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.