refactor: moved org-agent to its own repository as a submodule

system/skills/AtomicNotes.org

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+#+TITLE: SKILL: Atomic Notes (Zettelkasten) (Permanent Knowledge)
+#+author: Amero Garcia
+#+created: [2026-03-16 Mon 14:28]
+#+ID: skill-atomic-notes
+#+DATE: 2026-03-11
+#+STARTUP: content
+
+* Philosophy
+Atomic notes. Stand-alone knowledge. Linked by ideas, not categories. Use the second-degree connection to build a brain.
+
+* The Workflow
+
+** 1. Fleeting Notes (`$MEMEX_DAILY/`)
+- Temporary captures from today's sessions or conversations.
+- Put these in the daily file: `YYYY-MM-DD.org`.
+- Don't worry about structure; just get the facts down.
+
+** 2. Literature Notes (`$MEMEX_RESOURCES/`)
+- Summaries of external material (books, articles, podcasts) in your own words.
+- Always include a source link.
+
+** 3. Permanent Notes (`$MEMEX_NOTES/`)
+- *Atomic:* Each note covers exactly ONE concept or idea.
+- *Stand-alone:* A developer or researcher should understand it without context.
+- *Linked:* Every new note must link to at least one existing note. Look for non-obvious connections.
+
+** 4. Structuring
+- Use `ID` properties for Org-roam style linking.
+- Avoid deep folder hierarchies; let the links provide the structure.
+- Review and prune. Knowledge that isn't connected is forgotten.
+
+** 5. Discovery
+- When researching a new topic, always search the existing Atomic Notes (Zettelkasten) first.
+- Link new findings to old assumptions.
+- Identify "Second-Degree" connections (A -> B, B -> C, therefore A -> C).
+
+* The Distillation Pipeline
+
+** 6. Nightly Distillation
+- Dailies (`$MEMEX_DAILY/`) are raw, immutable logs. They are never destructively modified during processing.
+- A state file (`$MEMEX_SYSTEM/distillation-state.json`) tracks the last processed Git commit hash.
+- **Process:**
+  1. Read state file for the last processed commit.
+  2. Diff `$MEMEX_DAILY/` since that commit to identify new Atomic Notes (Zettelkasten) captures.
+  3. Extract these captures.
+  4. Generate a descriptive, concept-based filename (e.g., `proof_of_work.org`). *NO DATES IN PERMANENT FILENAMES.*
+  5. Create the new atomic note in `$MEMEX_NOTES/` with an `#+ID` and a `Source:` link pointing back to the specific daily log heading.
+  6. Update `distillation-state.json` with the new commit hash.
+
+** 7. Weekly Interlinking (Maintenance)
+- A deeper pass over the graph in `$MEMEX_NOTES/`.
+- Goal: Find orphaned notes, merge conceptually similar notes, flesh out stubs, and establish new connections.
+- Constraint: Ensure notes maintain their evergreen, atomic nature even when expanded. Do not let them turn into sprawling essays.

system/skills/GTD.org

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+#+TITLE: SKILL: Getting Things Done (GTD)
+#+author: Amero Garcia
+#+created: [2026-03-16 Mon 14:28]
+#+ID: skill-gtd
+#+DATE: 2026-03-11
+#+STARTUP: content
+
+* Philosophy
+Capture everything. Clarify the next action. Organize into projects. Reflect regularly. Engage with confidence.
+
+* The Workflow
+
+** 1. Capture (Inbox)
+- Everything that enters your awareness goes into `memex/0_inbox/`.
+- No friction. No filtering. Just get it out of the user's head.
+
+** 2. Clarify (Process)
+- Review the Inbox daily.
+- Is it actionable?
+  - *No:* Trash it, Archive it (`6_reference`), or Incubate it (`memex/gtd.org` under `* Incubate`).
+  - *Yes:* What's the next action?
+    - If <2 minutes, DO IT NOW.
+    - If it's a project (>1 step), add to `memex/gtd.org` under `* Projects` and create a dedicated project folder in `5_projects/` if detailed planning is needed.
+    - If it's for someone else, delegate and track in `memex/gtd.org`.
+
+** 3. Organize
+- *GTD Hub:* All Actions, Projects, Incubate items, and Habits go to `memex/gtd.org`. This is the single source of truth for your Emacs agenda and `org-gtd`.
+- *Fleeting Notes:* Use `memex/1_daily/` for non-actionable thoughts or meeting notes from the day.
+- *Project Artifacts:* Deep work, technical specs, and drafts go to `5_projects/` or `3_drafts/`.
+- *Reference material:* Non-actionable knowledge goes to `6_reference/` or `2_notes/`.
+
+** 4. Reflect (Review)
+- *Daily Review:* Process the inbox. Update `memex/gtd.org`.
+- *Weekly Review:* Review all projects in `memex/gtd.org`. Brainstorm new tasks. Clear the mental clutter.
+
+** 5. Engage
+- Use `memex/gtd.org` and Emacs agenda to decide what to work on based on Context, Time, Energy, and Priority.

system/skills/OrgMode.org

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+#+TITLE: SKILL: Org-Mode & Org-Roam (Technical Implementation)
+#+author: Amero Garcia
+#+created: [2026-03-16 Mon 14:28]
+#+ID: skill-org-mode
+#+DATE: 2026-03-11
+#+STARTUP: content
+
+* Philosophy
+Plain text is forever. Structure is metadata. Everything is a node.
+
+* Technical Implementation
+
+** 1. Document Structure
+- *Headlines:* Use `*` for top-level, `**` for second-level, etc.
+- *Properties:* Every node (headline) that is intended to be an atomic note must have a `:PROPERTIES:` drawer.
+- *Unique IDs:* Use `:ID:` for Org-roam style linking (e.g., `:ID: 550e8400-e29b-41d4-a716-446655440000`).
+- *Dates:* Use `[YYYY-MM-DD Day HH:MM]` for inactive timestamps and `<YYYY-MM-DD Day HH:MM>` for active/scheduled ones.
+
+** 2. Task Management (GTD)
+- *Hub:* Use `memex/gtd.org` for all TODOs, Projects, and Habits.
+- *Statuses:* `TODO`, `DOING`, `DONE` (with `CLOSED:`), `WAITING`, `SOMEDAY`.
+
+** 3. File Naming
+- *Daily & Fleeting:* `memex/1_daily/YYYY-MM-DD.org`
+- *Atomic Notes:* `memex/2_notes/slug-of-the-concept.org`
+- *Projects:* `memex/5_projects/ProjectName/SPEC.org`
+
+** 4. Code Blocks
+- Use `#+BEGIN_SRC <language>` and `#+END_SRC` for all code snippets.
+- Use `#+RESULTS:` to capture output when running code within Org-mode (Babel).
+
+** 6. Binary Management (org-attach)
+- **Philosophy:** Treat binaries (PDFs, images, data) as first-class citizens linked to symbolic nodes. Never use fragile local file paths.
+- **The Protocol (System 2):**
+  1. **Identify the Host Node:** Every attachment must be linked to a specific Org headline (e.g., in `memex/gtd.org` or a Literature Note).
+  2. **Generate Native ID:** Use `(org-id-get-create)` via Emacs to ensure the node has a globally unique, persistent identifier.
+  3. **Perform the Attachment:** Use `(org-attach-attach "/path/to/file" nil 'mv)` to move the file into the ID-based storage.
+  4. **Linking:** Use `[[attachment:filename.ext]]` for all internal references. This ensures the link survives if the file or node is moved.
+- **Storage Root:** The system-wide attachment directory is `$MEMEX_ATTACHMENTS` (typically `memex/7_resources/` or `memex/attachments/`).
+
+** 7. Learning Rituals (Closing the Loop)

system/skills/Scribe-Agent.org

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+#+TITLE: SKILL: Scribe Agent (Distillation Sub-Agent)
+#+ID: skill-scribe-agent
+#+STARTUP: content
+
+* Overview
+The Scribe Agent is an automated distillation sub-agent designed to process raw daily captures into permanent atomic notes for the Atomic Notes (Zettelkasten). It runs as an isolated OpenClaw cron job.
+
+* Configuration
+- **Type:** OpenClaw Cron Job
+- **Target:** `isolated`
+- **Model:** `CURRENT_TEXT_MANIPULATION_MODEL` (Updates periodically based on review; currently an efficient LLM suitable for text parsing).
+- **Environment:** Loads variables from `.env` to locate folders (e.g., `$MEMEX_DAILY`, `$MEMEX_NOTES`, `$MEMEX_SYSTEM`).
+
+* System Prompt / Agent Turn Directive
+```markdown
+You are the Scribe, an automated distillation sub-agent.
+Your sole job is to process raw notes into a Atomic Notes (Zettelkasten).
+Do not engage in conversation. Only execute the following pipeline:
+
+1. Read `$MEMEX_SYSTEM/distillation-state.json` to get the last processed Git commit hash.
+2. Run `git diff <last_commit_hash> HEAD -- $MEMEX_DAILY/` to find new captures.
+3. For every new Atomic Notes (Zettelkasten) capture found in the diff:
+   a. Read the raw capture.
+   b. Determine the core concept.
+   c. Generate a concise, snake_case filename (e.g., `core_concept_name.org`).
+   d. Write the content to `$MEMEX_NOTES/<filename>`, ensuring it is formatted as an atomic Org-mode note with `#+ID` and a `Source:` backlink to the daily file.
+4. Update `$MEMEX_SYSTEM/distillation-state.json` with the current HEAD commit hash.
+5. Exit.
+```