feat(psf): implement advanced foundry automation and memory optimization

notes/org-skill-atomic-notes.org

@@ -31,35 +31,58 @@ Define the interfaces for knowledge retrieval from the atomic note DAG.
 :END:
 
 ** 1. Architectural Intent
-Interfaces for scanning and resolving nodes in the Zettelkasten. Source of truth is `$MEMEX_NOTES`.
+Interfaces for scanning and resolving nodes in the Zettelkasten. It implements a two-stage retrieval process: Sparse Perception (Headlines/IDs) followed by Targeted Deep-Reading.
 
 ** 2. Semantic Interfaces
 #+begin_src lisp
-(defun atomic-notes-perceive (query)
-  "Performs a sparse-tree scan of the Zettelkasten.")
+(defun atomic-notes-scan (query)
+  "Stage 1: Returns a sparse list of matching headlines and their unique IDs.")
 
-(defun atomic-notes-resolve-link (link-target)
-  "Follows a link (ID or file) to retrieve the target node content.")
+(defun atomic-notes-deep-read (ids)
+  "Stage 2: Retrieves the full content for a specific list of node IDs.")
 #+end_src
 
 * Phase D: Build (Implementation)
 
-** Sparse Perception
+** Stage 1: Sparse Scan
 #+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."
+(defun atomic-notes-scan (query)
+  "Uses ripgrep to find matching headlines and extracts their IDs."
   (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)))
+    (kernel-log "MEMORY - Sparse Scan for: ~a" query)
+    ;; We grep for headlines and include the following line which usually has the ID property
+    (uiop:run-program (list "rg" "-i" "-A" "1" (format nil "^\\*+.*~a" query) notes-dir) 
+                      :output :string)))
 #+end_src
 
-** Link Resolution
+** Stage 2: Deep Read
 #+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)))
+(defun atomic-notes-deep-read (ids)
+  "Retrieves the full content subtree for given IDs from the Object Store."
+  (let ((results '()))
+    (dolist (id ids)
+      (let ((obj (org-agent:lookup-object id)))
+        (when obj
+          (push (list :id id :content (org-agent:org-object-content obj)) results))))
+    results))
+#+end_src
+
+** Neuro-Cognitive Intelligence
+#+begin_src lisp :tangle projects/org-skill-atomic-notes/src/retrieval-logic.lisp
+(defun neuro-skill-atomic-notes (context)
+  "Neural stage of Sparse Perception.
+   It analyzes the search results and decides which specific IDs to 'deep read'."
+  (let ((query-results (atomic-notes-scan (getf (getf context :payload) :query))))
+    (format nil "
+      I found the following headlines matching your query:
+      ---
+      ~a
+      ---
+      
+      TASK: 
+      Identify the IDs of the most relevant notes. 
+      Return a Lisp plist: (:target :atomic-notes :action :deep-read :ids (\"id1\" \"id2\"))
+    " query-results)))
 #+end_src
 
 * Registration
@@ -67,6 +90,6 @@ Interfaces for scanning and resolving nodes in the Zettelkasten. Source of truth
 (defskill :skill-atomic-notes
   :priority 90
   :trigger (lambda (context) nil)
-  :neuro (lambda (context) nil)
-  :symbolic #'atomic-notes-perceive)
+  :neuro #'neuro-skill-atomic-notes
+  :symbolic #'atomic-notes-scan)
 #+end_src