feat: stabilized org-agent two-way communication and UX

- Fixed kernel-to-Emacs communication bridge.
- Resolved boot-time crashes in multiple skeletal skills.
- Refined Chat skill prompt to eliminate conversational filler.
- Updated Emacs UI to automatically clean up status markers.
- Synchronized all fixes via Literate Org-mode documents.
- Verified physical two-way interaction via simulation.

inbox/flight-plan-flatten-env.org

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+#+TITLE: Flight Plan: Flatten & Generalize Memex Environment Architecture
+#+AUTHOR: Gemini CLI
+#+DATE: 2026-04-01
+#+FILETAGS: :psf:arch:refactor:generalization:
+#+STARTUP: content
+
+* Overview
+Refactor the =.env.example= and secure local =.env= to remove the legacy PARA structure and replace it with a generalized, anchor-based architecture. Move towards a unified =MEMEX_DIR= foundation while ensuring portability for different users and folder structures.
+
+* Phase A: Analysis (The Scientist)
+:PROPERTIES:
+:STATUS: COMPLETE
+:END:
+** Findings
+- Current =.env= relies on hardcoded absolute paths (=/home/user/memex/...=).
+- Direct removal of PARA variables breaks skills (=org-skill-project-foundry=, etc.).
+- The kernel's =context-resolve-path= already supports =$= expansion but needs to be the standard for all internal path lookups.
+
+* Phase B: Blueprint (The Architect)
+:PROPERTIES:
+:STATUS: PENDING_AUTHORIZATION
+:END:
+** [Coder] Surgical Implementation Tasks
+1. *Generalize .env.example:*
+   - Define =MEMEX_DIR= as the single mandatory anchor.
+   - Use variable references for all sub-directories (e.g., =PROJECTS_DIR="${MEMEX_DIR}/projects"=).
+   - Add documentation explaining how to override these for custom structures.
+2. *Harden Path Resolution (README.org):*
+   - Update =load-all-skills= to use =context-resolve-path= when reading the =SKILLS_DIR= environment variable.
+   - This ensures that if a user sets =SKILLS_DIR="$MEMEX_DIR/notes"=, the Lisp kernel expands it correctly regardless of the OS or username.
+3. *Sync Secure .env (~/.local/share/org-agent/.env):*
+   - Refactor the user's secure file to use this dynamic derivation.
+
+** [Tester] Verification Strategy
+1. *Portability Test:* Temporarily set =MEMEX_DIR=/tmp/memex-test= in the environment and verify that =(org-agent:context-get-skill-source "test")= attempts to read from the correct expanded path.
+2. *Boot Test:* Restart daemon and ensure all skills load via the new expanded paths.
+
+* NEXT Authorization Gate
+** Sovereign, do you approve this Generalized Flattening plan?
+- [ ] APPROVED
+- [ ] REJECTED