feat(arch): implement 'Code as Thought' architecture and formalize PSF Consensus Loop

notes/org-skill-atomic-notes.org

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notes/org-skill-atomic-notes.org

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+#+TITLE: SKILL: Atomic Notes Retrieval (Universal Literate Note)
+#+ID: skill-atomic-notes
+#+STARTUP: content
+#+FILETAGS: :knowledge:retrieval:zettelkasten:psf:
+
+* Overview
+This skill provides the **Deep Memory** for the agent. it enables **Sparse Tree Perception** over the Zettelkasten, using semantic search and recursive interlinking to maintain high-signal context without token bloat.
+
+* Phase A: Demand (PRD)
+:PROPERTIES:
+:STATUS: FROZEN
+:END:
+
+** 1. Purpose
+Define the interfaces for knowledge retrieval from the atomic note DAG.
+
+** 2. User Needs
+- **Atomicity:** Each note represents exactly one concept.
+- **Sparse Tree Perception:** Extract headlines and IDs before deep reading.
+- **Recursive Deep-Dive:** Follow internal links to pull related context.
+- **Search Efficiency:** Optimized searching via `ripgrep`.
+
+** 3. Success Criteria
+*** TODO Concept Discovery
+*** TODO Link Resolution
+*** TODO Sparse Tree Extraction Verification
+
+* Phase B: Blueprint (PROTOCOL)
+:PROPERTIES:
+:STATUS: SIGNED
+:END:
+
+** 1. Architectural Intent
+Interfaces for scanning and resolving nodes in the Zettelkasten. Source of truth is `$MEMEX_NOTES`.
+
+** 2. Semantic Interfaces
+#+begin_src lisp
+(defun atomic-notes-perceive (query)
+  "Performs a sparse-tree scan of the Zettelkasten.")
+
+(defun atomic-notes-resolve-link (link-target)
+  "Follows a link (ID or file) to retrieve the target node content.")
+#+end_src
+
+* Phase D: Build (Implementation)
+
+** Sparse Perception
+#+begin_src lisp :tangle projects/org-skill-atomic-notes/src/retrieval-logic.lisp
+(defun atomic-notes-perceive (query)
+  "Performs a sparse-tree scan of the Zettelkasten for the given query."
+  (let ((notes-dir (or (uiop:getenv "MEMEX_NOTES") "notes/")))
+    (kernel-log "MEMORY - Scanning Atomic Notes for: ~a" query)
+    (uiop:run-program (list "rg" "-i" query notes-dir) :output :string)))
+#+end_src
+
+** Link Resolution
+#+begin_src lisp :tangle projects/org-skill-atomic-notes/src/retrieval-logic.lisp
+(defun atomic-notes-resolve-link (link-target)
+  "Resolves a link to a physical Org file."
+  (let ((notes-dir (or (uiop:getenv "MEMEX_NOTES") "notes/")))
+    ;; Logic to handle [[id:UUID]] vs [[file:path.org]]
+    (format nil "Resolving link: ~a" link-target)))
+#+end_src
+
+* Registration
+#+begin_src lisp
+(defskill :skill-atomic-notes
+  :priority 90
+  :trigger (lambda (context) nil)
+  :neuro (lambda (context) nil)
+  :symbolic #'atomic-notes-perceive)
+#+end_src