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

system/ATOMIC_NOTES_SETUP.org

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+#+TITLE: Atomic Notes (Zettelkasten) & GTD Automation Setup Guide
+#+STARTUP: content
+#+DATE: 2026-03-17
+
+* Overview
+This system uses a hybrid approach to Personal Knowledge Management (PKM). It leverages Emacs Org-mode for low-friction, structured capture into daily logs, and an OpenClaw AI Sub-Agent ("The Scribe") to nightly distill these raw thoughts into an evergreen, atomic Atomic Notes (Zettelkasten).
+
+* 1. Environment Configuration (`.env`)
+To ensure Emacs, OpenClaw, and the Scribe Agent all agree on where files live, we use a single `.env` file at the root of the workspace.
+
+** Action:
+Ensure the following `.env` file exists in your workspace root:
+#+BEGIN_SRC env
+MEMEX_DIR="memex"
+MEMEX_INBOX="memex/inbox.org"
+MEMEX_DAILY="memex/1_daily"
+MEMEX_NOTES="memex/2_notes"
+MEMEX_DRAFTS="memex/3_drafts"
+MEMEX_PUBLISHED="memex/4_published"
+MEMEX_PROJECTS="memex/5_projects"
+MEMEX_AREAS="memex/6_areas"
+MEMEX_RESOURCES="memex/7_resources"
+MEMEX_ARCHIVES="memex/8_archives"
+MEMEX_SYSTEM="memex/9_system"
+MEMEX_ATTACHMENTS="memex/attachments"
+#+END_SRC
+
+* 2. Emacs Org-Capture Setup
+All captures route to the current day's log (`$MEMEX_DAILY/YYYY-MM-DD.org`), preserving the raw chronological context.
+
+** Action:
+Add this Emacs Lisp snippet to your `init.el` or `config.el` to set up your capture templates dynamically using the `.env` variables:
+#+BEGIN_SRC elisp
+(setq org-capture-templates
+      '(("z" "Atomic Notes (Zettelkasten) (Captures to Daily)")
+        ("zf" "Fleeting Note" entry (file+olp+datetree (expand-file-name (format "%s/%%<%%Y-%%m-%%d>.org" (getenv "MEMEX_DAILY"))))
+         "* Fleeting Note: %?\n  :PROPERTIES:\n  :ID: %u\n  :CREATED: %U\n  :END:\n\n  %i")
+        ("zl" "Draft Literature Note" entry (file+olp+datetree (expand-file-name (format "%s/%%<%%Y-%%m-%%d>.org" (getenv "MEMEX_DAILY"))))
+         "* Literature Note: %?\n  :PROPERTIES:\n  :ID: %u\n  :CREATED: %U\n  :AUTHOR: \n  :SOURCE: \n  :END:\n\n  *Summary:*\n  %?\n\n  *Key Insights:*\n  - ")
+        ("zp" "Draft Permanent Note" entry (file+olp+datetree (expand-file-name (format "%s/%%<%%Y-%%m-%%d>.org" (getenv "MEMEX_DAILY"))))
+         "* Permanent Note: %?\n  :PROPERTIES:\n  :ID: %u\n  :CREATED: %U\n  :LINKS: \n  :END:\n\n  *Concept:*\n  %?\n\n  *References:*\n  - ")
+        ("t" "GTD - Task / Inbox" entry (file (getenv "MEMEX_INBOX"))
+         "* TODO %?\n  :PROPERTIES:\n  :CREATED: %U\n  :END:\n\n  %i\n  %a")))
+#+END_SRC
+
+* 3. The Distillation State Tracker
+The Scribe Agent uses a JSON file to remember the last Git commit it processed, preventing it from distilling the same notes twice or modifying the daily logs directly.
+
+** Action:
+Ensure `memex/9_system/distillation-state.json` exists. It should look like this (the hash will update automatically):
+#+BEGIN_SRC json
+{
+  "lastProcessedCommit": "HEAD_HASH_GOES_HERE"
+}
+#+END_SRC
+
+* 4. OpenClaw Cron Job (The Scribe Agent)
+The final piece is the scheduled automation. We create a cron job in OpenClaw that runs every night, reads the diffs, and creates atomic notes.
+
+** Action:
+Ask the OpenClaw orchestrator (your AI assistant) to schedule the Scribe Agent using the `cron` tool. 
+The prompt it will execute is defined in `$MEMEX_SYSTEM/skills/Scribe-Agent.org`.
+
+** Architecture Rule:
+- *Dailies are Immutable:* The Scribe reads `$MEMEX_DAILY/` but NEVER writes to it.
+- *Evergreen Notes:* The Scribe extracts concepts, generates descriptive snake_case filenames (no dates), and writes them to `$MEMEX_NOTES/` with a `Source:` backlink to the original daily file.