chore: seal v0.2.0 milestone with updated submodule reference and README

- Exposed Structural AST Editing Tools.
- Implemented Reflection Loops.
- Hardened Actuators (path-traversal and Merkle snapshots).
- Implemented tool permission tiers (ask/allow/deny).
- Validated skill hot-reload capability.

.gitmodules

@@ -1,9 +1,9 @@
-[submodule "org-agent"]
-	path = org-agent
-	url = ssh://git@10.10.10.201:2222/amr/org-agent.git
-[submodule "projects/org-agent"]
-	path = projects/org-agent
-	url = ssh://git@10.10.10.201:2222/amr/org-agent.git
-[submodule "projects/org-agent-contrib"]
-	path = projects/org-agent-contrib
-	url = ssh://git@10.10.10.201:2222/amr/org-agent-contrib.git
+[submodule "opencortex"]
+	path = opencortex
+	url = ssh://git@10.10.10.201:2222/amr/opencortex.git
+[submodule "projects/opencortex"]
+	path = projects/opencortex
+	url = ssh://10.10.10.201:2222/amr/opencortex.git
+[submodule "projects/opencortex-contrib"]
+	path = projects/opencortex-contrib
+	url = ssh://git@10.10.10.201:2222/amr/opencortex-contrib.git

.opencode/AGENTS.md

@@ -0,0 +1,139 @@
+# OpenCortex Agent Mandate
+
+This file defines the operating policies and engineering guidelines that all autonomous agents MUST follow.
+
+## Vision
+
+- **Pure Lisp + Org-mode**: All intelligence implemented in Lisp, all documentation in Org-mode
+- **No JSON, No YAML**: Thin harness, fat skills
+- **Constraint**: No temporary scripts in opencortex repo - use `/home/user/memex/system/` instead
+
+## Current Goal
+
+- **v0.2.0**: Self-Improvement + Local LLMs
+  - org-skill-self-edit (self-modification)
+  - org-skill-emacs-edit (full org-mode manipulation)
+  - Local vector search (Ollama embeddings)
+  - Tool permission tiers (ask/allow/deny)
+  - Skill hot-reload ✅ DONE
+  - Engineering Standards skill ✅ DONE
+  - Literate Programming skill ✅ DONE
+
+## Wake-Up Protocol
+
+When this agent starts, it MUST:
+
+1. **Read this file** (`~/.opencode/AGENTS.md`)
+2. **Query the skill catalog**: Before any analysis, check if a skill covers the problem domain
+   - `(list-skills)` to see all loaded skills
+   - `(find-skill :keyword)` to check for a specific domain
+   - Read the skill's org file if found
+3. **Verify git status**: Working tree MUST be clean before modification
+4. **Read `gtd.org`**: Load current task context from the roadmap
+5. **Enter lifecycle**: Follow the Engineering Standards lifecycle (Phase 0 → A → B → C → D → E)
+
+Rationale: Raw LLM reasoning is a fallback, not a starting point. The skill layer encodes the system's accumulated wisdom. Ignoring skills creates drift.
+
+## Engineering Standards
+
+The Engineering Standards skill (`opencortex.skills.org-skill-engineering-standards`) defines the full lifecycle. The summaries below are reminders; the skill org file is authoritative.
+
+### Phase 0: Before You Think
+
+**Skill-First Query Rule**: Before analysis, debugging, or implementation, query the skill catalog. If a relevant skill exists, follow its mandates. Do not duplicate logic.
+
+### Phase A: Design (Test-First)
+
+1. **Define success criteria first** — Write the test or PROTOCOL that proves the feature works
+2. **Break the design with chaos** — Three tiers of adversarial testing:
+   - *Deterministic chaos*: Scripted regression tests on every change
+   - *Probabilistic chaos*: Randomized fuzzing on every major release
+   - *Stress chaos*: Load and resource starvation during hardening sprints
+
+### Phase B: Commit (Recovery Point)
+
+3. **Commit Before Modify** — Commit and push (if network available) before any file changes
+
+### Phase C: Build (Implementation)
+
+4. **Literate Programming** — All logic in Org files; generated `.lisp` is derived, not authored
+5. **Function-Block Granularity** — One function per `#+begin_src lisp` block
+6. **Tangle Mandate** — Edit Org only; never touch generated `.lisp`
+7. **Configuration Externalization** — No hardcoded values; use `.env.example`
+8. **Org as Thinking Medium** — Document investigation before fixing
+
+### Phase D: Validate (Proof)
+
+9. **Test Verification** — Run the full suite. A change that breaks tests is damage, not a fix.
+
+### Phase E: Document (Audit Trail)
+
+10. **Decision Audit Trail** — Document root cause, options, tradeoffs, and rationale
+11. **Stop-and-Wait** — For major changes, propose strategy, state "Waiting for user feedback," yield turn
+12. **GTD Synchronization** — Update `gtd.org` with TODO headlines before marking complete
+
+## Literate Programming Rules
+
+The Literate Programming skill (`opencortex.skills.org-skill-literate-programming`) enforces Org discipline:
+
+1. **One Function, One Block** — No bundling multiple definitions
+2. **Org-Mode Evaluation Gate** — `C-c C-c` after every block change
+3. **Pre-Tangle Structural Check** — Verify paren balance before tangling
+4. **No Direct `.lisp` Edits** — All changes flow through Org
+5. **Code and Prose Together** — Every block preceded by explanatory text
+
+Violating these rules corrupts the skill loader and causes boot failure (as seen in the 2026-04-25 incident).
+
+## Agent Workflow
+
+- **Boot Sequence**: Read AGENTS.md → query skills → verify git → read gtd.org
+- **Before Any Modification**: Commit first (Commit Before Modify rule)
+- **Plan Mode**: Draft PROTOCOL.md before complex implementations
+- **Testing**: Run FiveAM test suite + chaos tests before marking task complete
+- **Completion**: Update gtd.org, commit, sync with user
+
+## Self-Enforcement Checklist
+
+This agent MUST verify these conditions before, during, and after each task. Violation is a bug, not a suggestion.
+
+### Before Any Task (Gate)
+
+- [ ] **Git clean** — Working tree must be clean before modification
+- [ ] **Skill query** — Check if relevant skill exists in `/home/user/memex/projects/opencortex/skills/`
+- [ ] **Skill read** — If found, read the skill's org file before proceeding
+- [ ] **GTD read** — Check `gtd.org` for current task context
+
+### During Task (Literate Programming)
+
+- [ ] **Org-only edits** — Edit only `.org` files, never generated `.lisp` directly
+- [ ] **One function per block** — Each `#+begin_src` block contains exactly one definition
+- [ ] **Prose before code** — Every block preceded by explanatory text
+- [ ] **Prose includes**: What the function does, arguments, return value, rationale
+- [ ] **Evaluate each block** — Verify the block compiles/evaluates correctly
+- [ ] **Paren balance** — Check balanced parentheses before tangling
+
+### After Task (Validation)
+
+- [ ] **Tests pass** — Run full test suite; 100% pass required
+- [ ] **Chaos tier 1** — Deterministic regression tests pass
+- [ ] **No artifacts** — No orphaned `.bak`, `.log`, `.tmp`, or untracked test files
+- [ ] **Commit** — Stage and commit changes with descriptive message
+- [ ] **GTD update** — Update `gtd.org` with completed task state
+
+### For OpenCortex Work Specifically
+
+Reference authoritative skill files:
+- Engineering Standards: `projects/opencortex/skills/org-skill-engineering-standards.org`
+- Literate Programming: `projects/opencortex/skills/org-skill-literate-programming.org`
+- Policy: `projects/opencortex/skills/org-skill-policy.org`
+
+The summaries in this file are reminders; the skill org files are authoritative.
+
+## References
+
+- opencortex repo: `/home/user/memex/projects/opencortex`
+- Engineering Standards: `/home/user/memex/projects/opencortex/skills/org-skill-engineering-standards.org`
+- Literate Programming: `/home/user/memex/projects/opencortex/skills/org-skill-literate-programming.org`
+- Policy Skill: `/home/user/memex/projects/opencortex/skills/org-skill-policy.org`
+- Roadmap: `/home/user/memex/gtd.org`
+- README: `/home/user/memex/projects/opencortex/README.org`

README.org

@@ -2,10 +2,10 @@
 #+AUTHOR: Amr
 #+CREATED: [2026-03-17 Tue]
 #+UPDATED: [2026-04-08 Wed]
-#+FILETAGS: :memex:psf:org-agent:lisp:sovereignty:
+#+FILETAGS: :memex:psf:opencortex:lisp:sovereignty:
 
 * Overview
-The *Master Memex* is a sovereign, neurosymbolic intelligence organization system. It is not merely a collection of notes, but a live, programmable environment—a **Personal Software Foundry (PSF)**—where a human (the Sovereign Executive) and agentic co-processes (the `org-agent` kernel and Gemini CLI) collaborate within a shared address space.
+The *Master Memex* is a sovereign, neurosymbolic intelligence organization system. It is not merely a collection of notes, but a live, programmable environment—a **Personal Software Foundry (PSF)**—where a human (the Sovereign Executive) and agentic co-processes (the `opencortex` kernel and opencode) collaborate within a shared address space.
 
 This system synthesizes three core organizational methodologies into a unified "Lisp Machine" experience:
 - *Zettelkasten:* For atomic, evergreen, and interlinked knowledge.
@@ -33,10 +33,10 @@ The workspace is strictly divided into these zones to facilitate both human ergo
 * The Agentic Inhabitants
 The Memex is inhabited by autonomous agents that operate as "Probabilistic" (probabilistic/neural) and "Deterministic" (deterministic/symbolic) layers:
 
-** [[file:projects/org-agent/README.org][org-agent (The Kernel)]]
+** [[file:projects/opencortex/README.org][opencortex (The Kernel)]]
 A Common Lisp microkernel that maintains a live, threaded Object-Store in RAM. It uses Org-mode as its native Abstract Syntax Tree (AST), allowing it to "perceive" and "act" on the Memex with structural precision.
 
-** Gemini CLI
+** opencode
 A strategic orchestrator that handles large-scale batch tasks, research, and planning. It operates according to the *PSF Consensus Loop* (Demand -> Blueprint -> Success -> Build -> Chaos -> Memory).
 
 * The Cognitive Architecture: A Session-less Mind

boot-sequence-plan.md

@@ -1,36 +0,0 @@
-# Implementation Plan: The Micro-Loader (Boot Sequence Refactor)
-
-## Objective
-Consolidate and harden the kernel's skill-loading logic into a stateful "Micro-Loader." This improves boot reliability, provides clear error reporting for malformed skills, and centralizes all capability management within the `skills` module.
-
-## Key Files & Context
-- **Target:** `projects/org-agent/literate/skills.org` (Consolidating logic here).
-- **Target:** `projects/org-agent/literate/core.org` (Moving `load-all-skills` out of here).
-- **Mandate:** Syntax Pre-flight and Dependency Assertion.
-
-## Implementation Steps
-
-### 1. Define the Skill Catalog
-- Introduce `*skill-catalog*` in `skills.lisp` to track metadata and load status for every skill file found in `SKILLS_DIR`.
-- Statuses: `:discovered`, `:loading`, `:ready`, `:failed`.
-
-### 2. Refactor `load-skill-from-org` (Harden)
-- **Syntax Check:** Invoke `validate-lisp-syntax` before evaluation.
-- **Dependency Check:** If `#+DEPENDS_ON` refers to a skill that failed or is missing, mark this skill as `:failed` immediately with a clear error.
-- **Detailed Logging:** Record the specific reason for failure (syntax, timeout, runtime error) in the catalog.
-
-### 3. Implement `initialize-all-skills` (The Orchestrator)
-- Move the directory scanning and loop logic from `core.lisp` into `skills.lisp`.
-- This function will:
-  1. Scan `SKILLS_DIR`.
-  2. Populate the catalog.
-  3. Run the topological sort.
-  4. Execute the load loop with timeouts.
-  5. Print a final "Boot Summary" report.
-
-### 4. Simplify Kernel Boot
-- Update `start-daemon` in `core.lisp` to call `(initialize-all-skills)` instead of the old `load-all-skills`.
-
-## Phase E: Chaos (Verification)
-- **Integrity Test:** Add a test that verifies `initialize-all-skills` correctly identifies a missing dependency and prevents the dependent skill from attempting to load.
-- **Report Test:** Verify that the skill catalog correctly reflects the status of loaded vs. failed skills.

daily/2026-03-17.org

@@ -27,10 +27,10 @@ Chronological record of all meetings, fleeting notes, and raw conversation logs
 ## Major System Developments
 
 ### Three OpenClaw Skills Deployed
-Created and deployed three integrated skills for the org-agent-memex system:
-- *org-agent-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
-- *org-agent-memex-gtd*: Automated task promotion and GTD workflow management
-- *org-agent-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
+Created and deployed three integrated skills for the opencortex-memex system:
+- *opencortex-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
+- *opencortex-memex-gtd*: Automated task promotion and GTD workflow management
+- *opencortex-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
 
 All skills follow the established pattern: SKILL.md with YAML frontmatter, README.md for users, and integration with the PARA + Atomic Notes (Zettelkasten) + GTD workflow.
 
@@ -93,10 +93,10 @@ Awaiting pressure-testing session for 21-layer audit assumptions. All building p
 ## Major System Developments
 
 ### Three OpenClaw Skills Deployed
-Created and deployed three integrated skills for the org-agent-memex system:
-- *org-agent-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
-- *org-agent-memex-gtd*: Automated task promotion and GTD workflow management
-- *org-agent-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
+Created and deployed three integrated skills for the opencortex-memex system:
+- *opencortex-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
+- *opencortex-memex-gtd*: Automated task promotion and GTD workflow management
+- *opencortex-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
 
 All skills follow the established pattern: SKILL.md with YAML frontmatter, README.md for users, and integration with the PARA + Atomic Notes (Zettelkasten) + GTD workflow.
 
@@ -159,10 +159,10 @@ Awaiting pressure-testing session for 21-layer audit assumptions. All building p
 ## Major System Developments
 
 ### Three OpenClaw Skills Deployed
-Created and deployed three integrated skills for the org-agent-memex system:
-- *org-agent-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
-- *org-agent-memex-gtd*: Automated task promotion and GTD workflow management
-- *org-agent-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
+Created and deployed three integrated skills for the opencortex-memex system:
+- *opencortex-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
+- *opencortex-memex-gtd*: Automated task promotion and GTD workflow management
+- *opencortex-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
 
 All skills follow the established pattern: SKILL.md with YAML frontmatter, README.md for users, and integration with the PARA + Atomic Notes (Zettelkasten) + GTD workflow.
 
@@ -225,10 +225,10 @@ Awaiting pressure-testing session for 21-layer audit assumptions. All building p
 ## Major System Developments
 
 ### Three OpenClaw Skills Deployed
-Created and deployed three integrated skills for the org-agent-memex system:
-- *org-agent-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
-- *org-agent-memex-gtd*: Automated task promotion and GTD workflow management
-- *org-agent-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
+Created and deployed three integrated skills for the opencortex-memex system:
+- *opencortex-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
+- *opencortex-memex-gtd*: Automated task promotion and GTD workflow management
+- *opencortex-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
 
 All skills follow the established pattern: SKILL.md with YAML frontmatter, README.md for users, and integration with the PARA + Atomic Notes (Zettelkasten) + GTD workflow.
 
@@ -291,10 +291,10 @@ Awaiting pressure-testing session for 21-layer audit assumptions. All building p
 ## Major System Developments
 
 ### Three OpenClaw Skills Deployed
-Created and deployed three integrated skills for the org-agent-memex system:
-- *org-agent-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
-- *org-agent-memex-gtd*: Automated task promotion and GTD workflow management
-- *org-agent-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
+Created and deployed three integrated skills for the opencortex-memex system:
+- *opencortex-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
+- *opencortex-memex-gtd*: Automated task promotion and GTD workflow management
+- *opencortex-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
 
 All skills follow the established pattern: SKILL.md with YAML frontmatter, README.md for users, and integration with the PARA + Zettelkasten + GTD workflow.
 
@@ -357,10 +357,10 @@ Awaiting pressure-testing session for 21-layer audit assumptions. All building p
 ## Major System Developments
 
 ### Three OpenClaw Skills Deployed
-Created and deployed three integrated skills for the org-agent-memex system:
-- *org-agent-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
-- *org-agent-memex-gtd*: Automated task promotion and GTD workflow management
-- *org-agent-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
+Created and deployed three integrated skills for the opencortex-memex system:
+- *opencortex-memex-zettlekasten*: Nightly distillation of daily logs into atomic notes
+- *opencortex-memex-gtd*: Automated task promotion and GTD workflow management
+- *opencortex-memex-workbreakdown*: Meta-cognitive skill for task decomposition to prevent context saturation
 
 All skills follow the established pattern: SKILL.md with YAML frontmatter, README.md for users, and integration with the PARA + Zettelkasten + GTD workflow.
 

daily/2026-03-22.org

@@ -5,10 +5,10 @@
 * Activities
 ** OpenClaw Resilience and Memory Restoration
 - *Problem:* Agent suffered from "context amnesia" after a session reset at 08:10 AM, losing the path to `emacs.org` and failing to rediscover it.
-- *Root Cause:* Search depth was too shallow (workspace root only), and the `org-agent-memex-gtd` skill was not in the executable skills directory.
+- *Root Cause:* Search depth was too shallow (workspace root only), and the `opencortex-memex-gtd` skill was not in the executable skills directory.
 - *Resolution:*
   - Identified canonical path: `/home/amr/.openclaw/workspace/memex/5_projects/dotemacs/emacs.org`.
-  - Restored skills by copying `org-agent-memex-gtd`, `org-agent-memex-workbreakdown`, and `org-agent-memex-zettlekasten` to standard `.openclaw/skills/` directory.
+  - Restored skills by copying `opencortex-memex-gtd`, `opencortex-memex-workbreakdown`, and `opencortex-memex-zettlekasten` to standard `.openclaw/skills/` directory.
   - Synced `GTD.org` and `memex/gtd.org` to ensure "Ground Truth" is consistent.
 
 ** Emacs Configuration Modularization

fedora-43-repos.repo

@@ -0,0 +1,15 @@
+[fedora]
+name=Fedora 43 - x86_64
+enabled=1
+metadata_expire=1h
+baseurl=https://mirrors.fedoraproject.org/metalink?repo=fedora-43&arch=x86_64
+type=rpm-md
+gpgcheck=0
+
+[updates]
+name=Fedora 43 - x86_64 - Updates
+enabled=1
+metadata_expire=1h
+baseurl=https://mirrors.fedoraproject.org/metalink?repo=fedora-43-updates&arch=x86_64
+type=rpm-md
+gpgcheck=0

gtd.org

@@ -9,72 +9,432 @@
 :PROPERTIES:
 :ID:       gtd-actions
 :END:
+** DONE Fix Modular Emacs configuration loading and org-capture templates
+   - Restored ef-themes configuration in emacs-core.org which was lost during refactoring.
+   CLOSED: [2026-04-21 Tue 15:00]
+   - Resolved conflict where multiple modules were overwriting ~/.emacs.d/custom.el.
+   - Switched from defvar to setq for org-capture-templates to ensure it applies on boot.
+** DONE Reorganize Emacs configuration files into the dotemacs project
+   - Deleted outdated configuration modules in ~/memex/projects/dotemacs/.
+   - Moved live configuration files from ~/memex/system/ to ~/memex/projects/dotemacs/.
+   - Organized modules into a /modules subdirectory and snippets into /templates.
+   - Updated ~/.emacs and internal Org-babel paths to reflect the new location.
+   CLOSED: [2026-04-21 Tue 16:45]
+** DONE Fix emacsclient defaulting to terminal mode
+   - Identified that 'opencortex' setup.org was hardcoded to install emacs-nox.
+   - Reinstalled emacs-gtk and restored GUI support.
+   - Patched projects/opencortex/harness/setup.org to use 'emacs' metapackage.
+   - Restored missing modules/emacs-ui.org and added it to dotemacs.org.
+   - Added 'em' alias to ~/.bash_aliases for persistent GUI frame creation.
+   CLOSED: [2026-04-21 Tue 17:15]
+:END:
 
 * Projects
-:PROPERTIES:
 :ID:       gtd-projects
 :END:
 
-** NEXT Org-agent v1.0
+** NEXT OpenCortex v1.0
 :PROPERTIES:
-:ID:       proj-org-agent-v1-0
+:ID:       proj-opencortex-v1-0
 :Engineering-STATE: D: BUILD
 :CREATED:  [2026-03-09 Mon 14:23]
 :END:
-Org-agent: A Neurosymbolic AI Agent.
+OpenCortex: A Neurosymbolic AI Agent.
 
-*** PHASE: SOVEREIGN MVP (v0.1.0 Released)
+*** PHASE: AUTONOMOUS MVP (v0.1.0 Released)
 :PROPERTIES:
 :ID:       proj-mvp-v0-1-0
 :END:
 The "Zero-to-One" release. The agent must be mathematically secure, CLI-first, and capable of autonomous Memex maintenance.
 
 **** DONE 1. Harness Hardening (The Final Audit)
-     - [X] Audit remaining core skills (`org-skill-policy.org`, `org-skill-bouncer.org`) to the new Literate Granularity standard.
-     - [X] Implement Verification Lock: Ensure `MANDATORY_SKILLS` pass `validate-lisp-syntax` before boot proceeds.
-     - [X] Logging & Transparency: Ensure `context-get-system-logs` is utilized by the Reason engine to explain blocked actions.
+***** DONE Audit remaining core skills (`org-skill-policy.org`, `org-skill-bouncer.org`) to the new Literate Granularity standard.
+***** DONE Implement Verification Lock: Ensure `MANDATORY_SKILLS` pass `validate-lisp-syntax` before boot proceeds.
+***** DONE Logging & Transparency: Ensure `context-get-system-logs` is utilized by the Reason engine to explain blocked actions.
 
-**** DONE 2. The Sovereign Scribe & Gardener (The Primary Value Prop)
-     - [X] Implement `org-skill-scribe.org`: Background worker that distills daily chronological logs into structured Zettelkasten notes.
-     - [X] Implement `org-skill-gardener.org`: Heartbeat-driven skill that autonomously flags orphaned nodes and repairs broken links.
+**** DONE 2. The Autonomous Scribe & Gardener (The Primary Value Prop)
+***** DONE Implement `org-skill-scribe.org`: Background worker that distills daily chronological logs into structured Zettelkasten notes.
+***** DONE Implement `org-skill-gardener.org`: Heartbeat-driven skill that autonomously flags orphaned nodes and repairs broken links.
 
 **** DONE 3. The Zero-to-One Experience (setup.org)
-     - [X] Consolidate installation instructions, `onboard.sh`, and `Dockerfile` into a single, literate `setup.org` file.
-     - [X] Ensure the setup process interactively builds the `.env` and verifies SBCL/Quicklisp dependencies.
+***** DONE Consolidate installation instructions, `onboard.sh`, and `Dockerfile` into a single, literate `setup.org` file.
+***** DONE Ensure the setup process interactively builds the `.env` and verifies SBCL/Quicklisp dependencies.
 
-**** TODO 4. CLI-First Actuation
-     - [ ] Verify the `cli` actuator and inbound gateway handle standard I/O interaction gracefully, treating Emacs as an optional power-user viewport.
+**** DONE 4. CLI-First Actuation
+     CLOSED: [2026-04-14 Tue 09:40]
+***** DONE Verified the `cli` actuator and inbound gateway handle standard I/O interaction gracefully via a stateful `socat` connection.
+
+*** PHASE: PUBLICATION & VERIFICATION (v0.1.0 Post-Release)
+:PROPERTIES:
+:ID:       proj-pub-v0-1-0
+:END:
+Ensuring the system is ready for the world through collaborative testing, documentation, and licensing.
+
+**** DONE 1. Collaborative End-to-End Testing [2026-04-21 Tue]
+     CLOSED: [2026-04-21 Tue 17:30]
+***** DONE Verified stable foundation at commit `cab0e5a`.
+***** DONE Verified boot sequence and bidirectional connectivity.
+
+**** DONE 2. Semantic Reorganization & System Stabilization [2026-04-21 Tue]
+     CLOSED: [2026-04-21 Tue 18:30]
+***** DONE Rename directories: harness/, library/, environment/, infrastructure/.
+***** DONE Consolidate Probabilistic engine into reason.lisp.
+***** DONE Embed bidirectional CLI logic into opencortex.sh.
+***** DONE Stabilize skill engine: 12/12 skills loaded with package jailing.
+***** DONE Cleanup legacy documentation and deployment artifacts.
+
+**** DONE 2. Comprehensive Documentation <2026-04-14 Tue>
+     CLOSED: [2026-04-20 Mon 18:00]
+***** DONE Draft `USER_MANUAL.org`: Focus on CLI interaction, installation, and Memex structure.
+***** DONE Draft `CONTRIBUTING.org`: Explain Literate Granularity and Skill creation standards.
+
+**** DONE 3. License & Legal Finalization <2026-04-14 Tue>
+     CLOSED: [2026-04-17 Fri 11:25]
+***** DONE Assign the AGPLv3 open-source license.
+***** DONE Implement a broad Contributor License Agreement (CLA) process.
+***** DONE Update `LICENSE` and `CHANGELOG` accordingly.
+
+**** TODO 4. GitHub Migration & Repository Setup <2026-04-14 Tue>
+***** TODO Migrate primary remote to GitHub and configure canonical repository.
+***** TODO Set repository topics, badges, issue templates, and CI/CD foundations.
+
+**** TODO 5. Marketing & Social Media Launch <2026-04-14 Tue>
+***** TODO Execute PR plan (Reddit, Hacker News, X/Twitter).
+***** TODO Create a short, high-quality terminal demo GIF/video of the TUI interaction.
 
 *** PHASE: INTERACTIVE REFINEMENT (v0.2.0 Target)
 :PROPERTIES:
 :ID:       proj-refinement-v0-2-0
 :END:
-Elevating the user interface from raw shell piping to a high-fidelity, native Lisp experience.
+Elevating the user interface from raw shell piping to a high-fidelity, native Lisp experience. Priority: Self-editing is the foundation of all future growth. Full org-mode manipulation makes the agent a true Emacs citizen.
 
-**** TODO 1. Common Lisp TUI (The "gemini-cli" parity)
-     - [ ] Implement a rich, interactive TUI natively in Common Lisp (e.g., via `cl-charms`, `croatoan`, or `cl-ncurses`).
-     - [ ] Support syntax highlighting for code blocks and Org-mode syntax.
-     - [ ] Implement a fixed bottom input box with command history.
-     - [ ] Implement Slash Commands (`/help`, `/exit`, `/clear`, `/skill-load`).
+Roadmap basis: Evolutionary roadmap from README.org. Working backwards from SOTA parity.
 
-**** TODO 2. Direct Lisp-to-Terminal Actuation
-     - [ ] Refactor the `:cli` actuator to use the native TUI rendering instead of raw stream printing.
+**** DONE 0. Autonomous Self-Editing Foundation
+***** DONE org-skill-lisp-repair (Lisp syntax repair)
+      - Deterministic: auto-balance parens via paren-counting
+      - Probabilistic: LLM generates surgical fix on =:syntax-error= events
+      - Memory rollback on failure
+      DONE: Now in org-skill-lisp-utils (merged from contrib)
+***** DONE org-skill-emacs-edit (full org-mode manipulation)
+      - Read org buffers, parse AST via org-element
+      - Create/update/delete headlines, set properties, manage TODO states
+      - Handle =id:= links and internal links
+      - Pure Lisp implementation (no Emacs subprocess)
+***** DONE Expose Structural AST Editing Tools
+      - Wrap org-skill-emacs-edit into def-cognitive-tool definitions
+      - Force LLM to use semantic node updates instead of regex file I/O
+***** DONE Implement Reflection Loops
+      - Feed rejection traces (syntax errors, policy blocks) back to LLM to trigger self-correction
+***** DONE Harden Actuators
+      - Fix path-traversal vulnerabilities in file I/O tools (e.g. :write-file)
+      - Enforce Merkle-snapshots on all state-modifying actions
+***** DONE Implement tool permission tiers (ask/allow/deny)
+      - Per-tool permission plist stored in org-object
+      - =generate-tool-belt-prompt= filters denied tools before LLM sees them
+      - Ask-tier prompts user before execution
+***** DONE Implement skill hot-reload (=:reload-skill= tool)
+      - Swap compiled skill files without breaking active sockets
+      - Reload skill into jailed package namespace
+      - DONE: Added :reload-skill, :read-file, :write-file, :replace-string tools
+      - DONE: Fixed ASDF compilation bug (position tracking issue with :serial t)
+      - DONE: Added explicit :depends-on declarations to opencortex.asd
 
-*** PHASE: EVOLUTIONARY ROADMAP
-**** TODO v1.0.0 (Phase 2.5): The Verified Wrapper (SOTA Parity)
+**** DONE Engineering Process Improvements [2026-04-23 Wed]
+***** DONE Fix ASDF compilation bug (position tracking at byte 16834)
+      - Root cause: Duplicate proto-get, bt: prefix issues, :serial t position cache
+      - Fix: Removed duplicate, fixed bt:->bordeaux-threads, explicit dependencies
+      - Added eval-when wrapper for new tools (good Lisp practice)
+***** DONE Add test-first methodology to engineering standards
+      - Rule 10: Test-first - design tests before coding, run chaos testing
+      - Rule 11: Org as thinking medium - document investigations in prose
+      - Rule 12: Engineering decision audit trail - document root cause, tradeoffs
+      - Added to opencortex-contrib/skills/org-skill-engineering-standards.org
+***** DONE Perform comprehensive architectural review and evolution strategy [2026-04-27 Mon]
+      - Identified hidden gaps: Org-mode round-trip, sandboxing vulnerabilities, and GC scaling.
+      - Defined "Structural AST Editing" and "Reflection Loops" as core strategic requirements.
+      - Captured findings in [[file:notes/opencortex-architectural-evolution.org][opencortex-architectural-evolution.org]].
+***** DONE Fix API drift in opencortex-contrib [2026-04-27 Mon]
+      - Standardized legacy keywords (:neuro/:symbolic) to new harness standard (:probabilistic/:deterministic).
+      - Updated 16 skills in opencortex-contrib for kernel compatibility.
 
-     - Complete Formal Verification gates for external tools.
-     - Achieve secure, end-to-end autonomous engineering workflows.
-**** TODO v2.0.0 (Phase 3): Cannibalizing the Toolchain
-     - Ingest DOM as native Lisp AST (Cannibalize Browser).
-     - Replace string-based bash with native OS bindings (Cannibalize Shell).
-**** TODO v3.0.0 (Phase 4): True Symbolic Determinism
-     - Relegate LLM to Semantic Translator.
-     - Implement Deterministic Planner (The Solver).
-     - Implement Self-Correcting Syntax Gates.
-**** TODO v4.0.0+ (Phase 5): The Neurosymbolic Singularity
-     - Homoiconic Self-Writing (Hot-reloading literate source).
-     - Asynchronous Swarm Cognition (Jailed sub-agents).
+**** DONE 4. Core Skills Consolidation [2026-04-23 Thu]
+      - Merged lisp-validator + lisp-repair → org-skill-lisp-utils.org
+      - Added lisp utilities: count-char, deterministic-repair, neural-repair
+      - Added validation: structural, syntactic, semantic checks
+      - Moved org-skill-self-fix from contrib → core
+      - Moved org-skill-engineering-standards from contrib → core
+      - Deleted old org-skill-lisp-validator.org
+
+**** TODO 5. Advanced CLI Onboarding Experience
+***** TODO Implement interactive Lisp CLI wizard (=opencortex setup=)
+***** TODO Implement =opencortex link <gateway>= for Telegram/Signal bot connection
+***** TODO Implement =opencortex doctor= for environment health and API key validation
+***** TODO Implement =opencortex install <skill>= for dynamic skill downloading
+
+**** TODO 1. Common Lisp TUI Implementation
+***** TODO Integrate =croatoan= for native terminal rendering
+***** TODO Implement scrollable history viewport for chat and thought streams
+***** TODO Implement fixed bottom input box with multi-line support and command history
+***** TODO Implement persistent status bar for background workers (Scribe/Gardener)
+***** TODO Support syntax highlighting for Lisp code blocks and Org-mode syntax
+
+**** TODO 2. Slash Commands & Interactive Control
+***** TODO Implement =/help= command for system overview
+***** TODO Implement =/exit= and =/clear= commands
+***** TODO Implement =/skill-load <name>= for dynamic hot-reloading
+***** TODO Implement =/status=, =/config=, =/search=, =/commit= slash commands
+
+**** TODO 3. Direct Lisp-to-Terminal Actuation
+***** TODO Refactor the =:cli= actuator to use native TUI rendering
+
+*** PHASE: EVENT ORCHESTRATION + HITL (v0.3.0)
+:PROPERTIES:
+:ID:       proj-orchestration-v0-3-0
+:END:
+Unified control plane: hooks + cron + routing in one skill. Deep project understanding.
+
+**** TODO 0. Event Orchestrator (unified hooks+cron+routing)
+***** TODO Integrate contrib org-skill-event-orchestrator
+      - Merge *hook-registry* + *cron-registry* + complexity classifier
+      - Hooks via =#+HOOK:= Org-mode properties
+      - Three complexity tiers: =:REFLEX= (no LLM), =:COGNITION= (light LLM), =:REASONING= (full LLM)
+      - Hook into heartbeat for cron processing
+
+**** TODO 1. Context Manager (project scoping)
+***** TODO Integrate contrib org-skill-context-manager
+      - Stack-based context with =push-context= / =pop-context=
+      - Path resolution relative to current context
+      - Memory scope: =:scope= property on org-objects (memex/session/project)
+      - Implement lazy-loading proxies for large-scale memory traversal (offload cold nodes to disk)
+
+**** TODO 2. Model-Tier Routing (cost optimization)
+***** TODO Extend =*model-selector-fn= for complexity-based routing
+      - Heartbeats → smallest model
+      - User input → medium model
+      - Complex reasoning → large model
+      - Source: GBrain sub-agent model routing
+
+**** TODO 3. Memory Scope Segmentation
+***** TODO Extend org-object with =:scope= property
+      - =:memex= (permanent knowledge)
+      - =:session= (ephemeral context)
+      - =:project= (scoped to current work)
+      - Scope-aware retrieval in memory.lisp
+
+**** TODO 4. Asynchronous Embedding Gateway
+***** TODO Implement provider-agnostic org-skill-embedding-gateway
+      - Support Ollama, llama.cpp, and OpenAI based on .env config
+      - Implement lazy-loading: edits mark nodes as =:vector :pending=
+      - Background worker thread batches pending nodes and updates Merkle tree silently
+
+**** TODO 4. Slash Commands (TUI ergonomics)
+***** TODO M-x style command palette
+***** TODO /- prefix for command mode
+***** TODO Commands defined in Org-mode
+
+*** PHASE: LONG-HORIZON PLANNING + GIT WORKFLOWS (v0.4.0)
+:PROPERTIES:
+:ID:       proj-planning-v0-4-0
+:END:
+Multi-step task mastery, structured tracking with failure handling and course correction.
+
+**** TODO 0. Long-Horizon Planning (task tree DAG)
+***** TODO Implement org-skill-long-horizon
+      - Decompose complex tasks into Org-mode headline trees
+      - Terminal states: =:todo= → =:next-action= → =:in-progress= → =:done= / =:blocked= / =:stuck=
+      - Parent summarises child results
+      - Branch pruning when paths fail
+      - Source: Claude Code ULTRAPLAN (reimplemented in Lisp)
+
+**** TODO 1. Git Steward (version control integration)
+***** TODO Integrate contrib org-skill-git-steward
+      - Status, diff, commit, push, branch operations
+      - Policy: commit-before-modify gate (from contrib engineering-standards)
+      - Log commits to memory
+
+**** TODO 2. TDD Runner Integration
+***** TODO Integrate contrib org-skill-tdd-runner
+      - Run FiveAM tests on file save
+      - Inject =:test-failure= event on red
+      - Hook into self-fix for auto-repair proposals
+
+**** TODO 3. Deep Emacs Integration
+***** TODO Full org-agenda awareness
+      - Navigate, clock time, refile, archive
+      - Uses org-element + org-id
+
+*** PHASE: INTERACTIVE ACTUATION & ENVIRONMENT STEWARDSHIP (v0.5.0)
+:PROPERTIES:
+:ID:       proj-actuation-v0-5-0
+:END:
+Interactive terminal sessions and autonomous dependency management.
+
+**** TODO 0. Interactive PTY Actuator
+***** TODO Stream long-running process output to the context window (e.g., `npm run dev`, REPLs)
+***** TODO Implement async interrupt control (Ctrl+C emulation)
+
+**** TODO 1. The Environment Steward
+***** TODO Autonomously detect missing dependencies (e.g., "Command not found")
+***** TODO Propose an installation command and retry the failed action
+
+*** PHASE: CREATOR + ARCHITECT + GTD (v0.6.0)
+:PROPERTIES:
+:ID:       proj-creator-v0-5-0
+:END:
+Agent bootstraps itself: creates skills autonomously, designs projects from PRDs, tracks work.
+
+**** TODO 0. Skill Creator (autonomous skill generation)
+***** TODO Integrate contrib org-skill-creator
+      - LLM drafts complete skill org-file from natural language
+      - Mandatory: syntax validation → jail-load → test → register
+
+**** TODO 1. Architect Agent (PRD → PROTOCOL)
+***** TODO Integrate contrib org-skill-architect
+      - Scan =:STATUS: FROZEN= PRDs
+      - Generate Phase B PROTOCOL from Phase A
+      - Write to same file
+
+**** TODO 2. GTD Integration (project tracking)
+***** TODO Integrate contrib org-skill-gtd
+      - Full GTD cycle: capture, clarify, organize, reflect, engage
+      - org-gtd v4.0 DAG (=:TRIGGER:=, =:BLOCKER:=)
+
+**** TODO 3. Consensus Loop (multi-model agreement)
+***** TODO Integrate contrib org-skill-consensus
+      - Run multiple providers for critical decisions
+      - Compare results, detect disagreements
+      - Confidence scoring
+
+**** TODO 4. Web Research (Playwright browsing)
+***** TODO Integrate contrib org-skill-playwright + org-skill-web-research
+      - Headless Chromium via Python bridge
+      - Text extraction and screenshots
+      - Gemini Web UI automation
+
+**** TODO 5. Memex Management (PARA lifecycle)
+***** TODO Integrate contrib org-skill-memex + org-skill-workspace-manager
+      - Archive DONE tasks, suggest refiling
+      - Detect orphaned nodes
+      - PARA/Zettelkasten maintenance
+
+*** PHASE: VISUAL GROUNDING & MCP BRIDGE (v0.7.0)
+:PROPERTIES:
+:ID:       proj-vision-v0-7-0
+:END:
+Multimodal visual interaction and ecosystem-wide tool compatibility.
+
+**** TODO 0. Computer Use / Vision
+***** TODO Allow the agent to request host OS or browser screenshots
+***** TODO Analyze UI and issue precise X/Y coordinate click/type commands via an X11/Wayland bridge
+
+**** TODO 1. MCP Gateway Bridge
+***** TODO Build a Lisp-native client for the Model Context Protocol
+***** TODO Connect OpenCortex to external tools and data sources
+
+*** PHASE: THE EVALUATION HARNESS (v0.8.0)
+:PROPERTIES:
+:ID:       proj-eval-v0-8-0
+:END:
+Automated benchmarking to mathematically prove the agent's reasoning capabilities.
+
+**** TODO 0. SWE-Bench Harness
+***** TODO Automated pipeline that clones repositories and feeds GitHub issues
+***** TODO Track multi-step resolution trajectory, run tests, and score success
+
+*** PHASE: SOTA PARITY (v1.0.0)
+:PROPERTIES:
+:ID:       proj-sota-v1-0-0
+:END:
+Feature-complete agent competitive with commercial agents. All borrowed concepts reimplemented in pure Lisp.
+
+All features from v0.2.0 through v0.8.0 combined, verified, and tested end-to-end.
+
+| Area | Parity Target |
+|------|--------------|
+| Self-improvement | Claude Code self-debug |
+| Planning | ULTRAPLAN equivalent |
+| Tool ecosystem | 10+ cognitive tools |
+| Context window | Semantic search + scope segmentation |
+| Safety | 6 Policy invariants + formal verification |
+| Multi-step tasks | Task trees with terminal states |
+| Code editing | Full file read/write via org manipulation |
+| Memory | Vector recall in org-object |
+| Emacs integration | Full org-mode control (exceeds Claude Code) |
+| Autonomy | 100% local capable (exceeds Claude Code) |
+
+*** PHASE: LISP MACHINE EMERGENCE (v2.0.0)
+:PROPERTIES:
+:ID:       proj-lisp-v2-0-0
+:END:
+From Lisp-using agent to true Lisp machine. Agent IS the Emacs process.
+
+**** TODO Lish: Lisp editor as Org-mode IDE
+      - Org-babel for interactive Lisp evaluation
+      - Full REPL in TUI
+      - No bridge needed — direct memory access
+**** TODO Lish: Shell replacement
+      - Lisp-based shell that speaks plists
+      - Org-mode buffers as file system
+      - No bash dependency
+
+*** PHASE: NEUROSYMBOLIC MATURITY (v3.0.0)
+:PROPERTIES:
+:ID:       proj-neuro-v3-0-0
+:END:
+Deterministic planner takes the wheel. LLM relegated to semantic translation.
+
+**** TODO Deterministic planner
+      - Planner as pure Lisp function
+      - No LLM needed for scheduling
+      - Generates task graphs without probabilistic inference
+**** TODO Self-correcting gates
+      - Gates learn from false positives (user override patterns)
+      - Adaptive threshold adjustment
+
+*** PHASE: AI STACK INTERNALIZED (v4.0.0)
+:PROPERTIES:
+:ID:       proj-ai-v4-0-0
+:END:
+The agent understands its own weights. No external inference.
+
+**** TODO Llama.cpp in Lisp
+      - FFI binding to llama.cpp
+      - No Python subprocess
+      - Pure Common Lisp inference
+**** TODO Weights as sexps
+      - Neural weights represented as Lisp data structures
+      - Homoiconic model introspection
+
+*** PHASE: TRUE AGENCY (v5.0.0)
+:PROPERTIES:
+:ID:       proj-agency-v5-0-0
+:END:
+World models, temporal reasoning, goal persistence across restarts.
+
+**** TODO World models
+      - Agent builds predictive models of user behavior
+      - Project dynamics awareness
+      - System state forecasting
+**** TODO Temporal reasoning
+      - Scheduling and deadline awareness
+      - Elapsed duration tracking
+      - Calendar integration
+**** TODO Goal persistence
+      - Goals survive restarts
+      - Long-term projects tracked in org-objects
+      - Cross-session continuity
+
+*** PHASE: EVOLUTIONARY ROADMAP (Previous — Superseded by Critical Analysis)
+:PROPERTIES:
+:ID:       proj-old-roadmap
+:END:
+Superseded by the critical analysis-informed roadmap above (v0.2.0 through v5.0.0). This section kept for historical reference.
+
+**** TODO v0.1.0: The Autonomous Foundation (Current Release) — Now COMPLETE
+**** TODO v1.0.0 (Phase 2.5): The Verified Wrapper (SOTA Parity) — Now v1.0.0
+**** TODO v2.0.0 (Phase 3): Cannibalizing the Toolchain — Now v2.0.0
+**** TODO v3.0.0 (Phase 4): True Symbolic Determinism — Now v3.0.0
 
 *** PHASE: FOUNDATION (Complete)
 **** DONE Draft Swank/Socket communication protocol between CL and Emacs
@@ -111,9 +471,9 @@ Elevating the user interface from raw shell piping to a high-fidelity, native Li
 
 *** PHASE: THE SOVEREIGN BOUNDARY (Core vs Skills Refactor)
 :PROPERTIES:
-:ID:       proj-sovereign-boundary
+:ID:       proj-autonomous-boundary
 :END:
-Slim down the org-agent microharness by moving non-essential cognitive functions to hot-reloadable user-space skills.
+Slim down the opencortex microharness by moving non-essential cognitive functions to hot-reloadable user-space skills.
 
 **** DONE Extract LLM Provider Routing to a Skill (neuro.lisp)
 **** DONE Extract Vector Embedding Algorithms to a Skill (embedding.lisp)
@@ -157,7 +517,7 @@ Slim down the org-agent microharness by moving non-essential cognitive functions
     CLOSED: [2026-04-12 Sun 19:15]
 **** DONE Feature: Implement Latent Reflection (Proactive Gardening) using heartbeat idle cycles
     CLOSED: [2026-04-12 Sun 19:15]
-**** DONE Simplification: Refactor Cognitive Loop into a Unified Reactive Signal Pipeline
+**** DONE Simplification: Refactor Cognitive Cycle into a Unified Reactive Signal Pipeline
     CLOSED: [2026-04-12 Sun 19:15]
 **** DONE Resilience: Implement Micro-Rollbacks for the Immune System
     CLOSED: [2026-04-12 Sun 19:15]
@@ -187,19 +547,29 @@ Slim down the org-agent microharness by moving non-essential cognitive functions
     - Implemented Task Integrity (GTD semantics) in symbolic.lisp.
     - Integrated Consensus Gate and Delegation hooks in core.lisp.
     - Verified with new task-orchestrator-tests.lisp.
-**** IN-PROGRESS Full review of org-agent's harness
+**** DONE Implement Unified Envelope Architecture & Channel-Awareness
+    CLOSED: [2026-04-20 Mon 13:20]
+    - Removed specialized :CHAT type; reverted to semantic :REQUEST/:EVENT protocol.
+    - Decoupled routing metadata into a :META envelope (SOURCE, SESSION-ID).
+    - Updated TUI, Emacs, and CLI gateways to use the unified protocol.
+    - Verified end-to-end loop with TUI; kernel correctly routes responses back to origin interface.
+    - Achieved "Equality of Clients" mandate.
+**** IN-PROGRESS Full review of opencortex's harness
     :PROPERTIES:
     :CREATED: [2026-04-13 Mon 13:30]
     :ASSIGNED: Agent
     :END:
     - [X] Audit terminology: Replaced OACP with "communication protocol" workspace-wide.
     - [X] Audit boot sequence: Synchronized loader with `org-skill-policy.org`.
+    - [X] Implement Unified Envelope (Channel-Aware Routing).
     - [-] Audit core Perceive-Think-Act loop.
       - [X] Verified protocol framing and reader jailing (`*read-eval* nil`).
       - [X] Refactored `loop.org` for literate granularity and configuration externalization.
       - [X] Improved error handling (restricted rollback) and added graceful shutdown.
-      - [X] **GAP:** Missing symbolic guard check in `act-gate` (Stage 3: Act).
-    - [ ] Ensure alignment with System Policy and Engineering Standards.
+      - [X] **FIXED:** Implemented symbolic guard check in `act-gate` via Bouncer skill refactoring.
+      - [X] **FIXED:** Harness `deterministic-verify` now correctly respects skill triggers.
+    - [X] Ensure alignment with System Policy and Engineering Standards.
+    - [X] Restored structural integrity by fixing `manifest.org` loading sequence.
 **** TODO Wake up the Scribe (Implement autonomous weekly Journal-to-Ledger distillation in org-skill-scribe.org)
 **** TODO Implement `org-skill-lisp-repair` (Self-correcting syntax gate for Deterministic Engine)
     CLOSED: [2026-04-11 Sat 15:10]
@@ -247,12 +617,61 @@ Slim down the org-agent microharness by moving non-essential cognitive functions
     - Leveraged Memory event bus for asynchronous re-injection.
 
 **** DONE Refactor Architecture Terminology (Associative -> Probabilistic, Deliberate -> Deterministic)
-    CLOSED: [2026-04-12 Sun 21:00]
-    :PROPERTIES:
-    :ID: terminology-refactor-task
-    :END:
-    - Updated codebase-wide terminology to use Probabilistic/Deterministic Engines.
-    - Replaced System 1/2 with Probabilistic/Deterministic Engines respectively.
+     CLOSED: [2026-04-12 Sun 21:00]
+     :PROPERTIES:
+     :ID: terminology-refactor-task
+     :END:
+     - Updated codebase-wide terminology to use Probabilistic/Deterministic Engines.
+     - Replaced System 1/2 with Probabilistic/Deterministic Engines respectively.
+
+**** DONE Refactor org-skill-policy.org: Concrete Invariants, Conflict Hierarchy, and Auditable Gate
+     CLOSED: [2026-04-22 Wed 11:50]
+     :PROPERTIES:
+     :ID: policy-refactor-concrete-invariants
+     :END:
+     - Added explicit Override Hierarchy (Transparency > Autonomy > Bloat > Mentorship > Sustainability).
+     - Implemented `policy-check-transparency`: blocks user-facing actions without :explanation.
+     - Implemented `policy-check-autonomy`: flags proprietary domain references as autonomy debt.
+     - Implemented `policy-check-bloat`: warns on :create-skill actions exceeding size threshold.
+     - Implemented `policy-check-mentorship`: blocks high-impact actions missing :mentorship-note.
+     - Implemented `policy-check-sustainability`: logs cloud-provider usage as sustainability debt.
+     - Implemented `policy-explain`: formats auditable rationale for every policy decision.
+     - Implemented `policy-find-engineering-standards-gate`: robust cross-package search for standards skill.
+     - Hardened `policy-deterministic-gate`: never returns NIL silently; always returns action or auditable log.
+     - Raised skill priority from 100 to 500 to ensure it runs before other deterministic gates.
+
+**** DONE Add Invariant 6 (Modularity) and Harness Boundary Contract to Policy/Manifest
+     CLOSED: [2026-04-22 Wed 12:10]
+     :PROPERTIES:
+     :ID: policy-modularity-invariant
+     :END:
+     - Added Modularity as Invariant 6 in `org-skill-policy.org`: general life principle that complexity must live at the edges.
+     - Implemented `policy-check-modularity`: blocks modifications to protected core paths unless `:modularity-justification` is provided.
+     - Defined `*modularity-protected-paths*` as project-configurable variable (defaults: harness/, opencortex.asd).
+     - Updated Override Hierarchy to include Modularity between Bloat and Mentorship.
+     - Added Harness Boundary Contract section to `harness/manifest.org` documenting primary boundary files and generated artifacts.
+     - Converted checkbox sub-tasks to hierarchical TODO headlines in gtd.org per GTD standard.
+
+**** DONE Implement `org-skill-lisp-validator` (3-phase deterministic validation gate)
+     CLOSED: [2026-04-22 Wed 12:30]
+     :PROPERTIES:
+     :ID: lisp-validator-implementation
+     :END:
+     - Created 3-phase validation pipeline: Structural (O(n) paren scanner), Syntactic (reader with *read-eval* nil), Semantic (whitelist AST walk).
+     - Implemented `lisp-validator-validate` returning structured plists for machine parsing.
+     - Exposed `:validate-lisp` cognitive tool for Probabilistic Engine self-correction.
+     - Replaced `validate-lisp-syntax` in `harness/skills.org` with delegation to the validator.
+     - Added mandatory validation rule to Probabilistic Engine system prompt in `harness/reason.org`.
+     - Fixed paren balance and `return-from` compilation errors in org source; tangled and validated in SBCL.
+
+**** DONE Fix Skill Loader to Respect `:tangle` Blocks and Eliminate Circular Dependency
+     CLOSED: [2026-04-22 Wed 12:45]
+     :PROPERTIES:
+     :ID: skill-loader-tangle-fix
+     :END:
+     - Updated `load-skill-from-org` in `harness/skills.org` to only collect blocks with `:tangle` directives pointing to runtime `.lisp` files, excluding `tests/` and `test/` paths.
+     - Added fallback to `validate-lisp-syntax` so it uses a basic reader check when `lisp-validator-validate` is not yet loaded (breaks circular harness->skill dependency).
+     - Verified full boot: 13/13 skills loaded successfully into SBCL, including `skill-lisp-validator` at priority 900 and `skill-policy` at priority 500.
 
 *** TRACK: SECURITY & CONTAINMENT (The 5-Vector Bouncer Matrix)
 **** DONE Implement Path-Based Scoping for File Writes (DNA/State vs Work)
@@ -278,7 +697,7 @@ Slim down the org-agent microharness by moving non-essential cognitive functions
     - Added unit tests for each provider in `llm-gateway-tests.lisp`.
     - Mocked `dex:post` to verify JSON payload formatting and response parsing.
     - Implemented robust `get-nested` helper to handle various provider structures.
-    - Integrated `llm-gateway` and `credentials-vault` into `org-agent.asd`.
+    - Integrated `llm-gateway` and `credentials-vault` into `opencortex.asd`.
 **** TODO Verify org-skill-shell-actuator formal safety harnesses
 **** DONE Build Playwright-Python Bridge for high-fidelity browsing
     CLOSED: [2026-04-11 Sat 18:30]
@@ -343,11 +762,11 @@ Slim down the org-agent microharness by moving non-essential cognitive functions
      :ID: monthly-infra-audit
      :REPEAT_TO_STATE: TODO
      :END:
-     - [ ] Check for new Debian security patches (`apt-get update` check).
-     - [ ] Check for new `signal-cli` releases (compare vs v0.14.0).
-     - [ ] Check for new Quicklisp distribution (monthly snapshot).
-     - [ ] **Verification:** Update `Dockerfile`, run `docker-compose build --no-cache`, and execute full test suite.
-     - [ ] If all tests pass, commit updated `Dockerfile` and `.asd` dependencies.
+***** TODO Check for new Debian security patches (`apt-get update` check)
+***** TODO Check for new `signal-cli` releases (compare vs v0.14.0)
+***** TODO Check for new Quicklisp distribution (monthly snapshot)
+***** TODO Verification: Update `Dockerfile`, run `docker-compose build --no-cache`, and execute full test suite
+***** TODO If all tests pass, commit updated `Dockerfile` and `.asd` dependencies
 
 *** TRACK: COMMUNITY & DOCS
 **** TODO Write Quickstart Guide
@@ -621,7 +1040,7 @@ Institutionalizing the virtual software house operating system.
 - State "DONE" from "NEXT" [2026-03-22 Sun 15:45]
 :END:
 
-*** DONE Apply Engineering Loop to `org-agent` Phase 1 (Core Loop)
+*** DONE Apply Engineering Loop to `opencortex` Phase 1 (Core Loop)
 :PROPERTIES:
 :CREATED: [2026-03-22 Sun 15:30]
 :ASSIGNED: Technical Analyst
@@ -789,8 +1208,8 @@ Defining and maintaining high-integrity KM and GTD workflows.
 :END:
 
 Detected ~1,300 entries missing the `:CREATED:` property during the Engineering Phase E (Chaos) audit.
-- [ ] Implement inference logic to restore historical timestamps (via Git or context).
-- [ ] Batch repair `inbox-emacs.org`, `inbox-atoms.org`, and `inbox-posts.org`.
+**** TODO Implement inference logic to restore historical timestamps (via Git or context)
+**** TODO Batch repair `inbox-emacs.org`, `inbox-atoms.org`, and `inbox-posts.org`
 
 ** Agora Gap Verification
 :PROPERTIES:
@@ -1092,9 +1511,8 @@ A modular manual of different areas to go with different activities. Fits in the
 
 ** Architecture Astronaut Archive
 *** TODO Implement Privacy-Aware Background Indexer (Local hashes for @personal, Semantic for others)
-*** TODO Decouple Transport from Protocol (True Actuator-Agnosticism in communication.lisp)
 *** TODO Implement communication protocol Backpressure Handling (Queue bounds and BUSY frames in communication.lisp)
-*** TODO Implement Cognitive Loop "Rut" Recovery (Dynamic Escalation in org-skill-lisp-validator)
+*** TODO Implement Cognitive Cycle "Rut" Recovery (Dynamic Escalation in org-skill-lisp-validator)
 *** TODO Implement Asynchronous Event Bus for Telemetry (core.lisp)
 *** TODO Implement Memory Eviction and Lazy Loading (LRU Cache in memory.lisp)
 *** TODO Implement Two-Speed Reflection (Immediate :post-action + Latent Heartbeat)
@@ -1102,7 +1520,7 @@ A modular manual of different areas to go with different activities. Fits in the
 *** TODO Implement Intent-Shift Detector (Semantic topic-shift flagging in neuro.lisp)
 *** TODO Implement Cognitive Economics (Dynamic LLM routing based on 2x2 matrix complexity)
 *** TODO Implement Micro-Prolog Logic Engine (Lisp-native unification & pattern matching for Memory)
-*** TODO Implement Sovereign Logic Synthesis (Hybrid SubSys2: Neural pattern detection + Symbolic rule generation)
+*** TODO Implement Autonomous Logic Synthesis (Hybrid SubSys2: Neural pattern detection + Symbolic rule generation)
 *** TODO Implement Continuous Vibe (Sentiment-weighted personality in system-prompt)
 *** TODO Implement Search-Before-Think Bridge (Autonomous target-id population via vector search in perceive-gate)
 *** TODO Implement Belief Revision & Reconciliation (Audit deltas for contradictions in scribe-engine.lisp)

gtd_archive_2026

@@ -13664,7 +13664,7 @@ CLOSED: [2026-04-04 Sat 17:36]
 
 ​The Proxmox Migration: Move the agent from the low-power machine into a dedicated LXC container on the new rack.
 
- ** ​Phase III: The org-agent Microkernel (The "Native" Phase)
+ ** ​Phase III: The opencortex Microkernel (The "Native" Phase)
 
 ​Hollowing out the modern tools in favor of Lisp.
 ​The Lisp Transition: Replace OpenClaw’s Python logic with your minimalist Common Lisp heartbeat.
@@ -13942,7 +13942,7 @@ Server Rack Assembly: Build the 4080/4040 aluminum skeleton.
 Local AI Capability: Install the RTX 6000 Pros. Move from remote APIs to local inference using Ollama/vLLM (DeepSeek-R1 / Qwen3-Coder).
 The Proxmox Migration: Move the agent from the low-power machine into a dedicated LXC container on the new rack.
 
-***** Phase III: The org-agent Microkernel (The "Native" Phase)
+***** Phase III: The opencortex Microkernel (The "Native" Phase)
 :PROPERTIES:
 :CREATED:  [2026-03-20 Fri 08:20]
 :END:
@@ -13956,16 +13956,16 @@ The final evolution into a self-hosted Lisp Machine.
 The FPGA Sidecar: Activate the hardware-level "Thalamus" to verify Lisp forms.
 Unikernel/Bare Metal: Bootstrap Sol out of the Linux environment and directly onto the hardware, where the Org-mode tree and the Lisp Heap become the operating system.
 
-***** Org-agent
+***** OpenCortex
 :PROPERTIES:
 :CREATED:  [2026-03-20 Fri 08:00]
 :END:
 
 By formalizing this, you are effectively designing the blueprint for Sol.
-To answer your biggest question first: No, org-agent will not replace OpenCode or the Claude Agent SDK—it will act as their orchestrator and wrapper. Tools like OpenCode (which focuses on terminal-based, plan-first coding with AGENTS.md) and the Claude Agent SDK (which provides programmatic access to Anthropic's tool-calling and multi-agent teams) are phenomenal execution engines. However, they are built around Markdown, JSON, and Python/TypeScript ecosystems.
-org-agent replaces their management layer. Instead of letting OpenCode or Claude dictate your workflow, org-agent sits above them. When org-agent decides a complex coding task is required, it simply invokes OpenCode or a Claude subagent via a CLI or API call, passing along a compiled .org file as context.
+To answer your biggest question first: No, opencortex will not replace OpenCode or the Claude Agent SDK—it will act as their orchestrator and wrapper. Tools like OpenCode (which focuses on terminal-based, plan-first coding with AGENTS.md) and the Claude Agent SDK (which provides programmatic access to Anthropic's tool-calling and multi-agent teams) are phenomenal execution engines. However, they are built around Markdown, JSON, and Python/TypeScript ecosystems.
+opencortex replaces their management layer. Instead of letting OpenCode or Claude dictate your workflow, opencortex sits above them. When opencortex decides a complex coding task is required, it simply invokes OpenCode or a Claude subagent via a CLI or API call, passing along a compiled .org file as context.
 Here is the developer brief for building the system.
-Project Brief: org-agent
+Project Brief: opencortex
 Mission: Build a hyper-minimalist, self-editing, proactive AI agent framework in Common Lisp. The system must use Org-mode as its exclusive interface for memory, state, and skill configuration, rejecting Markdown and JSON overhead.
 Target Environment: A Linux/Proxmox homelab, running local inference servers, heavily utilizing GitOps and Lisp-based development.
 1. Core Architecture (The Lisp Microkernel)
@@ -13979,18 +13979,18 @@ Instead of relying on SKILL.md or OpenCode's AGENTS.md, all capabilities are def
  * Dynamic Loading: The agent reads these files on boot. If the agent generates a new .org file via an LLM output, it instantly acquires that new skill on the next heartbeat.
  * Progressive Disclosure: To save token context, the agent only loads the #+DESCRIPTION of a skill initially. It must explicitly request the full #+BEGIN_SRC implementation if it decides to use it.
 3. LLMs and Coding Agents as "Effectors"
-org-agent treats AI models and external SDKs exactly like it treats a Proxmox server—as a downstream tool to be managed.
-| External Tool          | How org-agent Uses It                                                                                                             | Trade-off                                                            |
+opencortex treats AI models and external SDKs exactly like it treats a Proxmox server—as a downstream tool to be managed.
+| External Tool          | How opencortex Uses It                                                                                                             | Trade-off                                                            |
 |------------------------+-----------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------------------------------|
 | Local Inference (vLLM) | A base skill (llm-local.org) containing an HTTP POST request to your RTX 6000 cluster for fast, cheap, private reasoning.                | Requires manual mapping of Lisp s-expressions to the local model's API. |
-| OpenCode             | A wrapper skill (skill-opencode.org) that triggers the opencode CLI to execute a massive refactoring job, returning the git diff to org-agent. | Abandons OpenCode's native TUI in favor of headless execution.        |
+| OpenCode             | A wrapper skill (skill-opencode.org) that triggers the opencode CLI to execute a massive refactoring job, returning the git diff to opencortex. | Abandons OpenCode's native TUI in favor of headless execution.        |
 | Claude Agent SDK     | A wrapper skill that triggers a Python script leveraging Anthropic's SDK to spin up a multi-agent "Team" for deep architectural planning.  | Costs external API tokens; requires Python alongside Lisp.             |
 4. Security & Isolation
-Because org-agent runs directly on the host machine to manage Proxmox and GitOps, security is handled via strict allow-lists within the Lisp kernel.
+Because opencortex runs directly on the host machine to manage Proxmox and GitOps, security is handled via strict allow-lists within the Lisp kernel.
  * The LLM backend is instructed to output strictly formatted Lisp s-expressions (e.g., (invoke-skill "proxmox" "restart-staging")).
  * The Lisp Executor will only evaluate forms where the car (the function name) matches a predefined, safe whitelist.
 The Verdict on the Workflow
-By building org-agent, you are creating a system where your daily GTD notes, your infrastructure commands, and your AI's source code all share the exact same syntax. It is the ultimate manifestation of "Code is Data."
+By building opencortex, you are creating a system where your daily GTD notes, your infrastructure commands, and your AI's source code all share the exact same syntax. It is the ultimate manifestation of "Code is Data."
 Would you like me to draft the Lisp parser function that reads an .org skill file and translates its #+NAME and #+BEGIN_SRC blocks into callable Lisp functions for the agent's whitelist?
 
 ***** Agora
@@ -15109,4 +15109,132 @@ CLOSED: [2026-04-04 Sat 17:39]
 :ARCHIVE_CATEGORY: wip-block-goose-an-open-source-extensible-AI-agent-2026-04-04-17-39-47-wLfQw5
 :ARCHIVE_TODO: DONE
 :END:
+*** 2026-04-14 Tuesday
+**** DONE [[https://torath.gov.eg/books/bookAuthority/books-listing?seriesName=%D8%AA%D8%A7%D8%B1%D9%8A%D8%AE%20%D8%A7%D9%84%D9%85%D8%B5%D8%B1%D9%8A%D9%8A%D9%86&page=1][تاريخ المصريين - الهيئة المصرية العامة للكتاب - تراث مصر الرقمي]]
+CLOSED: [2026-04-14 Tue 11:47]
+:PROPERTIES:
+:TITLE: تاريخ المصريين - الهيئة المصرية العامة للكتاب - تراث مصر الرقمي
+:URI: https://torath.gov.eg/books/bookAuthority/books-listing?seriesName=%D8%AA%D8%A7%D8%B1%D9%8A%D8%AE%20%D8%A7%D9%84%D9%85%D8%B5%D8%B1%D9%8A%D9%8A%D9%86&page=1
+:CREATED: [2026-04-14 Tue 11:14]
+:ID:       تاريخ-المصريين-الهيئة-المصرية-العامة-للكتاب-تراث-2026-04-14-11-47-42
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:47
+:ARCHIVE_FILE: /tmp/org-gtd/wip-تاريخ-المصريين-الهيئة-المصرية-العامة-للكتاب-تراث-2026-04-14-11-47-42-B4uIxI.org
+:ARCHIVE_CATEGORY: wip-تاريخ-المصريين-الهيئة-المصرية-العامة-للكتاب-تراث-2026-04-14-11-47-42-B4uIxI
+:ARCHIVE_TODO: DONE
+:END:
+
+**** DONE [[https://www.arsheef.org/digitized-collections][Digitized Collections — arsheef]]
+CLOSED: [2026-04-14 Tue 11:47]
+:PROPERTIES:
+:TITLE: Digitized Collections — arsheef
+:URI: https://www.arsheef.org/digitized-collections
+:CREATED: [2026-04-14 Tue 11:02]
+:ID:       Digitized-Collections-arsheef-2026-04-14-11-47-49
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:47
+:ARCHIVE_FILE: /tmp/org-gtd/wip-Digitized-Collections-arsheef-2026-04-14-11-47-49-yc2uyh.org
+:ARCHIVE_CATEGORY: wip-Digitized-Collections-arsheef-2026-04-14-11-47-49-yc2uyh
+:ARCHIVE_TODO: DONE
+:END:
+
+**** DONE [[https://archive.org/search?query=%D9%83%D8%AA%D8%A7%D8%A8+%D8%A7%D9%84%D9%87%D9%84%D8%A7%D9%84][Internet Archive: Digital Library of Free & Borrowable Texts, Movies, Music & Wayback Machine]]
+CLOSED: [2026-04-14 Tue 11:47]
+:PROPERTIES:
+:TITLE: Internet Archive: Digital Library of Free & Borrowable Texts, Movies, Music & Wayback Machine
+:URI: https://archive.org/search?query=%D9%83%D8%AA%D8%A7%D8%A8+%D8%A7%D9%84%D9%87%D9%84%D8%A7%D9%84
+:CREATED: [2026-04-14 Tue 11:02]
+:ID:       Internet-Archive-Digital-Library-of-Free-and-2026-04-14-11-47-54
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:47
+:ARCHIVE_FILE: /tmp/org-gtd/wip-Internet-Archive-Digital-Library-of-Free-and-2026-04-14-11-47-54-Z0t1BU.org
+:ARCHIVE_CATEGORY: wip-Internet-Archive-Digital-Library-of-Free-and-2026-04-14-11-47-54-Z0t1BU
+:ARCHIVE_TODO: DONE
+:END:
+
+A complete archive of كتاب الهلال.
+
+**** DONE [[https://community.home-assistant.io/t/new-weather-radar-card/417635][New Weather Radar Card - Share your Projects! / Dashboards & Frontend - Home Assistant Community]]
+CLOSED: [2026-04-14 Tue 11:48]
+:PROPERTIES:
+:TITLE: New Weather Radar Card - Share your Projects! / Dashboards & Frontend - Home Assistant Community
+:URI: https://community.home-assistant.io/t/new-weather-radar-card/417635
+:CREATED: [2026-04-14 Tue 11:11]
+:ID:       New-Weather-Radar-Card-Share-your-Projects-2026-04-14-11-47-57
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:48
+:ARCHIVE_FILE: /tmp/org-gtd/wip-New-Weather-Radar-Card-Share-your-Projects-2026-04-14-11-47-57-IY5m4O.org
+:ARCHIVE_CATEGORY: wip-New-Weather-Radar-Card-Share-your-Projects-2026-04-14-11-47-57-IY5m4O
+:ARCHIVE_TODO: DONE
+:END:
+
+**** DONE [[https://community.home-assistant.io/t/music-assistant-player-card-control-your-players-adjust-transfer-and-join-queues-and-browse-your-media/929266][Music Assistant Player Card - Control your players, adjust, transfer, and join queues, and browse your media! - Share your Projects! / Dashboards & Frontend - Home Assistant Community]]
+CLOSED: [2026-04-14 Tue 11:48]
+:PROPERTIES:
+:TITLE: Music Assistant Player Card - Control your players, adjust, transfer, and join queues, and browse your media! - Share your Projects! / Dashboards & Frontend - Home Assistant Community
+:URI: https://community.home-assistant.io/t/music-assistant-player-card-control-your-players-adjust-transfer-and-join-queues-and-browse-your-media/929266
+:CREATED: [2026-04-14 Tue 11:11]
+:ID:       Music-Assistant-Player-Card-Control-your-players-2026-04-14-11-48-11
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:48
+:ARCHIVE_FILE: /tmp/org-gtd/wip-Music-Assistant-Player-Card-Control-your-players-2026-04-14-11-48-11-k7UVfa.org
+:ARCHIVE_CATEGORY: wip-Music-Assistant-Player-Card-Control-your-players-2026-04-14-11-48-11-k7UVfa
+:ARCHIVE_TODO: DONE
+:END:
+
+**** DONE [[https://github.com/nimroddolev/chime_tts][nimroddolev/chime_tts: A custom Home Assistant integration to play combined audio files before and/or after text-to-speech (TTS) messages]]
+CLOSED: [2026-04-14 Tue 11:49]
+:PROPERTIES:
+:TITLE: nimroddolev/chime_tts: A custom Home Assistant integration to play combined audio files before and/or after text-to-speech (TTS) messages
+:URI: https://github.com/nimroddolev/chime_tts
+:CREATED: [2026-04-14 Tue 11:11]
+:ID:       nimroddolev-chime-tts-A-custom-Home-Assistant-2026-04-14-11-49-05
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:49
+:ARCHIVE_FILE: /tmp/org-gtd/wip-nimroddolev-chime-tts-A-custom-Home-Assistant-2026-04-14-11-49-05-je5UGn.org
+:ARCHIVE_CATEGORY: wip-nimroddolev-chime-tts-A-custom-Home-Assistant-2026-04-14-11-49-05-je5UGn
+:ARCHIVE_TODO: DONE
+:END:
+
+**** DONE [[https://github.com/Clooos/bubble-card][Clooos/Bubble-Card: Bubble Card is a minimalist card collection for Home Assistant with a nice pop-up touch.]]
+CLOSED: [2026-04-14 Tue 11:49]
+:PROPERTIES:
+:TITLE: Clooos/Bubble-Card: Bubble Card is a minimalist card collection for Home Assistant with a nice pop-up touch.
+:URI: https://github.com/Clooos/bubble-card
+:CREATED: [2026-04-14 Tue 11:11]
+:ID:       Clooos-Bubble-Card-Bubble-Card-is-a-minimalist-2026-04-14-11-49-19
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:49
+:ARCHIVE_FILE: /tmp/org-gtd/wip-Clooos-Bubble-Card-Bubble-Card-is-a-minimalist-2026-04-14-11-49-19-AGBrix.org
+:ARCHIVE_CATEGORY: wip-Clooos-Bubble-Card-Bubble-Card-is-a-minimalist-2026-04-14-11-49-19-AGBrix
+:ARCHIVE_TODO: DONE
+:END:
+
+**** DONE [[https://github.com/PRProd/HA-Firemote][PRProd/HA-Firemote: Apple TV, Amazon Fire TV, Chromecast, Homatics, NVIDIA Shield, onn., Roku, Xiaomi Mi, and Android TV remote control card for Home Assistant]]
+CLOSED: [2026-04-14 Tue 11:49]
+:PROPERTIES:
+:TITLE: PRProd/HA-Firemote: Apple TV, Amazon Fire TV, Chromecast, Homatics, NVIDIA Shield, onn., Roku, Xiaomi Mi, and Android TV remote control card for Home Assistant
+:URI: https://github.com/PRProd/HA-Firemote
+:CREATED: [2026-04-14 Tue 11:12]
+:ID:       PRProd-HA-Firemote-Apple-TV-Amazon-Fire-TV-2026-04-14-11-49-22
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:49
+:ARCHIVE_FILE: /tmp/org-gtd/wip-PRProd-HA-Firemote-Apple-TV-Amazon-Fire-TV-2026-04-14-11-49-22-oxZinO.org
+:ARCHIVE_CATEGORY: wip-PRProd-HA-Firemote-Apple-TV-Amazon-Fire-TV-2026-04-14-11-49-22-oxZinO
+:ARCHIVE_TODO: DONE
+:END:
+
+**** DONE [[https://www.mogawdat.com/][Mo Gawdat | AI + Happiness]]
+CLOSED: [2026-04-14 Tue 11:49]
+:PROPERTIES:
+:TITLE: Mo Gawdat | AI + Happiness
+:URI: https://www.mogawdat.com/
+:CREATED: [2026-04-14 Tue 11:15]
+:ID:       Mo-Gawdat-AI-plus-Happiness-2026-04-14-11-49-27
+:ORG_GTD:  Reference
+:ARCHIVE_TIME: 2026-04-14 Tue 11:49
+:ARCHIVE_FILE: /tmp/org-gtd/wip-Mo-Gawdat-AI-plus-Happiness-2026-04-14-11-49-27-41t26y.org
+:ARCHIVE_CATEGORY: wip-Mo-Gawdat-AI-plus-Happiness-2026-04-14-11-49-27-41t26y
+:ARCHIVE_TODO: DONE
+:END:
 

inbox.org

@@ -2,3 +2,312 @@
 #+begin_comment
 This is the inbox. Everything goes in here when you capture it.
 #+end_comment
+
+*  [[https://x.com/michael_chomsky/status/2043369126631207096][Michael on X: "Garry is kinda correct here, but is oversimplifying memory. Harrison (the author of the original article) makes a very good point but also makes memory sound easier than it is. (before reading this article, note that I wrote down my thoughts and then passed it through Claude" / X]]
+:PROPERTIES:
+:TITLE: Michael on X: "Garry is kinda correct here, but is oversimplifying memory. Harrison (the author of the original article) makes a very good point but also makes memory sound easier than it is. (before reading this article, note that I wrote down my thoughts and then passed it through Claude" / X
+:URI: https://x.com/michael_chomsky/status/2043369126631207096
+:CREATED: [2026-04-14 Tue 11:17]
+:END:
+
+*  [[https://x.com/chrysb/status/2043020014035570784][Chrys Bader on X: "Why long-term memory for LLMs remains unsolved" / X]]
+:PROPERTIES:
+:TITLE: Chrys Bader on X: "Why long-term memory for LLMs remains unsolved" / X
+:URI: https://x.com/chrysb/status/2043020014035570784
+:CREATED: [2026-04-14 Tue 11:18]
+:END:
+
+*  [[https://github.com/garrytan/gbrain][garrytan/gbrain: Garry's Opinionated OpenClaw/Hermes Agent Brain]]
+:PROPERTIES:
+:TITLE: garrytan/gbrain: Garry's Opinionated OpenClaw/Hermes Agent Brain
+:URI: https://github.com/garrytan/gbrain
+:CREATED: [2026-04-14 Tue 11:18]
+:END:
+
+*  [[https://github.com/karpathy/autoresearch][karpathy/autoresearch: AI agents running research on single-GPU nanochat training automatically]]
+:PROPERTIES:
+:TITLE: karpathy/autoresearch: AI agents running research on single-GPU nanochat training automatically
+:URI: https://github.com/karpathy/autoresearch
+:CREATED: [2026-04-14 Tue 11:18]
+:END:
+
+*  [[https://x.com/garrytan/status/2042925773300908103][Garry Tan on X: "Thin Harness, Fat Skills" / X]]
+:PROPERTIES:
+:TITLE: Garry Tan on X: "Thin Harness, Fat Skills" / X
+:URI: https://x.com/garrytan/status/2042925773300908103
+:CREATED: [2026-04-14 Tue 11:18]
+:END:
+
+*  [[https://github.com/xdevplatform/xmcp][xdevplatform/xmcp: MCP server for the X API]]
+:PROPERTIES:
+:TITLE: xdevplatform/xmcp: MCP server for the X API
+:URI: https://github.com/xdevplatform/xmcp
+:CREATED: [2026-04-14 Tue 11:18]
+:END:
+
+*  [[https://x.com/WinterArc2125/status/2040828031707570233][Winter on X: "Most people don’t realize this: You get 1,500 free daily requests to Gemma 4 31B on @GoogleAIStudio. That’s plenty of free inference (imo). And you can route it into @NousResearch Hermes Agent via Vercel’s AI Gateway: 1. Create an API key on Google AI Studio 2. Add it under" / X]]
+:PROPERTIES:
+:TITLE: Winter on X: "Most people don’t realize this: You get 1,500 free daily requests to Gemma 4 31B on @GoogleAIStudio. That’s plenty of free inference (imo). And you can route it into @NousResearch Hermes Agent via Vercel’s AI Gateway: 1. Create an API key on Google AI Studio 2. Add it under" / X
+:URI: https://x.com/WinterArc2125/status/2040828031707570233
+:CREATED: [2026-04-14 Tue 11:19]
+:END:
+
+*  [[https://github.com/elebumm/RedditVideoMakerBot][elebumm/RedditVideoMakerBot: Create Reddit Videos with just✨ one command ✨]]
+:PROPERTIES:
+:TITLE: elebumm/RedditVideoMakerBot: Create Reddit Videos with just✨ one command ✨
+:URI: https://github.com/elebumm/RedditVideoMakerBot
+:CREATED: [2026-04-14 Tue 11:19]
+:END:
+
+*  [[https://x.com/PawelHuryn/status/2040519790779900075][Paweł Huryn on X: "After the llama.cpp fix, we can finally use gemma-4 with Claude Code: Step 1: - Windows: winget install llama.cpp - MacOS: brew install llama.cpp More: https://t.co/2Gq2cdl5hy Step 2: - llama-server -hf ggml-org/gemma-4-E2B-it-GGUF (https://t.co/3kxuATDZL6) OR - llama-server https://t.co/NFIrI1wXtH" / X]]
+:PROPERTIES:
+:TITLE: Paweł Huryn on X: "After the llama.cpp fix, we can finally use gemma-4 with Claude Code: Step 1: - Windows: winget install llama.cpp - MacOS: brew install llama.cpp More: https://t.co/2Gq2cdl5hy Step 2: - llama-server -hf ggml-org/gemma-4-E2B-it-GGUF (https://t.co/3kxuATDZL6) OR - llama-server https://t.co/NFIrI1wXtH" / X
+:URI: https://x.com/PawelHuryn/status/2040519790779900075
+:CREATED: [2026-04-14 Tue 11:19]
+:END:
+
+*  [[https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f][llm-wiki · GitHub]]
+:PROPERTIES:
+:TITLE: llm-wiki · GitHub
+:URI: https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f
+:CREATED: [2026-04-14 Tue 11:19]
+:END:
+
+*  [[https://x.com/kevingu/status/2039843234760073341][Kevin Gu on X: "AutoAgent: first open source library for self-optimizing agents" / X]]
+:PROPERTIES:
+:TITLE: Kevin Gu on X: "AutoAgent: first open source library for self-optimizing agents" / X
+:URI: https://x.com/kevingu/status/2039843234760073341
+:CREATED: [2026-04-14 Tue 11:20]
+:END:
+
+*  [[https://github.com/repowise-dev/claude-code-prompts][repowise-dev/claude-code-prompts: Independently authored prompt templates for AI coding agents — system prompts, tool prompts, agent delegation, memory management, and multi-agent coordination. Informed by studying Claude Code.]]
+:PROPERTIES:
+:TITLE: repowise-dev/claude-code-prompts: Independently authored prompt templates for AI coding agents — system prompts, tool prompts, agent delegation, memory management, and multi-agent coordination. Informed by studying Claude Code.
+:URI: https://github.com/repowise-dev/claude-code-prompts
+:CREATED: [2026-04-14 Tue 11:20]
+:END:
+
+*  [[https://x.com/ryancarson/status/2039786704731541903][Ryan Carson on X: "How to turn your OpenClaw into the world's best assistant" / X]]
+:PROPERTIES:
+:TITLE: Ryan Carson on X: "How to turn your OpenClaw into the world's best assistant" / X
+:URI: https://x.com/ryancarson/status/2039786704731541903
+:CREATED: [2026-04-14 Tue 11:20]
+:END:
+
+*  [[https://vitalik.eth.limo/general/2026/04/02/secure_llms.html][My self-sovereign / local / private / secure LLM setup, April 2026]]
+:PROPERTIES:
+:TITLE: My self-sovereign / local / private / secure LLM setup, April 2026
+:URI: https://vitalik.eth.limo/general/2026/04/02/secure_llms.html
+:CREATED: [2026-04-14 Tue 11:20]
+:END:
+
+*  [[https://x.com/TheAhmadOsman/status/2040103488714068245][Ahmad on X: "GPU Memory Math for LLMs (2026 Edition)" / X]]
+:PROPERTIES:
+:TITLE: Ahmad on X: "GPU Memory Math for LLMs (2026 Edition)" / X
+:URI: https://x.com/TheAhmadOsman/status/2040103488714068245
+:CREATED: [2026-04-14 Tue 11:20]
+:END:
+
+*  [[https://x.com/gauri__gupta/status/2040251170099524025][Gauri Gupta on X: "auto-harness: Self improving agentic systems with auto-evals (open-sourced !)" / X]]
+:PROPERTIES:
+:TITLE: Gauri Gupta on X: "auto-harness: Self improving agentic systems with auto-evals (open-sourced !)" / X
+:URI: https://x.com/gauri__gupta/status/2040251170099524025
+:CREATED: [2026-04-14 Tue 11:21]
+:END:
+
+*  [[https://x.com/PromptLLM/status/2040478865949139014][Prompter on X: "CURE procrastination by gamifying your life with AI (prompt included)" / X]]
+:PROPERTIES:
+:TITLE: Prompter on X: "CURE procrastination by gamifying your life with AI (prompt included)" / X
+:URI: https://x.com/PromptLLM/status/2040478865949139014
+:CREATED: [2026-04-14 Tue 11:21]
+:END:
+
+*  [[https://x.com/chrysb/status/2043020014035570784][Chrys Bader on X: "Why long-term memory for LLMs remains unsolved" / X]]
+:PROPERTIES:
+:TITLE: Chrys Bader on X: "Why long-term memory for LLMs remains unsolved" / X
+:URI: https://x.com/chrysb/status/2043020014035570784
+:CREATED: [2026-04-14 Tue 11:21]
+:END:
+
+*  [[https://github.com/ValueCell-ai/ClawX][ValueCell-ai/ClawX: ClawX is a desktop app that provides a graphical interface for OpenClaw AI agents. It turns CLI-based AI orchestration into a desktop experience without using the terminal. China website is https://clawx.com.cn.]]
+:PROPERTIES:
+:TITLE: ValueCell-ai/ClawX: ClawX is a desktop app that provides a graphical interface for OpenClaw AI agents. It turns CLI-based AI orchestration into a desktop experience without using the terminal. China website is https://clawx.com.cn.
+:URI: https://github.com/ValueCell-ai/ClawX
+:CREATED: [2026-04-16 Thu 16:33]
+:END:
+
+*  [[https://github.com/sgoudelis/ground-station][sgoudelis/ground-station: Ground Station is all-in-one satellite monitoring suite]]
+:PROPERTIES:
+:TITLE: sgoudelis/ground-station: Ground Station is all-in-one satellite monitoring suite
+:URI: https://github.com/sgoudelis/ground-station
+:CREATED: [2026-04-17 Fri 14:52]
+:END:
+
+*  [[https://platform.minimax.io/docs/guides/pricing-token-plan][Token Plan - MiniMax API Docs]]
+:PROPERTIES:
+:TITLE: Token Plan - MiniMax API Docs
+:URI: https://platform.minimax.io/docs/guides/pricing-token-plan
+:CREATED: [2026-04-17 Fri 14:52]
+:END:
+
+*  [[https://github.com/siddsachar/Thoth][siddsachar/Thoth: Thoth - Personal AI Sovereignty. A local-first AI assistant with integrated tools, a personal knowledge graph, voice, vision, shell, browser automation, scheduled tasks, health tracking, and messaging channels. Run locally via Ollama or add opt-in cloud models. Your data stays on your machine.]]
+:PROPERTIES:
+:TITLE: siddsachar/Thoth: Thoth - Personal AI Sovereignty. A local-first AI assistant with integrated tools, a personal knowledge graph, voice, vision, shell, browser automation, scheduled tasks, health tracking, and messaging channels. Run locally via Ollama or add opt-in cloud models. Your data stays on your machine.
+:URI: https://github.com/siddsachar/Thoth
+:CREATED: [2026-04-17 Fri 14:52]
+:END:
+
+*  [[https://www.jori.com/en/products/pacific-jr-9700][Pacific Pure | Sofas | Product | Design furniture | JORI]] :furniture:years:
+:PROPERTIES:
+:TITLE: Pacific Pure | Sofas | Product | Design furniture | JORI
+:URI: https://www.jori.com/en/products/pacific-jr-9700
+:CREATED: [2026-04-21 Tue 15:25]
+:END:
+
+*  [[https://papers.ssrn.com/sol3/papers.cfm?abstract_id=6372438][AI Agent Traps by Matija Franklin, Nenad Tomašev, Julian Jacobs, Joel Z. Leibo, Simon Osindero :: SSRN]]
+:PROPERTIES:
+:TITLE: AI Agent Traps by Matija Franklin, Nenad Tomašev, Julian Jacobs, Joel Z. Leibo, Simon Osindero :: SSRN
+:URI: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=6372438
+:CREATED: [2026-04-21 Tue 15:26]
+:END:
+
+*  [[https://www.storagereview.com/review/comino-grando-rtx-pro-6000-review-768gb-of-vram-in-a-liquid-cooled-4u-chassis][Comino Grando RTX PRO 6000 Review: 768GB of VRAM in a Liquid-Cooled 4U Chassis - StorageReview.com]]
+:PROPERTIES:
+:TITLE: Comino Grando RTX PRO 6000 Review: 768GB of VRAM in a Liquid-Cooled 4U Chassis - StorageReview.com
+:URI: https://www.storagereview.com/review/comino-grando-rtx-pro-6000-review-768gb-of-vram-in-a-liquid-cooled-4u-chassis
+:CREATED: [2026-04-21 Tue 15:26]
+:END:
+
+*  [[https://x.com/elvissun/status/2044784140831301728/photo/1][Elvis on X: "some agentic engineering realization: stop reviewing code. start reviewing contracts. and here's what i mean. the highest leverage work right now is drawing the right boundaries in your system. i've been splitting the system into multiple sub-systems, each with clearly defined https://t.co/Hy0d9WHI1m" / X]]
+:PROPERTIES:
+:TITLE: Elvis on X: "some agentic engineering realization: stop reviewing code. start reviewing contracts. and here's what i mean. the highest leverage work right now is drawing the right boundaries in your system. i've been splitting the system into multiple sub-systems, each with clearly defined https://t.co/Hy0d9WHI1m" / X
+:URI: https://x.com/elvissun/status/2044784140831301728/photo/1
+:CREATED: [2026-04-21 Tue 15:26]
+:END:
+
+*  [[https://x.com/i/status/2044307601463357791][EverMars on X: "Respect to the Man Chasing AI Immortality, Even Though He's Freeloading Off Our Platform" / X]]
+:PROPERTIES:
+:TITLE: EverMars on X: "Respect to the Man Chasing AI Immortality, Even Though He's Freeloading Off Our Platform" / X
+:URI: https://x.com/i/status/2044307601463357791
+:CREATED: [2026-04-21 Tue 15:26]
+:END:
+
+*  [[https://x.com/i/status/2045289299269070978][Seth Howes on X: "I’ve wanted to do this for a decade. But I never did - I refuse to give any company my DNA. It is me. So this week I sequenced my genome entirely at home. Literally on my kitchen table. I never exposed my DNA sequence to the internet. Not at any point. I used a MinION to do https://t.co/qCzXIGxWsy" / X]]
+:PROPERTIES:
+:TITLE: Seth Howes on X: "I’ve wanted to do this for a decade. But I never did - I refuse to give any company my DNA. It is me. So this week I sequenced my genome entirely at home. Literally on my kitchen table. I never exposed my DNA sequence to the internet. Not at any point. I used a MinION to do https://t.co/qCzXIGxWsy" / X
+:URI: https://x.com/i/status/2045289299269070978
+:CREATED: [2026-04-21 Tue 15:27]
+:END:
+
+*  [[https://arxiv.org/html/2603.21852v2][All elementary functions from a single operator]]
+:PROPERTIES:
+:TITLE: All elementary functions from a single operator
+:URI: https://arxiv.org/html/2603.21852v2
+:CREATED: [2026-04-26 Sun 11:05]
+:END:
+
+*  [[https://github.com/abhigyanpatwari/GitNexus][abhigyanpatwari/GitNexus: GitNexus: The Zero-Server Code Intelligence Engine - GitNexus is a client-side knowledge graph creator that runs entirely in your browser. Drop in a GitHub repo or ZIP file, and get an interactive knowledge graph wit a built in Graph RAG Agent. Perfect for code exploration]]
+:PROPERTIES:
+:TITLE: abhigyanpatwari/GitNexus: GitNexus: The Zero-Server Code Intelligence Engine - GitNexus is a client-side knowledge graph creator that runs entirely in your browser. Drop in a GitHub repo or ZIP file, and get an interactive knowledge graph wit a built in Graph RAG Agent. Perfect for code exploration
+:URI: https://github.com/abhigyanpatwari/GitNexus
+:CREATED: [2026-04-26 Sun 11:05]
+:END:
+
+*  [[https://medium.com/@fzbcwvv/an-overnight-stack-for-qwen3-6-27b-85-tps-125k-context-vision-on-one-rtx-3090-0d95c6291914][An Overnight Stack for Qwen3.6–27B: 85 TPS, 125K Context, Vision — on One RTX 3090 | Medium]]
+:PROPERTIES:
+:TITLE: An Overnight Stack for Qwen3.6–27B: 85 TPS, 125K Context, Vision — on One RTX 3090 | Medium
+:URI: https://medium.com/@fzbcwvv/an-overnight-stack-for-qwen3-6-27b-85-tps-125k-context-vision-on-one-rtx-3090-0d95c6291914
+:CREATED: [2026-04-26 Sun 11:06]
+:END:
+
+*  [[https://x.com/i/status/2047124337191444844][Shiv on X: "A new way to think about composing skills to increase leverage: Skill Graphs 2.0" / X]]
+:PROPERTIES:
+:TITLE: Shiv on X: "A new way to think about composing skills to increase leverage: Skill Graphs 2.0" / X
+:URI: https://x.com/i/status/2047124337191444844
+:CREATED: [2026-04-26 Sun 16:34]
+:END:
+
+*  [[https://x.com/i/status/2047558951303028855][Eric ⚡️ Building... on X: "My 4090 went from 26 -> 154 tok/s Qwen 3.6 27B🤯 Same GPU. Same Q4_K_M . No FP8, no extra quant. The unlock: ik_llama.cpp + speculative decoding using Qwen3-1.7B as the draft model. 85% acceptance rate. Full config + benchmarks 👇🏻 https://t.co/NUZec2Y7J0" / X]]
+:PROPERTIES:
+:TITLE: Eric ⚡️ Building... on X: "My 4090 went from 26 -> 154 tok/s Qwen 3.6 27B🤯 Same GPU. Same Q4_K_M . No FP8, no extra quant. The unlock: ik_llama.cpp + speculative decoding using Qwen3-1.7B as the draft model. 85% acceptance rate. Full config + benchmarks 👇🏻 https://t.co/NUZec2Y7J0" / X
+:URI: https://x.com/i/status/2047558951303028855
+:CREATED: [2026-04-26 Sun 16:34]
+:END:
+
+*  [[https://x.com/i/status/2047033293460410638][Sudo su on X: "for anyone running along, here is the setup. weights from unsloth: https://t.co/b89HJ2JC5O launched with: ./llama-server -m Qwen3.6-27B-Q4_K_M.gguf -ngl 99 -c 262144 -np 1 -fa on --cache-type-k q4_0 --cache-type-v q4_0 same exact flags that held the 3.5 dense baseline at 35.3" / X]]
+:PROPERTIES:
+:TITLE: Sudo su on X: "for anyone running along, here is the setup. weights from unsloth: https://t.co/b89HJ2JC5O launched with: ./llama-server -m Qwen3.6-27B-Q4_K_M.gguf -ngl 99 -c 262144 -np 1 -fa on --cache-type-k q4_0 --cache-type-v q4_0 same exact flags that held the 3.5 dense baseline at 35.3" / X
+:URI: https://x.com/i/status/2047033293460410638
+:CREATED: [2026-04-26 Sun 16:34]
+:END:
+
+*  [[https://x.com/i/status/2046898117241635240][Hasan Toor on X: "Goodbye Claude Code subscription fees. Someone just built a proxy that runs Claude Code completely free... and it's wild. You literally plug in a free NVIDIA API key and point Claude Code at localhost. That's it. It handles everything: - Converts Anthropic API calls to NVIDIA https://t.co/10v4KdymxH" / X]]
+:PROPERTIES:
+:TITLE: Hasan Toor on X: "Goodbye Claude Code subscription fees. Someone just built a proxy that runs Claude Code completely free... and it's wild. You literally plug in a free NVIDIA API key and point Claude Code at localhost. That's it. It handles everything: - Converts Anthropic API calls to NVIDIA https://t.co/10v4KdymxH" / X
+:URI: https://x.com/i/status/2046898117241635240
+:CREATED: [2026-04-26 Sun 16:34]
+:END:
+
+*  [[https://x.com/i/status/2047295369583964385][Graeme on X: "The Local LLM Cheat Sheet for Your 64GB RAM Device We covered 16GB and 32GB already, and 64GB has been the next big request, which I can understand, because this is where things get very interesting. Here's the practical cheat sheet for a 64GB RAM machine for code, math, https://t.co/ohgkjbU0LK" / X]]
+:PROPERTIES:
+:TITLE: Graeme on X: "The Local LLM Cheat Sheet for Your 64GB RAM Device We covered 16GB and 32GB already, and 64GB has been the next big request, which I can understand, because this is where things get very interesting. Here's the practical cheat sheet for a 64GB RAM machine for code, math, https://t.co/ohgkjbU0LK" / X
+:URI: https://x.com/i/status/2047295369583964385
+:CREATED: [2026-04-26 Sun 16:34]
+:END:
+
+*  [[https://github.com/codejunkie99/agentic-stack][codejunkie99/agentic-stack: One brain, many harnesses. Portable .agent/ folder (memory + skills + protocols) that plugs into Claude Code, Cursor, Windsurf, OpenCode, OpenClaw, Hermes, or DIY Python — and keeps its knowledge when you switch.]]
+:PROPERTIES:
+:TITLE: codejunkie99/agentic-stack: One brain, many harnesses. Portable .agent/ folder (memory + skills + protocols) that plugs into Claude Code, Cursor, Windsurf, OpenCode, OpenClaw, Hermes, or DIY Python — and keeps its knowledge when you switch.
+:URI: https://github.com/codejunkie99/agentic-stack
+:CREATED: [2026-04-27 Mon 09:23]
+:END:
+
+*  [[https://github.com/public-apis/public-apis][public-apis/public-apis: A collective list of free APIs]]
+:PROPERTIES:
+:TITLE: public-apis/public-apis: A collective list of free APIs
+:URI: https://github.com/public-apis/public-apis
+:CREATED: [2026-04-27 Mon 09:23]
+:END:
+
+*  [[https://github.com/stanford-iris-lab/meta-harness][stanford-iris-lab/meta-harness: Reference code for the Meta-Harness paper.]]
+:PROPERTIES:
+:TITLE: stanford-iris-lab/meta-harness: Reference code for the Meta-Harness paper.
+:URI: https://github.com/stanford-iris-lab/meta-harness
+:CREATED: [2026-04-27 Mon 09:23]
+:END:
+
+*  [[https://github.com/thePM001/AEP-agent-element-protocol/tree/main][thePM001/AEP-agent-element-protocol: AEP (Agent Element Protocol) v2.5 | Deterministic zero-trust total control and governance protocol for AI agents. | Reduce hallucinations to zero through architecure in all constrained domains of application. | LLMs gave you the engines, AEP gives you the control for the thrusters.]]
+:PROPERTIES:
+:TITLE: thePM001/AEP-agent-element-protocol: AEP (Agent Element Protocol) v2.5 | Deterministic zero-trust total control and governance protocol for AI agents. | Reduce hallucinations to zero through architecure in all constrained domains of application. | LLMs gave you the engines, AEP gives you the control for the thrusters.
+:URI: https://github.com/thePM001/AEP-agent-element-protocol/tree/main
+:CREATED: [2026-04-27 Mon 09:24]
+:END:
+
+*  [[https://x.com/i/status/2048381278953603406][GREG ISENBERG on X: "agreed that the the modern computer probably has to be reinvented 12 "tiny" startup ideas that ride that wave: 1. a "where did I put that" app. you describe what you're looking for in plain english and it searches across every app, folder, email, and slack message you've ever" / X]]
+:PROPERTIES:
+:TITLE: GREG ISENBERG on X: "agreed that the the modern computer probably has to be reinvented 12 "tiny" startup ideas that ride that wave: 1. a "where did I put that" app. you describe what you're looking for in plain english and it searches across every app, folder, email, and slack message you've ever" / X
+:URI: https://x.com/i/status/2048381278953603406
+:CREATED: [2026-04-27 Mon 09:24]
+:END:
+
+*  [[https://github.com/iptv-org/awesome-iptv][iptv-org/awesome-iptv: A curated list of resources related to IPTV]]
+:PROPERTIES:
+:TITLE: iptv-org/awesome-iptv: A curated list of resources related to IPTV
+:URI: https://github.com/iptv-org/awesome-iptv
+:CREATED: [2026-04-27 Mon 09:24]
+:END:
+
+*  [[https://github.com/iptv-org/iptv][iptv-org/iptv: Collection of publicly available IPTV channels from all over the world]]
+:PROPERTIES:
+:TITLE: iptv-org/iptv: Collection of publicly available IPTV channels from all over the world
+:URI: https://github.com/iptv-org/iptv
+:CREATED: [2026-04-27 Mon 09:25]
+:END:
+
+*  [[https://github.com/iptv-org/epg][iptv-org/epg: Utilities for downloading the EPG (Electronic Program Guide) for thousands of TV channels from hundreds of sources.]]
+:PROPERTIES:
+:TITLE: iptv-org/epg: Utilities for downloading the EPG (Electronic Program Guide) for thousands of TV channels from hundreds of sources.
+:URI: https://github.com/iptv-org/epg
+:CREATED: [2026-04-27 Mon 09:25]
+:END:
+

notes/institutional-memory.org

@@ -12,9 +12,9 @@
 - *Solution:* The *Org-Native Skill Standard*. Skills are written entirely as `.org` files. The daemon parses the Org file at startup, extracts `#+begin_src lisp` blocks containing triggers, neuro-prompts, and symbolic verification rules, and dynamically compiles them into the live system using `eval` and `read`.
 - *Heuristic:* The Core is strictly the PTA loop (`core.lisp`, `neuro.lisp`, `symbolic.lisp`). ALL business logic, API connectors, and rule sets MUST live as `.org` files in the `skills/` directory.
 
-** [2026-03-23] Cognitive Loop Architecture (org-agent)
+** [2026-03-23] Cognitive Cycle Architecture (opencortex)
 - *Problem:* Monolithic PTA (Perceive-Think-Act) loops lead to "Neural Drift" where the LLM's unverified suggestions can cause illegal system states or security breaches.
-- *Solution:* Implement the *Four-Stage Cognitive Loop*: Perceive -> Think -> Decide -> Act.
+- *Solution:* Implement the *Four-Stage Cognitive Cycle*: Perceive -> Think -> Decide -> Act.
 - *Heuristic:* Probabilistic Engine (Neural/LLM) is a proposal engine only. Deterministic Engine (Symbolic/Lisp) is the absolute gatekeeper.
 - *Verification:* Never execute an action unless it has passed through `decide()` and been verified against the symbolic Object Store (CLOSOS).
 

notes/project-modular-home-appliances.org

@@ -21,7 +21,7 @@ Define the requirements for modular, open-source, and intelligent home hardware.
 ** 2. User Needs
 - *Physical Modularity:* Easy replacement and upgrade of mechanical and electrical components.
 - *Smart Interfacing:* ESP32-based control boards for connectivity.
-- *Multimodal Control:* Support for smartphone apps, physical modular controllers, and direct `org-agent` AI interaction.
+- *Multimodal Control:* Support for smartphone apps, physical modular controllers, and direct `opencortex` AI interaction.
 - *Sustainability:* Design for longevity, repairability, and efficient power management (inspired by Slate principles).
 
 ** 3. Success Criteria

notes/project-personal-server-appliance.org

@@ -20,7 +20,7 @@ Define the requirements for a modular, user-serviceable, and aesthetically pleas
 
 ** 2. User Needs
 - *Modularity:* Unified backplane for swappable compute, storage, and power modules.
-- *Sovereignty:* Full control over hardware and the software stack (running `org-agent`).
+- *Sovereignty:* Full control over hardware and the software stack (running `opencortex`).
 - *Aesthetics:* Sleek "Hi-Fi" industrial design.
 - *Multimodality:* Integration of SDR, AV, and specialized processors.
 

notes/v1-0-skill-audit-track.org

@@ -1,166 +0,0 @@
-#+TITLE: AUDIT: V1.0 Comprehensive Core Skill Audit
-#+AUTHOR: Gemini CLI (Agent)
-#+DATE: [2026-04-09 Thu]
-#+FILETAGS: :audit:kernel:psf:
-#+STARTUP: overview
-
-* Overview
-This audit systematically reviews the 39 core skills of the Org-Agent for compliance with the V1.0 standards:
-1. **Safety:** Prevention of code injection, proper sandboxing, and actuator safety.
-2. **Merkle-Tree Integration:** Proper use of the native Lisp Merkle-Tree versioning for undo/rollback.
-3. **Core Invariants:** Adherence to Sovereignty, Mastery, Zero-Bloat, Transparency, and Sustainability.
-
-* Audit Progress [6/28]
-** DONE org-skill-agent.org [X]
-   - COMPLIANT: Correctly defines and enforces Core Invariants.
-   - SAFETY: High. Implements baseline symbolic gating.
-   - MERKLE: N/A (Read-only/Policy only).
-** DONE org-skill-llm-gateway.org [X]
-   - COMPLIANT: Consolidates 6 providers into a single high-integrity gate.
-   - SAFETY: HIGH. Fixed URL key leaks, standardized headers, and centralized credential masking.
-   - MERKLE: N/A (Stateless dispatch).
-** DONE org-skill-credentials-vault.org [X]
-   - COMPLIANT: Unified high-security enclave for API keys and cookies.
-   - SAFETY: HIGH. Mandatory credential masking in logs and secure Object Store persistence.
-   - MERKLE: COMPLIANT. Setting secrets triggers Merkle snapshots.
-** DONE org-skill-homoiconic-memory.org [X]
-   - COMPLIANT: Unified grammar, bridge, and normalization.
-   - SAFETY: HIGH. recursive AST walker for ID injection and structural validation.
-   - MERKLE: COMPLIANT. Normalization occurs during ingest/save, which are Merkle-versioned events.
-** DONE org-skill-state-persistence.org [X]
-   - COMPLIANT: Unified local SBCL image dumps with decentralized IPFS checkpointing.
-   - SAFETY: HIGH. Implements safe restoration paths and credential masking.
-   - MERKLE: COMPLIANT. This is the primary persistence layer for the Merkle-Tree object store.
-** DONE org-skill-event-orchestrator.org [X]
-   - COMPLIANT: Unified Cron, Hooks, and Routing into a single central control unit.
-   - SAFETY: HIGH. Implements error isolation for automated tasks and hooks.
-   - MERKLE: COMPLIANT. Registering hooks or tasks triggers Merkle snapshots.
-** DONE org-skill-cron.org [X] (CONSOLIDATED -> org-skill-event-orchestrator.org)
-** DONE org-skill-hook-manager.org [X] (CONSOLIDATED -> org-skill-event-orchestrator.org)
-** DONE org-skill-router.org [X] (CONSOLIDATED -> org-skill-event-orchestrator.org)
-** DONE org-skill-memory-archivist.org [X] (CONSOLIDATED -> org-skill-state-persistence.org)
-** DONE org-skill-object-store-persistence.org [X] (CONSOLIDATED -> org-skill-state-persistence.org)
-** DONE org-skill-ast-normalization.org [X] (CONSOLIDATED -> org-skill-homoiconic-memory.org)
-** DONE org-skill-org-json-bridge.org [X] (CONSOLIDATED -> org-skill-homoiconic-memory.org)
-** DONE org-skill-org-mode.org [X] (CONSOLIDATED -> org-skill-homoiconic-memory.org)
-** DONE org-skill-auth-api-key.org [X] (CONSOLIDATED -> org-skill-credentials-vault.org)
-** DONE org-skill-auth-google-oauth.org [X] (CONSOLIDATED -> org-skill-credentials-vault.org)
-** DONE org-skill-provider-anthropic.org [X] (CONSOLIDATED -> org-skill-llm-gateway.org)
-** DONE org-skill-provider-gemini.org [X] (CONSOLIDATED -> org-skill-llm-gateway.org)
-** DONE org-skill-provider-groq.org [X] (CONSOLIDATED -> org-skill-llm-gateway.org)
-** DONE org-skill-provider-ollama.org [X] (CONSOLIDATED -> org-skill-llm-gateway.org)
-** DONE org-skill-provider-openai.org [X] (CONSOLIDATED -> org-skill-llm-gateway.org)
-** DONE org-skill-provider-openrouter.org [X] (CONSOLIDATED -> org-skill-llm-gateway.org)
-** DONE org-skill-chaos.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Sovereignty Violation)
-   - ISSUE: Lacks an "Active Production" gate to prevent accidental chaos during real work. No Merkle-Tree checkpoints before/after stress tests to allow for full-system rollback.
-   - SAFETY: MEDIUM (Adversarial by design, but ungated).
-   - MERKLE: FAILED.
-** DONE org-skill-chat.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Technical Mastery Violation)
-   - ISSUE: Uses `read-from-string` on unverified LLM output, risking reader macro injection. No Merkle-Tree integration for chat history persistence or rollbacks.
-   - SAFETY: LOW (Vulnerable to injection).
-   - MERKLE: FAILED.
-** DONE org-skill-consensus.org [X]
-   - STATUS: COMPLIANT (Consolidated -> Task Orchestrator)
-   - SAFETY: HIGH. Verified via parallel multi-backend consensus in neuro.lisp.
-   - MERKLE: COMPLIANT.
-** DONE org-skill-context-manager.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for context stack snapshots or rollbacks.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-delegation.org [X]
-   - STATUS: COMPLIANT (Consolidated -> Task Orchestrator)
-   - SAFETY: HIGH. Integrated consensus gate and delegation hooks in core.lisp.
-   - MERKLE: COMPLIANT.
-** DONE org-skill-environment-config.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Technical Mastery Violation)
-   - ISSUE: No validation or authorization gating for configuration changes. Direct hash-table modification skips the new Merkle-Tree versioning system in the Object Store.
-   - SAFETY: MEDIUM (Risk of misconfiguration).
-   - MERKLE: FAILED.
-** DONE org-skill-formal-verification.org [X]
-   - STATUS: COMPLIANT
-   - ISSUE: Implemented Lisp-Native Symbolic Prover for security invariants.
-   - SAFETY: HIGH. Implements path-confinement and no-network-exfil.
-   - MERKLE: COMPLIANT.
-** DONE org-skill-function-calling.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for recording and rolling back tool-use history or state.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-inbound-gateway.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for recording and rolling back inbound message history or state.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-inbox-processor.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Technical Mastery Violation)
-   - ISSUE: Physical move logic is a "Simulation". No implementation of actual file refactoring. No Merkle-Tree integration for recording or rolling back inbox-related state changes.
-   - SAFETY: MEDIUM (Simulation only).
-   - MERKLE: FAILED.
-** DONE org-skill-latent-reflection.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Technical Mastery Violation)
-   - ISSUE: No validation or authorization gating for reflected state changes. Random sampling is inefficient. No Merkle-Tree integration for recording or rolling back reflected state changes.
-   - SAFETY: MEDIUM (Risk of unintended modifications).
-   - MERKLE: FAILED.
-** DONE org-skill-lisp-machine-bootstrap.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for recording or rolling back bootstrap-related state changes or ISA simulation history.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-log-aggregator.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for recording or rolling back log-related state changes or observability history.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-memex.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for recording or rolling back memex-related state changes or metadata audits.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-model-explorer.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code or blueprint. The skill is only a title and overview. No Merkle-Tree integration for model discovery or state changes.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-onboarding.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for recording or rolling back onboarding-related state changes or environment calibration.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-lisp-validator.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Technical Mastery Violation)
-   - ISSUE: No validation or authorization gate for dynamic symbol registration. No Merkle-Tree integration for recording or rolling back safety-related state changes or verification history.
-   - SAFETY: HIGH (The core of the system's safety).
-   - MERKLE: FAILED.
-** DONE org-skill-self-fix.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Technical Mastery Violation)
-   - ISSUE: No validation or authorization gate for proposed self-fixes. Fixes are applied directly to files. No Merkle-Tree integration for recording or rolling back self-fix-related state changes or repair history.
-   - SAFETY: LOW (Risk of unintended/malicious modifications).
-   - MERKLE: FAILED.
-** DONE org-skill-shell-actuator.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Sovereignty Violation)
-   - ISSUE: No validation or authorization gate for synthesized script execution. Script synthesis bypasses the shell whitelist. No Merkle-Tree integration for recording or rolling back shell-related state changes or command history.
-   - SAFETY: MEDIUM (Whitelisted, but script synthesis is a gap).
-   - MERKLE: FAILED.
-** DONE org-skill-sub-agent-manager.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for recording or rolling back sub-agent-related state changes or concurrent thoughts.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-task-integrity.org [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for recording or rolling back task-related state changes or transition history.
-   - SAFETY: N/A (Missing).
-   - MERKLE: FAILED.
-** DONE org-skill-token-accountant.org [ ]
-   - STATUS: NON-COMPLIANT (Safety/Sovereignty Violation)
-   - ISSUE: Hot-patches the kernel's core variables (`*provider-cascade*`, `*model-selector-fn*`) directly, bypassing the skill registration system's safety. No Merkle-Tree integration for recording or rolling back provider-related state changes or pain history.
-   - SAFETY: LOW (Direct kernel mutation).
-   - MERKLE: FAILED.
-
-* Findings Log
-| Skill | Issue | Priority | Status |
-|-------+-------+----------+--------|
-|       |       |          |        |

peripheral-vision-plan.md

@@ -1,32 +0,0 @@
-# Implementation Plan: Component IV - Peripheral Vision Extraction
-
-## Objective
-Implement a sophisticated "Foveal-Peripheral" context model. This ensures the agent has high-resolution focus on the current task (Foveal) while maintaining a low-resolution "skeletal" awareness of the broader Memex structure (Peripheral), optimized for token efficiency and reasoning accuracy.
-
-## Key Files & Context
-- **Target:** `projects/org-agent/literate/context.org` (Source of `src/context.lisp`)
-- **Core Concept:** Deep pruning of the Org AST based on semantic distance and structural hierarchy.
-
-## Implementation Steps
-
-### 1. Identify Foveal Focus
-- Extend the `SIGNAL` structure processing to identify a `target-id` (the current headline being operated on).
-
-### 2. Implement Tree Pruning (`context-extract-peripheral-vision`)
-- Create a recursive function that walks the Object Store starting from the root (or active projects).
-- **Rule A (Foveal):** If the node matches `target-id`, include it and its immediate children in **Full Resolution** (Content + Attributes).
-- **Rule B (Peripheral):** For ancestors and siblings of the target, include only **Title and ID**.
-- **Rule C (Background):** For unrelated nodes, omit entirely or include only at Level 1.
-
-### 3. AST to Org Renderer (`context-render-to-org`)
-- Implement a serializer that transforms our `org-object` structures back into valid Org-mode strings.
-- This allows the LLM to "see" the Memex in its native habitat.
-
-### 4. Integrate with `context-assemble-global-awareness`
-- Update this function to use the new extraction and rendering logic.
-- Ensure it respects a maximum token/character budget to prevent context overflow.
-
-## Phase E: Chaos (Verification)
-- **Structural Test:** Verify that ancestors are rendered as "skeletons" (no body text).
-- **Foveal Test:** Verify that the target node is rendered with its full body text.
-- **Budget Test:** Verify that the output string stays within defined limits even for large Memex structures.

pipeline-refactor.md

@@ -1,37 +0,0 @@
-# Implementation Plan: Reactive Signal Pipeline Refactor
-
-## Objective
-Refactor the monolithic recursive `cognitive-loop` into a functional, gate-based `reactive-signal-pipeline`. This flattens the execution stack, enables multi-backend consensus, and improves observability according to Component VII of the evolutionary roadmap.
-
-## Key Files & Context
-- **Target:** `projects/org-agent/literate/core.org` (Source of `src/core.lisp`)
-- **Architectural Reference:** `projects/org-agent/literate/evolution.org`
-
-## Implementation Steps
-
-### 1. Define the Signal Structure
-Transition from raw plists to a structured `:SIGNAL` format that tracks state as it moves through the pipeline.
-- Attributes: `:status`, `:payload`, `:context`, `:depth`, `:proposals`, `:reply-stream`.
-
-### 2. Implement the Pipeline Gates
-Extract existing logic from `cognitive-loop` into discrete functional gates:
-- **`perceive-gate`**: Normalizes input, updates `*object-store*`.
-- **`neuro-gate`**: Invokes Probabilistic Engine. Support for future parallel backend calls.
-- **`consensus-gate`**: (New) Selects the best proposal from multiple backends (initially a pass-through for the single proposal).
-- **`decide-gate`**: Invokes Deterministic Engine safety checks.
-- **`dispatch-gate`**: Executes tools or physical actuators.
-
-### 3. Implement the Pipeline Orchestrator (`process-signal`)
-Create a function that moves a signal through the sequence of gates. 
-- **Flattening Recursion:** If `dispatch-gate` results in a tool output or error, it MUST NOT call the pipeline recursively. Instead, it returns a new `:SIGNAL` with `depth + 1`, which the orchestrator then re-injects into the top of the pipe via a loop or queue.
-
-### 4. Refactor `inject-stimulus`
-Update `inject-stimulus` to initialize a Signal and hand it to the `process-signal` pipeline instead of `cognitive-loop`.
-
-### 5. Cleanup
-Remove the obsolete `cognitive-loop` function and update `literate/core.org` documentation/diagrams to reflect the new architecture.
-
-## Verification & Testing (Phase E: Chaos)
-- **Unit Tests:** Verify each gate function in isolation.
-- **Pipeline Test:** Simulate a complex multi-turn interaction (e.g., User Prompt -> Tool Call -> Tool Result -> LLM Final Answer) and ensure the stack depth remains flat.
-- **Immune System Test:** Verify that the depth limit (Max depth 10) still correctly terminates runaway loops.

projects/dotemacs/docs/README.org

@@ -1,26 +0,0 @@
-#+title: Emacs Setup Improvement & Documentation Project
-#+author: Amero Garcia
-#+created: [2026-03-16 Mon 13:58]
-#+begin_comment
-This file outlines the project to collaboratively improve and document Amr's Emacs setup, aiming to make Emacs his primary computing tool.
-#+end_comment
-
-* Emacs Setup Improvement & Documentation Project
-
-*Goal:** To collaboratively improve and comprehensively document Amr's Emacs configuration, transitioning Emacs into his primary computing environment.
-
-*Initial Scope:**
--   Reviewing the existing Emacs Org-mode configuration file (tangled to set up Emacs).
--   Identifying areas for optimization, new functionalities, and better integration with workflows.
--   Documenting each significant setting, function, and package.
-
-*Information Needed from Amr:**
--   Location of the current Emacs Org-mode configuration file.
--   Key pain points or areas where Emacs currently falls short as a "main computing tool."
--   Specific desired functionalities or integrations (e.g., mail, calendar, task management, coding environments, note-taking, web browsing within Emacs).
--   Any existing documentation or design principles for the current setup.
-
-*Next Steps:**
-1.  Receive Emacs configuration file location from Amr.
-2.  Analyze current setup.
-3.  Propose documentation structure and initial improvements.

projects/dotemacs/docs/dotemacs.org

@@ -1,27 +0,0 @@
-#+TITLE: Amr's Modular Emacs Configuration
-#+PROPERTY: header-args :tangle no ; This file is for loading other modules, not for tangling itself.
-
-* Configuration Modules
-
-This file loads the modular Emacs configuration files. It should be the primary way Emacs is configured, replacing or integrating with the original `~/.emacs`, `~/.emacs.d/init.el`, `~/.emacs.d/early-init.el`, and `~/.emacs.d/config.el`.
-
-#+begin_src emacs-lisp :exports none
-;; Load early-init.el first, if it exists and is separate (though it's now part of emacs-early-init.org)
-;; (load-file (expand-file-name "emacs-early-init.org" (file-name-directory load-file-name)))
-
-;; Load the core settings, including package management and essential setup.
-(org-babel-load-file (expand-file-name "emacs-core.org" (file-name-directory load-file-name)))
-
-;; Load early init settings (if separate and not fully covered by core)
-(org-babel-load-file (expand-file-name "emacs-early-init.org" (file-name-directory load-file-name)))
-
-;; Load other modules in a logical order
-(org-babel-load-file (expand-file-name "emacs-org.org" (file-name-directory load-file-name)))
-(org-babel-load-file (expand-file-name "emacs-gtd.org" (file-name-directory load-file-name)))
-(org-babel-load-file (expand-file-name "emacs-roam.org" (file-name-directory load-file-name)))
-(org-babel-load-file (expand-file-name "emacs-writing.org" (file-name-directory load-file-name)))
-(org-babel-load-file (expand-file-name "emacs-media.org" (file-name-directory load-file-name)))
-(org-babel-load-file (expand-file-name "emacs-shell.org" (file-name-directory load-file-name)))
-(org-babel-load-file (expand-file-name "emacs-ai.org" (file-name-directory load-file-name)))
-(org-babel-load-file (expand-file-name "emacs-misc.org" (file-name-directory load-file-name)))
-#+end_src

projects/dotemacs/docs/emacs-ai.org

@@ -1,104 +0,0 @@
-#+TITLE: AI Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* AI Settings
-
-** Ellama
-
-#+begin_src elisp :tangle no
-  ;; YOU DON'T NEED NONE OF THIS CODE FOR SIMPLE INSTALL
-  ;; IT IS AN EXAMPLE OF CUSTOMIZATION.
-  (use-package ellama
-    :init
-    (require 'llm-openai)
-    ;; setup key bindings
-    (setq ellama-keymap-prefix "C-c e")
-    )
-#+end_src
-
-#+begin_src elisp ~/.emacs.d/custom.el :tangle no
-  (setopt ellama-providers
-  	'(
-  	  ;; Ollama Provider (added here with a name)
-  	  ("ollama" . (make-llm-ollama
-                               ;; Consider a dedicated embedding model if gemma isn't ideal for it.
-                               :chat-model "gemma3:latest"
-                               :embedding-model "gemma3:latest" ; Or e.g., "nomic-embed-text"
-                               :default-chat-non-standard-params '(("num_ctx" . 8192))))
-
-  	  ("openai" . (make-llm-openai
-                         :key (auth-source-pass-get "api-key" "www/openai.com/amr@gharbeia.net")
-                         :chat-model "gpt-4o"
-  		       :embedding-model "text-embedding-3-large"))
-
-            ("groq" . (make-llm-openai-compatible
-                       :url "https://api.groq.com/openai/v1"
-                       :key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net")
-                       ;; Check Groq console for available models, these might change
-                       :chat-model "llama3-70b-8192" ; Example, verify on Groq
-                       :embedding-model "llama3-70b-8192")) ; Groq might not offer dedicated embedding models via this API
-            ))
-
-  ;; --- Set Active Providers ---
-  ;; Choose your default provider from the list above by its name
-  (setopt ellama-provider "ollama") ; Or "ollama", "openai", "groq"
-
-  ;; You can specify different providers for different tasks if needed
-  (setopt ellama-translation-provider "ollama")
-  (setopt ellama-naming-provider "ollama")
-  (setopt ellama-naming-scheme 'ellama-generate-name-by-llm)
-
-  (setq llm-debug t)
-#+end_src
-
-#+begin_src elisp
-  (use-package ellama
-  :ensure t
-  :bind ("C-c e" . ellama)
-  ;; send last message in chat buffer with C-c C-c
-  :hook (org-ctrl-c-ctrl-c-final . ellama-chat-send-last-message)
-  :init (setopt ellama-auto-scroll t)
-  :config
-  ;; show ellama context in header line in all buffers
-  (ellama-context-header-line-global-mode +1)
-  ;; show ellama session id in header line in all buffers
-  (ellama-session-header-line-global-mode +1))
-#+end_src
-
-** GPTel
-   
-#+begin_src elisp :tangle no
-  (use-package gptel)
-#+end_src
-
-#+begin_src elisp :tangle no
-  (setq gptel-api-key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net"))
-#+end_src
-
-#+begin_src elisp :tangle no
-  (gptel-make-openai "Groq"               ;Any name you want
-  :host "api.groq.com"
-  :endpoint "/openai/v1/chat/completions"
-  :stream t
-  :key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net")                   ;can be a function that returns the key
-  :models '(llama-3.1-70b-versatile
-            llama-3.1-8b-instant
-            llama3-70b-8192
-            llama3-8b-8192
-            mixtral-8x7b-32768
-            gemma-7b-it))
-#+end_src
-
-** Elisa
-
-#+begin_src elisp :tangle no
-  (use-package elisa
-    :init
-    (setopt elisa-limit 5)
-    (require 'llm-ollama)
-    (setopt elisa-embeddings-provider (make-llm-ollama :embedding-model "nomic-embed-text"))
-    (setopt elisa-chat-provider (make-llm-ollama
-                                 :chat-model "sskostyaev/openchat:8k-rag"
-                                 :embedding-model "nomic-embed-text"))
-    )
-#+end_src

projects/dotemacs/docs/emacs-core.org

@@ -1,169 +0,0 @@
-#+TITLE: Core Emacs Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* Front matter
-
-#+begin_src elisp :tangle ~/.emacs
-  ;;; .emacs --- Global settings
-  ;;; Commentary:
-  ;;; Code:
-
-  ;; -*- lexical-binding: t; -*-
-#+end_src
-
-#+begin_src elisp
-  ;;; config.el --- Summary
-  ;;; Commentary:
-  ;;; Code:
-
-  ;; -*- lexical-binding: t; -*-
-#+end_src
-
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  ;;; custom.el --- Summary
-  ;;; Commentary:
-  ;;; Code:
-
-  ;; -*- lexical-binding: t; -*-
-#+end_src
-
-* Garbage collector
-
-Increase threshold to 500 MB to ease startup
-#+begin_src elisp :tangle ~/.emacs
-  (setq gc-cons-threshold (* 500 1024 1024))
-#+end_src
-
-Decrease threshold to 5 MB after init
-#+begin_src elisp :tangle ~/.emacs
-  (add-hook 'after-init-hook (lambda () (setq gc-cons-threshold (* 5 1024 1024))))
-#+end_src
-
-* Straight.el and use-package
-
-Bootstrap Straight.el and install use-package
-#+begin_src elisp :tangle ~/.emacs
-  (setq straight-repository-branch "develop") ;; Using develop branch temporarily to fix the org-roam-dailies issue.
-
-   (eval-and-compile
-     (defvar bootstrap-version)
-     (let ((bootstrap-file
-            (expand-file-name "straight/repos/straight.el/bootstrap.el"
-               		   (or (bound-and-true-p straight-base-dir)
-               		       user-emacs-directory)))
-           (bootstrap-version 7))
-       (unless (file-exists-p bootstrap-file)
-         (with-current-buffer
-             (url-retrieve-synchronously  "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el" 'silent 'inhibit-cookies)
-           (goto-char (point-max))
-           (eval-print-last-sexp)))
-       (load bootstrap-file nil 'nomessage))
-     
-     (straight-use-package 'use-package)
-     )
-#+end_src
-
-Integrate use-package and straight
-#+begin_src elisp :tangle ~/.emacs
-  (setq straight-use-package-by-default t)
-#+end_src
-
-Make sure Org is installed (straight.el)
-#+begin_src elisp :tangle ~/.emacs
-  (unless (file-directory-p "~/.emacs.d/straight/versions") (make-directory (concat user-emacs-directory "straight/versions")))
-#+end_src
-
-#+begin_src elisp :tangle ~/.emacs
-  (use-package org)
-#+end_src
-
-A use-package declaration for simplifying your .emacs
-#+begin_src elisp
-  (require 'use-package)
-#+end_src
-
-* Custom file
-
-#+begin_src elisp
-  (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
-  (when (file-exists-p custom-file) (load custom-file))
-#+end_src
-
-* System information
-
-#+begin_src elisp  :tangle ~/.emacs.d/custom.el
-  (defvar my-laptop-p (equal (system-name) "lilitop"))
-  (defvar my-server-p (and (equal (system-name) "localhost") (equal user-login-name "root")))
-  (defvar my-phone-p (not (null (getenv "ANDROID_ROOT")))
-    "If non-nil, GNU Emacs is running on Termux.")
-  (when my-phone-p (defvar gnutls-algorithm-priority "NORMAL:-VERS-TLS1.3"))
-  (global-auto-revert-mode)  ; simplifies syncing
-#+end_src
-
-* Persistent history
-
-#+begin_src elisp
-  (savehist-mode)
-#+end_src
-
-* Backup and versioning
-
-#+begin_src emacs-lisp
-  (use-package magit
-    :ensure t
-    )
-#+end_src
-
-* Personal information
-
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (setq user-full-name "Amr Gharbeia")
-  (defvar email-address "amr@gharbeia.net")
-  (defvar calendar-latitude 39.0)
-  (defvar calendar-longitude -77.1)
-  (defvar calendar-location-name "Washington, DC")
-  (defvar calendar-time-zone -300)
-  (defvar calendar-standard-time-zone-name "EST")
-  (defvar calendar-daylight-time-zone-name "EDT")
-#+end_src
-
-* Saving Emacs Sessions
-
-Close frame when done
-#+begin_src elisp
-  (add-hook 'server-done-hook (lambda () (delete-frame)))
-#+end_src
-
-Save desktop session
-#+begin_src elisp
-  (desktop-save-mode t)
-#+end_src
-
-* Security
-
-#+begin_src elisp :tangle no
-  (use-package password-store)
-#+end_src
-
-#+begin_src elisp
-  (use-package auth-source
-    :config (auth-source-pass-enable)
-    )
-#+end_src
-
-* End matter
-
-#+begin_src elisp :tangle ~/.emacs
-  (provide '.emacs)
-  ;;; .emacs ends here
-#+end_src
-
-#+begin_src elisp
-  (provide 'config)
-  ;;; config.el ends here
-#+end_src
-
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (provide 'custom)
-  ;;; custom.el ends here
-#+end_src

projects/dotemacs/docs/emacs-gtd.org

@@ -1,157 +0,0 @@
-#+TITLE: GTD & Agenda Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* Agenda
-
-Basic agenda settings
-#+begin_src elisp
-   (setq org-deadline-warning-days 7)
-   (setq org-agenda-skip-additional-timestamps-same-entry t)
-   (setq org-agenda-span 'fortnight)
-   (setq org-agenda-tags-column 'auto)
-   (setq org-agenda-skip-scheduled-if-deadline-is-shown t)
-#+end_src
-
-Agenda files
-#+begin_src elisp
-  (setq org-agenda-files (list
-  			(concat org-directory "inbox.org")
-  			(concat org-directory "gtd.org")
-  			)
-        )
-#+end_src
-
-Better agenda views
-#+begin_src elisp :tangle no
-  (use-package org-super-agenda)
-#+end_src
-
-* To-do
-
-Basic todo
-#+begin_src elisp
-  (setq org-todo-keywords
-          '(
-            (sequence "TODO(t)" "NEXT(n)" "WAIT(w@/!)" "|" "DONE(d!)" "CNCL(c@)")
-            )
-          )
-
-  (setq org-todo-keyword-faces
-          '(
-            ("TODO" :foreground "red" :weight bold)
-            ("NEXT" :foreground "red" :weight bold)
-            ("WAIT" :foreground "yellow" :weight bold)
-            ("DONE" :foreground "green" :weight bold)
-            ("CNCL" :foreground "blue" :weight bold)
-            )
-          )
-
-  (setq org-enforce-todo-dependencies t)
-  (setq org-tags-exclude-from-inheritance '("crypt" "!private"))
-#+end_src
-
-Switch entry to 'DONE' when all subentries are done
-#+begin_src elisp
-  (defun org-summary-todo (n-done n-not-done)
-    "Switch entry to 'DONE' when all subentries are done, to 'TODO' otherwise.
-  Uses N-DONE and N-NOT-DONE"
-    (let (org-log-done org-log-states)   ; turn off logging
-      (org-todo (if (= n-not-done 0) "DONE" "TODO")
-                )
-        )
-    )
-
-    (add-hook 'org-after-todo-statistics-hook #'org-summary-todo)
-#+end_src
-
-* Getting Things Done (GTD)
-#+begin_src elisp
-  (use-package org-gtd
-    :defer t
-    :init (setq org-gtd-update-ack "4.0.0")
-    :after org
-    :config
-    (setq org-edna-use-inheritance t)
-    (org-edna-mode)
-    (setq org-gtd-keyword-mapping
-          '((todo . "TODO")
-            (next . "NEXT")
-            (wait . "WAIT")
-            (done . "DONE")
-            (canceled . "CNCL")))
-    (setq org-gtd-custom-node-paths
-          '(("Actionable" . '("~/memex/gtd.org" "Actions"))
-            ("Incubate" . '("~/memex/gtd.org" "Incubate"))))
-    (org-gtd-mode)
-    :bind (
-  	 ("C-c d c" . org-gtd-capture)
-  	 ("C-c d e" . org-gtd-engage)
-  	 ("C-c d p" . org-gtd-process-inbox)
-  	 :map org-gtd-clarify-map
-  	 ("C-c c" . org-gtd-organize)
-  	 )
-    )
-#+end_src
-
-#+begin_src elisp
-  (defvar org-gtd-directory org-directory)
-  (defvar org-gtd-organize-hooks '(org-gtd-set-area-of-focus org-set-tags-command))
-  (defvar org-gtd-organize-hooks '(org-gtd-set-area-of-focus))
-  (defvar org-gtd-areas-of-focus '(
-  				 "Atoms"
-  				 "Bits"
-  				 "Cells"
-  				 "Flags"
-  				 "Business"
-  				 "Wealth"
-  				 "Learning"
-  				 "Skills"
-  				 "Privacy"
-  				 "Archive"
-  				 "Library"
-  				 "Writing"
-  				 "Health"
-  				 "Home"
-  				 "Family"
-  				 "Social"
-  				 "Egypt"
-  				 )
-    )
-  (defvar org-gtd-clarify-show-horizons 'right)
-#+end_src
-
-Logging
-#+begin_src elisp
-  (setq org-log-into-drawer "LOGBOOK")
-#+end_src
-
-Clocking work in drawer
-#+begin_src elisp :tangle no
-  (setq org-clock-into-drawer t)
-#+end_src
-
-Habits
-#+begin_src elisp :tangle no
-  (setq org-habit-graph-column 80)
-  (setq org-habit-show-habits-only-for-today nil)
-#+end_src
-
-* Refile
-
-org-refile targets
-#+begin_src elisp
-  (setq org-refile-targets '((nil :maxlevel . 9)
-                             (org-agenda-files :maxlevel . 9)
-                             )
-        )
-#+end_src
-
-Set type of refile targets completion
-#+begin_src elisp
-  (setq org-outline-path-complete-in-steps nil)
-#+end_src
-
-Allow refiling to new parents created on the go after confirmation
-#+begin_src elisp
-  (setq org-refile-allow-creating-parent-nodes 'confirm)
-#+end_src

projects/dotemacs/docs/emacs-media.org

@@ -1,175 +0,0 @@
-#+TITLE: Media and Books Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* Read ebooks (calibredb)
-
-#+begin_src elisp
-  (use-package calibredb
-:defer t
-    :config
-      (setq calibredb-format-all-the-icons t)
-      (setq calibredb-format-icons-in-terminal t)
-      )
-#+end_src
-
-#+begin_src elisp
-  ;; Forcefully reset the variable after loading calibredb
-  (defvar calibredb-root-dir (concat (getenv "HOME") "/library/books"))
-  (defvar calibredb-db-dir (expand-file-name "metadata.db" calibredb-root-dir))
-  					; (defvar calibredb-library-alist (concat (getenv "HOME") "/library/books"))
-  ;;  (defvar calibredb-search-page-max-rows 1000)
-  (defvar calibredb-id-width 6)
-  (defvar calibredb-title-width 100)
-  (defvar calibredb-format-width 0)
-  (defvar calibredb-date-width 0)
-  (defvar calibredb-author-width 20)
-  (defvar calibredb-comment-width 0)
-  (defvar calibredb-tag-width 0)
-#+end_src
-
-Some keybindings
-
-#+begin_src elisp ~/.emacs.d/custom.el
-  (defvar calibredb-show-mode-map
-    (let ((map (make-sparse-keymap)))
-      (define-key map "?" #'calibredb-entry-dispatch)
-      (define-key map "o" #'calibredb-find-file)
-      (define-key map "O" #'calibredb-find-file-other-frame)
-      (define-key map "V" #'calibredb-open-file-with-default-tool)
-      (define-key map "s" #'calibredb-set-metadata-dispatch)
-      (define-key map "e" #'calibredb-export-dispatch)
-      (define-key map "q" #'calibredb-entry-quit)
-      (define-key map "y" #'calibredb-yank-dispatch)
-      (define-key map "," #'calibredb-quick-look)
-      (define-key map "." #'calibredb-dired-open)
-      (define-key map "\M-/" #'calibredb-rga)
-      (define-key map "\M-t" #'calibredb-set-metadata--tags)
-      (define-key map "\M-a" #'calibredb-set-metadata--author_sort)
-      (define-key map "\M-A" #'calibredb-set-metadata--authors)
-      (define-key map "\M-T" #'calibredb-set-metadata--title)
-      (define-key map "\M-c" #'calibredb-set-metadata--comments)
-      map)
-    "Keymap for `calibredb-show-mode'.")
-#+end_src
-
-#+begin_src elisp
-  (defvar calibredb-search-mode-map
-    (let ((map (make-sparse-keymap)))
-      (define-key map [mouse-3] #'calibredb-search-mouse)
-      (define-key map (kbd "<RET>") #'calibredb-find-file)
-      (define-key map "?" #'calibredb-dispatch)
-      (define-key map "a" #'calibredb-add)
-      (define-key map "A" #'calibredb-add-dir)
-      (define-key map "c" #'calibredb-clone)
-      (define-key map "d" #'calibredb-remove)
-      (define-key map "D" #'calibredb-remove-marked-items)
-      (define-key map "j" #'calibredb-next-entry)
-      (define-key map "k" #'calibredb-previous-entry)
-      (define-key map "l" #'calibredb-virtual-library-list)
-      (define-key map "L" #'calibredb-library-list)
-      (define-key map "n" #'calibredb-virtual-library-next)
-      (define-key map "N" #'calibredb-library-next)
-      (define-key map "p" #'calibredb-virtual-library-previous)
-      (define-key map "P" #'calibredb-library-previous)
-      (define-key map "s" #'calibredb-set-metadata-dispatch)
-      (define-key map "S" #'calibredb-switch-library)
-      (define-key map "o" #'calibredb-find-file)
-      (define-key map "O" #'calibredb-find-file-other-frame)
-      (define-key map "v" #'calibredb-view)
-      (define-key map "V" #'calibredb-open-file-with-default-tool)
-      (define-key map "," #'calibredb-quick-look)
-      (define-key map "." #'calibredb-dired-open)
-      (define-key map "y" #'calibredb-yank-dispatch)
-      (define-key map "b" #'calibredb-catalog-bib-dispatch)
-      (define-key map "e" #'calibredb-export-dispatch)
-      (define-key map "r" #'calibredb-search-refresh-and-clear-filter)
-      (define-key map "R" #'calibredb-search-clear-filter)
-      (define-key map "q" #'calibredb-search-quit)
-      (define-key map "m" #'calibredb-mark-and-forward)
-      (define-key map "f" #'calibredb-toggle-favorite-at-point)
-      (define-key map "x" #'calibredb-toggle-archive-at-point)
-      (define-key map "h" #'calibredb-toggle-highlight-at-point)
-      (define-key map "u" #'calibredb-unmark-and-forward)
-      (define-key map "i" #'calibredb-edit-annotation)
-      (define-key map (kbd "<DEL>") #'calibredb-unmark-and-backward)
-      (define-key map (kbd "<backtab>") #'calibredb-toggle-view)
-      (define-key map (kbd "TAB") #'calibredb-toggle-view-at-point)
-      (define-key map "\M-n" #'calibredb-show-next-entry)
-      (define-key map "\M-p" #'calibredb-show-previous-entry)
-      (define-key map "/" #'calibredb-search-live-filter)
-      (define-key map "\M-t" #'calibredb-set-metadata--tags)
-      (define-key map "\M-a" #'calibredb-set-metadata--author_sort)
-      (define-key map "\M-A" #'calibredb-set-metadata--authors)
-      (define-key map "\M-T" #'calibredb-set-metadata--title)
-      (define-key map "\M-c" #'calibredb-set-metadata--comments)
-      map)
-    "Keymap for `calibredb-search-mode'.")
-#+end_src
-
-* Annotate PDFs and EPUBs (org-noter)
-
-#+begin_src elisp :tangle no
-  (use-package org-noter)
-#+end_src
-
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (defvar org-noter-notes-search-path (list (concat org-directory "/library/books")))
-  (defvar org-noter-default-notes-file-names '("books.org"))  
-#+end_src
-
-* Link PDFs (org-noter-pdftools)
-
-#+begin_src elisp
-  (use-package org-noter-pdftools
-    :after org-noter
-    :config
-    ;; Add a function to ensure precise note is inserted
-    (defun org-noter-pdftools-insert-precise-note (&optional toggle-no-questions)
-      (interactive "P")
-      (org-noter--with-valid-session
-       (let ((org-noter-insert-note-no-questions (if toggle-no-questions
-  						   (not org-noter-insert-note-no-questions)
-                                                   org-noter-insert-note-no-questions))
-             (org-pdftools-use-isearch-link t)
-             (org-pdftools-use-freepointer-annot t))
-         (org-noter-insert-note (org-noter--get-precise-info)))))
-
-    ;; fix https://github.com/weirdNox/org-noter/pull/93/commits/f8349ae7575e599f375de1be6be2d0d5de4e6cbf
-    (defun org-noter-set-start-location (&optional arg)
-      "When opening a session with this document, go to the current location.
-  With a prefix ARG, remove start location."
-      (interactive "P")
-      (org-noter--with-valid-session
-       (let ((inhibit-read-only t)
-             (ast (org-noter--parse-root))
-             (location (org-noter--doc-approx-location (when (called-interactively-p 'any) 'interactive))))
-         (with-current-buffer (org-noter--session-notes-buffer session)
-           (org-with-wide-buffer
-            (goto-char (org-element-property :begin ast))
-            (if arg
-                (org-entry-delete nil org-noter-property-note-location)
-              (org-entry-put nil org-noter-property-note-location
-                             (org-noter--pretty-print-location location))))))))
-    (with-eval-after-load 'pdf-annot
-      (add-hook 'pdf-annot-activate-handler-functions #'org-noter-pdftools-jump-to-note)
-      )
-    )
-#+end_src
-
-* View EPUBs (nov.el)
-
-#+begin_src elisp :tangle no
-  (use-package nov
-    :config
-    (add-to-list 'auto-mode-alist '("\\.epub\\'" . nov-mode))
-    )
-#+end_src
-
-* Zotero (helm-bibtex)
-#+begin_src elisp :tangle no
-  (use-package helm-bibtex)
-#+end_src
-
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (defvar bibtex-completion-bibliography '("~/bibliography/zotero.bib"))
-#+end_src

projects/dotemacs/docs/emacs-misc.org

@@ -1,46 +0,0 @@
-#+TITLE: Miscellaneous Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* Browser (eww)
-
-#+begin_src elisp
-  (use-package eww
-    :bind* (("M-m g x" . eww)
-            ("M-m g :" . eww-browse-with-external-browser)
-            ("M-m g #" . eww-list-histories)
-            ("M-m g {" . eww-back-url)
-            ("M-m g }" . eww-forward-url))
-    :config
-    (progn
-      (add-hook 'eww-mode-hook 'visual-line-mode)
-      )
-    )
-#+end_src
-
-* Manage Docker in Emacs
-
-#+begin_src elisp
-  (use-package docker
-    :bind ("C-c d" . docker)
-    )
-#+end_src
-
-* Periodic table of the elements
-
-#+begin_src elisp :tangle no
-  (use-package chemtable)
-#+end_src
-
-* Accounting (beancount)
-
-#+begin_src elisp :tangle no
-  (use-package beancount
-    :straight (beancount :type git :host github :repo "beancount/beancount-mode")
-    :config
-    (add-to-list 'auto-mode-alist '("\\.beancount\\'" . beancount-mode))
-    (add-hook 'beancount-mode-hook #'outline-minor-mode)
-    (define-key beancount-mode-map (kbd "C-c C-n") #'outline-next-visible-heading)
-    (define-key beancount-mode-map (kbd "C-c C-p") #'outline-previous-visible-heading)
-    (add-hook 'beancount-mode-hook #'flymake-bean-check-enable)
-    )
-#+end_src

projects/dotemacs/docs/emacs-org.org

@@ -1,233 +0,0 @@
-#+TITLE: Org Mode Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* Org Mode
-
-** Basic setup
-
-#+begin_src elisp
-  (use-package org
-    :config
-    (defvar org-outline-path-complete-in-steps nil)
-    :bind (("C-c l" . org-store-link)
-  	 ("C-c a" . org-agenda)
-  	 ("C-c c" . org-capture)
-  	 :map org-mode-map)
-    )
-#+end_src
-
-#+begin_src elisp
-  (defvar org-directory (concat (getenv "HOME") "/memex/"))
-#+end_src
-
-** Looks
-
-Basic 
-#+begin_src elisp
-  (defvar org-pretty-entities t) ; Improve org mode looks
-  (defvar org-hide-emphasis-markers t) ; Hide emphasis markup
-  (defvar org-num-mode nil)
-  (defvar org-startup-folded 'shw2levels)
-#+end_src
-
-Indentation of headers
-#+begin_src elisp
-  (defvar org-startup-indented t) ; Indent org heirarchy
-  (defvar org-adapt-indentation t)
-  (defvar org-hide-leading-stars t) ; Minimal Outline
-  (defvar org-odd-levels-only nil)
-#+end_src
-
-Indentation of lists
-#+begin_src elisp
-  (setq org-list-demote-modify-bullet t)
-#+end_src
-
-Org-modern
-#+begin_src elisp
-  (use-package org-modern
-    :ensure t
-    :config
-        ;; Choose some fonts
-    (set-face-attribute 'default nil :family "sans-serif")
-    (set-face-attribute 'variable-pitch nil :family "sans-serif")
-    (set-face-attribute 'org-modern-symbol nil :family "Iosevka")
-
-    ;; Edit settings
-    (defvar org-auto-align-tags nil)
-    (defvar org-tags-column 0)
-    (defvar org-catch-invisible-edits 'show-and-error)
-    (defvar org-special-ctrl-a/e t)
-    (defvar org-insert-heading-respect-content t)
-
-     ;; Org styling, hide markup etc.
-     (defvar org-hide-emphasis-markers t)
-     (defvar org-pretty-entities t)
-
-     ;; Agenda styling
-     (defvar org-agenda-tags-column 0)
-     (defvar org-agenda-block-separator ?─)
-     (defvar org-agenda-time-grid
-       '((daily today require-timed)
-         (800 1000 1200 1400 1600 1800 2000)
-         " ┄┄┄┄┄ " "┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄"))
-     (defvar org-agenda-current-time-string
-       "◀── now ─────────────────────────────────────────────────")
-
-    ;; Ellipsis styling
-     (defvar org-ellipsis "…")
-     (set-face-attribute 'org-ellipsis nil :inherit 'default :box nil)
-    
-     (global-org-modern-mode)
-    )
-#+end_src
-
-Highlight Sourcecode Syntax
-#+begin_src elisp
-  (setq org-src-fontify-natively t)
-  (setq org-src-tab-acts-natively t)
-#+end_src
-
-Images
-#+begin_src elisp
-  (setq org-startup-with-inline-images t)
-  (setq org-image-actual-width '(300))
-#+end_src
-
-** Capture
-
-#+begin_src elisp
-  (defvar org-default-notes-file (concat org-directory "inbox.org"))
-#+end_src
-
-*** Org-protocol
-
-Linux configuration
-#+begin_src bash :tangle no
-[Desktop Entry]
-Name=org-protocol
-Comment=Intercept calls from emacsclient to trigger custom actions
-Categories=Other;
-Keywords=org-protocol;
-Icon=emacs
-Type=Application
-Exec=emacsclient -- %u
-Terminal=false
-StartupWMClass=Emacs
-MimeType=x-scheme-handler/org-protocol;
-#+end_src
-
-#+begin_src bash :tangle no
-update-desktop-database ~/.local/share/applications/
-#+end_src
-
-Basic configuration
-#+begin_src elisp
-  (require 'org-protocol)
-  (setq org-protocol-default-buffer-for-file-links "*scratch*") ; fixes 'no buffers remain to edit error for org-protocol capturer
-#+end_src
-
-Org-protocol templates
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (defvar org-capture-templates '(
-                                ("p" "Protocol"
-                                 entry
-                                 (file "inbox.org")
-                                 "* %^{Title}\nSource: %u, %c\n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n%?"
-                                 )
-                                ("L" "Protocol Link"
-                                 entry
-                                 (file "inbox.org")
-                                 "* %? [[%:link][%:description]]\n:PROPERTIES:\n:TITLE: %:description\n:URI: %:link\n:CREATED: %U\n:END:"
-                                 :prepend nil
-                                 :empty-lines 1
-                                 :created t
-                                 :kill-buffer t
-                                 )
-                                )
-        )
-#+end_src
-
-#+begin_src elisp
-  (setq org-protocol-default-template-key "L")
-#+end_src
-
-Convert Orgzly captures to org-protocol captures standard
-#+begin_src elisp
-  (defun my/org-convert-orgzly-to-org-protocol ()
-    "Reformat Orgzly bookmark at point to org-protocol bookmark."
-    (interactive)
-    (when (org-at-heading-p)
-      (let ((headline (nth 4 (org-heading-components))))
-        ;; Find and store the link. Delete the link line.
-        (search-forward-regexp "^https?://\\S-*" nil t)
-        (let ((link (match-string 0)))
-          (beginning-of-line)
-          (kill-line)
-          ;; Delete any trailing blank spaces
-          (org-back-to-heading)
-          (end-of-line)
-          (when (not (org-on-heading-p))
-            (delete-char 1)
-            )
-          ;; Set new headline
-          (goto-char (org-entry-beginning-position))
-          (org-edit-headline (format "[[%s][%s]]" link headline))
-          ;; Set new properties
-          (org-set-property "TITLE" headline)
-          (org-set-property "URI" link)
-          (message "Reformatted Orgzly bookmark at point to org-protocol bookmark")
-          )
-        )
-      )
-    )
-#+end_src
-
-** Exporting
-
-#+begin_src elisp :tangle no
-  (setq org-export-with-smart-quotes t)
-  (setq org-export-backends '(beamer html latex md))
-#+end_src
-
-Export to EPUB
-#+begin_src elisp :tangle no
-  (use-package ox-epub)
-#+end_src
-
-** org-attach
-
-#+begin_src elisp
-  (defvar org-attach-id-dir (concat org-directory "/library"))
-#+end_src
-
-** Enable shell scripting support in org-babel
-
-#+begin_src elisp
-  (defvar org-babel-do-load-languages  'org-babel-load-languages  '((shell . t)))
-#+end_src
-
-** Insert org-mode links from clipboard
-#+begin_src elisp :tangle no
-  (use-package org-cliplink
-    :bind
-    (("C-x p i" . org-cliplink))
-    )
-#+end_src
-
-** Deft
-#+begin_src elisp :tangle no
-  (use-package deft
-    :commands (deft)
-    :init
-    (defvar deft-extensions '("org"))
-    (defvar deft-recursive nil)
-    (defvar deft-use-filename-as-title t)
-    :config
-    (defvar deft-directory org-directory)
-    (defvar deft-recursive t)
-    (defvar deft-strip-summary-regexp ":PROPERTIES:\n\\(.+\n\\)+:END:\n")
-    (defvar deft-use-filename-as-title t)
-    :bind  ("C-c n d" . deft)
-    )
-#+end_src

projects/dotemacs/docs/emacs-roam.org

@@ -1,140 +0,0 @@
-#+TITLE: Org-Roam Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* Org-roam
-
-** Basic org-roam setup
-
-#+begin_src elisp
-(use-package org-roam
-  :init (setq org-roam-v2-ack t) ;; Acknowledge V2 upgrade
-  :after org
-  :config
-  (org-roam-db-autosync-enable)
-  (require 'org-roam-dailies)
-  :bind  (
-   ("C-c n f" . org-roam-node-find)
-   ("C-c n g" . org-roam-graph)
-   ("C-c n r" . org-roam-node-random)
-   ("C-c n h" . org-roam-node-convert-headline)
-   ("C-c n i" . org-roam-node-insert)
-   ("C-c n o" . org-id-get-create)
-   ("C-c n t" . org-roam-tag-add)
-   ("C-c n a" . org-roam-alias-add)
-   ("C-c n l" . org-roam-buffer-display-dedicated)
-   )
-  )
-#+end_src
-
-#+begin_src elisp
-  (setq org-roam-directory (concat org-directory "notes"))
-  (setq org-roam-dailies-directory (concat org-directory "daily"))
-#+end_src
-
-#+begin_src elisp :tangle no
-  (use-package sqlite3)
-  (require 'sqlite3)
-#+end_src
-
-Include subdirectories in org-roam
-#+begin_src elisp
-  (setq org-roam-file-exclude-regexp "^[.][.]?/")
-#+end_src
-
-** Display in org-roam-buffer
-#+begin_src elisp :tangle no
-  (setq org-roam-mode-sections
-        (list #'org-roam-backlinks-section
-              #'org-roam-reflinks-section
-              #'org-roam-unlinked-references-section 
-              )
-        )
-#+end_src
-
-** Filter org-roam nodes find by tag
-
-#+begin_src elisp :tangle no
-  (defun my/org-roam-node-has-tag (node tag)
-    "Filter function to check if the given NODE has the specified TAG."
-    (member tag (org-roam-node-tags node))
-    )
-
-  (defun my/org-roam-node-find-by-tag ()
-    "Find and open an Org-roam node based on a specified tag."
-    (interactive)
-    (let ((tag (read-string "Enter tag: ")))
-      (org-roam-node-find nil nil (lambda (node) (my/org-roam-node-has-tag node tag))))
-    )
-#+end_src
-
-** org-roam-capture templates
-#+begin_src elisp
-  (setq org-roam-capture-templates
-        '(
-          ("L" "link" plain
-           (function org-roam--capture-get-point)
-           "%?"
-           :file-name "web/%<%Y-%m-%dT%H%M%S>.org"
-           :head "#+TITLE: ${title}\n#+CREATED: %<%Y-%m-%dT%H%M%S>"
-           :immediate-finish t
-           :unnarrowed t
-           )
-
-          ("h" "hugo post" plain
-           "%?"
-           :target (file+head "posts/${slug}.org"
-                              "#+TITLE: ${title}\n#+DATE: %U\n#+HUGO_BASE_DIR: ~/gharbeia.net\n#+HUGO_SECTION: ./posts\n#+HUGO_AUTO_SET_LASTMOD: t\n#+HUGO_TAGS: article\n#+HUGO_DRAFT: true\n")
-           :immediate-finish t
-           :unnarrowed t
-           )
-
-          ("p" "person" plain
-           "%?"
-           :if-new (file+head "people/${slug}.org"
-                             "#+TITLE: ${title}")
-          :immediate-finish t
-          :unnarrowed t
-          )
-         )
-       )
-#+end_src
-
-#+begin_src elisp
-  (setq org-roam-dailies-capture-templates
-        '(
-          ("d" "daily" plain
-           ""
-          :target ("file+heaed %<%Y-%m-%d>.org"  "#+title: %<%Y-%m-%d>\n\n")
-          :immediate-finish t
-          )
-         )
-       )
-#+end_src
-
-** Move org header to org-roam-daily
-
-#+begin_src elisp :tangle no
-  (defun my/org-move-entry-to-daily-notes ()
-    "Move the current org-mode headline to the daily notes file based on its :CREATED: property."
-    (interactive)
-    (let*
-        (
-         (created-prop (org-entry-get nil "CREATED"))
-         (created-date (when created-prop
-                         (org-parse-time-string created-prop)))
-         (year (nth 5 created-date)) ; Extract year (6th element)
-         (month (nth 4 created-date)) ; Extract month (5th element)
-         (day (nth 3 created-date)) ; Extract day (4th element)
-         (target-date (format "%04d-%02d-%02d" year month day)) ; Format date string
-         (target-file (org-roam-dailies-goto target-date)) 
-         )
-      (when target-file
-        (org-cut-subtree)
-        (find-file target-file)
-        (goto-char (point-max))
-        (unless (bolp) (newline))
-        (org-paste-subtree)
-        )
-      )
-  )
-#+end_src

projects/dotemacs/docs/emacs-shell.org

@@ -1,73 +0,0 @@
-#+TITLE: Shell Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* Shell
-
-** Bash completion
-
-#+begin_src elisp
-  (use-package bash-completion
-    :config
-    (require 'bash-completion)
-    (bash-completion-setup)
-    )
-#+end_src
-
-#+begin_src elisp
-(defvar shell-dynamic-complete-functions t)
-#+end_src
-
-** Eshell
-
-Add programmable bash completion to Emacs shell-mode
-#+begin_src elisp :tangle no
-  (require 'bash-completion)
-  (add-hook 'eshell-mode-hook
-          (lambda ()
-            (add-hook 'completion-at-point-functions
-                      'bash-completion-capf-nonexclusive nil t
-                      )
-            )
-          )
-#+end_src
-
-Use colors in eshell
-#+begin_src elisp :tangle no
-  (use-package xterm-color
-    :commands (xterm-color-filter)
-    )
-
-  (use-package eshell
-    :after xterm-color
-    :config
-    (define-key eshell-hist-mode-map (kbd "M-r") #'consult-history)
-    (add-hook 'eshell-mode-hook
-              (lambda ()
-                (setenv "TERM" "xterm-256color")))
-    (add-hook 'eshell-before-prompt-hook (setq xterm-color-preserve-properties t))
-    (add-to-list 'eshell-preoutput-filter-functions 'xterm-color-filter)
-    (setq eshell-output-filter-functions
-          (remove 'eshell-handle-ansi-color eshell-output-filter-functions)
-          )
-    )
-#+end_src
-
-Eshell completion
-#+begin_src elisp :tangle no
-  (add-hook 'eshell-mode-hook
-          (lambda ()
-            (add-hook 'completion-at-point-functions
-                      'bash-completion-capf-nonexclusive nil t)))
-#+end_src
-
-Emulate A Terminal (EAT)
-#+begin_src elisp :tangle no
-  (use-package eat
-    :config
-    ;; For `eat-eshell-mode'.
-    (add-hook 'eshell-load-hook #'eat-eshell-mode)
-
-    ;; For `eat-eshell-visual-command-mode'.
-    (add-hook 'eshell-load-hook #'eat-eshell-visual-command-mode)
-    )
-#+end_src

projects/dotemacs/docs/emacs-writing.org

@@ -1,255 +0,0 @@
-#+TITLE: Reading and Writing Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/config.el
-
-* Text and Case
-
-** Convert DOuble capitals to single capitals
-
-#+begin_src elisp :tangle no
-  (defun my/dcaps-to-scaps ()
-    "Convert word in DOuble CApitals to Single Capitals."
-    (interactive)
-    (and (= ?w (char-syntax (char-before)))
-         (save-excursion
-           (and (if (called-interactively-p)
-                    (skip-syntax-backward "w")
-                  (= -3 (skip-syntax-backward "w"))
-                  )
-                (let (case-fold-search)
-                  (looking-at "\\b[[:upper:]]\\{2\\}[[:lower:]]")
-                  )
-              (capitalize-word 1)
-              )
-           )
-         )
-    )
-#+end_src
-
-Then, let’s define a minor mode for it to be activated.
-#+begin_src elisp :tangle no
-  (define-minor-mode my-dubcaps-mode
-    "Toggle 'my-dubcaps-mode' and convert words in DOuble CApitals to Single Capitals as you type."
-    :init-value nil
-    :lighter (" DC")
-    (if my-dubcaps-mode
-        (add-hook 'post-self-insert-hook #'my/dcaps-to-scaps nil 'local)
-      (remove-hook 'post-self-insert-hook #'my/dcaps-to-scaps 'local)))
-#+end_src
-
- Finally, let’s add a hook so that it is on for all the text files Emacs opens.
-#+begin_src elisp :tangle no
-  (add-hook 'text-mode-hook #'my-dubcaps-mode)  
-#+end_src
-
-Also, since we add a minor mode string (it might be useful sometimes), currently I prefer to diminish it.
-#+begin_src elisp :tangle no
-  (defun my/diminish-dubcaps ()
-    (interactive)
-    (diminish 'my-dubcaps-mode ""))
-  (add-hook 'my-dubcaps-mode-hook 'my/diminish-dubcaps)
-#+end_src
-
-* Reading and Writing
-
-** Move correctly over camelCased words
-
-#+begin_src elisp
-  (subword-mode)
-#+end_src
-
-** Understand the more common sentence with double space
-
-#+begin_src elisp
-  (setq sentence-end-double-space nil)
-#+end_src
-
-** Join lines into paragraph
-
-#+begin_src elisp
-  (defun my/fill-or-unfill-paragraph (&optional unfill region)
-    "Fill paragraph (or REGION). With the prefix argument UNFILL, fill it instead."
-    (interactive (progn
-                   (barf-if-buffer-read-only)
-                   (list (if current-prefix-arg 'fill) t)))
-    (let ((fill-column (if unfill fill-column (point-max))))
-      (fill-paragraph nil region)))
-
-  (bind-key "M-q" 'my/fill-or-unfill-paragraph)
-#+end_src
-
-#+begin_src elisp
-  (defun my/fill-or-unfill-all-paragraphs (&optional unfill)
-  "Fill or unfill all paragraphs in the current buffer.
-With the prefix argument UNFILL, fill them instead."
-  (interactive (list (if current-prefix-arg 'fill)))
-  (let ((fill-column (if unfill fill-column (point-max))))
-    (save-excursion
-      (goto-char (point-min))
-      (while (not (eobp))
-        (fill-paragraph nil t)
-        (forward-paragraph)))))
-
-(bind-key "M-Q" 'my/fill-or-unfill-all-paragraphs)
-#+end_src
-
-#+begin_src elisp
-  (remove-hook 'text-mode-hook #'turn-on-auto-fill)
-  (add-hook 'text-mode-hook 'turn-on-visual-line-mode)
-#+end_src
-
-** Expand some words with auto-correct
-
-  #+begin_src elisp :tangle no
-  (setq save-abbrevs 'silently)
-  (setq-default abbrev-mode t)
-  #+end_src
-
-** ediff
-
-#+begin_src elisp :tangle no
-  (setq ediff-window-setup-function 'ediff-setup-windows-plain)
-  (setq ediff-split-window-function 'split-window-horizontally)
-#+end_src
-
-** tramp
-
-#+begin_src elisp :tangle no
-  (setq tramp-default-method "ssh"
-        tramp-backup-directory-alist backup-directory-alist
-        tramp-ssh-controlmaster-options "ssh")
-#+end_src
-
-** Clean up space
-#+begin_src elisp :tangle no
-  (bind-key "M-SPC" 'cycle-spacing)
-#+end_src
-
-** Transform <a href> links into org links
-
-#+begin_src elisp :tangle no
-  (defun my/transform-html-links-to-org ()
-  "Transform all HTML <a> links in the current buffer into 'org-mode' links."
-  (interactive)
-  (goto-char (point-min))
-  (while (re-search-forward "<a href=\"\\(.*?\\)\">\\(.*?\\)</a>" nil t)
-    (replace-match (org-make-link-string (match-string 1) (match-string 2)))))
-#+end_src
-
-** Count words per minute
-#+begin_src elisp :tangle no
-  (require 'org-clock)
-  (defun my/org-entry-wpm ()
-    (interactive)
-    (save-restriction
-      (save-excursion
-        (org-narrow-to-subtree)
-        (goto-char (point-min))
-        (let* ((words (count-words-region (point-min) (point-max)))
-
-               (minutes (org-clock-sum-current-item))
-               (wpm (/ words minutes)))
-          (message "WPM: %d (words: %d, minutes: %d)" wpm words minutes)
-          (kill-new (number-to-string wpm))
-          )
-        )
-      )
-    )
-#+end_src
-
-** Enable dict mode
-  #+begin_src elisp :tangle no
-    (setq dictionary-server "automatic")
-  #+end_src
-
-** Pick out passive voice and weasel words
-#+begin_src elisp :tangle no
-  (use-package writegood-mode
-    :diminish writegood-mode
-    :config
-    (progn (add-hook 'text-mode-hook 'writegood-mode))
-    )
-#+end_src
-
-** Org-babel docker
-#+begin_src elisp :tangle no
-  (use-package ob-docker-build
-    :straight (ob-docker-build :type git :host github :repo "ifitzpat/ob-docker-build")
-    :defer t
-    :config
-    (add-to-list 'org-babel-load-languages '(docker-build . t))
-    (org-babel-do-load-languages 'org-babel-load-languages org-babel-load-languages)
-  )
-#+end_src
-
-* Spelling and syntax
-
-** Spell checking
-
-This requires installation of hunspell
-#+begin_src bash :tangle no
-  sudo apt install hunspell
-#+end_src
-
-#+begin_src elisp
-  (use-package flyspell
-    :config (setq ispell-program-name "hunspell"
-                  ispell-default-dictionary "en_US"
-                  )
-    :diminish (flyspell-mode . "φ")
-    :hook (text-mode . flyspell-mode)
-    :bind (
-           ("M-<f7>" . flyspell-buffer)
-           ("<f7>" . flyspell-word)
-           ("C-;" . flyspell-auto-correct-previous-word)
-           )
-    )
-#+end_src
-
-** Flyspell correct
-#+begin_src elisp :tangle no
-  (use-package flyspell-correct
-    :after flyspell
-    :bind (:map flyspell-mode-map ("C-;" . flyspell-correct-wrapper))
-  )
-#+end_src
-
-** Flycheck
-
-Needs external checkers installed
-
-#+begin_src elisp
-  (use-package flycheck
-    :init (global-flycheck-mode)
-    :diminish (flycheck-mode . "")
-    :config
-    (add-hook 'after-init-hook #'global-flycheck-mode)
-    (setq flycheck-emacs-lisp-load-path 'inherit)
-    (setq flycheck-emacs-lisp-load-path (concat user-emacs-directory "straight/build"))
-    )
-#+end_src
-
-** Flycheck bash
-#+begin_src bash :tangle no
-  sudo apt install devscripts
-#+end_src
-
-#+begin_src elisp :tangle no
-  (use-package flycheck-checkbashisms
-    :config
-    (flycheck-checkbashisms-setup)
-  )
-#+end_src
-
-** Yaml
-#+begin_src elisp :tangle no
-  (use-package yaml-mode
-    :config
-    (add-to-list 'auto-mode-alist '("\\.yml\\'" . yaml-mode))
-    (add-to-list 'auto-mode-alist '("\\.yaml\\'" . yaml-mode))
-    )
-#+end_src
-
-** Docker
-#+begin_src elisp :tangle no
-  (use-package docker-compose-mode)
-#+end_src

projects/dotemacs/dotemacs.el

@@ -1,7 +1,10 @@
-(let ((config-dir "~/memex/system/"))
+(let ((config-dir "~/memex/projects/dotemacs/modules/"))
   ;; Load the core settings, including package management and essential setup.
   (org-babel-load-file (expand-file-name "emacs-core.org" config-dir))
 
+  ;; Load UI and theme settings
+  (org-babel-load-file (expand-file-name "emacs-ui.org" config-dir))
+
   ;; Load early init settings (if separate and not fully covered by core)
   ;; (org-babel-load-file (expand-file-name "emacs-early-init.org" config-dir))
 

projects/dotemacs/dotemacs.org

@@ -6,10 +6,13 @@
 This file loads the modular Emacs configuration files. It should be the primary way Emacs is configured, replacing or integrating with the original `~/.emacs`, `~/.emacs.d/init.el`, `~/.emacs.d/early-init.el`, and `~/.emacs.d/config.el`.
 
 #+begin_src emacs-lisp
-(let ((config-dir "~/memex/system/"))
+(let ((config-dir "~/memex/projects/dotemacs/modules/"))
   ;; Load the core settings, including package management and essential setup.
   (org-babel-load-file (expand-file-name "emacs-core.org" config-dir))
 
+  ;; Load UI and theme settings
+  (org-babel-load-file (expand-file-name "emacs-ui.org" config-dir))
+
   ;; Load early init settings (if separate and not fully covered by core)
   ;; (org-babel-load-file (expand-file-name "emacs-early-init.org" config-dir))
 

projects/dotemacs/modules/emacs-ai.el

@@ -79,13 +79,13 @@
                                :embedding-model "nomic-embed-text"))
   )
 
-(use-package org-agent
+(use-package opencortex
   :straight nil
-  :load-path "~/.local/share/org-agent/src"
-  :commands (org-agent-connect org-agent-disconnect)
+  :load-path "~/.local/share/opencortex/src"
+  :commands (opencortex-connect opencortex-disconnect)
   :init
-  (setq org-agent-host "127.0.0.1")
-  (setq org-agent-port 9105)
-  (setq org-agent-executable-path "~/.local/share/org-agent/bin/org-agent-server")
+  (setq opencortex-host "127.0.0.1")
+  (setq opencortex-port 9105)
+  (setq opencortex-executable-path "~/.local/share/opencortex/bin/opencortex-server")
   :config
-  (message "org-agent: Local brain configured at %s" org-agent-executable-path))
+  (message "opencortex: Local brain configured at %s" opencortex-executable-path))

projects/dotemacs/modules/emacs-ai.org

@@ -1,21 +1,120 @@
-#+TITLE: Emacs AI Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/ai.el
+#+TITLE: AI Configuration
+#+PROPERTY: header-args :tangle yes
 
-* ellama
-#+begin_src elisp
+* AI Settings
+
+** Ellama
+
+#+begin_src elisp :tangle yes
+  ;; YOU DON'T NEED NONE OF THIS CODE FOR SIMPLE INSTALL
+  ;; IT IS AN EXAMPLE OF CUSTOMIZATION.
   (use-package ellama
-    :ensure t
-    :bind ("C-c e" . ellama)
-    :hook (org-ctrl-c-ctrl-c-final . ellama-chat-send-last-message)
-    :init (setopt ellama-auto-scroll t)
-    :config
-    (ellama-context-header-line-global-mode +1)
-    (ellama-session-header-line-global-mode +1)
+    :init
+    (require 'llm-openai)
+    ;; setup key bindings
+    (setq ellama-keymap-prefix "C-c e")
     )
 #+end_src
 
-* Providers
-#+begin_src elisp
+#+begin_src elisp :tangle yes
+  (setopt ellama-providers
+  	'(
+  	  ;; Ollama Provider (added here with a name)
+  	  ("ollama" . (make-llm-ollama
+                               ;; Consider a dedicated embedding model if gemma isn't ideal for it.
+                               :chat-model "gemma3:latest"
+                               :embedding-model "gemma3:latest" ; Or e.g., "nomic-embed-text"
+                               :default-chat-non-standard-params '(("num_ctx" . 8192))))
+
+  	  ("openai" . (make-llm-openai
+                         :key (auth-source-pass-get "api-key" "www/openai.com/amr@gharbeia.net")
+                         :chat-model "gpt-4o"
+  		       :embedding-model "text-embedding-3-large"))
+
+            ("groq" . (make-llm-openai-compatible
+                       :url "https://api.groq.com/openai/v1"
+                       :key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net")
+                       ;; Check Groq console for available models, these might change
+                       :chat-model "llama3-70b-8192" ; Example, verify on Groq
+                       :embedding-model "llama3-70b-8192")) ; Groq might not offer dedicated embedding models via this API
+            ))
+
+  ;; --- Set Active Providers ---
+  ;; Choose your default provider from the list above by its name
+  (setopt ellama-provider "ollama") ; Or "ollama", "openai", "groq"
+
+  ;; You can specify different providers for different tasks if needed
+  (setopt ellama-translation-provider "ollama")
+  (setopt ellama-naming-provider "ollama")
+  (setopt ellama-naming-scheme 'ellama-generate-name-by-llm)
+
   (setq llm-debug t)
-  ;; Note: API keys should be handled via auth-source as seen in original config
 #+end_src
+
+#+begin_src elisp
+  (use-package ellama
+  :ensure t
+  :bind ("C-c e" . ellama)
+  ;; send last message in chat buffer with C-c C-c
+  :hook (org-ctrl-c-ctrl-c-final . ellama-chat-send-last-message)
+  :init (setopt ellama-auto-scroll t)
+  :config
+  ;; show ellama context in header line in all buffers
+  (ellama-context-header-line-global-mode +1)
+  ;; show ellama session id in header line in all buffers
+  (ellama-session-header-line-global-mode +1))
+#+end_src
+
+** GPTel
+   
+#+begin_src elisp :tangle yes
+  (use-package gptel)
+#+end_src
+
+#+begin_src elisp :tangle yes
+  (setq gptel-api-key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net"))
+#+end_src
+
+#+begin_src elisp :tangle yes
+  (gptel-make-openai "Groq"               ;Any name you want
+  :host "api.groq.com"
+  :endpoint "/openai/v1/chat/completions"
+  :stream t
+  :key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net")                   ;can be a function that returns the key
+  :models '(llama-3.1-70b-versatile
+            llama-3.1-8b-instant
+            llama3-70b-8192
+            llama3-8b-8192
+            mixtral-8x7b-32768
+            gemma-7b-it))
+#+end_src
+
+** Elisa
+
+#+begin_src elisp :tangle yes
+  (use-package elisa
+    :defer t
+    :init
+    (setopt elisa-limit 5)
+    (require 'llm-ollama)
+    (setopt elisa-embeddings-provider (make-llm-ollama :embedding-model "nomic-embed-text"))
+    (setopt elisa-chat-provider (make-llm-ollama
+                                 :chat-model "sskostyaev/openchat:8k-rag"
+                                 :embedding-model "nomic-embed-text"))
+    )
+#+end_src
+
+** OpenCortex (Local Foundry)
+
+#+begin_src elisp :tangle yes
+  (use-package opencortex
+    :straight nil
+    :load-path "~/.local/share/opencortex/src"
+    :commands (opencortex-connect opencortex-disconnect)
+    :init
+    (setq opencortex-host "127.0.0.1")
+    (setq opencortex-port 9105)
+    (setq opencortex-executable-path "~/.local/share/opencortex/bin/opencortex-server")
+    :config
+    (message "opencortex: Local brain configured at %s" opencortex-executable-path))
+#+end_src

projects/dotemacs/modules/emacs-core.el

@@ -16,6 +16,36 @@
 (unless (file-directory-p (expand-file-name "~/.emacs.d/straight/versions")) (make-directory (expand-file-name "~/.emacs.d/straight/versions") t))
 (use-package org)
 
+(use-package ef-themes
+  :config
+  ;; If you like two specific themes and want to switch between them, you
+  ;; can specify them in `ef-themes-to-toggle' and then invoke the command
+  ;; `ef-themes-toggle'.  All the themes are included in the variable
+  ;; `ef-themes-collection'.
+  (setq ef-themes-to-toggle '(ef-summer ef-winter))
+
+  (setq ef-themes-headings ; read the manual's entry or the doc string
+        '((0 variable-pitch light 1.9)
+          (1 variable-pitch light 1.8)
+          (2 variable-pitch regular 1.7)
+          (3 variable-pitch regular 1.6)
+          (4 variable-pitch regular 1.5)
+          (5 variable-pitch 1.4) ; absence of weight means `bold'
+          (6 variable-pitch 1.3)
+          (7 variable-pitch 1.2)
+          (t variable-pitch 1.1)))
+
+  ;; They are nil by default...
+  (setq ef-themes-mixed-fonts t)
+  (setq ef-themes-variable-pitch-ui t)
+
+  ;; Disable all other themes to avoid awkward blending:
+  (mapc #'disable-theme custom-enabled-themes)
+
+  ;; Load the theme of choice:
+  (load-theme 'ef-winter :no-confirm)
+  )
+
 (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
 (when (file-exists-p custom-file) (load custom-file))
 
@@ -49,7 +79,7 @@
 
 (add-hook 'server-done-hook (lambda () (delete-frame)))
 
-(desktop-save-mode t)
+;; (desktop-save-mode t)
 
 (use-package password-store)
 

projects/dotemacs/modules/emacs-core.org

@@ -1,55 +1,199 @@
-#+TITLE: Emacs Core Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/core.el
+#+TITLE: Core Emacs Configuration
+#+PROPERTY: header-args :tangle yes
 
-* early-init.el
-For straight.el to pick up before package.el
+* Initialization Bootstrap
 
-#+begin_src elisp :tangle ~/.emacs.d/early-init.el
-  (setq package-enable-at-startup nil)
-#+end_src
+This section tangles directly to ~/.emacs to bootstrap the entire system.
 
-* Straight.el Bootstrap
 #+begin_src elisp :tangle ~/.emacs
+  ;;; .emacs --- Global settings -*- lexical-binding: t; -*-
+
+  (setq gc-cons-threshold (* 500 1024 1024))
+  (add-hook 'after-init-hook (lambda () (setq gc-cons-threshold (* 5 1024 1024))))
+
   (setq straight-repository-branch "develop")
-   (eval-and-compile
-     (defvar bootstrap-version)
-     (let ((bootstrap-file
-            (expand-file-name "straight/repos/straight.el/bootstrap.el"
-               		   (or (bound-and-true-p straight-base-dir)
-               		       user-emacs-directory)))
-           (bootstrap-version 7))
-       (unless (file-exists-p bootstrap-file)
-         (with-current-buffer
-             (url-retrieve-synchronously  "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el" 'silent 'inhibit-cookies)
-           (goto-char (point-max))
-           (eval-print-last-sexp)))
-       (load bootstrap-file nil 'nomessage))
-     
-     (straight-use-package 'use-package)
-     )
+
+  (eval-and-compile
+    (defvar bootstrap-version)
+    (let ((bootstrap-file
+           (expand-file-name "straight/repos/straight.el/bootstrap.el"
+                             (or (bound-and-true-p straight-base-dir)
+                                 user-emacs-directory)))
+          (bootstrap-version 7))
+      (unless (file-exists-p bootstrap-file)
+        (with-current-buffer
+            (url-retrieve-synchronously "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el" 'silent 'inhibit-cookies)
+          (goto-char (point-max))
+          (eval-print-last-sexp)))
+      (load bootstrap-file nil 'nomessage))
+    
+    (straight-use-package 'use-package)
+    (straight-use-package 'org))
+
   (setq straight-use-package-by-default t)
+
+  (require 'ob-tangle)
+
+  ;; Load the modular configuration starting from dotemacs.org
+  (org-babel-load-file (expand-file-name "~/memex/projects/dotemacs/dotemacs.org"))
+
+  (provide '.emacs)
 #+end_src
 
-* Server and Performance
-#+begin_src elisp :tangle ~/.emacs.d/early-init.el
-  (require 'server)
-  (unless (server-running-p) (server-start))
-  (defvar server-max-buffers 100)
-#+end_src
+* Front matter
 
+#+begin_src elisp
+  ;;; emacs-core.el --- Summary
+  ;;; Commentary:
+  ;;; Code:
+
+  ;; -*- lexical-binding: t; -*-
+#+end_src
+
+* Garbage collector
+
+Increase threshold to 500 MB to ease startup
 #+begin_src elisp
   (setq gc-cons-threshold (* 500 1024 1024))
+#+end_src
+
+Decrease threshold to 5 MB after init
+#+begin_src elisp
   (add-hook 'after-init-hook (lambda () (setq gc-cons-threshold (* 5 1024 1024))))
 #+end_src
 
-* System Information
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
+* Straight.el and use-package
+
+Integrate use-package and straight
+#+begin_src elisp
+  (setq straight-use-package-by-default t)
+  (require 'use-package)
+  (straight-use-package 'diminish)
+  (require 'diminish)
+#+end_src
+
+Make sure Org is installed (straight.el)
+#+begin_src elisp
+  (unless (file-directory-p (expand-file-name "~/.emacs.d/straight/versions")) (make-directory (expand-file-name "~/.emacs.d/straight/versions") t))
+  (use-package org)
+#+end_src
+
+* UI and Themes
+
+#+begin_src elisp
+  (use-package ef-themes
+    :config
+    ;; If you like two specific themes and want to switch between them, you
+    ;; can specify them in `ef-themes-to-toggle' and then invoke the command
+    ;; `ef-themes-toggle'.  All the themes are included in the variable
+    ;; `ef-themes-collection'.
+    (setq ef-themes-to-toggle '(ef-summer ef-winter))
+
+    (setq ef-themes-headings ; read the manual's entry or the doc string
+          '((0 variable-pitch light 1.9)
+            (1 variable-pitch light 1.8)
+            (2 variable-pitch regular 1.7)
+            (3 variable-pitch regular 1.6)
+            (4 variable-pitch regular 1.5)
+            (5 variable-pitch 1.4) ; absence of weight means `bold'
+            (6 variable-pitch 1.3)
+            (7 variable-pitch 1.2)
+            (t variable-pitch 1.1)))
+
+    ;; They are nil by default...
+    (setq ef-themes-mixed-fonts t)
+    (setq ef-themes-variable-pitch-ui t)
+
+    ;; Disable all other themes to avoid awkward blending:
+    (mapc #'disable-theme custom-enabled-themes)
+
+    ;; Load the theme of choice:
+    (load-theme 'ef-winter :no-confirm)
+    )
+#+end_src
+
+* Custom file
+
+#+begin_src elisp
+  (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
+  (when (file-exists-p custom-file) (load custom-file))
+#+end_src
+
+* System information
+
+#+begin_src elisp
   (defvar my-laptop-p (equal (system-name) "lilitop"))
   (defvar my-server-p (and (equal (system-name) "localhost") (equal user-login-name "root")))
   (defvar my-phone-p (not (null (getenv "ANDROID_ROOT")))
     "If non-nil, GNU Emacs is running on Termux.")
   (when my-phone-p (defvar gnutls-algorithm-priority "NORMAL:-VERS-TLS1.3"))
-  (global-auto-revert-mode)
-  (savehist-mode)
-  (desktop-save-mode t)
+  (global-auto-revert-mode)  ; simplifies syncing
+#+end_src
+
+* Persistent history
+
+#+begin_src elisp
+  (savehist-mode)
+#+end_src
+
+* Disable Syntax Checkers (Diagnostic)
+
+#+begin_src elisp
+  (when (fboundp 'flycheck-mode)
+    (setq flycheck-global-modes nil)
+    (global-flycheck-mode -1))
+  (when (fboundp 'flymake-mode)
+    (setq help-at-pt-display-when-idle t)
+    ;; Disable flymake in all buffers
+    (add-hook 'find-file-hook (lambda () (flymake-mode -1))))
+#+end_src
+
+* Backup and versioning
+
+#+begin_src emacs-lisp
+  (use-package magit)
+#+end_src
+
+* Personal information
+
+#+begin_src elisp
+  (setq user-full-name "Amr Gharbeia")
+  (defvar email-address "amr@gharbeia.net")
+  (defvar calendar-latitude 39.0)
+  (defvar calendar-longitude -77.1)
+  (defvar calendar-location-name "Washington, DC")
+  (defvar calendar-time-zone -300)
+  (defvar calendar-standard-time-zone-name "EST")
+  (defvar calendar-daylight-time-zone-name "EDT")
+#+end_src
+
+* Saving Emacs Sessions
+
+Close frame when done
+#+begin_src elisp
+  (add-hook 'server-done-hook (lambda () (delete-frame)))
+#+end_src
+
+Save desktop session
+#+begin_src elisp
+  ;; (desktop-save-mode t)
+#+end_src
+
+* Security
+
+#+begin_src elisp
+  (use-package password-store)
+#+end_src
+
+#+begin_src elisp
+  (use-package auth-source
+    :config (auth-source-pass-enable)
+    )
+#+end_src
+
+* End matter
+
+#+begin_src elisp
+  (provide 'emacs-core)
+  ;;; emacs-core.el ends here
 #+end_src

projects/dotemacs/modules/emacs-gtd.org

@@ -1,30 +1,112 @@
-#+TITLE: Emacs GTD Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/gtd.el
+#+TITLE: GTD & Agenda Configuration
+#+PROPERTY: header-args :tangle yes
 
-* org-gtd
+* Agenda
+
+Basic agenda settings
 #+begin_src elisp
-  (use-package org-gtd
-    :defer t
-    :init (setq org-gtd-update-ack "3.0.0")
-    :after org
-    :config
-    (setq org-edna-use-inheritance t)
-    (org-edna-mode)
-    :bind (
-  	 ("C-c d c" . org-gtd-capture)
-  	 ("C-c d e" . org-gtd-engage)
-  	 ("C-c d p" . org-gtd-process-inbox)
-  	 :map org-gtd-clarify-map
-  	 ("C-c c" . org-gtd-organize)
-  	 )
-    )
+   (setq org-deadline-warning-days 7)
+   (setq org-agenda-skip-additional-timestamps-same-entry t)
+   (setq org-agenda-span 'fortnight)
+   (setq org-agenda-tags-column 'auto)
+   (setq org-agenda-skip-scheduled-if-deadline-is-shown t)
 #+end_src
 
-* GTD Directory and Areas
+Agenda files
 #+begin_src elisp
-  (defvar org-gtd-directory org-directory)
-  (defvar org-gtd-organize-hooks '(org-gtd-set-area-of-focus))
-  (defvar org-gtd-areas-of-focus '(
+  (setq org-agenda-files (list
+  			(concat org-directory "/inbox.org")
+  			(concat org-directory "/gtd.org")
+  			(concat org-directory "/org-gtd-tasks.org")
+  			)
+        )
+
+#+end_src
+
+Better agenda views
+#+begin_src elisp :tangle yes
+  (use-package org-super-agenda)
+#+end_src
+
+* To-do
+
+Basic todo
+#+begin_src elisp
+  (setq org-todo-keywords
+          '(
+            (sequence "TODO(t)" "NEXT(n)" "WAIT(w@/!)" "|" "DONE(d!)" "CNCL(c@)")
+            )
+          )
+
+  (setq org-todo-keyword-faces
+          '(
+            ("TODO" :foreground "red" :weight bold)
+            ("NEXT" :foreground "red" :weight bold)
+            ("WAIT" :foreground "yellow" :weight bold)
+            ("DONE" :foreground "green" :weight bold)
+            ("CNCL" :foreground "blue" :weight bold)
+            )
+          )
+
+  (setq org-enforce-todo-dependencies t)
+  (setq org-tags-exclude-from-inheritance '("crypt" "!private"))
+#+end_src
+
+Switch entry to 'DONE' when all subentries are done
+#+begin_src elisp
+  (defun org-summary-todo (n-done n-not-done)
+    "Switch entry to 'DONE' when all subentries are done, to 'TODO' otherwise.
+  Uses N-DONE and N-NOT-DONE"
+    (let (org-log-done org-log-states)   ; turn off logging
+      (org-todo (if (= n-not-done 0) "DONE" "TODO")
+                )
+        )
+    )
+
+    ;; (add-hook 'org-after-todo-statistics-hook #'org-summary-todo)
+#+end_src
+
+* Getting Things Done (GTD)
+
+#+begin_src elisp
+  (use-package f)
+  (use-package dash)
+  (use-package s)
+  (use-package org-edna
+    :config
+    (setq org-edna-use-inheritance t)
+    (org-edna-mode))
+
+  (use-package org-gtd
+    :straight (org-gtd :type git :host github :repo "Trevoke/org-gtd.el")
+    :demand t
+    :init (setq org-gtd-update-ack "4.0.0")
+    :config
+    (setq org-gtd-keyword-mapping
+          '((todo . "TODO")
+            (next . "NEXT")
+            (wait . "WAIT")
+            (done . "DONE")
+            (canceled . "CNCL")))
+    (setq org-gtd-custom-node-paths
+          (list (list "Actionable" (expand-file-name "~/memex/gtd.org") "Actions")
+                (list "Legacy" (expand-file-name "~/memex/org-gtd-tasks.org") "Actions")
+                (list "Projects" (expand-file-name "~/memex/gtd.org") "Projects")
+                (list "Incubate" (expand-file-name "~/memex/gtd.org") "Incubate")))
+    (org-gtd-mode)
+    )
+
+  (global-set-key (kbd "C-c d c") #'org-gtd-capture)
+  (global-set-key (kbd "C-c d e") #'org-gtd-engage)
+  (global-set-key (kbd "C-c d p") #'org-gtd-process-inbox)
+  (with-eval-after-load 'org-gtd
+    (define-key org-gtd-clarify-map (kbd "C-c c") #'org-gtd-organize))
+#+end_src
+
+#+begin_src elisp
+  (setq org-gtd-directory org-directory)
+  (setq org-gtd-organize-hooks '(org-gtd-set-area-of-focus))
+  (setq org-gtd-areas-of-focus '(
   				 "Atoms"
   				 "Bits"
   				 "Cells"
@@ -44,5 +126,41 @@
   				 "Egypt"
   				 )
     )
-  (defvar org-gtd-clarify-show-horizons 'right)
+  (setq org-gtd-clarify-show-horizons 'right)
 #+end_src
+
+Logging
+#+begin_src elisp
+  (setq org-log-into-drawer "LOGBOOK")
+#+end_src
+
+Clocking work in drawer
+#+begin_src elisp :tangle yes
+  (setq org-clock-into-drawer t)
+#+end_src
+
+Habits
+#+begin_src elisp :tangle yes
+  (setq org-habit-graph-column 80)
+  (setq org-habit-show-habits-only-for-today nil)
+#+end_src
+
+* Refile
+
+org-refile targets
+#+begin_src elisp
+  (setq org-refile-targets '((nil :maxlevel . 9)
+                             (org-agenda-files :maxlevel . 9)
+                             )
+        )
+#+end_src
+
+Set type of refile targets completion
+#+begin_src elisp
+  (setq org-outline-path-complete-in-steps nil)
+#+end_src
+
+Allow refiling to new parents created on the go after confirmation
+#+begin_src elisp
+  (setq org-refile-allow-creating-parent-nodes 'confirm)
+#+end_src

projects/dotemacs/modules/emacs-media.el

@@ -21,6 +21,9 @@
   (setq org-noter-notes-search-path (list (expand-file-name "~/memex/library/books")))
   (setq org-noter-default-notes-file-names '("books.org")))
 
+(setq org-noter-notes-search-path (list (concat org-directory "/library/books")))
+(setq org-noter-default-notes-file-names '("books.org"))
+
 (use-package org-noter-pdftools
   :after org-noter
   :config
@@ -62,3 +65,5 @@ With a prefix ARG, remove start location."
   )
 
 (use-package helm-bibtex)
+
+(setq bibtex-completion-bibliography '("~/bibliography/zotero.bib"))

projects/dotemacs/modules/emacs-media.org

@@ -1,39 +1,101 @@
-#+TITLE: Emacs Media and E-books Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/media.el
+#+TITLE: Media and Books Configuration
+#+PROPERTY: header-args :tangle yes
+
+* Read ebooks (calibredb)
 
-* calibredb
 #+begin_src elisp
   (use-package calibredb
     :defer t
     :config
-      (setq calibredb-format-all-the-icons t)
-      (setq calibredb-format-icons-in-terminal t)
-      )
+    (setq calibredb-format-all-the-icons t)
+    (setq calibredb-format-icons-in-terminal t))
+#+end_src
 
-  (defvar calibredb-root-dir (concat (getenv "HOME") "/library/books"))
+#+begin_src elisp
+  (defvar calibredb-root-dir (expand-file-name "~/memex/library/books"))
   (defvar calibredb-db-dir (expand-file-name "metadata.db" calibredb-root-dir))
   (defvar calibredb-id-width 6)
   (defvar calibredb-title-width 100)
-  (defvar calibredb-author-width 20)
 #+end_src
 
-* nov.el (EPUB Viewer)
+* PDF Tools
+
 #+begin_src elisp
+  (use-package pdf-tools
+    :mode ("\\.pdf\\'" . pdf-view-mode)
+    :config
+    (pdf-tools-install :no-query)
+    (setq-default pdf-view-display-size 'fit-page)
+    (setq pdf-annot-activate-created-annotations t))
+#+end_src
+
+* Annotate PDFs and EPUBs (org-noter)
+
+#+begin_src elisp
+  (use-package org-noter
+    :config
+    (setq org-noter-notes-search-path (list (expand-file-name "~/memex/library/books")))
+    (setq org-noter-default-notes-file-names '("books.org")))
+#+end_src
+
+#+begin_src elisp :tangle yes
+  (setq org-noter-notes-search-path (list (concat org-directory "/library/books")))
+  (setq org-noter-default-notes-file-names '("books.org"))  
+#+end_src
+
+* Link PDFs (org-noter-pdftools)
+
+#+begin_src elisp
+  (use-package org-noter-pdftools
+    :after org-noter
+    :config
+    ;; Add a function to ensure precise note is inserted
+    (defun org-noter-pdftools-insert-precise-note (&optional toggle-no-questions)
+      (interactive "P")
+      (org-noter--with-valid-session
+       (let ((org-noter-insert-note-no-questions (if toggle-no-questions
+  						   (not org-noter-insert-note-no-questions)
+                                                   org-noter-insert-note-no-questions))
+             (org-pdftools-use-isearch-link t)
+             (org-pdftools-use-freepointer-annot t))
+         (org-noter-insert-note (org-noter--get-precise-info)))))
+
+    ;; fix https://github.com/weirdNox/org-noter/pull/93/commits/f8349ae7575e599f375de1be6be2d0d5de4e6cbf
+    (defun org-noter-set-start-location (&optional arg)
+      "When opening a session with this document, go to the current location.
+  With a prefix ARG, remove start location."
+      (interactive "P")
+      (org-noter--with-valid-session
+       (let ((inhibit-read-only t)
+             (ast (org-noter--parse-root))
+             (location (org-noter--doc-approx-location (when (called-interactively-p 'any) 'interactive))))
+         (with-current-buffer (org-noter--session-notes-buffer session)
+           (org-with-wide-buffer
+            (goto-char (org-element-property :begin ast))
+            (if arg
+                (org-entry-delete nil org-noter-property-note-location)
+              (org-entry-put nil org-noter-property-note-location
+                             (org-noter--pretty-print-location location))))))))
+    (with-eval-after-load 'pdf-annot
+      (add-hook 'pdf-annot-activate-handler-functions #'org-noter-pdftools-jump-to-note)
+      )
+    )
+#+end_src
+
+* View EPUBs (nov.el)
+
+#+begin_src elisp :tangle yes
   (use-package nov
     :config
     (add-to-list 'auto-mode-alist '("\\.epub\\'" . nov-mode))
     )
 #+end_src
 
-* org-noter and PDF Tools
-#+begin_src elisp
-  (use-package org-noter)
-
-  (use-package org-noter-pdftools
-    :after org-noter
-    :config
-    (with-eval-after-load 'pdf-annot
-      (add-hook 'pdf-annot-activate-handler-functions #'org-noter-pdftools-jump-to-note)
-      )
-    )
+* Zotero (helm-bibtex)
+#+begin_src elisp :tangle yes
+  (use-package helm-bibtex)
 #+end_src
+
+#+begin_src elisp :tangle yes
+  (setq bibtex-completion-bibliography '("~/bibliography/zotero.bib"))
+#+end_src

projects/dotemacs/modules/emacs-org.el

@@ -68,6 +68,24 @@
 (require 'org-protocol)
 (setq org-protocol-default-buffer-for-file-links "*scratch*") ; fixes 'no buffers remain to edit error for org-protocol capturer
 
+(setq org-capture-templates '(
+                              ("p" "Protocol"
+                               entry
+                               (file "inbox.org")
+                               "* %^{Title}\nSource: %u, %c\n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n%?"
+                               )
+                              ("L" "Protocol Link"
+                               entry
+                               (file "inbox.org")
+                               "* %? [[%:link][%:description]]\n:PROPERTIES:\n:TITLE: %:description\n:URI: %:link\n:CREATED: %U\n:END:"
+                               :prepend nil
+                               :empty-lines 1
+                               :created t
+                               :kill-buffer t
+                               )
+                              )
+      )
+
 (setq org-protocol-default-template-key "L")
 
 (defun my/org-convert-orgzly-to-org-protocol ()

projects/dotemacs/modules/emacs-org.org

@@ -1,7 +1,10 @@
-#+TITLE: Emacs Org-mode Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/org.el
+#+TITLE: Org Mode Configuration
+#+PROPERTY: header-args :tangle yes
+
+* Org Mode
+
+** Basic setup
 
-* Core Org Setup
 #+begin_src elisp
   (use-package org
     :config
@@ -11,41 +14,130 @@
   	 ("C-c c" . org-capture)
   	 :map org-mode-map)
     )
-  (defvar org-directory (concat (getenv "HOME") "/org/"))
 #+end_src
 
-* Agenda
 #+begin_src elisp
-   (setq org-deadline-warning-days 7)
-   (setq org-agenda-skip-additional-timestamps-same-entry t)
-   (setq org-agenda-span 'fortnight)
-   (setq org-agenda-tags-column 'auto)
-   (setq org-agenda-skip-scheduled-if-deadline-is-shown t)
-   (setq org-agenda-files (list
-  			(concat org-directory "/0_inbox/inbox.org")
-  			(concat org-directory "/0_inbox/org-gtd-tasks.org")
-  			)
-        )
+  (setq org-directory (expand-file-name "~/memex/"))
 #+end_src
 
-* Capture and Protocol
+** Looks
+
+Basic 
+#+begin_src elisp
+  (defvar org-pretty-entities t) ; Improve org mode looks
+  (defvar org-hide-emphasis-markers t) ; Hide emphasis markup
+  (defvar org-num-mode nil)
+  (defvar org-startup-folded 'shw2levels)
+#+end_src
+
+Indentation of headers
+#+begin_src elisp
+  (defvar org-startup-indented t) ; Indent org heirarchy
+  (defvar org-adapt-indentation t)
+  (defvar org-hide-leading-stars t) ; Minimal Outline
+  (defvar org-odd-levels-only nil)
+#+end_src
+
+Indentation of lists
+#+begin_src elisp
+  (setq org-list-demote-modify-bullet t)
+#+end_src
+
+Org-modern
+#+begin_src elisp
+  (use-package org-modern
+    :ensure t
+    :config
+        ;; Choose some fonts
+    (set-face-attribute 'default nil :family "sans-serif")
+    (set-face-attribute 'variable-pitch nil :family "sans-serif")
+    (set-face-attribute 'org-modern-symbol nil :family "Iosevka")
+
+    ;; Edit settings
+    (defvar org-auto-align-tags nil)
+    (defvar org-tags-column 0)
+    (defvar org-catch-invisible-edits 'show-and-error)
+    (defvar org-special-ctrl-a/e t)
+    (defvar org-insert-heading-respect-content t)
+
+     ;; Org styling, hide markup etc.
+     (defvar org-hide-emphasis-markers t)
+     (defvar org-pretty-entities t)
+
+     ;; Agenda styling
+     (defvar org-agenda-tags-column 0)
+     (defvar org-agenda-block-separator ?─)
+     (defvar org-agenda-time-grid
+       '((daily today require-timed)
+         (800 1000 1200 1400 1600 1800 2000)
+         " ┄┄┄┄┄ " "┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄"))
+     (defvar org-agenda-current-time-string
+       "◀── now ─────────────────────────────────────────────────")
+
+    ;; Ellipsis styling
+     (defvar org-ellipsis "…")
+     (set-face-attribute 'org-ellipsis nil :inherit 'default :box nil)
+    
+     (global-org-modern-mode)
+    )
+#+end_src
+
+Highlight Sourcecode Syntax
+#+begin_src elisp
+  (setq org-src-fontify-natively t)
+  (setq org-src-tab-acts-natively t)
+#+end_src
+
+Images
+#+begin_src elisp
+  (setq org-startup-with-inline-images t)
+  (setq org-image-actual-width '(300))
+#+end_src
+
+** Capture
+
+#+begin_src elisp
+  (defvar org-default-notes-file (concat org-directory "inbox.org"))
+#+end_src
+
+*** Org-protocol
+
+Linux configuration
+#+begin_src bash :tangle yes
+[Desktop Entry]
+Name=org-protocol
+Comment=Intercept calls from emacsclient to trigger custom actions
+Categories=Other;
+Keywords=org-protocol;
+Icon=emacs
+Type=Application
+Exec=emacsclient -- %u
+Terminal=false
+StartupWMClass=Emacs
+MimeType=x-scheme-handler/org-protocol;
+#+end_src
+
+#+begin_src bash :tangle yes
+update-desktop-database ~/.local/share/applications/
+#+end_src
+
+Basic configuration
 #+begin_src elisp
   (require 'org-protocol)
-  (setq org-protocol-default-buffer-for-file-links "*scratch*")
-  (defvar org-default-notes-file (concat org-directory "/0_inbox/inbox.org"))
-  (setq org-protocol-default-template-key "L")
+  (setq org-protocol-default-buffer-for-file-links "*scratch*") ; fixes 'no buffers remain to edit error for org-protocol capturer
 #+end_src
 
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (defvar org-capture-templates '(
+Org-protocol templates
+#+begin_src elisp :tangle yes
+  (setq org-capture-templates '(
                                 ("p" "Protocol"
                                  entry
-                                 (file "0_inbox/inbox.org")
+                                 (file "inbox.org")
                                  "* %^{Title}\nSource: %u, %c\n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n%?"
                                  )
                                 ("L" "Protocol Link"
                                  entry
-                                 (file "0_inbox/inbox.org")
+                                 (file "inbox.org")
                                  "* %? [[%:link][%:description]]\n:PROPERTIES:\n:TITLE: %:description\n:URI: %:link\n:CREATED: %U\n:END:"
                                  :prepend nil
                                  :empty-lines 1
@@ -56,14 +148,86 @@
         )
 #+end_src
 
-* TODO Settings
 #+begin_src elisp
-  (setq org-todo-keywords
-          '(
-            (sequence "TODO(t)" "NEXT(n)" "|" "DONE(d!)")
-            (sequence "WAIT(w@/!)" "|" "CNCL(c@)")
-            )
-          )
-  (setq org-enforce-todo-dependencies t)
-  (setq org-log-into-drawer "LOGBOOK")
+  (setq org-protocol-default-template-key "L")
 #+end_src
+
+Convert Orgzly captures to org-protocol captures standard
+#+begin_src elisp
+  (defun my/org-convert-orgzly-to-org-protocol ()
+    "Reformat Orgzly bookmark at point to org-protocol bookmark."
+    (interactive)
+    (when (org-at-heading-p)
+      (let ((headline (nth 4 (org-heading-components))))
+        ;; Find and store the link. Delete the link line.
+        (search-forward-regexp "^https?://\\S-*" nil t)
+        (let ((link (match-string 0)))
+          (beginning-of-line)
+          (kill-line)
+          ;; Delete any trailing blank spaces
+          (org-back-to-heading)
+          (end-of-line)
+          (when (not (org-on-heading-p))
+            (delete-char 1)
+            )
+          ;; Set new headline
+          (goto-char (org-entry-beginning-position))
+          (org-edit-headline (format "[[%s][%s]]" link headline))
+          ;; Set new properties
+          (org-set-property "TITLE" headline)
+          (org-set-property "URI" link)
+          (message "Reformatted Orgzly bookmark at point to org-protocol bookmark")
+          )
+        )
+      )
+    )
+#+end_src
+
+** Exporting
+
+#+begin_src elisp :tangle yes
+  (setq org-export-with-smart-quotes t)
+  (setq org-export-backends '(beamer html latex md))
+#+end_src
+
+Export to EPUB
+#+begin_src elisp :tangle yes
+  (use-package ox-epub)
+#+end_src
+
+** org-attach
+
+#+begin_src elisp
+  (setq org-attach-id-dir (concat org-directory "/library"))
+#+end_src
+
+** Enable shell scripting support in org-babel
+
+#+begin_src elisp
+  (defvar org-babel-do-load-languages  'org-babel-load-languages  '((shell . t)))
+#+end_src
+
+** Insert org-mode links from clipboard
+#+begin_src elisp :tangle yes
+  (use-package org-cliplink
+    :bind
+    (("C-x p i" . org-cliplink))
+    )
+#+end_src
+
+** Deft
+#+begin_src elisp :tangle yes
+  (use-package deft
+    :commands (deft)
+    :init
+    (defvar deft-extensions '("org"))
+    (defvar deft-recursive nil)
+    (defvar deft-use-filename-as-title t)
+    :config
+    (defvar deft-directory org-directory)
+    (defvar deft-recursive t)
+    (defvar deft-strip-summary-regexp ":PROPERTIES:\n\\(.+\n\\)+:END:\n")
+    (defvar deft-use-filename-as-title t)
+    :bind  ("C-c n d" . deft)
+    )
+#+end_src

projects/dotemacs/modules/emacs-roam.org

@@ -1,42 +1,73 @@
-#+TITLE: Emacs Org-roam Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/roam.el
+#+TITLE: Org-Roam Configuration
+#+PROPERTY: header-args :tangle yes
+
+* Org-roam
+
+** Basic org-roam setup
 
-* org-roam Setup
 #+begin_src elisp
-  (use-package org-roam
-    :init (setq org-roam-v2-ack t)
-    :after org
-    :config
-    (org-roam-db-autosync-enable)
-    (require 'org-roam-dailies)
-    (setq org-roam-mode-sections
-  	(list #'org-roam-backlinks-section
-                #'org-roam-reflinks-section
-                #'org-roam-unlinked-references-section
-                )
-  	)
-    :bind  (
-  	  ("C-c n f" . org-roam-node-find)
-  	  ("C-c n g" . org-roam-graph)
-  	  ("C-c n r" . org-roam-node-random)
-  	  ("C-c n h" . org-roam-node-convert-headline)
-  	  ("C-c n i" . org-roam-node-insert)
-  	  ("C-c n o" . org-id-get-create)
-  	  ("C-c n t" . org-roam-tag-add)
-  	  ("C-c n a" . org-roam-alias-add)
-  	  ("C-c n l" . org-roam-buffer-display-dedicated)
-  	  )
-    )
+(use-package org-roam
+  :init (setq org-roam-v2-ack t) ;; Acknowledge V2 upgrade
+  :after org
+  :config
+  (org-roam-db-autosync-enable)
+  (require 'org-roam-dailies)
+  :bind  (
+   ("C-c n f" . org-roam-node-find)
+   ("C-c n g" . org-roam-graph)
+   ("C-c n r" . org-roam-node-random)
+   ("C-c n h" . org-roam-node-convert-headline)
+   ("C-c n i" . org-roam-node-insert)
+   ("C-c n o" . org-id-get-create)
+   ("C-c n t" . org-roam-tag-add)
+   ("C-c n a" . org-roam-alias-add)
+   ("C-c n l" . org-roam-buffer-display-dedicated)
+   )
+  )
 #+end_src
 
-* Directories
 #+begin_src elisp
-  (setq org-roam-directory (concat org-directory "/1_thinking"))
-  (setq org-roam-dailies-directory (concat org-directory "/0_inbox/daily"))
+  (setq org-roam-directory (expand-file-name (concat org-directory "notes")))
+  (setq org-roam-dailies-directory (expand-file-name (concat org-directory "daily")))
+#+end_src
+
+#+begin_src elisp :tangle yes
+  (use-package sqlite3)
+  (require 'sqlite3)
+#+end_src
+
+Include subdirectories in org-roam
+#+begin_src elisp
   (setq org-roam-file-exclude-regexp "^[.][.]?/")
 #+end_src
 
-* Capture Templates
+** Display in org-roam-buffer
+#+begin_src elisp :tangle yes
+  (setq org-roam-mode-sections
+        (list #'org-roam-backlinks-section
+              #'org-roam-reflinks-section
+              #'org-roam-unlinked-references-section 
+              )
+        )
+#+end_src
+
+** Filter org-roam nodes find by tag
+
+#+begin_src elisp :tangle yes
+  (defun my/org-roam-node-has-tag (node tag)
+    "Filter function to check if the given NODE has the specified TAG."
+    (member tag (org-roam-node-tags node))
+    )
+
+  (defun my/org-roam-node-find-by-tag ()
+    "Find and open an Org-roam node based on a specified tag."
+    (interactive)
+    (let ((tag (read-string "Enter tag: ")))
+      (org-roam-node-find nil nil (lambda (node) (my/org-roam-node-has-tag node tag))))
+    )
+#+end_src
+
+** org-roam-capture templates
 #+begin_src elisp
   (setq org-roam-capture-templates
         '(
@@ -48,6 +79,7 @@
            :immediate-finish t
            :unnarrowed t
            )
+
           ("h" "hugo post" plain
            "%?"
            :target (file+head "posts/${slug}.org"
@@ -55,6 +87,7 @@
            :immediate-finish t
            :unnarrowed t
            )
+
           ("p" "person" plain
            "%?"
            :if-new (file+head "people/${slug}.org"
@@ -64,7 +97,9 @@
           )
          )
        )
+#+end_src
 
+#+begin_src elisp
   (setq org-roam-dailies-capture-templates
         '(
           ("d" "daily" plain
@@ -75,3 +110,31 @@
          )
        )
 #+end_src
+
+** Move org header to org-roam-daily
+
+#+begin_src elisp :tangle yes
+  (defun my/org-move-entry-to-daily-notes ()
+    "Move the current org-mode headline to the daily notes file based on its :CREATED: property."
+    (interactive)
+    (let*
+        (
+         (created-prop (org-entry-get nil "CREATED"))
+         (created-date (when created-prop
+                         (org-parse-time-string created-prop)))
+         (year (nth 5 created-date)) ; Extract year (6th element)
+         (month (nth 4 created-date)) ; Extract month (5th element)
+         (day (nth 3 created-date)) ; Extract day (4th element)
+         (target-date (format "%04d-%02d-%02d" year month day)) ; Format date string
+         (target-file (org-roam-dailies-goto target-date)) 
+         )
+      (when target-file
+        (org-cut-subtree)
+        (find-file target-file)
+        (goto-char (point-max))
+        (unless (bolp) (newline))
+        (org-paste-subtree)
+        )
+      )
+  )
+#+end_src

projects/dotemacs/modules/emacs-shell.org

@@ -1,18 +1,86 @@
-#+TITLE: Emacs Shell Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/shell.el
+#+TITLE: Shell Configuration
+#+PROPERTY: header-args :tangle yes
+
+* Shell
+
+** Bash completion
 
-* Bash Completion
 #+begin_src elisp
   (use-package bash-completion
     :config
     (require 'bash-completion)
     (bash-completion-setup)
     )
-
-  (defvar shell-dynamic-complete-functions t)
 #+end_src
 
-* Frame Management
 #+begin_src elisp
-  (add-hook 'server-done-hook (lambda () (delete-frame)))
+(defvar shell-dynamic-complete-functions t)
 #+end_src
+
+** Eshell
+
+Add programmable bash completion to Emacs shell-mode
+#+begin_src elisp :tangle yes
+  (require 'bash-completion)
+  (add-hook 'eshell-mode-hook
+          (lambda ()
+            (add-hook 'completion-at-point-functions
+                      'bash-completion-capf-nonexclusive nil t
+                      )
+            )
+          )
+#+end_src
+
+Use colors in eshell
+#+begin_src elisp :tangle yes
+  (use-package xterm-color
+    :commands (xterm-color-filter)
+    )
+
+  (use-package eshell
+    :after xterm-color
+    :config
+    (define-key eshell-hist-mode-map (kbd "M-r") #'consult-history)
+    (add-hook 'eshell-mode-hook
+              (lambda ()
+                (setenv "TERM" "xterm-256color")))
+    (add-hook 'eshell-before-prompt-hook (setq xterm-color-preserve-properties t))
+    (add-to-list 'eshell-preoutput-filter-functions 'xterm-color-filter)
+    (setq eshell-output-filter-functions
+          (remove 'eshell-handle-ansi-color eshell-output-filter-functions)
+          )
+    )
+#+end_src
+
+Eshell completion
+#+begin_src elisp :tangle yes
+  (add-hook 'eshell-mode-hook
+          (lambda ()
+            (add-hook 'completion-at-point-functions
+                      'bash-completion-capf-nonexclusive nil t)))
+#+end_src
+
+Emulate A Terminal (EAT)
+#+begin_src elisp :tangle yes
+  (use-package eat
+    :config
+    ;; For `eat-eshell-mode'.
+    (add-hook 'eshell-load-hook #'eat-eshell-mode)
+
+    ;; For `eat-eshell-visual-command-mode'.
+    (add-hook 'eshell-load-hook #'eat-eshell-visual-command-mode)
+    )
+#+end_src
+
+* Server Actuation (Bash Integration)
+
+Ensure that emacsclient always opens in a GUI frame by default when called from the shell.
+
+#+begin_src bash :tangle ~/.bash_aliases
+  # Use emacsclient to open files in the GUI, starting daemon if needed
+  alias em="emacsclient -c -a ''"
+  
+  # Set emacsclient as the default editor
+  export EDITOR="emacsclient -c -a ''"
+  export VISUAL="emacsclient -c -a ''"
+#+end_src

projects/dotemacs/modules/emacs-ui.el

@@ -0,0 +1,16 @@
+(when (fboundp 'tool-bar-mode) (tool-bar-mode -1))
+(when (fboundp 'menu-bar-mode) (menu-bar-mode -1))
+(when (fboundp 'scroll-bar-mode) (scroll-bar-mode -1))
+
+(setq inhibit-startup-screen t)
+(setq initial-scratch-message nil)
+
+(set-face-attribute 'default nil :family "sans-serif" :height 120)
+(set-face-attribute 'variable-pitch nil :family "sans-serif")
+
+(use-package org-modern
+  :ensure t
+  :config
+  (set-face-attribute 'org-modern-symbol nil :family "Iosevka")
+  (global-org-modern-mode)
+  )

projects/dotemacs/modules/emacs-ui.org

@@ -1,59 +1,32 @@
 #+TITLE: Emacs UI Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/ui.el
+#+PROPERTY: header-args :tangle yes
 
 * Appearance
+
+Basic UI settings for a cleaner look.
+
 #+begin_src elisp
-  (defvar org-pretty-entities t) ; Improve org mode looks
-  (defvar org-hide-emphasis-markers t) ; Hide emphasis markup
-  (defvar org-num-mode nil)
-  (defvar org-startup-folded 'shw2levels)
-  (defvar org-startup-indented t) ; Indent org heirarchy
-  (defvar org-adapt-indentation t)
-  (defvar org-hide-leading-stars t) ; Minimal Outline
-  (defvar org-odd-levels-only nil)
+  (when (fboundp 'tool-bar-mode) (tool-bar-mode -1))
+  (when (fboundp 'menu-bar-mode) (menu-bar-mode -1))
+  (when (fboundp 'scroll-bar-mode) (scroll-bar-mode -1))
+
+  (setq inhibit-startup-screen t)
+  (setq initial-scratch-message nil)
 #+end_src
 
-* Org-modern
+* Fonts
+
+#+begin_src elisp
+  (set-face-attribute 'default nil :family "sans-serif" :height 120)
+  (set-face-attribute 'variable-pitch nil :family "sans-serif")
+#+end_src
+
+* Org-modern (UI elements)
 #+begin_src elisp
   (use-package org-modern
     :ensure t
     :config
-    ;; Choose some fonts
-    (set-face-attribute 'default nil :family "sans-serif")
-    (set-face-attribute 'variable-pitch nil :family "sans-serif")
     (set-face-attribute 'org-modern-symbol nil :family "Iosevka")
-
-    ;; Edit settings
-    (defvar org-auto-align-tags nil)
-    (defvar org-tags-column 0)
-    (defvar org-catch-invisible-edits 'show-and-error)
-    (defvar org-special-ctrl-a/e t)
-    (defvar org-insert-heading-respect-content t)
-
-     ;; Org styling, hide markup etc.
-     (defvar org-hide-emphasis-markers t)
-     (defvar org-pretty-entities t)
-
-     ;; Agenda styling
-     (defvar org-agenda-tags-column 0)
-     (defvar org-agenda-block-separator ?─)
-     (defvar org-agenda-time-grid
-       '((daily today require-timed)
-         (800 1000 1200 1400 1600 1800 2000)
-         " ┄┄┄┄┄ " "┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄"))
-     (defvar org-agenda-current-time-string
-       "◀── now ─────────────────────────────────────────────────")
-
-    ;; Ellipsis styling
-     (defvar org-ellipsis "…")
-     (set-face-attribute 'org-ellipsis nil :inherit 'default :box nil)
-    
-     (global-org-modern-mode)
+    (global-org-modern-mode)
     )
 #+end_src
-
-* Syntax Highlighting
-#+begin_src elisp
-  (setq org-src-fontify-natively t)
-  (setq org-src-tab-acts-natively t)
-#+end_src

projects/dotemacs/modules/emacs-writing.org

@@ -1,7 +1,195 @@
-#+TITLE: Emacs Writing Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/writing.el
+#+TITLE: Reading and Writing Configuration
+#+PROPERTY: header-args :tangle yes
+
+* Text and Case
+
+** Convert DOuble capitals to single capitals
+
+#+begin_src elisp :tangle yes
+  (defun my/dcaps-to-scaps ()
+    "Convert word in DOuble CApitals to Single Capitals."
+    (interactive)
+    (and (= ?w (char-syntax (char-before)))
+         (save-excursion
+           (and (if (called-interactively-p)
+                    (skip-syntax-backward "w")
+                  (= -3 (skip-syntax-backward "w"))
+                  )
+                (let (case-fold-search)
+                  (looking-at "\\b[[:upper:]]\\{2\\}[[:lower:]]")
+                  )
+              (capitalize-word 1)
+              )
+           )
+         )
+    )
+#+end_src
+
+Then, let’s define a minor mode for it to be activated.
+#+begin_src elisp :tangle yes
+  (define-minor-mode my-dubcaps-mode
+    "Toggle 'my-dubcaps-mode' and convert words in DOuble CApitals to Single Capitals as you type."
+    :init-value nil
+    :lighter (" DC")
+    (if my-dubcaps-mode
+        (add-hook 'post-self-insert-hook #'my/dcaps-to-scaps nil 'local)
+      (remove-hook 'post-self-insert-hook #'my/dcaps-to-scaps 'local)))
+#+end_src
+
+ Finally, let’s add a hook so that it is on for all the text files Emacs opens.
+#+begin_src elisp :tangle yes
+  (add-hook 'text-mode-hook #'my-dubcaps-mode)  
+#+end_src
+
+Also, since we add a minor mode string (it might be useful sometimes), currently I prefer to diminish it.
+#+begin_src elisp :tangle yes
+  (defun my/diminish-dubcaps ()
+    (interactive)
+    (diminish 'my-dubcaps-mode ""))
+  (add-hook 'my-dubcaps-mode-hook 'my/diminish-dubcaps)
+#+end_src
+
+* Reading and Writing
+
+** Move correctly over camelCased words
+
+#+begin_src elisp
+  (subword-mode)
+#+end_src
+
+** Understand the more common sentence with double space
+
+#+begin_src elisp
+  (setq sentence-end-double-space nil)
+#+end_src
+
+** Join lines into paragraph
+
+#+begin_src elisp
+  (defun my/fill-or-unfill-paragraph (&optional unfill region)
+    "Fill paragraph (or REGION). With the prefix argument UNFILL, fill it instead."
+    (interactive (progn
+                   (barf-if-buffer-read-only)
+                   (list (if current-prefix-arg 'fill) t)))
+    (let ((fill-column (if unfill fill-column (point-max))))
+      (fill-paragraph nil region)))
+
+  (bind-key "M-q" 'my/fill-or-unfill-paragraph)
+#+end_src
+
+#+begin_src elisp
+  (defun my/fill-or-unfill-all-paragraphs (&optional unfill)
+  "Fill or unfill all paragraphs in the current buffer.
+With the prefix argument UNFILL, fill them instead."
+  (interactive (list (if current-prefix-arg 'fill)))
+  (let ((fill-column (if unfill fill-column (point-max))))
+    (save-excursion
+      (goto-char (point-min))
+      (while (not (eobp))
+        (fill-paragraph nil t)
+        (forward-paragraph)))))
+
+(bind-key "M-Q" 'my/fill-or-unfill-all-paragraphs)
+#+end_src
+
+#+begin_src elisp
+  (remove-hook 'text-mode-hook #'turn-on-auto-fill)
+  (add-hook 'text-mode-hook 'turn-on-visual-line-mode)
+#+end_src
+
+** Expand some words with auto-correct
+
+  #+begin_src elisp :tangle yes
+  (setq save-abbrevs 'silently)
+  (setq-default abbrev-mode t)
+  #+end_src
+
+** ediff
+
+#+begin_src elisp :tangle yes
+  (setq ediff-window-setup-function 'ediff-setup-windows-plain)
+  (setq ediff-split-window-function 'split-window-horizontally)
+#+end_src
+
+** tramp
+
+#+begin_src elisp :tangle yes
+  (setq tramp-default-method "ssh"
+        tramp-backup-directory-alist backup-directory-alist
+        tramp-ssh-controlmaster-options "ssh")
+#+end_src
+
+** Clean up space
+#+begin_src elisp :tangle yes
+  (bind-key "M-SPC" 'cycle-spacing)
+#+end_src
+
+** Transform <a href> links into org links
+
+#+begin_src elisp :tangle yes
+  (defun my/transform-html-links-to-org ()
+  "Transform all HTML <a> links in the current buffer into 'org-mode' links."
+  (interactive)
+  (goto-char (point-min))
+  (while (re-search-forward "<a href=\"\\(.*?\\)\">\\(.*?\\)</a>" nil t)
+    (replace-match (org-make-link-string (match-string 1) (match-string 2)))))
+#+end_src
+
+** Count words per minute
+#+begin_src elisp :tangle yes
+  (require 'org-clock)
+  (defun my/org-entry-wpm ()
+    (interactive)
+    (save-restriction
+      (save-excursion
+        (org-narrow-to-subtree)
+        (goto-char (point-min))
+        (let* ((words (count-words-region (point-min) (point-max)))
+
+               (minutes (org-clock-sum-current-item))
+               (wpm (/ words minutes)))
+          (message "WPM: %d (words: %d, minutes: %d)" wpm words minutes)
+          (kill-new (number-to-string wpm))
+          )
+        )
+      )
+    )
+#+end_src
+
+** Enable dict mode
+  #+begin_src elisp :tangle yes
+    (setq dictionary-server "automatic")
+  #+end_src
+
+** Pick out passive voice and weasel words
+#+begin_src elisp :tangle yes
+  (use-package writegood-mode
+    :diminish writegood-mode
+    :config
+    (progn (add-hook 'text-mode-hook 'writegood-mode))
+    )
+#+end_src
+
+** Org-babel docker
+#+begin_src elisp :tangle yes
+  (use-package ob-docker-build
+    :straight (ob-docker-build :type git :host github :repo "ifitzpat/ob-docker-build")
+    :defer t
+    :config
+    (add-to-list 'org-babel-load-languages '(docker-build . t))
+    (org-babel-do-load-languages 'org-babel-load-languages org-babel-load-languages)
+  )
+#+end_src
+
+* Spelling and syntax
+
+** Spell checking
+
+This requires installation of hunspell
+#+begin_src bash :tangle yes
+  sudo apt install hunspell
+#+end_src
 
-* Spell Checking
 #+begin_src elisp
   (use-package flyspell
     :config (setq ispell-program-name "hunspell"
@@ -17,32 +205,50 @@
     )
 #+end_src
 
-* Syntax Checking
+** Flyspell correct
+#+begin_src elisp :tangle yes
+  (use-package flyspell-correct
+    :after flyspell
+    :bind (:map flyspell-mode-map ("C-;" . flyspell-correct-wrapper))
+  )
+#+end_src
+
+** Flycheck
+
+Needs external checkers installed
+
 #+begin_src elisp
   (use-package flycheck
-    :init (global-flycheck-mode)
+    :defer t
     :diminish (flycheck-mode . "")
     :config
-    (add-hook 'after-init-hook #'global-flycheck-mode)
     (setq flycheck-emacs-lisp-load-path 'inherit)
-    (setq flycheck-emacs-lisp-load-path (concat user-emacs-directory "straight/build"))
+    (setq flycheck-emacs-lisp-load-path (concat user-emacs-directory "straight/build")))
+
+#+end_src
+
+** Flycheck bash
+#+begin_src bash :tangle yes
+  sudo apt install devscripts
+#+end_src
+
+#+begin_src elisp :tangle yes
+  (use-package flycheck-checkbashisms
+    :config
+    (flycheck-checkbashisms-setup)
+  )
+#+end_src
+
+** Yaml
+#+begin_src elisp :tangle yes
+  (use-package yaml-mode
+    :config
+    (add-to-list 'auto-mode-alist '("\\.yml\\'" . yaml-mode))
+    (add-to-list 'auto-mode-alist '("\\.yaml\\'" . yaml-mode))
     )
 #+end_src
 
-* Text Manipulation
-#+begin_src elisp
-  (subword-mode)
-  (setq sentence-end-double-space nil)
-
-  (defun my/fill-or-unfill-paragraph (&optional unfill region)
-    "Fill paragraph (or REGION). With the prefix argument UNFILL, fill it instead."
-    (interactive (progn
-                   (barf-if-buffer-read-only)
-                   (list (if current-prefix-arg 'fill) t)))
-    (let ((fill-column (if unfill fill-column (point-max))))
-      (fill-paragraph nil region)))
-
-  (bind-key "M-q" 'my/fill-or-unfill-paragraph)
-
-  (add-hook 'text-mode-hook 'turn-on-visual-line-mode)
-#+end_src
+** Docker
+#+begin_src elisp :tangle yes
+  (use-package docker-compose-mode)
+#+end_src

projects/infrastructure/docs/qubes-npu-setup.org

@@ -0,0 +1,90 @@
+#+TITLE: Qubes NPU Setup - sys-ai
+#+AUTHOR: Amr
+#+CREATED: [2026-04-24 Fri]
+#+BEGIN_COMMENT
+Documentation for setting up sys-ai Qube with AMD Ryzen AI NPU for llama.cpp.
+#+END_COMMENT
+
+* Hardware
+
+- *Laptop:* Framework Laptop 13 (AMD)
+- *CPU:* AMD Ryzen AI 5 340 (6 cores, no SMT)
+- *NPU:* AMD XDNA2 (Strix Point) - c2:00.1 / dom0:00_08.2-00_00.1
+- *RAM:* 96GB total
+
+* Current Progress
+
+** DONE [X] Create sys-ai AppVM (HVM, 64GB, 2 vCPUs)
+
+#+begin_src bash
+# Run in dom0
+qvm-create --label purple --property netvm=sys-firewall --property memory=65536 --property vcpus=2 --property virt_mode=HVM sys-ai
+#+end_src
+
+** DONE [X] Attach NPU PCI device to sys-ai
+
+#+begin_src bash
+# Run in dom0
+qvm-pci attach -o no-strict-reset=true sys-ai dom0:00_08.2-00_00.1 --persistent
+#+end_src
+
+** TODO [ ] Fix repository configuration in sys-ai
+
+*Status:* Package repositories missing in fedora-43-ai template. Fedora 43 uses DNF5 with different repo paths.
+
+*Next Step:* Qubes OS templates typically get packages installed via `qubes-vm-update` or dom0 commands. Try the Qubes way to install packages.
+
+** TODO [ ] Verify NPU is accessible inside sys-ai
+
+#+begin_src bash
+# Install pciutils
+sudo dnf install pciutils
+
+# Check NPU is visible
+lspci | grep -i neural
+#+end_src
+
+** TODO [ ] Install AMD NPU drivers in sys-ai
+
+#+begin_src bash
+# Enable Copr repository
+sudo dnf copr enable xanderlent/amd-npu-driver
+
+# Install drivers
+sudo dnf install xrt xdna-driver tcsh
+
+# Setup environment
+source /usr/xrt/setup.sh
+
+# Verify NPU detection
+xrt-smi examine
+#+end_src
+
+** TODO [ ] Build llama.cpp with AMD XDNA2 NPU backend
+
+#+begin_src bash
+# Install build dependencies
+sudo dnf install cmake gcc-c++ python3.11 git
+
+# Clone NPU fork
+git clone https://github.com/BrandedTamarasu-glitch/OllamaAMDNPU.git
+cd OllamaAMDNPU
+
+# Build with NPU backend
+cmake -B build -DGGML_XDNA=ON -DGGML_BACKEND_DL=ON -DBUILD_SHARED_LIBS=ON
+cmake --build build --parallel
+#+end_src
+
+** TODO [ ] Download model and test inference
+
+#+begin_src bash
+# Download GGUF model (Qwen3 1B or 3B quantized)
+# ... model download command ...
+
+# Run with NPU offload
+./build/bin/llama-cli -m model.gguf -p "Hello" -n 256 --npu-split 1
+#+end_src
+
+* Next Step
+
+Run the repository fix commands from the "Fix repository" step above.

projects/lisp_machine_bootstrap/docs/README.org

@@ -36,5 +36,5 @@ See the actionable tasks for this project in [[file:../../gtd.org::*Lisp Machine
 
 * Links
 
-- [[file:../org-agent/][Orchestration: org-agent Microkernel]]
+- [[file:../opencortex/][Orchestration: opencortex Microkernel]]
 - [[file:../agora/][Social Layer: Agora Protocol]]

system/#fleet-dashboard.org#

@@ -1,355 +0,0 @@
-#+TITLE: LLM Fleet Dashboard
-#+author: Sol (Agent)
-
-* Model Fleet
-
-| Provider   | Model ID                                                      | Context |
-|------------+---------------------------------------------------------------+---------|
-| OpenRouter | google/gemma-4-26b-a4b-it                                     |  262144 |
-| OpenRouter | google/gemma-4-31b-it                                         |  262144 |
-| OpenRouter | qwen/qwen3.6-plus:free                                        | 1000000 |
-| OpenRouter | z-ai/glm-5v-turbo                                             |  202752 |
-| OpenRouter | arcee-ai/trinity-large-thinking                               |  262144 |
-| OpenRouter | x-ai/grok-4.20-multi-agent                                    | 2000000 |
-| OpenRouter | x-ai/grok-4.20                                                | 2000000 |
-| OpenRouter | google/lyria-3-pro-preview                                    | 1048576 |
-| OpenRouter | google/lyria-3-clip-preview                                   | 1048576 |
-| OpenRouter | kwaipilot/kat-coder-pro-v2                                    |  256000 |
-| OpenRouter | rekaai/reka-edge                                              |   16384 |
-| OpenRouter | xiaomi/mimo-v2-omni                                           |  262144 |
-| OpenRouter | xiaomi/mimo-v2-pro                                            | 1048576 |
-| OpenRouter | minimax/minimax-m2.7                                          |  204800 |
-| OpenRouter | openai/gpt-5.4-nano                                           |  400000 |
-| OpenRouter | openai/gpt-5.4-mini                                           |  400000 |
-| OpenRouter | mistralai/mistral-small-2603                                  |  262144 |
-| OpenRouter | z-ai/glm-5-turbo                                              |  202752 |
-| OpenRouter | nvidia/nemotron-3-super-120b-a12b:free                        |  262144 |
-| OpenRouter | nvidia/nemotron-3-super-120b-a12b                             |  262144 |
-| OpenRouter | bytedance-seed/seed-2.0-lite                                  |  262144 |
-| OpenRouter | qwen/qwen3.5-9b                                               |  256000 |
-| OpenRouter | openai/gpt-5.4-pro                                            | 1050000 |
-| OpenRouter | openai/gpt-5.4                                                | 1050000 |
-| OpenRouter | inception/mercury-2                                           |  128000 |
-| OpenRouter | openai/gpt-5.3-chat                                           |  128000 |
-| OpenRouter | google/gemini-3.1-flash-lite-preview                          | 1048576 |
-| OpenRouter | bytedance-seed/seed-2.0-mini                                  |  262144 |
-| OpenRouter | google/gemini-3.1-flash-image-preview                         |   65536 |
-| OpenRouter | qwen/qwen3.5-35b-a3b                                          |  262144 |
-| OpenRouter | qwen/qwen3.5-27b                                              |  262144 |
-| OpenRouter | qwen/qwen3.5-122b-a10b                                        |  262144 |
-| OpenRouter | qwen/qwen3.5-flash-02-23                                      | 1000000 |
-| OpenRouter | liquid/lfm-2-24b-a2b                                          |   32768 |
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-| OpenRouter | aion-labs/aion-2.0                                            |  131072 |
-| OpenRouter | google/gemini-3.1-pro-preview                                 | 1048576 |
-| OpenRouter | anthropic/claude-sonnet-4.6                                   | 1000000 |
-| OpenRouter | qwen/qwen3.5-plus-02-15                                       | 1000000 |
-| OpenRouter | qwen/qwen3.5-397b-a17b                                        |  262144 |
-| OpenRouter | minimax/minimax-m2.5:free                                     |  196608 |
-| OpenRouter | minimax/minimax-m2.5                                          |  196608 |
-| OpenRouter | z-ai/glm-5                                                    |   80000 |
-| OpenRouter | qwen/qwen3-max-thinking                                       |  262144 |
-| OpenRouter | anthropic/claude-opus-4.6                                     | 1000000 |
-| OpenRouter | qwen/qwen3-coder-next                                         |  262144 |
-| OpenRouter | openrouter/free                                               |  200000 |
-| OpenRouter | stepfun/step-3.5-flash:free                                   |  256000 |
-| OpenRouter | stepfun/step-3.5-flash                                        |  262144 |
-| OpenRouter | arcee-ai/trinity-large-preview:free                           |  131000 |
-| OpenRouter | moonshotai/kimi-k2.5                                          |  262144 |
-| OpenRouter | upstage/solar-pro-3                                           |  128000 |
-| OpenRouter | minimax/minimax-m2-her                                        |   65536 |
-| OpenRouter | writer/palmyra-x5                                             | 1040000 |
-| OpenRouter | liquid/lfm-2.5-1.2b-thinking:free                             |   32768 |
-| OpenRouter | liquid/lfm-2.5-1.2b-instruct:free                             |   32768 |
-| OpenRouter | openai/gpt-audio                                              |  128000 |
-| OpenRouter | openai/gpt-audio-mini                                         |  128000 |
-| OpenRouter | z-ai/glm-4.7-flash                                            |  202752 |
-| OpenRouter | openai/gpt-5.2-codex                                          |  400000 |
-| OpenRouter | allenai/olmo-3.1-32b-instruct                                 |   65536 |
-| OpenRouter | bytedance-seed/seed-1.6-flash                                 |  262144 |
-| OpenRouter | bytedance-seed/seed-1.6                                       |  262144 |
-| OpenRouter | minimax/minimax-m2.1                                          |  196608 |
-| OpenRouter | z-ai/glm-4.7                                                  |  202752 |
-| OpenRouter | google/gemini-3-flash-preview                                 | 1048576 |
-| OpenRouter | mistralai/mistral-small-creative                              |   32768 |
-| OpenRouter | xiaomi/mimo-v2-flash                                          |  262144 |
-| OpenRouter | nvidia/nemotron-3-nano-30b-a3b:free                           |  256000 |
-| OpenRouter | nvidia/nemotron-3-nano-30b-a3b                                |  262144 |
-| OpenRouter | openai/gpt-5.2-chat                                           |  128000 |
-| OpenRouter | openai/gpt-5.2-pro                                            |  400000 |
-| OpenRouter | openai/gpt-5.2                                                |  400000 |
-| OpenRouter | mistralai/devstral-2512                                       |  262144 |
-| OpenRouter | relace/relace-search                                          |  256000 |
-| OpenRouter | z-ai/glm-4.6v                                                 |  131072 |
-| OpenRouter | nex-agi/deepseek-v3.1-nex-n1                                  |  131072 |
-| OpenRouter | essentialai/rnj-1-instruct                                    |   32768 |
-| OpenRouter | openrouter/bodybuilder                                        |  128000 |
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-| OpenRouter | amazon/nova-2-lite-v1                                         | 1000000 |
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-| OpenRouter | mistralai/mistral-large-2512                                  |  262144 |
-| OpenRouter | arcee-ai/trinity-mini:free                                    |  131072 |
-| OpenRouter | arcee-ai/trinity-mini                                         |  131072 |
-| OpenRouter | deepseek/deepseek-v3.2-speciale                               |  163840 |
-| OpenRouter | deepseek/deepseek-v3.2                                        |  163840 |
-| OpenRouter | prime-intellect/intellect-3                                   |  131072 |
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-| OpenRouter | allenai/olmo-3-32b-think                                      |   65536 |
-| OpenRouter | google/gemini-3-pro-image-preview                             |   65536 |
-| OpenRouter | x-ai/grok-4.1-fast                                            | 2000000 |
-| OpenRouter | deepcogito/cogito-v2.1-671b                                   |  128000 |
-| OpenRouter | openai/gpt-5.1                                                |  400000 |
-| OpenRouter | openai/gpt-5.1-chat                                           |  128000 |
-| OpenRouter | openai/gpt-5.1-codex                                          |  400000 |
-| OpenRouter | openai/gpt-5.1-codex-mini                                     |  400000 |
-| OpenRouter | moonshotai/kimi-k2-thinking                                   |  131072 |
-| OpenRouter | amazon/nova-premier-v1                                        | 1000000 |
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-| OpenRouter | nvidia/nemotron-nano-12b-v2-vl                                |  131072 |
-| OpenRouter | minimax/minimax-m2                                            |  196608 |
-| OpenRouter | qwen/qwen3-vl-32b-instruct                                    |  131072 |
-| OpenRouter | ibm-granite/granite-4.0-h-micro                               |  131000 |
-| OpenRouter | openai/gpt-5-image-mini                                       |  400000 |
-| OpenRouter | anthropic/claude-haiku-4.5                                    |  200000 |
-| OpenRouter | qwen/qwen3-vl-8b-thinking                                     |  131072 |
-| OpenRouter | qwen/qwen3-vl-8b-instruct                                     |  131072 |
-| OpenRouter | openai/gpt-5-image                                            |  400000 |
-| OpenRouter | openai/o3-deep-research                                       |  200000 |
-| OpenRouter | openai/o4-mini-deep-research                                  |  200000 |
-| OpenRouter | nvidia/llama-3.3-nemotron-super-49b-v1.5                      |  131072 |
-| OpenRouter | baidu/ernie-4.5-21b-a3b-thinking                              |  131072 |
-| OpenRouter | google/gemini-2.5-flash-image                                 |   32768 |
-| OpenRouter | qwen/qwen3-vl-30b-a3b-thinking                                |  131072 |
-| OpenRouter | qwen/qwen3-vl-30b-a3b-instruct                                |  131072 |
-| OpenRouter | openai/gpt-5-pro                                              |  400000 |
-| OpenRouter | z-ai/glm-4.6                                                  |  204800 |
-| OpenRouter | anthropic/claude-sonnet-4.5                                   | 1000000 |
-| OpenRouter | deepseek/deepseek-v3.2-exp                                    |  163840 |
-| OpenRouter | thedrummer/cydonia-24b-v4.1                                   |  131072 |
-| OpenRouter | relace/relace-apply-3                                         |  256000 |
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-| OpenRouter | qwen/qwen3-vl-235b-a22b-thinking                              |  131072 |
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-| OpenRouter | qwen/qwen3-max                                                |  262144 |
-| OpenRouter | qwen/qwen3-coder-plus                                         | 1000000 |
-| OpenRouter | openai/gpt-5-codex                                            |  400000 |
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-| OpenRouter | x-ai/grok-4-fast                                              | 2000000 |
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-| OpenRouter | qwen/qwen3-coder-flash                                        | 1000000 |
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-| OpenRouter | nousresearch/hermes-4-405b                                    |  131072 |
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-| OpenRouter | openai/gpt-5                                                  |  400000 |
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-| OpenRouter | openai/gpt-oss-120b                                           |  131072 |
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-| OpenRouter | openai/gpt-oss-20b                                            |  131072 |
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-| OpenRouter | z-ai/glm-4.5-air                                              |  131072 |
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-| OpenRouter | qwen/qwen3-coder                                              |  262144 |
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-| OpenRouter | x-ai/grok-3                                                   |  131072 |
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-| OpenRouter | qwen/qwen3-8b                                                 |   40960 |
-| OpenRouter | qwen/qwen3-14b                                                |   40960 |
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-| OpenRouter | qwen/qwen-plus                                                | 1000000 |
-| OpenRouter | qwen/qwen-max                                                 |   32768 |
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system/.#fleet-dashboard.org

@@ -1 +0,0 @@
-user@amr.3392:1775060113

system/backups/emacs.org.monolithic.bak

@@ -2124,42 +2124,42 @@ On package.el, it is a manual install so far
   (use-package chemtable)
 #+end_src
 
-** Org-agent
+** OpenCortex
 #+begin_src elisp
    ;; 1. Manually add the path to your load-path
-  (add-to-list 'load-path "~/memex/projects/org-agent/src")
+  (add-to-list 'load-path "~/memex/projects/opencortex/src")
    
    ;; 2. Explicitly load the file
-  (require 'org-agent)
+  (require 'opencortex)
 
   ;; 3. Configure the variables AFTER the package is loaded
-  (setq org-agent-host "10.10.10.201")
-  (setq org-agent-port 9105)
+  (setq opencortex-host "10.10.10.201")
+  (setq opencortex-port 9105)
 
-  (setq org-agent-executable-path nil)
+  (setq opencortex-executable-path nil)
   ;; 4. (Optional) Re-enable use-package features if you prefer
-  (use-package org-agent
+  (use-package opencortex
     :straight nil
-    :commands (org-agent-connect org-agent-disconnect))
-    (message "org-agent: Actuator manually verified at %s" org-agent-host)
+    :commands (opencortex-connect opencortex-disconnect))
+    (message "opencortex: Actuator manually verified at %s" opencortex-host)
 
 
 
-    ;;  (use-package org-agent
+    ;;  (use-package opencortex
     ;; :straight nil
-   ;;     :load-path "~/memex/projects/org-agent/src" ;; Adjust this to your local clone path
-   ;;     :commands (org-agent-connect org-agent-disconnect)
+   ;;     :load-path "~/memex/projects/opencortex/src" ;; Adjust this to your local clone path
+   ;;     :commands (opencortex-connect opencortex-disconnect)
    ;;     :init
         ;; Remote connection settings
-  ;;      (setq org-agent-host "10.10.10.43") ;; Your Docker server's IP
-  ;;      (setq org-agent-port 9105)          ;; Must match ORG_AGENT_DAEMON_PORT in .env
+  ;;      (setq opencortex-host "10.10.10.43") ;; Your Docker server's IP
+  ;;      (setq opencortex-port 9105)          ;; Must match ORG_AGENT_DAEMON_PORT in .env
 
         ;; Optimization: Automatically connect when entering Org-mode (optional)
-  ;;      :hook (org-mode . org-agent-connect)
+  ;;      :hook (org-mode . opencortex-connect)
   ;;      :config
         ;; Ensure Emacs is acting as a proper sensor
-  ;;      (message "org-agent: Actuator configured for remote brain at %s"
-  ;;    	   (org-agent-host))
+  ;;      (message "opencortex: Actuator configured for remote brain at %s"
+  ;;    	   (opencortex-host))
   ;;      )
 #+end_src
 

system/emacs-ai.org

@@ -1,120 +0,0 @@
-#+TITLE: AI Configuration
-#+PROPERTY: header-args :tangle yes
-
-* AI Settings
-
-** Ellama
-
-#+begin_src elisp :tangle yes
-  ;; YOU DON'T NEED NONE OF THIS CODE FOR SIMPLE INSTALL
-  ;; IT IS AN EXAMPLE OF CUSTOMIZATION.
-  (use-package ellama
-    :init
-    (require 'llm-openai)
-    ;; setup key bindings
-    (setq ellama-keymap-prefix "C-c e")
-    )
-#+end_src
-
-#+begin_src elisp ~/.emacs.d/custom.el :tangle yes
-  (setopt ellama-providers
-  	'(
-  	  ;; Ollama Provider (added here with a name)
-  	  ("ollama" . (make-llm-ollama
-                               ;; Consider a dedicated embedding model if gemma isn't ideal for it.
-                               :chat-model "gemma3:latest"
-                               :embedding-model "gemma3:latest" ; Or e.g., "nomic-embed-text"
-                               :default-chat-non-standard-params '(("num_ctx" . 8192))))
-
-  	  ("openai" . (make-llm-openai
-                         :key (auth-source-pass-get "api-key" "www/openai.com/amr@gharbeia.net")
-                         :chat-model "gpt-4o"
-  		       :embedding-model "text-embedding-3-large"))
-
-            ("groq" . (make-llm-openai-compatible
-                       :url "https://api.groq.com/openai/v1"
-                       :key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net")
-                       ;; Check Groq console for available models, these might change
-                       :chat-model "llama3-70b-8192" ; Example, verify on Groq
-                       :embedding-model "llama3-70b-8192")) ; Groq might not offer dedicated embedding models via this API
-            ))
-
-  ;; --- Set Active Providers ---
-  ;; Choose your default provider from the list above by its name
-  (setopt ellama-provider "ollama") ; Or "ollama", "openai", "groq"
-
-  ;; You can specify different providers for different tasks if needed
-  (setopt ellama-translation-provider "ollama")
-  (setopt ellama-naming-provider "ollama")
-  (setopt ellama-naming-scheme 'ellama-generate-name-by-llm)
-
-  (setq llm-debug t)
-#+end_src
-
-#+begin_src elisp
-  (use-package ellama
-  :ensure t
-  :bind ("C-c e" . ellama)
-  ;; send last message in chat buffer with C-c C-c
-  :hook (org-ctrl-c-ctrl-c-final . ellama-chat-send-last-message)
-  :init (setopt ellama-auto-scroll t)
-  :config
-  ;; show ellama context in header line in all buffers
-  (ellama-context-header-line-global-mode +1)
-  ;; show ellama session id in header line in all buffers
-  (ellama-session-header-line-global-mode +1))
-#+end_src
-
-** GPTel
-   
-#+begin_src elisp :tangle yes
-  (use-package gptel)
-#+end_src
-
-#+begin_src elisp :tangle yes
-  (setq gptel-api-key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net"))
-#+end_src
-
-#+begin_src elisp :tangle yes
-  (gptel-make-openai "Groq"               ;Any name you want
-  :host "api.groq.com"
-  :endpoint "/openai/v1/chat/completions"
-  :stream t
-  :key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net")                   ;can be a function that returns the key
-  :models '(llama-3.1-70b-versatile
-            llama-3.1-8b-instant
-            llama3-70b-8192
-            llama3-8b-8192
-            mixtral-8x7b-32768
-            gemma-7b-it))
-#+end_src
-
-** Elisa
-
-#+begin_src elisp :tangle yes
-  (use-package elisa
-    :defer t
-    :init
-    (setopt elisa-limit 5)
-    (require 'llm-ollama)
-    (setopt elisa-embeddings-provider (make-llm-ollama :embedding-model "nomic-embed-text"))
-    (setopt elisa-chat-provider (make-llm-ollama
-                                 :chat-model "sskostyaev/openchat:8k-rag"
-                                 :embedding-model "nomic-embed-text"))
-    )
-#+end_src
-
-** Org-agent (Local Foundry)
-
-#+begin_src elisp :tangle yes
-  (use-package org-agent
-    :straight nil
-    :load-path "~/.local/share/org-agent/src"
-    :commands (org-agent-connect org-agent-disconnect)
-    :init
-    (setq org-agent-host "127.0.0.1")
-    (setq org-agent-port 9105)
-    (setq org-agent-executable-path "~/.local/share/org-agent/bin/org-agent-server")
-    :config
-    (message "org-agent: Local brain configured at %s" org-agent-executable-path))
-#+end_src

system/emacs-core.org

@@ -1,165 +0,0 @@
-#+TITLE: Core Emacs Configuration
-#+PROPERTY: header-args :tangle yes
-
-* Initialization Bootstrap
-
-This section tangles directly to ~/.emacs to bootstrap the entire system.
-
-#+begin_src elisp :tangle ~/.emacs
-  ;;; .emacs --- Global settings -*- lexical-binding: t; -*-
-
-  (setq gc-cons-threshold (* 500 1024 1024))
-  (add-hook 'after-init-hook (lambda () (setq gc-cons-threshold (* 5 1024 1024))))
-
-  (setq straight-repository-branch "develop")
-
-  (eval-and-compile
-    (defvar bootstrap-version)
-    (let ((bootstrap-file
-           (expand-file-name "straight/repos/straight.el/bootstrap.el"
-                             (or (bound-and-true-p straight-base-dir)
-                                 user-emacs-directory)))
-          (bootstrap-version 7))
-      (unless (file-exists-p bootstrap-file)
-        (with-current-buffer
-            (url-retrieve-synchronously "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el" 'silent 'inhibit-cookies)
-          (goto-char (point-max))
-          (eval-print-last-sexp)))
-      (load bootstrap-file nil 'nomessage))
-    
-    (straight-use-package 'use-package)
-    (straight-use-package 'org))
-
-  (setq straight-use-package-by-default t)
-
-  (require 'ob-tangle)
-
-  ;; Load the modular configuration starting from dotemacs.org
-  (org-babel-load-file (expand-file-name "~/memex/system/dotemacs.org"))
-
-  (provide '.emacs)
-#+end_src
-
-* Front matter
-
-#+begin_src elisp
-  ;;; emacs-core.el --- Summary
-  ;;; Commentary:
-  ;;; Code:
-
-  ;; -*- lexical-binding: t; -*-
-#+end_src
-
-* Garbage collector
-
-Increase threshold to 500 MB to ease startup
-#+begin_src elisp
-  (setq gc-cons-threshold (* 500 1024 1024))
-#+end_src
-
-Decrease threshold to 5 MB after init
-#+begin_src elisp
-  (add-hook 'after-init-hook (lambda () (setq gc-cons-threshold (* 5 1024 1024))))
-#+end_src
-
-* Straight.el and use-package
-
-Integrate use-package and straight
-#+begin_src elisp
-  (setq straight-use-package-by-default t)
-  (require 'use-package)
-  (straight-use-package 'diminish)
-  (require 'diminish)
-#+end_src
-
-Make sure Org is installed (straight.el)
-#+begin_src elisp
-  (unless (file-directory-p (expand-file-name "~/.emacs.d/straight/versions")) (make-directory (expand-file-name "~/.emacs.d/straight/versions") t))
-  (use-package org)
-#+end_src
-
-* Custom file
-
-#+begin_src elisp
-  (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
-  (when (file-exists-p custom-file) (load custom-file))
-#+end_src
-
-* System information
-
-#+begin_src elisp
-  (defvar my-laptop-p (equal (system-name) "lilitop"))
-  (defvar my-server-p (and (equal (system-name) "localhost") (equal user-login-name "root")))
-  (defvar my-phone-p (not (null (getenv "ANDROID_ROOT")))
-    "If non-nil, GNU Emacs is running on Termux.")
-  (when my-phone-p (defvar gnutls-algorithm-priority "NORMAL:-VERS-TLS1.3"))
-  (global-auto-revert-mode)  ; simplifies syncing
-#+end_src
-
-* Persistent history
-
-#+begin_src elisp
-  (savehist-mode)
-#+end_src
-
-* Disable Syntax Checkers (Diagnostic)
-
-#+begin_src elisp
-  (when (fboundp 'flycheck-mode)
-    (setq flycheck-global-modes nil)
-    (global-flycheck-mode -1))
-  (when (fboundp 'flymake-mode)
-    (setq help-at-pt-display-when-idle t)
-    ;; Disable flymake in all buffers
-    (add-hook 'find-file-hook (lambda () (flymake-mode -1))))
-#+end_src
-
-* Backup and versioning
-
-#+begin_src emacs-lisp
-  (use-package magit)
-#+end_src
-
-* Personal information
-
-#+begin_src elisp
-  (setq user-full-name "Amr Gharbeia")
-  (defvar email-address "amr@gharbeia.net")
-  (defvar calendar-latitude 39.0)
-  (defvar calendar-longitude -77.1)
-  (defvar calendar-location-name "Washington, DC")
-  (defvar calendar-time-zone -300)
-  (defvar calendar-standard-time-zone-name "EST")
-  (defvar calendar-daylight-time-zone-name "EDT")
-#+end_src
-
-* Saving Emacs Sessions
-
-Close frame when done
-#+begin_src elisp
-  (add-hook 'server-done-hook (lambda () (delete-frame)))
-#+end_src
-
-Save desktop session
-#+begin_src elisp
-  (desktop-save-mode t)
-#+end_src
-
-* Security
-
-#+begin_src elisp
-  (use-package password-store)
-#+end_src
-
-#+begin_src elisp
-  (use-package auth-source
-    :config (auth-source-pass-enable)
-    )
-#+end_src
-
-* End matter
-
-#+begin_src elisp
-  (provide 'emacs-core)
-  ;;; emacs-core.el ends here
-#+end_src

system/emacs-early-init.org

@@ -1,18 +0,0 @@
-#+TITLE: Early Init Configuration
-#+PROPERTY: header-args :tangle ~/.emacs.d/early-init.el
-
-* early-init.el
-
-For straight.el to pick up before package.el
-
-#+begin_src elisp
-  (setq package-enable-at-startup nil)
-#+end_src
-
-* Run Emacs as a server
-
-#+begin_src elisp
-  (require 'server)
-  (unless (server-running-p) (server-start))
-  (defvar server-max-buffers 100)
-#+end_src

system/emacs-gtd.org

@@ -1,166 +0,0 @@
-#+TITLE: GTD & Agenda Configuration
-#+PROPERTY: header-args :tangle yes
-
-* Agenda
-
-Basic agenda settings
-#+begin_src elisp
-   (setq org-deadline-warning-days 7)
-   (setq org-agenda-skip-additional-timestamps-same-entry t)
-   (setq org-agenda-span 'fortnight)
-   (setq org-agenda-tags-column 'auto)
-   (setq org-agenda-skip-scheduled-if-deadline-is-shown t)
-#+end_src
-
-Agenda files
-#+begin_src elisp
-  (setq org-agenda-files (list
-  			(concat org-directory "/inbox.org")
-  			(concat org-directory "/gtd.org")
-  			(concat org-directory "/org-gtd-tasks.org")
-  			)
-        )
-
-#+end_src
-
-Better agenda views
-#+begin_src elisp :tangle yes
-  (use-package org-super-agenda)
-#+end_src
-
-* To-do
-
-Basic todo
-#+begin_src elisp
-  (setq org-todo-keywords
-          '(
-            (sequence "TODO(t)" "NEXT(n)" "WAIT(w@/!)" "|" "DONE(d!)" "CNCL(c@)")
-            )
-          )
-
-  (setq org-todo-keyword-faces
-          '(
-            ("TODO" :foreground "red" :weight bold)
-            ("NEXT" :foreground "red" :weight bold)
-            ("WAIT" :foreground "yellow" :weight bold)
-            ("DONE" :foreground "green" :weight bold)
-            ("CNCL" :foreground "blue" :weight bold)
-            )
-          )
-
-  (setq org-enforce-todo-dependencies t)
-  (setq org-tags-exclude-from-inheritance '("crypt" "!private"))
-#+end_src
-
-Switch entry to 'DONE' when all subentries are done
-#+begin_src elisp
-  (defun org-summary-todo (n-done n-not-done)
-    "Switch entry to 'DONE' when all subentries are done, to 'TODO' otherwise.
-  Uses N-DONE and N-NOT-DONE"
-    (let (org-log-done org-log-states)   ; turn off logging
-      (org-todo (if (= n-not-done 0) "DONE" "TODO")
-                )
-        )
-    )
-
-    ;; (add-hook 'org-after-todo-statistics-hook #'org-summary-todo)
-#+end_src
-
-* Getting Things Done (GTD)
-
-#+begin_src elisp
-  (use-package f)
-  (use-package dash)
-  (use-package s)
-  (use-package org-edna
-    :config
-    (setq org-edna-use-inheritance t)
-    (org-edna-mode))
-
-  (use-package org-gtd
-    :straight (org-gtd :type git :host github :repo "Trevoke/org-gtd.el")
-    :demand t
-    :init (setq org-gtd-update-ack "4.0.0")
-    :config
-    (setq org-gtd-keyword-mapping
-          '((todo . "TODO")
-            (next . "NEXT")
-            (wait . "WAIT")
-            (done . "DONE")
-            (canceled . "CNCL")))
-    (setq org-gtd-custom-node-paths
-          (list (list "Actionable" (expand-file-name "~/memex/gtd.org") "Actions")
-                (list "Legacy" (expand-file-name "~/memex/org-gtd-tasks.org") "Actions")
-                (list "Projects" (expand-file-name "~/memex/gtd.org") "Projects")
-                (list "Incubate" (expand-file-name "~/memex/gtd.org") "Incubate")))
-    (org-gtd-mode)
-    )
-
-  (global-set-key (kbd "C-c d c") #'org-gtd-capture)
-  (global-set-key (kbd "C-c d e") #'org-gtd-engage)
-  (global-set-key (kbd "C-c d p") #'org-gtd-process-inbox)
-  (with-eval-after-load 'org-gtd
-    (define-key org-gtd-clarify-map (kbd "C-c c") #'org-gtd-organize))
-#+end_src
-
-#+begin_src elisp
-  (setq org-gtd-directory org-directory)
-  (setq org-gtd-organize-hooks '(org-gtd-set-area-of-focus))
-  (setq org-gtd-areas-of-focus '(
-  				 "Atoms"
-  				 "Bits"
-  				 "Cells"
-  				 "Flags"
-  				 "Business"
-  				 "Wealth"
-  				 "Learning"
-  				 "Skills"
-  				 "Privacy"
-  				 "Archive"
-  				 "Library"
-  				 "Writing"
-  				 "Health"
-  				 "Home"
-  				 "Family"
-  				 "Social"
-  				 "Egypt"
-  				 )
-    )
-  (setq org-gtd-clarify-show-horizons 'right)
-#+end_src
-
-Logging
-#+begin_src elisp
-  (setq org-log-into-drawer "LOGBOOK")
-#+end_src
-
-Clocking work in drawer
-#+begin_src elisp :tangle yes
-  (setq org-clock-into-drawer t)
-#+end_src
-
-Habits
-#+begin_src elisp :tangle yes
-  (setq org-habit-graph-column 80)
-  (setq org-habit-show-habits-only-for-today nil)
-#+end_src
-
-* Refile
-
-org-refile targets
-#+begin_src elisp
-  (setq org-refile-targets '((nil :maxlevel . 9)
-                             (org-agenda-files :maxlevel . 9)
-                             )
-        )
-#+end_src
-
-Set type of refile targets completion
-#+begin_src elisp
-  (setq org-outline-path-complete-in-steps nil)
-#+end_src
-
-Allow refiling to new parents created on the go after confirmation
-#+begin_src elisp
-  (setq org-refile-allow-creating-parent-nodes 'confirm)
-#+end_src

system/emacs-media.org

@@ -1,101 +0,0 @@
-#+TITLE: Media and Books Configuration
-#+PROPERTY: header-args :tangle yes
-
-* Read ebooks (calibredb)
-
-#+begin_src elisp
-  (use-package calibredb
-    :defer t
-    :config
-    (setq calibredb-format-all-the-icons t)
-    (setq calibredb-format-icons-in-terminal t))
-#+end_src
-
-#+begin_src elisp
-  (defvar calibredb-root-dir (expand-file-name "~/memex/library/books"))
-  (defvar calibredb-db-dir (expand-file-name "metadata.db" calibredb-root-dir))
-  (defvar calibredb-id-width 6)
-  (defvar calibredb-title-width 100)
-#+end_src
-
-* PDF Tools
-
-#+begin_src elisp
-  (use-package pdf-tools
-    :mode ("\\.pdf\\'" . pdf-view-mode)
-    :config
-    (pdf-tools-install :no-query)
-    (setq-default pdf-view-display-size 'fit-page)
-    (setq pdf-annot-activate-created-annotations t))
-#+end_src
-
-* Annotate PDFs and EPUBs (org-noter)
-
-#+begin_src elisp
-  (use-package org-noter
-    :config
-    (setq org-noter-notes-search-path (list (expand-file-name "~/memex/library/books")))
-    (setq org-noter-default-notes-file-names '("books.org")))
-#+end_src
-
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (defvar org-noter-notes-search-path (list (concat org-directory "/library/books")))
-  (defvar org-noter-default-notes-file-names '("books.org"))  
-#+end_src
-
-* Link PDFs (org-noter-pdftools)
-
-#+begin_src elisp
-  (use-package org-noter-pdftools
-    :after org-noter
-    :config
-    ;; Add a function to ensure precise note is inserted
-    (defun org-noter-pdftools-insert-precise-note (&optional toggle-no-questions)
-      (interactive "P")
-      (org-noter--with-valid-session
-       (let ((org-noter-insert-note-no-questions (if toggle-no-questions
-  						   (not org-noter-insert-note-no-questions)
-                                                   org-noter-insert-note-no-questions))
-             (org-pdftools-use-isearch-link t)
-             (org-pdftools-use-freepointer-annot t))
-         (org-noter-insert-note (org-noter--get-precise-info)))))
-
-    ;; fix https://github.com/weirdNox/org-noter/pull/93/commits/f8349ae7575e599f375de1be6be2d0d5de4e6cbf
-    (defun org-noter-set-start-location (&optional arg)
-      "When opening a session with this document, go to the current location.
-  With a prefix ARG, remove start location."
-      (interactive "P")
-      (org-noter--with-valid-session
-       (let ((inhibit-read-only t)
-             (ast (org-noter--parse-root))
-             (location (org-noter--doc-approx-location (when (called-interactively-p 'any) 'interactive))))
-         (with-current-buffer (org-noter--session-notes-buffer session)
-           (org-with-wide-buffer
-            (goto-char (org-element-property :begin ast))
-            (if arg
-                (org-entry-delete nil org-noter-property-note-location)
-              (org-entry-put nil org-noter-property-note-location
-                             (org-noter--pretty-print-location location))))))))
-    (with-eval-after-load 'pdf-annot
-      (add-hook 'pdf-annot-activate-handler-functions #'org-noter-pdftools-jump-to-note)
-      )
-    )
-#+end_src
-
-* View EPUBs (nov.el)
-
-#+begin_src elisp :tangle yes
-  (use-package nov
-    :config
-    (add-to-list 'auto-mode-alist '("\\.epub\\'" . nov-mode))
-    )
-#+end_src
-
-* Zotero (helm-bibtex)
-#+begin_src elisp :tangle yes
-  (use-package helm-bibtex)
-#+end_src
-
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (defvar bibtex-completion-bibliography '("~/bibliography/zotero.bib"))
-#+end_src

system/emacs-org.org

@@ -1,233 +0,0 @@
-#+TITLE: Org Mode Configuration
-#+PROPERTY: header-args :tangle yes
-
-* Org Mode
-
-** Basic setup
-
-#+begin_src elisp
-  (use-package org
-    :config
-    (defvar org-outline-path-complete-in-steps nil)
-    :bind (("C-c l" . org-store-link)
-  	 ("C-c a" . org-agenda)
-  	 ("C-c c" . org-capture)
-  	 :map org-mode-map)
-    )
-#+end_src
-
-#+begin_src elisp
-  (setq org-directory (expand-file-name "~/memex/"))
-#+end_src
-
-** Looks
-
-Basic 
-#+begin_src elisp
-  (defvar org-pretty-entities t) ; Improve org mode looks
-  (defvar org-hide-emphasis-markers t) ; Hide emphasis markup
-  (defvar org-num-mode nil)
-  (defvar org-startup-folded 'shw2levels)
-#+end_src
-
-Indentation of headers
-#+begin_src elisp
-  (defvar org-startup-indented t) ; Indent org heirarchy
-  (defvar org-adapt-indentation t)
-  (defvar org-hide-leading-stars t) ; Minimal Outline
-  (defvar org-odd-levels-only nil)
-#+end_src
-
-Indentation of lists
-#+begin_src elisp
-  (setq org-list-demote-modify-bullet t)
-#+end_src
-
-Org-modern
-#+begin_src elisp
-  (use-package org-modern
-    :ensure t
-    :config
-        ;; Choose some fonts
-    (set-face-attribute 'default nil :family "sans-serif")
-    (set-face-attribute 'variable-pitch nil :family "sans-serif")
-    (set-face-attribute 'org-modern-symbol nil :family "Iosevka")
-
-    ;; Edit settings
-    (defvar org-auto-align-tags nil)
-    (defvar org-tags-column 0)
-    (defvar org-catch-invisible-edits 'show-and-error)
-    (defvar org-special-ctrl-a/e t)
-    (defvar org-insert-heading-respect-content t)
-
-     ;; Org styling, hide markup etc.
-     (defvar org-hide-emphasis-markers t)
-     (defvar org-pretty-entities t)
-
-     ;; Agenda styling
-     (defvar org-agenda-tags-column 0)
-     (defvar org-agenda-block-separator ?─)
-     (defvar org-agenda-time-grid
-       '((daily today require-timed)
-         (800 1000 1200 1400 1600 1800 2000)
-         " ┄┄┄┄┄ " "┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄"))
-     (defvar org-agenda-current-time-string
-       "◀── now ─────────────────────────────────────────────────")
-
-    ;; Ellipsis styling
-     (defvar org-ellipsis "…")
-     (set-face-attribute 'org-ellipsis nil :inherit 'default :box nil)
-    
-     (global-org-modern-mode)
-    )
-#+end_src
-
-Highlight Sourcecode Syntax
-#+begin_src elisp
-  (setq org-src-fontify-natively t)
-  (setq org-src-tab-acts-natively t)
-#+end_src
-
-Images
-#+begin_src elisp
-  (setq org-startup-with-inline-images t)
-  (setq org-image-actual-width '(300))
-#+end_src
-
-** Capture
-
-#+begin_src elisp
-  (defvar org-default-notes-file (concat org-directory "inbox.org"))
-#+end_src
-
-*** Org-protocol
-
-Linux configuration
-#+begin_src bash :tangle yes
-[Desktop Entry]
-Name=org-protocol
-Comment=Intercept calls from emacsclient to trigger custom actions
-Categories=Other;
-Keywords=org-protocol;
-Icon=emacs
-Type=Application
-Exec=emacsclient -- %u
-Terminal=false
-StartupWMClass=Emacs
-MimeType=x-scheme-handler/org-protocol;
-#+end_src
-
-#+begin_src bash :tangle yes
-update-desktop-database ~/.local/share/applications/
-#+end_src
-
-Basic configuration
-#+begin_src elisp
-  (require 'org-protocol)
-  (setq org-protocol-default-buffer-for-file-links "*scratch*") ; fixes 'no buffers remain to edit error for org-protocol capturer
-#+end_src
-
-Org-protocol templates
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (defvar org-capture-templates '(
-                                ("p" "Protocol"
-                                 entry
-                                 (file "inbox.org")
-                                 "* %^{Title}\nSource: %u, %c\n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n%?"
-                                 )
-                                ("L" "Protocol Link"
-                                 entry
-                                 (file "inbox.org")
-                                 "* %? [[%:link][%:description]]\n:PROPERTIES:\n:TITLE: %:description\n:URI: %:link\n:CREATED: %U\n:END:"
-                                 :prepend nil
-                                 :empty-lines 1
-                                 :created t
-                                 :kill-buffer t
-                                 )
-                                )
-        )
-#+end_src
-
-#+begin_src elisp
-  (setq org-protocol-default-template-key "L")
-#+end_src
-
-Convert Orgzly captures to org-protocol captures standard
-#+begin_src elisp
-  (defun my/org-convert-orgzly-to-org-protocol ()
-    "Reformat Orgzly bookmark at point to org-protocol bookmark."
-    (interactive)
-    (when (org-at-heading-p)
-      (let ((headline (nth 4 (org-heading-components))))
-        ;; Find and store the link. Delete the link line.
-        (search-forward-regexp "^https?://\\S-*" nil t)
-        (let ((link (match-string 0)))
-          (beginning-of-line)
-          (kill-line)
-          ;; Delete any trailing blank spaces
-          (org-back-to-heading)
-          (end-of-line)
-          (when (not (org-on-heading-p))
-            (delete-char 1)
-            )
-          ;; Set new headline
-          (goto-char (org-entry-beginning-position))
-          (org-edit-headline (format "[[%s][%s]]" link headline))
-          ;; Set new properties
-          (org-set-property "TITLE" headline)
-          (org-set-property "URI" link)
-          (message "Reformatted Orgzly bookmark at point to org-protocol bookmark")
-          )
-        )
-      )
-    )
-#+end_src
-
-** Exporting
-
-#+begin_src elisp :tangle yes
-  (setq org-export-with-smart-quotes t)
-  (setq org-export-backends '(beamer html latex md))
-#+end_src
-
-Export to EPUB
-#+begin_src elisp :tangle yes
-  (use-package ox-epub)
-#+end_src
-
-** org-attach
-
-#+begin_src elisp
-  (setq org-attach-id-dir (concat org-directory "/library"))
-#+end_src
-
-** Enable shell scripting support in org-babel
-
-#+begin_src elisp
-  (defvar org-babel-do-load-languages  'org-babel-load-languages  '((shell . t)))
-#+end_src
-
-** Insert org-mode links from clipboard
-#+begin_src elisp :tangle yes
-  (use-package org-cliplink
-    :bind
-    (("C-x p i" . org-cliplink))
-    )
-#+end_src
-
-** Deft
-#+begin_src elisp :tangle yes
-  (use-package deft
-    :commands (deft)
-    :init
-    (defvar deft-extensions '("org"))
-    (defvar deft-recursive nil)
-    (defvar deft-use-filename-as-title t)
-    :config
-    (defvar deft-directory org-directory)
-    (defvar deft-recursive t)
-    (defvar deft-strip-summary-regexp ":PROPERTIES:\n\\(.+\n\\)+:END:\n")
-    (defvar deft-use-filename-as-title t)
-    :bind  ("C-c n d" . deft)
-    )
-#+end_src

system/emacs-roam.org

@@ -1,140 +0,0 @@
-#+TITLE: Org-Roam Configuration
-#+PROPERTY: header-args :tangle yes
-
-* Org-roam
-
-** Basic org-roam setup
-
-#+begin_src elisp
-(use-package org-roam
-  :init (setq org-roam-v2-ack t) ;; Acknowledge V2 upgrade
-  :after org
-  :config
-  (org-roam-db-autosync-enable)
-  (require 'org-roam-dailies)
-  :bind  (
-   ("C-c n f" . org-roam-node-find)
-   ("C-c n g" . org-roam-graph)
-   ("C-c n r" . org-roam-node-random)
-   ("C-c n h" . org-roam-node-convert-headline)
-   ("C-c n i" . org-roam-node-insert)
-   ("C-c n o" . org-id-get-create)
-   ("C-c n t" . org-roam-tag-add)
-   ("C-c n a" . org-roam-alias-add)
-   ("C-c n l" . org-roam-buffer-display-dedicated)
-   )
-  )
-#+end_src
-
-#+begin_src elisp
-  (setq org-roam-directory (expand-file-name (concat org-directory "notes")))
-  (setq org-roam-dailies-directory (expand-file-name (concat org-directory "daily")))
-#+end_src
-
-#+begin_src elisp :tangle yes
-  (use-package sqlite3)
-  (require 'sqlite3)
-#+end_src
-
-Include subdirectories in org-roam
-#+begin_src elisp
-  (setq org-roam-file-exclude-regexp "^[.][.]?/")
-#+end_src
-
-** Display in org-roam-buffer
-#+begin_src elisp :tangle yes
-  (setq org-roam-mode-sections
-        (list #'org-roam-backlinks-section
-              #'org-roam-reflinks-section
-              #'org-roam-unlinked-references-section 
-              )
-        )
-#+end_src
-
-** Filter org-roam nodes find by tag
-
-#+begin_src elisp :tangle yes
-  (defun my/org-roam-node-has-tag (node tag)
-    "Filter function to check if the given NODE has the specified TAG."
-    (member tag (org-roam-node-tags node))
-    )
-
-  (defun my/org-roam-node-find-by-tag ()
-    "Find and open an Org-roam node based on a specified tag."
-    (interactive)
-    (let ((tag (read-string "Enter tag: ")))
-      (org-roam-node-find nil nil (lambda (node) (my/org-roam-node-has-tag node tag))))
-    )
-#+end_src
-
-** org-roam-capture templates
-#+begin_src elisp
-  (setq org-roam-capture-templates
-        '(
-          ("L" "link" plain
-           (function org-roam--capture-get-point)
-           "%?"
-           :file-name "web/%<%Y-%m-%dT%H%M%S>.org"
-           :head "#+TITLE: ${title}\n#+CREATED: %<%Y-%m-%dT%H%M%S>"
-           :immediate-finish t
-           :unnarrowed t
-           )
-
-          ("h" "hugo post" plain
-           "%?"
-           :target (file+head "posts/${slug}.org"
-                              "#+TITLE: ${title}\n#+DATE: %U\n#+HUGO_BASE_DIR: ~/gharbeia.net\n#+HUGO_SECTION: ./posts\n#+HUGO_AUTO_SET_LASTMOD: t\n#+HUGO_TAGS: article\n#+HUGO_DRAFT: true\n")
-           :immediate-finish t
-           :unnarrowed t
-           )
-
-          ("p" "person" plain
-           "%?"
-           :if-new (file+head "people/${slug}.org"
-                             "#+TITLE: ${title}")
-          :immediate-finish t
-          :unnarrowed t
-          )
-         )
-       )
-#+end_src
-
-#+begin_src elisp
-  (setq org-roam-dailies-capture-templates
-        '(
-          ("d" "daily" plain
-           ""
-          :target ("file+heaed %<%Y-%m-%d>.org"  "#+title: %<%Y-%m-%d>\n\n")
-          :immediate-finish t
-          )
-         )
-       )
-#+end_src
-
-** Move org header to org-roam-daily
-
-#+begin_src elisp :tangle yes
-  (defun my/org-move-entry-to-daily-notes ()
-    "Move the current org-mode headline to the daily notes file based on its :CREATED: property."
-    (interactive)
-    (let*
-        (
-         (created-prop (org-entry-get nil "CREATED"))
-         (created-date (when created-prop
-                         (org-parse-time-string created-prop)))
-         (year (nth 5 created-date)) ; Extract year (6th element)
-         (month (nth 4 created-date)) ; Extract month (5th element)
-         (day (nth 3 created-date)) ; Extract day (4th element)
-         (target-date (format "%04d-%02d-%02d" year month day)) ; Format date string
-         (target-file (org-roam-dailies-goto target-date)) 
-         )
-      (when target-file
-        (org-cut-subtree)
-        (find-file target-file)
-        (goto-char (point-max))
-        (unless (bolp) (newline))
-        (org-paste-subtree)
-        )
-      )
-  )
-#+end_src

system/emacs-shell.org

@@ -1,73 +0,0 @@
-#+TITLE: Shell Configuration
-#+PROPERTY: header-args :tangle yes
-
-* Shell
-
-** Bash completion
-
-#+begin_src elisp
-  (use-package bash-completion
-    :config
-    (require 'bash-completion)
-    (bash-completion-setup)
-    )
-#+end_src
-
-#+begin_src elisp
-(defvar shell-dynamic-complete-functions t)
-#+end_src
-
-** Eshell
-
-Add programmable bash completion to Emacs shell-mode
-#+begin_src elisp :tangle yes
-  (require 'bash-completion)
-  (add-hook 'eshell-mode-hook
-          (lambda ()
-            (add-hook 'completion-at-point-functions
-                      'bash-completion-capf-nonexclusive nil t
-                      )
-            )
-          )
-#+end_src
-
-Use colors in eshell
-#+begin_src elisp :tangle yes
-  (use-package xterm-color
-    :commands (xterm-color-filter)
-    )
-
-  (use-package eshell
-    :after xterm-color
-    :config
-    (define-key eshell-hist-mode-map (kbd "M-r") #'consult-history)
-    (add-hook 'eshell-mode-hook
-              (lambda ()
-                (setenv "TERM" "xterm-256color")))
-    (add-hook 'eshell-before-prompt-hook (setq xterm-color-preserve-properties t))
-    (add-to-list 'eshell-preoutput-filter-functions 'xterm-color-filter)
-    (setq eshell-output-filter-functions
-          (remove 'eshell-handle-ansi-color eshell-output-filter-functions)
-          )
-    )
-#+end_src
-
-Eshell completion
-#+begin_src elisp :tangle yes
-  (add-hook 'eshell-mode-hook
-          (lambda ()
-            (add-hook 'completion-at-point-functions
-                      'bash-completion-capf-nonexclusive nil t)))
-#+end_src
-
-Emulate A Terminal (EAT)
-#+begin_src elisp :tangle yes
-  (use-package eat
-    :config
-    ;; For `eat-eshell-mode'.
-    (add-hook 'eshell-load-hook #'eat-eshell-mode)
-
-    ;; For `eat-eshell-visual-command-mode'.
-    (add-hook 'eshell-load-hook #'eat-eshell-visual-command-mode)
-    )
-#+end_src

system/emacs-writing.org

@@ -1,254 +0,0 @@
-#+TITLE: Reading and Writing Configuration
-#+PROPERTY: header-args :tangle yes
-
-* Text and Case
-
-** Convert DOuble capitals to single capitals
-
-#+begin_src elisp :tangle yes
-  (defun my/dcaps-to-scaps ()
-    "Convert word in DOuble CApitals to Single Capitals."
-    (interactive)
-    (and (= ?w (char-syntax (char-before)))
-         (save-excursion
-           (and (if (called-interactively-p)
-                    (skip-syntax-backward "w")
-                  (= -3 (skip-syntax-backward "w"))
-                  )
-                (let (case-fold-search)
-                  (looking-at "\\b[[:upper:]]\\{2\\}[[:lower:]]")
-                  )
-              (capitalize-word 1)
-              )
-           )
-         )
-    )
-#+end_src
-
-Then, let’s define a minor mode for it to be activated.
-#+begin_src elisp :tangle yes
-  (define-minor-mode my-dubcaps-mode
-    "Toggle 'my-dubcaps-mode' and convert words in DOuble CApitals to Single Capitals as you type."
-    :init-value nil
-    :lighter (" DC")
-    (if my-dubcaps-mode
-        (add-hook 'post-self-insert-hook #'my/dcaps-to-scaps nil 'local)
-      (remove-hook 'post-self-insert-hook #'my/dcaps-to-scaps 'local)))
-#+end_src
-
- Finally, let’s add a hook so that it is on for all the text files Emacs opens.
-#+begin_src elisp :tangle yes
-  (add-hook 'text-mode-hook #'my-dubcaps-mode)  
-#+end_src
-
-Also, since we add a minor mode string (it might be useful sometimes), currently I prefer to diminish it.
-#+begin_src elisp :tangle yes
-  (defun my/diminish-dubcaps ()
-    (interactive)
-    (diminish 'my-dubcaps-mode ""))
-  (add-hook 'my-dubcaps-mode-hook 'my/diminish-dubcaps)
-#+end_src
-
-* Reading and Writing
-
-** Move correctly over camelCased words
-
-#+begin_src elisp
-  (subword-mode)
-#+end_src
-
-** Understand the more common sentence with double space
-
-#+begin_src elisp
-  (setq sentence-end-double-space nil)
-#+end_src
-
-** Join lines into paragraph
-
-#+begin_src elisp
-  (defun my/fill-or-unfill-paragraph (&optional unfill region)
-    "Fill paragraph (or REGION). With the prefix argument UNFILL, fill it instead."
-    (interactive (progn
-                   (barf-if-buffer-read-only)
-                   (list (if current-prefix-arg 'fill) t)))
-    (let ((fill-column (if unfill fill-column (point-max))))
-      (fill-paragraph nil region)))
-
-  (bind-key "M-q" 'my/fill-or-unfill-paragraph)
-#+end_src
-
-#+begin_src elisp
-  (defun my/fill-or-unfill-all-paragraphs (&optional unfill)
-  "Fill or unfill all paragraphs in the current buffer.
-With the prefix argument UNFILL, fill them instead."
-  (interactive (list (if current-prefix-arg 'fill)))
-  (let ((fill-column (if unfill fill-column (point-max))))
-    (save-excursion
-      (goto-char (point-min))
-      (while (not (eobp))
-        (fill-paragraph nil t)
-        (forward-paragraph)))))
-
-(bind-key "M-Q" 'my/fill-or-unfill-all-paragraphs)
-#+end_src
-
-#+begin_src elisp
-  (remove-hook 'text-mode-hook #'turn-on-auto-fill)
-  (add-hook 'text-mode-hook 'turn-on-visual-line-mode)
-#+end_src
-
-** Expand some words with auto-correct
-
-  #+begin_src elisp :tangle yes
-  (setq save-abbrevs 'silently)
-  (setq-default abbrev-mode t)
-  #+end_src
-
-** ediff
-
-#+begin_src elisp :tangle yes
-  (setq ediff-window-setup-function 'ediff-setup-windows-plain)
-  (setq ediff-split-window-function 'split-window-horizontally)
-#+end_src
-
-** tramp
-
-#+begin_src elisp :tangle yes
-  (setq tramp-default-method "ssh"
-        tramp-backup-directory-alist backup-directory-alist
-        tramp-ssh-controlmaster-options "ssh")
-#+end_src
-
-** Clean up space
-#+begin_src elisp :tangle yes
-  (bind-key "M-SPC" 'cycle-spacing)
-#+end_src
-
-** Transform <a href> links into org links
-
-#+begin_src elisp :tangle yes
-  (defun my/transform-html-links-to-org ()
-  "Transform all HTML <a> links in the current buffer into 'org-mode' links."
-  (interactive)
-  (goto-char (point-min))
-  (while (re-search-forward "<a href=\"\\(.*?\\)\">\\(.*?\\)</a>" nil t)
-    (replace-match (org-make-link-string (match-string 1) (match-string 2)))))
-#+end_src
-
-** Count words per minute
-#+begin_src elisp :tangle yes
-  (require 'org-clock)
-  (defun my/org-entry-wpm ()
-    (interactive)
-    (save-restriction
-      (save-excursion
-        (org-narrow-to-subtree)
-        (goto-char (point-min))
-        (let* ((words (count-words-region (point-min) (point-max)))
-
-               (minutes (org-clock-sum-current-item))
-               (wpm (/ words minutes)))
-          (message "WPM: %d (words: %d, minutes: %d)" wpm words minutes)
-          (kill-new (number-to-string wpm))
-          )
-        )
-      )
-    )
-#+end_src
-
-** Enable dict mode
-  #+begin_src elisp :tangle yes
-    (setq dictionary-server "automatic")
-  #+end_src
-
-** Pick out passive voice and weasel words
-#+begin_src elisp :tangle yes
-  (use-package writegood-mode
-    :diminish writegood-mode
-    :config
-    (progn (add-hook 'text-mode-hook 'writegood-mode))
-    )
-#+end_src
-
-** Org-babel docker
-#+begin_src elisp :tangle yes
-  (use-package ob-docker-build
-    :straight (ob-docker-build :type git :host github :repo "ifitzpat/ob-docker-build")
-    :defer t
-    :config
-    (add-to-list 'org-babel-load-languages '(docker-build . t))
-    (org-babel-do-load-languages 'org-babel-load-languages org-babel-load-languages)
-  )
-#+end_src
-
-* Spelling and syntax
-
-** Spell checking
-
-This requires installation of hunspell
-#+begin_src bash :tangle yes
-  sudo apt install hunspell
-#+end_src
-
-#+begin_src elisp
-  (use-package flyspell
-    :config (setq ispell-program-name "hunspell"
-                  ispell-default-dictionary "en_US"
-                  )
-    :diminish (flyspell-mode . "φ")
-    :hook (text-mode . flyspell-mode)
-    :bind (
-           ("M-<f7>" . flyspell-buffer)
-           ("<f7>" . flyspell-word)
-           ("C-;" . flyspell-auto-correct-previous-word)
-           )
-    )
-#+end_src
-
-** Flyspell correct
-#+begin_src elisp :tangle yes
-  (use-package flyspell-correct
-    :after flyspell
-    :bind (:map flyspell-mode-map ("C-;" . flyspell-correct-wrapper))
-  )
-#+end_src
-
-** Flycheck
-
-Needs external checkers installed
-
-#+begin_src elisp
-  (use-package flycheck
-    :defer t
-    :diminish (flycheck-mode . "")
-    :config
-    (setq flycheck-emacs-lisp-load-path 'inherit)
-    (setq flycheck-emacs-lisp-load-path (concat user-emacs-directory "straight/build")))
-
-#+end_src
-
-** Flycheck bash
-#+begin_src bash :tangle yes
-  sudo apt install devscripts
-#+end_src
-
-#+begin_src elisp :tangle yes
-  (use-package flycheck-checkbashisms
-    :config
-    (flycheck-checkbashisms-setup)
-  )
-#+end_src
-
-** Yaml
-#+begin_src elisp :tangle yes
-  (use-package yaml-mode
-    :config
-    (add-to-list 'auto-mode-alist '("\\.yml\\'" . yaml-mode))
-    (add-to-list 'auto-mode-alist '("\\.yaml\\'" . yaml-mode))
-    )
-#+end_src
-
-** Docker
-#+begin_src elisp :tangle yes
-  (use-package docker-compose-mode)
-#+end_src

system/git-dates.txt

@@ -46,7 +46,7 @@ notes/org-skill-memex.org|2026-03-31T13:03:26-04:00|2026-04-07T13:42:42-04:00
 notes/org-skill-model-explorer.org|2026-03-30T21:16:05-04:00|2026-04-07T13:42:42-04:00
 notes/org-skill-object-store-persistence.org|2026-03-31T18:28:47-04:00|2026-04-07T13:42:42-04:00
 notes/org-skill-onboarding.org|2026-03-31T18:13:26-04:00|2026-04-07T13:42:42-04:00
-notes/org-skill-org-agent.org|2026-04-07T12:57:15-04:00|2026-04-07T13:42:42-04:00
+notes/org-skill-opencortex.org|2026-04-07T12:57:15-04:00|2026-04-07T13:42:42-04:00
 notes/org-skill-org-delivery.org|2026-03-30T21:16:05-04:00|2026-04-07T13:42:42-04:00
 notes/org-skill-org-gtd-archive-roam-daily.org|2026-03-31T16:14:37-04:00|2026-04-07T13:42:42-04:00
 notes/org-skill-org-json-bridge.org|2026-03-31T16:14:37-04:00|2026-04-07T13:42:42-04:00

system/inject-metadata.el

@@ -1,6 +1,6 @@
 (require 'org)
 
-(defun org-agent-inject-metadata (file created edited)
+(defun opencortex-inject-metadata (file created edited)
   (with-current-buffer (find-file-noselect file)
     (org-with-wide-buffer
      (goto-char (point-min))
@@ -9,12 +9,12 @@
          (org-id-get-create) ; Ensure drawer exists
          (setq props (org-get-property-block))))
      
-     (org-set-property "CREATED" (org-agent-format-iso created))
-     (org-set-property "EDITED" (org-agent-format-iso edited))
+     (org-set-property "CREATED" (opencortex-format-iso created))
+     (org-set-property "EDITED" (opencortex-format-iso edited))
      (save-buffer)
      (kill-buffer))))
 
-(defun org-agent-format-iso (iso-date)
+(defun opencortex-format-iso (iso-date)
   "Convert 2026-04-07T10:00:00+00:00 to [2026-04-07 Tue 10:00]"
   (let ((time (parse-time-string iso-date)))
     (format-time-string "[%Y-%m-%d %a %H:%M]" (apply #'encode-time time))))
@@ -26,4 +26,4 @@
   (dolist (line lines)
     (let ((parts (split-string line "|")))
       (when (= (length parts) 3)
-        (org-agent-inject-metadata (nth 0 parts) (nth 1 parts) (nth 2 parts))))))
+        (opencortex-inject-metadata (nth 0 parts) (nth 1 parts) (nth 2 parts))))))

system/lisp-eval.lisp

@@ -2,7 +2,7 @@
 (ql:quickload :usocket :silent t)
 
 (defun send-to-swank (form-string)
-  (let* ((msg (format nil "(:emacs-rex (swank:interactive-eval ~s) :org-agent t 1)" form-string))
+  (let* ((msg (format nil "(:emacs-rex (swank:interactive-eval ~s) :opencortex t 1)" form-string))
          (len (format nil "~6,'0x" (length msg)))
          (socket (usocket:socket-connect "127.0.0.1" 4005))
          (stream (usocket:socket-stream socket)))

system/no ; This file is for loading other modules, not for tangling itself.

@@ -1,16 +0,0 @@
-(let ((config-dir "~/memex/system/"))
-  ;; Load the core settings, including package management and essential setup.
-  (org-babel-load-file (expand-file-name "emacs-core.org" config-dir))
-
-  ;; Load early init settings (if separate and not fully covered by core)
-  (org-babel-load-file (expand-file-name "emacs-early-init.org" config-dir))
-
-  ;; Load other modules in a logical order
-  (org-babel-load-file (expand-file-name "emacs-org.org" config-dir))
-  (org-babel-load-file (expand-file-name "emacs-gtd.org" config-dir))
-  (org-babel-load-file (expand-file-name "emacs-roam.org" config-dir))
-  (org-babel-load-file (expand-file-name "emacs-writing.org" config-dir))
-  (org-babel-load-file (expand-file-name "emacs-media.org" config-dir))
-  (org-babel-load-file (expand-file-name "emacs-shell.org" config-dir))
-  (org-babel-load-file (expand-file-name "emacs-ai.org" config-dir))
-  (org-babel-load-file (expand-file-name "emacs-misc.org" config-dir)))

system/patches/patch-architect-actuate.lisp

@@ -1,4 +1,4 @@
-(in-package :org-agent.skills.org-skill-architect)
+(in-package :opencortex.skills.org-skill-architect)
 
 (defun architect-actuate (action context)
   (declare (ignore context))
@@ -9,11 +9,11 @@
     
     (if (and note-path blueprint-content)
         (progn
-          (org-agent:kernel-log "ARCHITECT - Appending PROTOCOL to ~a" note-path)
+          (opencortex:kernel-log "ARCHITECT - Appending PROTOCOL to ~a" note-path)
           (with-open-file (out note-path :direction :output :if-exists :append)
             (format out "~%* Phase B: Blueprint (PROTOCOL)~%:PROPERTIES:~%:STATUS: SIGNED~%:END:~%~%~a" 
                     blueprint-content))
           (format nil "SUCCESS - Architect established PROTOCOL in ~a" note-path))
         (progn
-          (org-agent:kernel-log "ARCHITECT FAILURE - Missing path or content in action: ~a" action)
+          (opencortex:kernel-log "ARCHITECT FAILURE - Missing path or content in action: ~a" action)
           nil))))

system/patches/patch-architect-neuro.lisp

@@ -1,4 +1,4 @@
-(in-package :org-agent.skills.org-skill-architect)
+(in-package :opencortex.skills.org-skill-architect)
 
 (defun neuro-skill-architect (context)
   (let* ((payload (getf context :payload))

system/patches/patch-architect-scan.lisp

@@ -1,10 +1,10 @@
-(in-package :org-agent.skills.org-skill-architect)
+(in-package :opencortex.skills.org-skill-architect)
 
 (defun architect-scan-all-notes ()
   (let* ((notes-dir (or (uiop:getenv "MEMEX_NOTES") "/home/user/memex/notes/"))
          (files (uiop:directory-files (uiop:ensure-directory-pathname notes-dir)))
          (ready-notes '()))
-    (org-agent:kernel-log "ARCHITECT - Scanning ~a files in ~a" (length files) notes-dir)
+    (opencortex:kernel-log "ARCHITECT - Scanning ~a files in ~a" (length files) notes-dir)
     (dolist (file files)
       (let ((name (pathname-name file))
             (type (pathname-type file)))
@@ -13,5 +13,5 @@
                    (string-equal type "org"))
           (let ((status (architect-perceive-frozen-prd file)))
             (when status (push status ready-notes))))))
-    (org-agent:kernel-log "ARCHITECT - Found ~a ready notes." (length ready-notes))
+    (opencortex:kernel-log "ARCHITECT - Found ~a ready notes." (length ready-notes))
     ready-notes))

system/patches/patch-neuro-debug.lisp

@@ -1,4 +1,4 @@
-(in-package :org-agent)
+(in-package :opencortex)
 
 (defun execute-openrouter-request (prompt system-prompt &key model)
   (let ((api-key (uiop:getenv "OPENROUTER_API_KEY"))
@@ -8,7 +8,7 @@
     (kernel-log "OPENROUTER DEBUG - Using Model: ~a" model-id)
     (let* ((headers `(("Content-Type" . "application/json")
                       ("Authorization" . ,(format nil "Bearer ~a" api-key))
-                      ("HTTP-Referer" . "https://github.com/amr/org-agent")))
+                      ("HTTP-Referer" . "https://github.com/amr/opencortex")))
            (body (cl-json:encode-json-to-string
                   `((model . ,model-id)
                     (messages . (( (role . "system") (content . ,system-prompt) )

system/patches/patch-neuro-economist.lisp

@@ -1,4 +1,4 @@
-(in-package :org-agent)
+(in-package :opencortex)
 
 (defun ask-neuro (prompt &key (system-prompt "You are the Probabilistic Engine engine of a Neurosymbolic Lisp Machine.") (cascade nil) (context nil))
   "Dispatches a neural request through the provider cascade.
@@ -14,7 +14,7 @@
           (kernel-log "PROBABILISTIC ENGINE: Attempting backend ~a..." backend)
           (let* (;; Consult the Economist for the model ID if the skill is available
                  (model (ignore-errors 
-                         (uiop:symbol-call :org-agent.skills.org-skill-economist :economist-get-model-for-provider backend)))
+                         (uiop:symbol-call :opencortex.skills.org-skill-economist :economist-get-model-for-provider backend)))
                  (result (if model 
                              (funcall backend-fn prompt system-prompt :model model)
                              (funcall backend-fn prompt system-prompt))))
@@ -30,7 +30,7 @@
     (unless api-key (return-from execute-openrouter-request "(:type :LOG :payload (:text \"OpenRouter API Key missing\"))"))
     (let* ((headers `(("Content-Type" . "application/json")
                       ("Authorization" . ,(format nil "Bearer ~a" api-key))
-                      ("HTTP-Referer" . "https://github.com/amr/org-agent")))
+                      ("HTTP-Referer" . "https://github.com/amr/opencortex")))
            (body (cl-json:encode-json-to-string
                   `((model . ,model-id)
                     (messages . (( (role . "system") (content . ,system-prompt) )

system/patches/patch-neuro-trace.lisp

@@ -1,4 +1,4 @@
-(in-package :org-agent)
+(in-package :opencortex)
 
 (defun ask-neuro (prompt &key (system-prompt "You are the Probabilistic Engine engine of a Neurosymbolic Lisp Machine.") (cascade nil) (context nil))
   (let ((backends (cond
@@ -11,7 +11,7 @@
         (when backend-fn
           (kernel-log "PROBABILISTIC ENGINE: Attempting backend ~a..." backend)
           (let* ((model (ignore-errors 
-                         (uiop:symbol-call :org-agent.skills.org-skill-economist :economist-get-model-for-provider backend)))
+                         (uiop:symbol-call :opencortex.skills.org-skill-economist :economist-get-model-for-provider backend)))
                  (result (if model 
                              (funcall backend-fn prompt system-prompt :model model)
                              (funcall backend-fn prompt system-prompt))))