feat(psf): transition to Order 2 (Sovereign Architect) with advanced skill graph and philosophical alignment

notes/org-skill-atomic-notes.org

@@ -67,22 +67,51 @@ Interfaces for scanning and resolving nodes in the Zettelkasten. It implements a
     results))
 #+end_src
 
+** Stage 3: Semantic Search (SOTA)
+#+begin_src lisp :tangle projects/org-skill-atomic-notes/src/retrieval-logic.lisp
+(defun atomic-notes-semantic-search (query &optional (top-k 5))
+  "Uses dense vector embeddings to find semantically related notes."
+  (let* ((query-vec (org-agent:get-embedding query))
+         (matches (when query-vec (org-agent:find-most-similar query-vec top-k))))
+    (mapcar (lambda (match)
+              (let* ((score (car match))
+                     (obj (cdr match))
+                     (attrs (org-agent:org-object-attributes obj)))
+                (list :score score 
+                      :id (org-agent:org-object-id obj)
+                      :title (getf attrs :TITLE))))
+            matches)))
+#+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))))
+  "Neural stage of Sparse and Semantic Perception.
+   It combines ripgrep hits and semantic matches to provide high-fidelity context."
+  (let* ((query (getf (getf context :payload) :query))
+         (sparse-results (atomic-notes-scan query))
+         (semantic-results (atomic-notes-semantic-search query)))
     (format nil "
-      I found the following headlines matching your query:
+      I have searched your Zettelkasten for '~a'.
+      
+      KEYWORD MATCHES (Sparse):
       ---
       ~a
       ---
       
+      SEMANTIC MATCHES (Dense):
+      ---
+      ~{~a (Score: ~f) [ID: ~a]~%~}
+      ---
+      
       TASK: 
-      Identify the IDs of the most relevant notes. 
+      Identify the IDs of the most relevant notes to answer the user's implicit or explicit question.
       Return a Lisp plist: (:target :atomic-notes :action :deep-read :ids (\"id1\" \"id2\"))
-    " query-results)))
+    " query sparse-results 
+      (loop for m in semantic-results 
+            collect (getf m :title) 
+            collect (getf m :score) 
+            collect (getf m :id)))))
 #+end_src
 
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