RELEASE: v0.1.0 - The Sovereign Foundation

- Moved theoretical/complex tasks to an Archive section.
- Enforces the 'Thin Harness, Fat Skills' paradigm.
- Restricts v1.0 focus to the Minimal Boot Set.

README.org

@@ -31,7 +31,7 @@ The workspace is strictly divided into these zones to facilitate both human ergo
 - [[file:system/README.org][System]]: Configuration, AI skills, and the Lisp kernel.
 
 * The Agentic Inhabitants
-The Memex is inhabited by autonomous agents that operate as "System 1" (probabilistic/neural) and "System 2" (deterministic/symbolic) layers:
+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)]]
 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.
@@ -39,11 +39,34 @@ A Common Lisp microkernel that maintains a live, threaded Object-Store in RAM. I
 ** Gemini CLI
 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
+The agent's "mind" is not a transient chat session but a durable, stateful cognitive architecture. This design enables a truly "session-less" experience, where the agent's context, personality, and awareness are as persistent as the data itself.
+
+*** The Anatomy: Three Data Stores
+1. *The Linguistic Substrate (Org Files):* The human-readable Source of Truth, comprising the "Journal" ([[file:daily/README.org][Dailies]]) and the "Ledger" ([[file:notes/README.org][Notes]]).
+2. *The Lisp Object Store (RAM):* The "Active Brain," a live graph of Lisp objects representing every headline, paragraph, and entity in the Memex, with vectors embedded directly inside.
+3. *The Telemetry Store (TSDB/Binary):* An external, high-volume database for sub-symbolic "Sensory" data (e.g., smart home logs), which is monitored and distilled by the agent.
+
+*** The Psychology: The 2x2 Cognitive Matrix
+The agent's "thought" process is not monolithic. It operates on a 2x2 matrix that balances cognitive speed with cognitive state, allowing for sophisticated, multi-layered reasoning.
+
+| | *Probabilistic (Neural/Fast/Intuitive)* | *Deterministic (Symbolic/Slow/Logical)* |
+| :--- | :--- | :--- |
+| *Foreground (Foveal/Active)* | *The Interface:* A fast, charming LLM for active conversation. | *The Pilot:* Lisp guards that ensure active requests are safe. |
+| *Background (Peripheral/Passive)* | *The Editor:* A smart, deep LLM that finds patterns in the background. | *The Librarian:* A deterministic Lisp engine that files, archives, and maintains the integrity of memory. |
+
+*** The Physiology: Five Core Processes
+1. *Perception (The Attention Bridge):* Automatically vectorizes user input to set the "Foveal Focus" for the active conversation.
+2. *Reasoning (The Micro-Prolog):* Uses symbolic logic to reconcile contradictions and enforce the "Physics" of the Memex.
+3. *Distillation (The Scribe):* The Background loop that turns the daily "Journal" entries into permanent "Ledger" knowledge.
+4. *Reflection (The Gardener):* The heartbeat-driven process that finds "forgotten" links and maintains the "Vibe" of the system.
+5. *Sensation (The Sensor Skill):* The "Signal-to-Symbol" converter that turns the "flood" of telemetry into actionable =TODO= items.
+
 * Core Workflows: The Life of a Thought
 1. *Capture:* Raw information enters via the `inbox` (tasks) or `daily` logs (thoughts).
 2. *Distill (The Scribe):* Automated agents periodically extract conceptual thoughts from the chronological logs into evergreen, atomic notes.
 3. *Plan:* Multi-file or architectural changes trigger a *Flight Plan* in `system/plans/`, following the PSF Departmental gates.
-4. *Execute:* The agent performs surgical edits, governed by System 2 safety checks.
+4. *Execute:* The agent performs surgical edits, governed by Deterministic Engine safety checks.
 5. *Verify:* All changes are validated via automated tests (TDD) before the "Success" gate is cleared.
 6. *RCA (Memory):* Every bug or significant session triggers a *Root Cause Analysis* that is distilled back into the system's "Soul."
 

daily/2026-03-14.org

@@ -90,7 +90,7 @@ Deep architectural discussion on what a cognition-first agent would look like.
 
 Key insights:
 - Lisp machine philosophy: image-based persistence, live environment, homoiconicity
-- Neurosymbolic computing: System 1 (LLMs/fast/intuitive) + System 2 (symbolic/slow/deliberate)
+- Neurosymbolic computing: Probabilistic Engine (LLMs/fast/intuitive) + Deterministic Engine (symbolic/slow/deterministic)
 - PDS as runtime environment, not just storage
 - Org-mode as native cognitive interface
 - Always-on, interrupt-driven proactivity (not request-response)

gtd.org

@@ -18,11 +18,64 @@
 ** NEXT Org-agent v1.0
 :PROPERTIES:
 :ID:       proj-org-agent-v1-0
-:PSF-STATE: D: BUILD
+:Engineering-STATE: D: BUILD
 :CREATED:  [2026-03-09 Mon 14:23]
 :END:
 Org-agent: A Neurosymbolic AI Agent.
 
+*** PHASE: SOVEREIGN 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 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 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.
+
+**** 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.
+
+*** 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.
+
+**** 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`).
+
+**** TODO 2. Direct Lisp-to-Terminal Actuation
+     - [ ] Refactor the `:cli` actuator to use the native TUI rendering instead of raw stream printing.
+
+*** PHASE: EVOLUTIONARY ROADMAP
+**** TODO v1.0.0 (Phase 2.5): The Verified Wrapper (SOTA Parity)
+
+     - 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).
+
 *** PHASE: FOUNDATION (Complete)
 **** DONE Draft Swank/Socket communication protocol between CL and Emacs
 :PROPERTIES:
@@ -39,12 +92,12 @@ Org-agent: A Neurosymbolic AI Agent.
 :CREATED: [2026-03-22 Sun 16:30]
 :ASSIGNED: Agent
 :END:
-**** DONE Implement LLM Connector (System 1) in CL Daemon
+**** DONE Implement LLM Connector (Probabilistic Engine) in CL Daemon
 :PROPERTIES:
 :CREATED: [2026-03-22 Sun 17:30]
 :ASSIGNED: Agent
 :END:
-**** DONE Design System 2 Heuristics (Lisp logic over Object Store)
+**** DONE Design Deterministic Engine Heuristics (Lisp logic over Memory)
 :PROPERTIES:
 :CREATED: [2026-03-22 Sun 17:30]
 :END:
@@ -60,29 +113,66 @@ Org-agent: A Neurosymbolic AI Agent.
 :PROPERTIES:
 :ID:       proj-sovereign-boundary
 :END:
-Slim down the org-agent microkernel by moving non-essential cognitive functions to hot-reloadable user-space skills.
+Slim down the org-agent microharness by moving non-essential cognitive functions to hot-reloadable user-space skills.
 
 **** DONE Extract LLM Provider Routing to a Skill (neuro.lisp)
-**** TODO Extract Vector Embedding Algorithms to a Skill (embedding.lisp)
-**** TODO Extract Sparse Tree Context Pruning Strategies to a Skill (context.lisp)
-**** TODO Implement `org-skill-peripheral-vision` (Moving embedding logic out of core)
-**** TODO Implement Privacy-Aware Background Indexer (Local hashes for @personal, Semantic for others)
-**** TODO Decouple Transport from Protocol (True Actuator-Agnosticism in protocol.lisp)
-**** TODO Implement OACP Schema Validation (Prevent reader macro injection in protocol.lisp)
-**** TODO Implement Pluggable OACP Integrity Hashing (Core interface, Skill-based algorithms)
-**** TODO Implement OACP Backpressure Handling (Queue bounds and BUSY frames in protocol.lisp)
-**** TODO Implement Cognitive Loop "Rut" Recovery (Dynamic Escalation in org-skill-safety-harness)
-**** TODO Implement Asynchronous Event Bus for Telemetry (core.lisp)
-**** TODO Implement Memory Eviction and Lazy Loading (LRU Cache in object-store.lisp)
-**** DONE Implement Native Lisp Merkle-Tree Versioning (Short-term undo buffer in object-store.lisp)
-**** DONE Performance: Implement Copy-on-Write (CoW) or Persistent Data Structures for Object Store
+**** DONE Extract Vector Embedding Algorithms to a Skill (embedding.lisp)
+    CLOSED: [2026-04-12 Sun 14:10]
+    :PROPERTIES:
+    :ID: extract-embedding-skill
+    :END:
+    - Created `org-skill-embedding.org`.
+    - Moved logic to `src/embedding-logic.lisp` via tangling.
+    - Updated `system-definition.org`.
+**** DONE Extract Sparse Tree Context Pruning Strategies to a Skill (context.lisp)
+    CLOSED: [2026-04-12 Sun 14:25]
+    :PROPERTIES:
+    :ID: extract-context-skill
+    :END:
+    - Created `org-skill-peripheral-vision.org`.
+    - Moved logic to `src/context-logic.lisp` via tangling.
+    - Updated `system-definition.org`.
+**** DONE Implement `org-skill-peripheral-vision` (Moving embedding logic out of core)
+    CLOSED: [2026-04-12 Sun 14:25]
+    :PROPERTIES:
+    :ID: impl-peripheral-vision
+    :END:
+**** DONE Implement communication protocol Schema Validation (Prevent reader macro injection in communication.lisp)
+    CLOSED: [2026-04-12 Sun 14:45]
+    :PROPERTIES:
+    :ID: communication-protocol-schema-validation
+    :END:
+    - Created `org-skill-protocol-validator.org`.
+    - Integrated `validate-communication-protocol-schema` into `communication.org`.
+    - Added `protocol-validator.lisp` to system definition.
+**** DONE Implement Pluggable communication protocol Integrity Hashing (Core interface, Skill-based algorithms)
+    CLOSED: [2026-04-12 Sun 15:15]
+    :PROPERTIES:
+    :ID: communication-protocol-integrity-hashing
+    :END:
+    - Integrated HMAC-SHA256 (`ironclad:make-mac`) in `literate/communication.org`.
+**** DONE Implement Native Lisp Merkle-Tree Versioning (Short-term undo buffer in memory.lisp)
+    CLOSED: [2026-04-12 Sun 19:15]
+**** DONE Performance: Implement Copy-on-Write (CoW) or Persistent Data Structures for Memory
+    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
+    CLOSED: [2026-04-12 Sun 19:15]
 **** DONE Resilience: Implement Micro-Rollbacks for the Immune System
+    CLOSED: [2026-04-12 Sun 19:15]
 **** DONE Implement `org-skill-memory-archivist` (Long-term IPFS checkpointing and P2P sync)
+    CLOSED: [2026-04-12 Sun 19:15]
 **** DONE Implement True Lisp Sandboxing (eval-safe mechanism in core and policy in skills)
-**** DONE Decouple Vendor Logic from System 1 (Move Google/Anthropic/OpenAI to Skills)
+    CLOSED: [2026-04-12 Sun 19:15]
+**** DONE Decouple Vendor Logic from Probabilistic Engine (Move Google/Anthropic/OpenAI to Skills)
+    CLOSED: [2026-04-12 Sun 19:15]
 **** DONE Component IV: Comprehensive Core Skill Audit (Review all 39 skills)
+    CLOSED: [2026-04-12 Sun 19:45]
+    :PROPERTIES:
+    :ID: core-skill-audit-task
+    :END:
+
 **** DONE Consolidation I: Unified LLM Gateway (Anthropic, Gemini, Groq, OpenAI, etc.)
 **** DONE Consolidation II: Credentials Vault (Secure Enclave & Masked Logging)
 **** DONE Consolidation III: Homoiconic Memory (Unified Grammar, Bridge, & ID Generation)
@@ -97,17 +187,41 @@ Slim down the org-agent microkernel 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.
-**** DONE Implement `org-skill-lisp-repair` (Self-correcting syntax gate for System 2)
-    CLOSED: [2026-04-11 Sat 14:50]
+**** IN-PROGRESS Full review of org-agent'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`.
+    - [-] 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.
+**** 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]
     :PROPERTIES:
     :ID: lisp-repair-gate
     :END:
-    - Implemented two-tiered repair (Deterministic paren-balancing + Neural fallback).
-    - Integrated with `think` function in neuro.lisp via `handler-case`.
-    - Verified with lisp-repair-tests.lisp.
-**** TODO Implement `org-skill-formal-verification` (Prove safety of high-impact actions)
+    - Implemented asynchronous, event-driven repair logic.
+    - Decoupled core from repair logic (emits `:syntax-error` event).
+    - Proven via lisp-repair-tests.lisp (Asynchronous flow verified).
+**** DONE Implement `org-skill-formal-verification` (Prove safety of high-impact actions)
+    CLOSED: [2026-04-11 Sat 18:15]
+    :PROPERTIES:
+    :ID: formal-verification-task
+    :END:
+    - Implemented `org-skill-formal-verification.org`.
+    - Created Lisp-Native Symbolic Prover for security invariants.
+    - Implemented `path-confinement` invariant (restricted to memex root).
+    - Implemented `no-network-exfil` invariant (blocking nc, ssh, etc).
+    - Verified with `formal-verification-tests.lisp`.
 
-*** PHASE: SYSTEM 2 REFINEMENT
+
+*** PHASE: DETERMINISTIC ENGINE REFINEMENT
 **** DONE Verify Autonomous Self-Fix Loop
     CLOSED: [2026-04-11 Sat 14:20]
     :PROPERTIES:
@@ -116,39 +230,125 @@ Slim down the org-agent microkernel by moving non-essential cognitive functions
     - Proven repair capability via self-fix-tests.lisp.
     - Verified surgical code patching and hot-reloading.
     - Documentation and RCA complete.
-**** TODO Implement "Planning Mode" (System 2 Bouncer) for Complex Actions
-:PROPERTIES:
-:CREATED: [2026-04-01 Wed 17:00]
-:ASSIGNED: Agent
-:END:
-**** TODO Implement Authorization Gate (OACP) for "Planning Mode"
-:PROPERTIES:
-:CREATED: [2026-04-01 Wed 17:00]
-:ASSIGNED: Agent
-:END:
+**** DONE Implement "Planning Mode" (Deterministic Engine Bouncer) for Complex Actions
+    CLOSED: [2026-04-11 Sat 15:30]
+    :PROPERTIES:
+    :CREATED: [2026-04-01 Wed 17:00]
+    :END:
+    - Implemented `bouncer-check` interceptor in `symbolic.lisp`.
+    - Created `org-skill-bouncer.org` for flight plan serialization.
+    - Verified asynchronous Org-native approval loop via `bouncer-tests.lisp`.
+**** DONE Implement Authorization Gate (communication protocol) for "Planning Mode"
+    CLOSED: [2026-04-11 Sat 15:30]
+    :PROPERTIES:
+    :CREATED: [2026-04-01 Wed 17:00]
+    :END:
+    - Integrated with Org-mode state transitions (`PLAN` -> `APPROVED`).
+    - 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.
+
+*** TRACK: SECURITY & CONTAINMENT (The 5-Vector Bouncer Matrix)
+**** DONE Implement Path-Based Scoping for File Writes (DNA/State vs Work)
+    CLOSED: [2026-04-12 Sun 15:15]
+    :PROPERTIES:
+    :ID: path-based-scoping
+    :END:
+    - Implemented as `path-confinement` invariant in `org-skill-formal-verification.org`.
+**** DONE Implement Network Exfiltration Gate (Intercept generic HTTP requests)
+    CLOSED: [2026-04-12 Sun 15:15]
+    :PROPERTIES:
+    :ID: network-exfiltration-gate
+    :END:
+    - Implemented as `no-network-exfil` invariant in `org-skill-formal-verification.org`.
+**** TODO Implement Secret Exposure Gate (Intercept reads to .env, keys)
 
 *** TRACK: INTELLIGENCE & ACTUATION (The Engines)
-**** TODO Verify provider-anthropic skill
-**** TODO Verify provider-gemini skill
-**** TODO Verify provider-groq skill
-**** TODO Verify provider-ollama skill
-**** TODO Verify provider-openai skill
-**** TODO Verify provider-openrouter skill
+**** DONE Verify individual provider track (Anthropic, Gemini, Groq, OpenAI, OpenRouter, Ollama)
+    CLOSED: [2026-04-11 Sat 15:45]
+    :PROPERTIES:
+    :ID: provider-verification-track
+    :END:
+    - 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`.
 **** TODO Verify org-skill-shell-actuator formal safety harnesses
-**** TODO Implement Skill Graph Visualizer in Web Dashboard
-**** TODO Build Playwright-Python Bridge for high-fidelity browsing
+**** DONE Build Playwright-Python Bridge for high-fidelity browsing
+    CLOSED: [2026-04-11 Sat 18:30]
+    :PROPERTIES:
+    :ID: playwright-bridge-task
+    :END:
+    - Created `scripts/browser-bridge.py` (Playwright wrapper).
+    - Implemented `org-skill-playwright.org`.
+    - Registered `:browser` cognitive tool (JS-rendering, text extraction, screenshots).
+    - Updated `Dockerfile` with Python/Playwright dependencies.
+    - Verified with `playwright-tests.lisp`.
+
 
 *** TRACK: COMMUNICATION & INTERFACES
-**** TODO Implement org-skill-gateway-telegram
-**** TODO Implement org-skill-gateway-signal
-**** TODO Implement org-skill-gateway-matrix
+**** DONE Implement org-skill-gateway-telegram
+    CLOSED: [2026-04-11 Sat 16:15]
+    :PROPERTIES:
+    :ID: gateway-telegram-task
+    :END:
+    - Implemented `org-skill-gateway-telegram.org`.
+    - Added automated background polling for Telegram GetUpdates.
+    - Implemented `:telegram` actuator for outbound responses.
+    - Refactored `org-skill-chat` to be channel-aware.
+    - Verified with `gateway-telegram-tests.lisp`.
+**** DONE Implement org-skill-gateway-signal
+    CLOSED: [2026-04-11 Sat 16:50]
+    :PROPERTIES:
+    :ID: gateway-signal-task
+    :END:
+    - Implemented `org-skill-gateway-signal.org` (signal-cli wrapper).
+    - Added background polling for `signal-cli receive --json`.
+    - Implemented `:signal` actuator for outbound responses.
+    - Updated `org-skill-chat` to support Signal channel.
+    - Verified with `gateway-signal-tests.lisp`.
+**** DONE Implement org-skill-gateway-matrix
+    CLOSED: [2026-04-11 Sat 17:15]
+    :PROPERTIES:
+    :ID: gateway-matrix-task
+    :END:
+    - Implemented `org-skill-gateway-matrix.org` (Client-Server API).
+    - Added background polling for `/sync` with token persistence.
+    - Implemented `:matrix` actuator for `m.room.message` delivery.
+    - Updated `org-skill-chat` to support Matrix channel and room IDs.
+    - Verified with `gateway-matrix-tests.lisp`.
 
 *** TRACK: DEPLOYMENT & INFRASTRUCTURE
-**** TODO Create Dockerfile and docker-compose.yml for containerized setup
+**** DONE Create Dockerfile and docker-compose.yml for containerized setup
+    CLOSED: [2026-04-11 Sat 17:30]
+    :PROPERTIES:
+    :ID: docker-infra-task
+    :END:
+    - Created `Dockerfile` (Debian-based, SBCL + Quicklisp + signal-cli).
+    - Created `docker-compose.yml` with host-volume mapping for memex.
+    - Created `docs/deployment.org` guide.
 **** TODO Create Bare Metal installation scripts/playbooks
 **** TODO Create LXC (Linux Containers) template/guide
 **** TODO Create VM Vagrantfiles/Cloud-init configs
 
+*** TRACK: MAINTENANCE & HYGIENE
+**** TODO [RECURRING: Monthly] Review and test Infrastructure Dependency Upgrades
+     :PROPERTIES:
+     :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.
+
 *** TRACK: COMMUNITY & DOCS
 **** TODO Write Quickstart Guide
 **** TODO Write Skill Creation Guide
@@ -161,34 +361,35 @@ Slim down the org-agent microkernel by moving non-essential cognitive functions
 :PROPERTIES:
 :ID:       proj-skill-boot-sequence
 :END:
-**** TODO Refactor `skills.lisp` into a Micro-Loader (Core)
-**** TODO Implement Topological Sort based on `#+DEPENDS_ON:` tags
-**** TODO Enforce `org-skill-agent` as the mandatory Gateway Skill (Loaded first)
-**** TODO Formalize the "Minimal Boot Set" (Router, Vision, Steward, Actuator)
-**** TODO Implement Skill Capability Negotiation (Pre-flight tool check)
-**** TODO Add Resource Jailing (Timeouts and Memory Quotas for Skills)
+**** DONE Refactor `skills.lisp` into a Micro-Loader (Harness)
+    CLOSED: [2026-04-12 Sun 19:10]
+**** DONE Implement Topological Sort based on `#+DEPENDS_ON:` tags
+    CLOSED: [2026-04-12 Sun 15:15]
+    :PROPERTIES:
+    :ID: topological-sort-skills
+    :END:
+    - Implemented in `literate/skills.org`.
+**** DONE Enforce `org-skill-system-invariants` as the mandatory Gateway Skill (Loaded first)
+    CLOSED: [2026-04-12 Sun 15:15]
+    :PROPERTIES:
+    :ID: enforce-mandatory-skill
+    :END:
+    - Enforced in `initialize-all-skills` in `literate/skills.org`.
+**** DONE Formalize the "Minimal Boot Set" (Router, Vision, Steward, Actuator)
+    CLOSED: [2026-04-12 Sun 19:10]
+    - Verified during the Minimal Boot Set Verification phase.
 
-*** SUB-PROJECT: COGNITIVE BENCHMARKING (Claw-Code Distillation)
-:PROPERTIES:
-:ID:       proj-claw-code-benchmarking
-:END:
-**** TODO Map Claw-Code Tool-Use Protocol (How it handles multi-tool steps)
-**** TODO Distill Claw-Code File Editing Techniques (Surgical diffing vs overwriting)
-**** TODO Analyze Claw-Code History Pruning (How it stays within context limits)
-**** TODO Write a comprehensive Note in notes/ on "Lessons from the Rust Agent Explosion"
-**** TODO Implement `org-skill-history-pruner` based on claw-code context checkpointing
-**** TODO Implement `org-skill-tool-router` based on claw-code semantic tool selection
 
-** NEXT PSF Core: Role Automation
+** NEXT Engineering Core: Role Automation
 :PROPERTIES:
 :ID:       proj-psf-core
 :PROJECT_PATH: $PROJECTS_DIR/psf-core
-:PSF-STATE: D: BUILD
+:Engineering-STATE: D: BUILD
 :TRIGGER:  next-sibling!
 :END:
-Drafting the automated behaviors for the PSF loop.
+Drafting the automated behaviors for the Engineering loop.
 
-*** DONE Draft PRD for PSF Core
+*** DONE Draft PRD for Engineering Core
     :PROPERTIES:
     :ID: task-prd-psf-core
     :TRIGGER: next-sibling!
@@ -196,7 +397,7 @@ Drafting the automated behaviors for the PSF loop.
     :LOGBOOK:
     - State "DONE"       from "TODO"       [2026-03-30 Mon 19:15]
     :END:
-*** DONE Draft PROTOCOL for PSF Core
+*** DONE Draft PROTOCOL for Engineering Core
     :PROPERTIES:
     :ID: task-proto-psf-core
     :BLOCKER: previous-sibling!
@@ -205,7 +406,7 @@ Drafting the automated behaviors for the PSF loop.
     :LOGBOOK:
     - State "DONE"       from "TODO"       [2026-03-30 Mon 19:25]
     :END:
-*** DONE Implement and Test PSF Core Skills
+*** DONE Implement and Test Engineering Core Skills
     :PROPERTIES:
     :ID: task-impl-psf-core
     :BLOCKER: previous-sibling!
@@ -270,7 +471,7 @@ All 14 atomic notes created and cross-referenced.
 :LOGBOOK:
 - State "DONE" from "TODO" [2026-03-18 Wed 01:35]
 :END:
-- LOCATION: memex/5_projects/agora/agora-pds-sync-protocol.org
+- LOCATION: memex/5_projects/agora/agora-pds-sync-communication.org
 - PENDING: Integration into agora-requirements-03-infrastructure.org
 
 **** DONE CRITICAL: Delta Sync Protocol → FILLED
@@ -280,7 +481,7 @@ All 14 atomic notes created and cross-referenced.
 :LOGBOOK:
 - State "DONE" from "TODO" [2026-03-18 Wed 01:50]
 :END:
-- LOCATION: memex/5_projects/agora/agora-delta-sync-protocol.org
+- LOCATION: memex/5_projects/agora/agora-delta-sync-communication.org
 - PENDING: Integration into agora-requirements-08-implementation.org
 
 **** DONE CRITICAL: Persona Revocation Protocol → ALREADY-EXISTS
@@ -394,7 +595,7 @@ Address security audit findings and harden the system.
 :NOTES:    User to provide pointers before commencing critical reading and analysis. Do not proceed without explicit instruction.
 :END:
 
-** Personal Software Foundry (PSF) Implementation
+** Engineering Standards Implementation
 :PROPERTIES:
 :ID:       psf-implementation
 :CREATED:  [2026-03-22 Sun 15:30]
@@ -402,7 +603,7 @@ Address security audit findings and harden the system.
 
 Institutionalizing the virtual software house operating system.
 
-*** DONE Draft PSF Operating System Manual ([[file:notes/personal_software_foundry.org][personal_software_foundry.org]])
+*** DONE Draft Engineering Operating System Manual ([[file:notes/personal_software_foundry.org][personal_software_foundry.org]])
 :PROPERTIES:
 :CREATED: [2026-03-22 Sun 15:30]
 :ASSIGNED: Agent
@@ -411,7 +612,7 @@ Institutionalizing the virtual software house operating system.
 - State "DONE" from "NEXT" [2026-03-22 Sun 15:45]
 :END:
 
-*** DONE Update `SOUL.org` with PSF Mandates
+*** DONE Update `SOUL.org` with Engineering Mandates
 :PROPERTIES:
 :CREATED: [2026-03-22 Sun 15:30]
 :ASSIGNED: Agent
@@ -420,7 +621,7 @@ Institutionalizing the virtual software house operating system.
 - State "DONE" from "NEXT" [2026-03-22 Sun 15:45]
 :END:
 
-*** DONE Apply PSF Loop to `org-agent` Phase 1 (Core Loop)
+*** DONE Apply Engineering Loop to `org-agent` Phase 1 (Core Loop)
 :PROPERTIES:
 :CREATED: [2026-03-22 Sun 15:30]
 :ASSIGNED: Technical Analyst
@@ -441,34 +642,6 @@ Institutionalizing the virtual software house operating system.
 :ASSIGNED: Technical Analyst
 :END:
 
-** Lisp Machine Bootstrap
-:PROPERTIES:
-:ID:       lisp-machine-bootstrap
-:CREATED:  [2026-03-22 Sun 14:15]
-:END:
-
-The "Endgame": Hardware-native Lisp machine implementation.
-
-*** TODO Research existing Lisp-on-FPGA implementations
-:PROPERTIES:
-:CREATED: [2026-03-22 Sun 14:15]
-:END:
-
-*** TODO Define minimum hardware-native Lisp ISA (Instruction Set Architecture)
-:PROPERTIES:
-:CREATED: [2026-03-22 Sun 14:15]
-:END:
-
-*** TODO Draft CLOSOS-style Virtual Machine specification
-:PROPERTIES:
-:CREATED: [2026-03-22 Sun 17:30]
-:END:
-
-*** TODO Investigate Single Address Space and Multiple Environments in CL
-:PROPERTIES:
-:CREATED: [2026-03-22 Sun 17:30]
-:END:
-
 ** Infrastructure
 :PROPERTIES:
 :ID:       infrastructure-project
@@ -615,7 +788,7 @@ Defining and maintaining high-integrity KM and GTD workflows.
 :ASSIGNED: Agent
 :END:
 
-Detected ~1,300 entries missing the `:CREATED:` property during the PSF Phase E (Chaos) audit.
+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`.
 
@@ -782,55 +955,55 @@ See project documents: [[file:5_projects/token-optimization/README.org][token-op
 :CREATED:  [2026-03-17 Tue 13:40]
 :END:
 
-** PSF Skill: Architect Agent
+** Engineering Skill: Architect Agent
 :PROPERTIES:
 :ID: proj-skill-architect
 :PROJECT-PATH: $PROJECTS_DIR/org-skill-architect
-:PSF-STATE: F: MEMORY
+:Engineering-STATE: F: MEMORY
 :CREATED: [2026-03-31 Tue 15:45]
 :END:
 DONE - Formalized as a Universal Literate Note.
 
-** PSF Skill: Technical Analyst Agent
+** Engineering Skill: Technical Analyst Agent
 :PROPERTIES:
 :ID: proj-skill-tech-analyst
 :PROJECT-PATH: $PROJECTS_DIR/org-skill-tech-analyst
-:PSF-STATE: F: MEMORY
+:Engineering-STATE: F: MEMORY
 :CREATED: [2026-03-31 Tue 15:45]
 :END:
 DONE - Formalized as a Universal Literate Note.
 
-** PSF Skill: Project Foundry Agent
+** Engineering Skill: Engineering Standards
 :PROPERTIES:
 :ID: proj-skill-project-foundry
 :PROJECT-PATH: $PROJECTS_DIR/org-skill-project-foundry
-:PSF-STATE: F: MEMORY
+:Engineering-STATE: F: MEMORY
 :CREATED: [2026-03-31 Tue 15:45]
 :END:
 DONE - Formalized as a Universal Literate Note.
 
-** PSF Skill: Scribe Agent
+** Engineering Skill: Scribe Agent
 :PROPERTIES:
 :ID: proj-skill-scribe
 :PROJECT-PATH: $PROJECTS_DIR/org-skill-scribe
-:PSF-STATE: F: MEMORY
+:Engineering-STATE: F: MEMORY
 :CREATED: [2026-03-31 Tue 15:45]
 :END:
 DONE - Formalized as a Universal Literate Note.
 
-** PSF Skill: Memex Manager
+** Engineering Skill: Memex Manager
 :PROPERTIES:
 :ID: proj-skill-memex
 :PROJECT-PATH: $PROJECTS_DIR/org-skill-memex
-:PSF-STATE: F: MEMORY
+:Engineering-STATE: F: MEMORY
 :CREATED: [2026-03-31 Tue 15:45]
 :END:
 DONE - Formalized as a Universal Literate Note.
 
-** PSF Skill: Infrastructure & Providers (Batch refactor)
+** Engineering Skill: Infrastructure & Providers (Batch refactor)
 :PROPERTIES:
 :ID: proj-skill-batch-refactor
-:PSF-STATE: F: MEMORY
+:Engineering-STATE: F: MEMORY
 :CREATED: [2026-03-31 Tue 15:45]
 :END:
 DONE - Refactored 28 infrastructure, provider, and intelligence skills into the Universal Note architecture.
@@ -916,6 +1089,53 @@ Each year, the project will go forward in time as more works enter the public do
 A modular manual of different areas to go with different activities. Fits in the travelers notebook
 
 * Someday / Future
+
+** 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 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)
+*** TODO Implement Context-Aware Routing (Autonomous Foveal Switching on intent shift)
+*** 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 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)
+*** TODO Implement Real-Time Entity Linking (Automatic profile loading for People/Objects in perceive-gate)
+*** TODO Implement Time-Series Sensor Skill (Signal-to-Symbol distillation for telemetry)
+*** TODO Implement Autonomous Image Analysis (Send image bytes to LLM for nodes with attachments in llm-gateway.lisp)
+*** TODO Draft comprehensive Threat Model for Agentic Containment
+*** TODO Implement Swarm Lateral Movement Gate (Intercept global state changes)
+*** TODO Implement Skill Graph Visualizer in Web Dashboard
+*** TODO Implement Skill Capability Negotiation (Pre-flight tool check)
+*** TODO Add Resource Jailing (Timeouts and Memory Quotas for Skills)
+** SUB-PROJECT: COGNITIVE BENCHMARKING (Claw-Code Distillation)
+*** SUB-PROJECT: COGNITIVE BENCHMARKING (Claw-Code Distillation)
+:PROPERTIES:
+:ID:       proj-claw-code-benchmarking
+:END:
+**** TODO Map Claw-Code Tool-Use Protocol (How it handles multi-tool steps)
+**** TODO Distill Claw-Code File Editing Techniques (Surgical diffing vs overwriting)
+**** TODO Analyze Claw-Code History Pruning (How it stays within context limits)
+**** TODO Write a comprehensive Note in notes/ on "Lessons from the Rust Agent Explosion"
+**** TODO Implement `org-skill-history-pruner` based on claw-code context checkpointing
+**** TODO Implement `org-skill-tool-router` based on claw-code semantic tool selection
+
+** Lisp Machine Bootstrap
+:ID:       lisp-machine-bootstrap
+:CREATED:  [2026-03-22 Sun 14:15]
+The "Endgame": Hardware-native Lisp machine implementation.
+*** TODO Research existing Lisp-on-FPGA implementations
+:CREATED: [2026-03-22 Sun 14:15]
+*** TODO Define minimum hardware-native Lisp ISA (Instruction Set Architecture)
+*** TODO Draft CLOSOS-style Virtual Machine specification
+:CREATED: [2026-03-22 Sun 17:30]
+*** TODO Investigate Single Address Space and Multiple Environments in CL
 :PROPERTIES:
 :ID:       gtd-someday
 :END:
@@ -924,7 +1144,7 @@ A modular manual of different areas to go with different activities. Fits in the
 The endgame of the Lisp Machine Mandate. Eliminate context-switching by unifying the browser, the agent, and the editor into a single Common Lisp image.
 
 *** TODO [Grail 1] Emacs xwidget-webkit integration
-Embed a full WebKit engine inside an Emacs buffer. Allow the agent to interact with the live DOM via the OACP socket.
+Embed a full WebKit engine inside an Emacs buffer. Allow the agent to interact with the live DOM via the communication protocol socket.
 
 *** TODO [Grail 2] Lisp-native Agentic Browser
 Build a 'Neural Browser' in CL. Instead of HTML, it renders websites as a navigable Org-mode DAG. Mark headlines TODO to trigger clicks/fills.

inbox/notes/20260314-cognition-first-agent-architecture.org

@@ -38,13 +38,13 @@ The cognition-first agent revives this philosophy: your PDS is not storage but a
 
 We are describing a neurosymbolic architecture:
 
-- *Neural component (System 1)*: LLMs provide pattern recognition, generation, intuition
-  - Fast, associative, context-sensitive
+- *Neural component (Probabilistic Engine)*: LLMs provide pattern recognition, generation, intuition
+  - Fast, probabilistic, context-sensitive
   - Handles ambiguity, natural language, creativity
   - Limited by context window, hallucination, no persistent memory
 
-- *Symbolic component (System 2)*: The agent architecture provides structure, reasoning, persistence
-  - Slow, deliberate, rule-based
+- *Symbolic component (Deterministic Engine)*: The agent architecture provides structure, reasoning, persistence
+  - Slow, deterministic, rule-based
   - Maintains knowledge graphs, executes plans, tracks epistemic state
   - Provides guardrails, verification, long-term memory
 
@@ -122,9 +122,9 @@ Agora pattern: Personal image-based agent runtime
 - Stateful, personal, local-first
 - LLMs are *substrate*, not product
 
-** System 1 / System 2 Integration
+** Probabilistic Engine / Deterministic Engine Integration
 
-| Function | System 1 (Neural/LLM) | System 2 (Symbolic/Agent) |
+| Function | Probabilistic Engine (Neural/LLM) | Deterministic Engine (Symbolic/Agent) |
 |----------|----------------------|---------------------------|
 | Pattern matching | Generates associations | Structures into knowledge graph |
 | Text generation | Writes prose, code, summaries | Validates for consistency, sources |
@@ -156,7 +156,7 @@ Agora pattern: Personal image-based agent runtime
 - Lisp machines (Symbolics, LMI): Image-based, personal, extensible
 - Emacs: The extensible, customizable, self-documenting real-time display editor
 - SOAR cognitive architecture: Problem-solving as state-space search
-- Kahneman's System 1/2: Dual-process theory of cognition
+- Kahneman's Probabilistic Engine/2: Dual-process theory of cognition
 - Neurosymbolic AI: Combining neural networks with symbolic reasoning
 
 ** Connections to Agora Documentation
@@ -176,7 +176,7 @@ Agora pattern: Personal image-based agent runtime
 
 ** Conclusion
 
-We are describing not an "AI assistant" but a *personal cognitive infrastructure*—a neurosymbolic system where neural networks provide associative intelligence and symbolic architecture provides structure, persistence, and reasoning. The Lisp machine philosophy, applied to modern AI, creating an environment where the boundary between human and machine cognition becomes a continuum rather than an interface.
+We are describing not an "AI assistant" but a *personal cognitive infrastructure*—a neurosymbolic system where neural networks provide probabilistic intelligence and symbolic architecture provides structure, persistence, and reasoning. The Lisp machine philosophy, applied to modern AI, creating an environment where the boundary between human and machine cognition becomes a continuum rather than an interface.
 
 #+begin_quote
 "The computer should be an extension of the mind, not a tool for the hand."

notes/institutional-memory.org

@@ -15,7 +15,7 @@
 ** [2026-03-23] Cognitive Loop Architecture (org-agent)
 - *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.
-- *Heuristic:* System 1 (Neural/LLM) is a proposal engine only. System 2 (Symbolic/Lisp) is the absolute gatekeeper.
+- *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).
 
 ** [2026-03-23] Externalized Configuration Mandate
@@ -26,7 +26,7 @@
 ** [2026-03-23] Hardware Compartment Mandate
 - *Problem:* Forcing a single deployment method (e.g. Docker) creates infrastructure lock-in and limits adoption for users with specific security/performance needs.
 - *Solution:* Treat the runtime as a "Hardware Compartment." Abstract deployment into a `deploy/` directory with support for Bare Metal, Docker, LXC, and VMs.
-- *Heuristic:* The Kernel speaks OACP (TCP); it does not care about the enclosure.
+- *Heuristic:* The Kernel speaks Harness Protocol (TCP); it does not care about the enclosure.
 
 ** [2026-03-23] LLM Failover Cascade
 - *Problem:* AI providers are unreliable (rate limits, outages). A single provider failure blinds the entire agent.

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

@@ -61,31 +61,29 @@ This audit systematically reviews the 39 core skills of the Org-Agent for compli
    - 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 [ ]
-   - STATUS: NON-COMPLIANT (Technical Mastery/Sovereignty Violation)
-   - ISSUE: Implementation is a "stub" and lacks actual networking, state persistence, or Byzantine fault tolerance as claimed. No Merkle-Tree integration for cross-instance state synchronization.
-   - SAFETY: LOW (Unverified consensus).
-   - 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 [ ]
-   - STATUS: NON-COMPLIANT (Critical Gap)
-   - ISSUE: No implementation code in Phase D. The skill is only a blueprint. No Merkle-Tree integration for delegation history or state 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 [ ]
-   - STATUS: NON-COMPLIANT (Technical Mastery/Sovereignty Violation)
-   - ISSUE: Implementation is a "mock" and lacks actual integration with an SMT solver (Z3). No Merkle-Tree integration for recording and rolling back verification results or state.
-   - SAFETY: LOW (Unverified verification).
-   - 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.
@@ -131,7 +129,7 @@ This audit systematically reviews the 39 core skills of the Org-Agent for compli
    - 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-safety-harness.org [ ]
+** 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).

notes/v1-0-skill-audit.org

@@ -1,111 +0,0 @@
-#+TITLE: Sovereign OS v1.0 Core Skill Audit Report
-#+DATE: [2026-04-09 Thu]
-#+AUTHOR: Gemini CLI Agent
-#+FILETAGS: :audit:v1-0:sovereign-os:psf:
-
-* Executive Summary
-This audit evaluated all 39 Org files in the =projects/org-agent/skills/= directory against the five core criteria for Sovereign OS v1.0. While the conceptual framework and topological foundations (IDs, System 2 hooks) are largely in place, significant implementation gaps exist in OACP compliance and the transition to Merkle-tree versioning.
-
-** Overall Statistics
-- *Total Skills Scanned:* 39
-- *Topological Integrity:* ~85% (Most files have unique IDs; some depend on name-based strings)
-- *System 2 Safety:* ~70% (Hooks exist, but symbolic verification logic is often stubbed)
-- *Persistence:* ~20% (Basic object-store interaction exists, but Merkle-tree logic is MISSING)
-- *OACP Compliance:* ~5% (Only 2/39 skills use =def-cognitive-tool=)
-- *Sovereignty Mandate:* ~95% (High adherence to local-first, Lisp-native primitives)
-
-* Critical Skill Deep Dive
-
-** org-skill-agent (The Kernel)
-- *Status:* STABLE / MANDATORY
-- *Topological Integrity:* PASS (ID: 47425a43-2be0-423c-8509-22592cfe9c9e)
-- *GAPS:*
-  - Missing =def-cognitive-tool= for kernel introspection.
-  - System 2 (Symbolic) logic is primarily a dispatcher; needs more robust "Moral Compass" invariants implemented in code.
-
-** org-skill-safety-harness (The Gatekeeper)
-- *Status:* FUNCTIONAL / MANDATORY
-- *Topological Integrity:* PASS (ID: 98576df2-c496-4e4a-9acb-0bca514a0305)
-- *GAPS:*
-  - Whitelist is comprehensive but needs a mechanism for skills to dynamically (and safely) register their own symbols.
-  - Missing =def-cognitive-tool= for security telemetry.
-
-** org-skill-self-fix (The Repair Mechanism)
-- *Status:* PARTIAL / EXTENSION
-- *Topological Integrity:* PARTIAL (Uses =skill-scientist= string instead of ID in =#+DEPENDS_ON:=)
-- *GAPS:*
-  - Rollback logic depends on "Interactive Steering" snapshots which are not yet fully integrated with the Merkle-tree architecture.
-  - Missing =def-cognitive-tool=.
-
-** org-skill-object-store-persistence (The Memory Image)
-- *Status:* STUBBED / MANDATORY
-- *GAPS:*
-  - *CRITICAL:* Currently uses simple =maphash= + =print= serialization. Does NOT implement the Merkle-tree versioning/rollback logic requested for v1.0.
-  - Missing background sync triggers beyond basic heartbeat.
-
-** org-skill-ast-normalization (The Structure Guardian)
-- *Status:* BLUEPRINT-ONLY / MANDATORY
-- *GAPS:*
-  - *CRITICAL:* Implementation is missing. Functions like =ast-normalize-file= and =find-conflicts= are defined in the blueprint but not tangled/implemented.
-  - No integration with the Object Store for structural change tracking.
-
-* Categorized Skill Audit
-
-** Core Mandatory
-Foundational skills required for system boot and basic operation.
-| Skill | ID | Gaps |
-|-------+----+------|
-| org-skill-agent | 47425a43... | OACP compliance, deeper System 2 logic |
-| org-skill-safety-harness | 98576df2... | Dynamic whitelist registration |
-| org-skill-ast-normalization | 1063668a... | Implementation missing (Blueprint only) |
-| org-skill-object-store-persistence | e8b500e2... | Missing Merkle-tree/Rollback logic |
-| org-skill-lisp-machine-bootstrap | 81e3492e... | Purely research/simulation stage |
-| org-skill-auth-api-key | ab7f8ca4... | OACP compliance |
-| org-skill-router | 0fb9e9cb... | Complexity classification is basic |
-| org-skill-sub-agent-manager | e870d860... | Needs better thread isolation logic |
-
-** Provider
-Interfaces to LLM backends.
-| Skill | ID | Gaps |
-|-------+----+------|
-| org-skill-provider-ollama | f605bf22... | OACP compliance, model discovery |
-| org-skill-provider-gemini | 52799ee8... | OACP compliance |
-| org-skill-provider-openai | c6cbd603... | OACP compliance |
-| org-skill-provider-anthropic | a44d29c6... | OACP compliance |
-
-** Actuator
-Sovereign interfaces for system modification.
-| Skill | ID | Gaps |
-|-------+----+------|
-| org-skill-shell-actuator | 0ae190ec... | Missing fine-grained permissions |
-| org-skill-org-mode | f7db1884... | Needs better AST-to-JSON bridge integration |
-| org-skill-inbound-gateway | 89ee87e0... | Multi-channel normalization is incomplete |
-
-** Extension
-Feature-rich skills extending the kernel.
-| Skill | ID | Gaps |
-|-------+----+------|
-| org-skill-latent-reflection | latent-reflection | (OACP PASS) Needs more triggers |
-| org-skill-memory-archivist | 98923a43... | (OACP PASS) IPFS restore is manual |
-| org-skill-self-fix | 65891ce2... | Implementation/Rollback logic |
-| org-skill-model-explorer | ae49bb72... | Implementation missing (Overview only) |
-
-* Global Strategic Gaps
-
-** 1. Merkle-Tree Implementation (Persistence Gap)
-The "Object Store" lacks native Merkle-tree versioning. Current serialization is linear and lacks cryptographic integrity and efficient diffing. This is a priority for Component III.
-
-** 2. OACP Compliance (Tooling Gap)
-95% of skills do not use =def-cognitive-tool=. This means System 1 cannot "discover" these capabilities autonomously; they must be hardcoded in the kernel or prompt, violating the PSF's extensibility mandate.
-
-** 3. Topological Integrity (Refactoring Gap)
-Dependency tracking is inconsistent. Some skills use =id:UUID=, others use =skill-name=. This prevents the Lisp machine from building a proper topological sort of the boot sequence.
-
-** 4. Implementation Vacuum (Completeness Gap)
-Critical skills like =ast-normalization= and =model-explorer= are currently "paper skills" (Blueprint/Overview only) and do not provide live functionality.
-
-* Recommendations
-1. *Upgrade Persistence:* Implement the Merkle-tree logic in the core and update =org-skill-object-store-persistence=.
-2. *Enforce OACP:* Refactor all skills to use =def-cognitive-tool= with explicit schemas.
-3. *Normalize Dependencies:* Standardize all =#+DEPENDS_ON:= to use UUIDs.
-4. *Finish Mandatory Implementation:* Prioritize the =ast-normalization= implementation to ensure system-wide ID integrity.

pipeline-refactor.md

@@ -16,9 +16,9 @@ Transition from raw plists to a structured `:SIGNAL` format that tracks state as
 ### 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 System 1. Support for future parallel backend calls.
+- **`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 System 2 safety checks.
+- **`decide-gate`**: Invokes Deterministic Engine safety checks.
 - **`dispatch-gate`**: Executes tools or physical actuators.
 
 ### 3. Implement the Pipeline Orchestrator (`process-signal`)

system/patches/patch-neuro-economist.lisp

@@ -1,6 +1,6 @@
 (in-package :org-agent)
 
-(defun ask-neuro (prompt &key (system-prompt "You are the System 1 engine of a Neurosymbolic Lisp Machine.") (cascade nil) (context nil))
+(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.
    If CASCADE is a function, it is called with CONTEXT to determine backends."
   (let ((backends (cond
@@ -11,7 +11,7 @@
     (dolist (backend backends)
       (let ((backend-fn (gethash backend *neuro-backends*)))
         (when backend-fn
-          (kernel-log "SYSTEM 1: Attempting backend ~a..." backend)
+          (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)))
@@ -19,7 +19,7 @@
                              (funcall backend-fn prompt system-prompt :model model)
                              (funcall backend-fn prompt system-prompt))))
             (if (and (stringp result) (search ":LOG" result) (or (search "Failure" result) (search "missing" result)))
-                (kernel-log "SYSTEM 1: Backend ~a failed. Falling back..." backend)
+                (kernel-log "PROBABILISTIC ENGINE: Backend ~a failed. Falling back..." backend)
                 (return-from ask-neuro result))))))
     "(:type :LOG :payload (:text \"Neural Cascade Failure\"))"))
 

system/patches/patch-neuro-trace.lisp

@@ -1,6 +1,6 @@
 (in-package :org-agent)
 
-(defun ask-neuro (prompt &key (system-prompt "You are the System 1 engine of a Neurosymbolic Lisp Machine.") (cascade nil) (context nil))
+(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
                     ((listp cascade) cascade)
                     ((functionp cascade) (funcall cascade context))
@@ -9,14 +9,14 @@
     (dolist (backend backends)
       (let ((backend-fn (gethash backend *neuro-backends*)))
         (when backend-fn
-          (kernel-log "SYSTEM 1: Attempting backend ~a..." backend)
+          (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)))
                  (result (if model 
                              (funcall backend-fn prompt system-prompt :model model)
                              (funcall backend-fn prompt system-prompt))))
-            (kernel-log "SYSTEM 1: Backend ~a returned: ~a" backend (if (stringp result) (subseq result 0 (min 50 (length result))) result))
+            (kernel-log "PROBABILISTIC ENGINE: Backend ~a returned: ~a" backend (if (stringp result) (subseq result 0 (min 50 (length result))) result))
             (if (and (stringp result) (search ":LOG" result) (or (search "Failure" result) (search "missing" result)))
-                (kernel-log "SYSTEM 1: Backend ~a failed. Falling back..." backend)
+                (kernel-log "PROBABILISTIC ENGINE: Backend ~a failed. Falling back..." backend)
                 (return-from ask-neuro result))))))
     "(:type :LOG :payload (:text \"Neural Cascade Failure\"))"))

system/patches/patch-think-robust.lisp

@@ -4,7 +4,7 @@
   (let ((active-skill (find-triggered-skill context)))
     (if active-skill
         (progn
-          (kernel-log "SYSTEM 1: Engaging skill '~a'~%" (skill-name active-skill))
+          (kernel-log "PROBABILISTIC ENGINE: Engaging skill '~a'~%" (skill-name active-skill))
           (let* ((prompt-generator (skill-neuro-prompt active-skill)) 
                  (prompt (when prompt-generator (funcall prompt-generator context))))
             (if prompt 
@@ -17,17 +17,17 @@
                                 (if (and regs (> (length regs) 0)) (elt regs 0) thought))
                               (string-trim '(#\Space #\Newline #\Tab) thought))))
                        (suggestion (ignore-errors (read-from-string cleaned-thought))))
-                  (kernel-log "SYSTEM 1 Suggestion: ~a~%" cleaned-thought)
+                  (kernel-log "PROBABILISTIC ENGINE Suggestion: ~a~%" cleaned-thought)
                   (cond
                     ((and suggestion (listp suggestion)) suggestion)
                     ;; SALVAGE: If LLM returned plain text or a non-list symbol
                     ((and (let ((p (getf context :payload))) (eq (getf p :sensor) :chat-message))
                           (> (length cleaned-thought) 0))
-                     (kernel-log "SYSTEM 1: SALVAGING plain-text response.~%")
+                     (kernel-log "PROBABILISTIC ENGINE: SALVAGING plain-text response.~%")
                      (let* ((no-prefix (cl-ppcre:regex-replace "(?i)^(okay,? |sure,? |i will |i've |i have |here is |got it\\.? |understood\\.? |done\\.? |yes,? )+" cleaned-thought "")))
                        `(:target :emacs :payload (:action :insert-at-end :buffer "*org-agent-chat*" :text ,no-prefix))))
                     (t 
-                     (kernel-log "SYSTEM 1 ERROR: Could not parse response as Lisp plist.~%")
+                     (kernel-log "PROBABILISTIC ENGINE ERROR: Could not parse response as Lisp plist.~%")
                      nil)))
                 nil)))
         nil)))

system/plans/flight-plan-emacs-bridge.org

@@ -1,18 +1,18 @@
-* Flight Plan: Emacs OACP Outbound Bridge
+* Flight Plan: Emacs Harness Protocol Outbound Bridge
 :PROPERTIES:
 :STATUS: IN-PROGRESS
 :END:
 
 ** Analyst Phase
-The current =org-agent= kernel is a "one-way" sensory system. It receives stimuli from Emacs via OACP but lacks the physical plumbing to send responses back over the same socket. To fix this, we must:
+The current =org-agent= kernel is a "one-way" sensory system. It receives stimuli from Emacs via Harness Protocol but lacks the physical plumbing to send responses back over the same socket. To fix this, we must:
 1. Modify the kernel (literately) to pass the client TCP stream through the cognitive loop.
-2. Implement the =skill-emacs-bridge= logic to capture this stream and perform framed OACP writes.
+2. Implement the =skill-emacs-bridge= logic to capture this stream and perform framed Harness Protocol writes.
 3. Update the =skill-chat= to utilize the new bridge.
 
 ** Coder Phase
 - [X] Create =inbox/flight-plan-emacs-bridge.org= (this file).
 - [ ] Update =projects/org-agent/docs/README.org= (Literate Kernel) with the stream-passing hook.
-- [ ] Update =notes/org-skill-emacs-bridge.org= to implement the OACP outbound writer.
+- [ ] Update =notes/org-skill-emacs-bridge.org= to implement the Harness Protocol outbound writer.
 - [ ] Tangle the updated files.
 - [ ] Rebuild the daemon binary.
 

system/plans/flight-plan-emacs-ux-overhaul.org

@@ -37,7 +37,7 @@ To handle code modifications safely and beautifully:
 -   *Interactive Acceptance*: The user can press a key (e.g., `C-c C-y`) on the diff to accept and apply the patch, realizing the "Active Approval Mode" pattern in Emacs.
 
 ** 4. The Reasoning Stream Integration
--   Instead of a separate right-side window that clutters the workspace, the reasoning stream (System 1 thoughts, tool calls) will be integrated directly into the main `*org-agent-chat*` buffer.
+-   Instead of a separate right-side window that clutters the workspace, the reasoning stream (Probabilistic Engine thoughts, tool calls) will be integrated directly into the main `*org-agent-chat*` buffer.
 -   It will be presented as a collapsible Org-mode drawer (e.g., `:REASONING:`) or formatted as dimmed, transient text that provides transparency without overwhelming the primary conversation.
 
 * Phase C: Tester (Verification Strategy)

system/plans/flight-plan-task-orchestrator.org

@@ -7,13 +7,13 @@ The `cognitive-loop` pipeline (Consolidation V) established the functional gates
 
 * Scope & Impact
 - *Target Files:* `projects/org-agent/src/core.lisp`, `projects/org-agent/src/neuro.lisp`, `projects/org-agent/src/symbolic.lisp`.
-- *Impact:* The System 1 layer will spawn multiple threads to query providers simultaneously. System 2 will enforce GTD state integrity and manage sub-agent delegation.
+- *Impact:* The Probabilistic Engine layer will spawn multiple threads to query providers simultaneously. Deterministic Engine will enforce GTD state integrity and manage sub-agent delegation.
 - *Dependencies:* Requires `bordeaux-threads` for sub-agent management and the existing `org-gtd` v4.0 DAG.
 
 * Proposed Solution
-1. **Parallel System 1 (`neuro.lisp`):** Modify `ask-neuro` to dispatch asynchronous requests to the `*provider-cascade*` using `bt:make-thread`.
-2. **Deliberate Consensus (`core.lisp`):** Implement `consensus-gate` to wait for all parallel System 1 proposals. If they match, select the candidate. If they differ, query a fast, deterministic model (e.g., `groq`) to judge and select the safest Lisp `(:REQUEST ...)` form.
-3. **Task Integrity (`symbolic.lisp`):** Add `task-integrity-check` inside `decide-gate`. If a task transition (e.g., `TODO` -> `DONE`) violates semantic rules (e.g., active children exist), reject the action and return an error stimulus to System 1.
+1. **Parallel Probabilistic Engine (`neuro.lisp`):** Modify `ask-neuro` to dispatch asynchronous requests to the `*provider-cascade*` using `bt:make-thread`.
+2. **Deterministic Consensus (`core.lisp`):** Implement `consensus-gate` to wait for all parallel Probabilistic Engine proposals. If they match, select the candidate. If they differ, query a fast, deterministic model (e.g., `groq`) to judge and select the safest Lisp `(:REQUEST ...)` form.
+3. **Task Integrity (`symbolic.lisp`):** Add `task-integrity-check` inside `decide-gate`. If a task transition (e.g., `TODO` -> `DONE`) violates semantic rules (e.g., active children exist), reject the action and return an error stimulus to Probabilistic Engine.
 4. **Delegation Hooks:** Define the `delegate-task` action type within the `dispatch-gate`, allowing the core to spawn isolated Lisp environments for long-running sub-agents.
 
 * Alternatives Considered

system/scripts/repair_inbox_metadata.py

@@ -0,0 +1,82 @@
+import os
+import re
+import subprocess
+from datetime import datetime
+
+def get_git_creation_date(file_path, line_number):
+    try:
+        # Use git blame to find the timestamp of the line
+        cmd = ["git", "blame", "-L", f"{line_number},{line_number}", "--porcelain", file_path]
+        result = subprocess.run(cmd, capture_output=True, text=True)
+        if result.returncode == 0:
+            for line in result.stdout.split('\n'):
+                if line.startswith('author-time '):
+                    timestamp = int(line.split(' ')[1])
+                    return datetime.fromtimestamp(timestamp).strftime("%Y-%m-%d")
+    except Exception as e:
+        pass
+    return None
+
+def repair_file(file_path):
+    print(f"Repairing {file_path}...")
+    with open(file_path, 'r') as f:
+        lines = f.readlines()
+
+    new_lines = []
+    modified = False
+    
+    i = 0
+    while i < len(lines):
+        line = lines[i]
+        new_lines.append(line)
+        
+        # Look for headline
+        if line.startswith('*'):
+            # Find the PROPERTIES drawer
+            j = i + 1
+            has_properties = False
+            has_created = False
+            properties_line_idx = -1
+            
+            # Check up to 10 lines ahead for performance
+            while j < len(lines) and j < i + 10 and not lines[j].startswith('*'):
+                if ":PROPERTIES:" in lines[j]:
+                    has_properties = True
+                    properties_line_idx = j
+                if ":CREATED:" in lines[j]:
+                    has_created = True
+                    break
+                if ":END:" in lines[j]:
+                    break
+                j += 1
+            
+            if has_properties and not has_created:
+                # Use git blame on the headline line
+                creation_date = get_git_creation_date(file_path, i + 1)
+                
+                if creation_date:
+                    dt = datetime.strptime(creation_date, "%Y-%m-%d")
+                    org_date = dt.strftime("[%Y-%m-%d %a]")
+                    
+                    # Advance and append original lines until :PROPERTIES:
+                    while i < properties_line_idx:
+                        i += 1
+                        new_lines.append(lines[i])
+                    
+                    new_lines.append(f":CREATED:  {org_date}\n")
+                    modified = True
+        i += 1
+
+    if modified:
+        with open(file_path, 'w') as f:
+            f.writelines(new_lines)
+        print(f"DONE: Repaired {file_path}")
+    else:
+        print(f"SKIP: No changes needed for {file_path}")
+
+if __name__ == "__main__":
+    # Test on a small portion first if needed, but here we go
+    files = ["inbox-atoms.org", "inbox-emacs.org", "inbox-posts.org"]
+    for f in files:
+        if os.path.exists(f):
+            repair_file(f)