docs: Document ASDF fix and engineering methodology additions

- Added 4 cognitive tools: reload-skill, read-file, write-file, replace-string
- Fixed ASDF compilation bug with explicit dependencies
- Added test-first methodology rules to engineering standards

gtd.org

@@ -9,9 +9,27 @@
 :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+   - Deleted outdated configuration modules in ~/memex/projects/dotemacs/.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:
 
@@ -52,15 +70,23 @@ The "Zero-to-One" release. The agent must be mathematically secure, CLI-first, a
 :END:
 Ensuring the system is ready for the world through collaborative testing, documentation, and licensing.
 
-**** TODO 1. Collaborative End-to-End Testing <2026-04-14 Tue>
-***** TODO Perform a full walkthrough: Install via one-liner `opencortex.sh`, boot, and chat.
-***** TODO Verify boot sequence, environment variable parsing, and LLM gateway connectivity.
-***** TODO Verify Scribe background distillation on real journal data.
-***** TODO Verify Gardener audit reports (orphaned nodes and broken links).
+**** 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.
 
-**** TODO 2. Comprehensive Documentation <2026-04-14 Tue>
-***** TODO Draft `USER_MANUAL.md`: Focus on CLI interaction, installation, and Memex structure.
-***** TODO Draft `CONTRIBUTING.md`: Explain Literate Granularity and Skill creation standards.
+**** 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]
@@ -80,45 +106,270 @@ Ensuring the system is ready for the world through collaborative testing, docume
 :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 4. Advanced CLI Onboarding Experience (Hermes/OpenClaw parity)
-***** TODO Implement interactive Lisp CLI wizard (`opencortex setup`) to replace bash prompts.
-***** TODO Implement `opencortex link <gateway>` for secure Telegram/Signal bot connection.
-***** TODO Implement `opencortex doctor` for environment health and API key validation.
-***** TODO Implement `opencortex install <skill>` for ClawHub-style dynamic skill downloading.
-***** TODO Implement migration logic to ingest OpenClaw or Obsidian existing memory vaults.
+Roadmap basis: Evolutionary roadmap from README.org. Working backwards from SOTA parity.
+
+**** TODO 0. Autonomous Self-Editing Foundation
+***** TODO Implement org-skill-self-edit (self-modification)
+      - Deterministic: auto-balance parens via paren-counting
+      - Probabilistic: LLM generates surgical fix on =:syntax-error= events
+      - Memory rollback on failure
+***** TODO Implement 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
+      - Makes agent a true Emacs citizen
+***** TODO Implement local vector search (Ollama embeddings)
+      - =generate-embeddings= via Ollama API
+      - Add =:vector= slot to org-object
+      - Semantic search with cosine similarity over memory
+***** TODO 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
+***** TODO 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
+
+**** 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
+
+**** TODO 4. 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 a persistent status bar for background workers (Scribe/Gardener).
-***** TODO Support syntax highlighting for Lisp code blocks and Org-mode syntax.
+***** 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 of literate skills.
-***** TODO Implement `/status`, `/config`, `/search`, and `/commit` slash commands.
+***** 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 the native TUI rendering instead of raw stream printing.
+***** TODO Refactor the =:cli= actuator to use native TUI rendering
 
-*** PHASE: EVOLUTIONARY ROADMAP
-**** TODO v0.1.0: The Autonomous Foundation (Current Release)
-     - estabelecer a base segura do Lisp kernel.
-**** TODO v1.0.0 (Phase 2.5): The Verified Wrapper (SOTA Parity)
+*** PHASE: EVENT ORCHESTRATION (v0.3.0)
+:PROPERTIES:
+:ID:       proj-orchestration-v0-3-0
+:END:
+Unified control plane: hooks + cron + routing in one skill. Deep project understanding.
 
-     - 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 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)
+
+**** 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. 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 (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: CREATOR + ARCHITECT (v0.5.0)
+: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: 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 v0.5.0 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
@@ -231,6 +482,13 @@ Slim down the opencortex microharness by moving non-essential cognitive function
     - 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 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]
@@ -238,6 +496,7 @@ Slim down the opencortex microharness by moving non-essential cognitive function
     :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.
@@ -293,12 +552,61 @@ Slim down the opencortex microharness by moving non-essential cognitive function
     - 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)
@@ -389,11 +697,11 @@ Slim down the opencortex microharness by moving non-essential cognitive function
      :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
@@ -835,8 +1143,8 @@ 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:
@@ -1138,7 +1446,6 @@ 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 Cycle "Rut" Recovery (Dynamic Escalation in org-skill-lisp-validator)
 *** TODO Implement Asynchronous Event Bus for Telemetry (core.lisp)