refactor: Move Emacs config from system/ to projects/dotemacs/

- Delete deprecated system/ configuration files
- Update projects/dotemacs/modules/ with reorganized config
- Add .opencode/ directory for agent state
- Clean up attachments and unused documentation files

.opencode/AGENTS.md

@@ -0,0 +1,102 @@
+# 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
+
+## 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`