Add v0.2.0 features: vector search + tool permissions

- Local vector search: Ollama embeddings + semantic search
  - get-embedding with caching
  - cosine-similarity computation
  - semantic-search cognitive tool
  - :semantic-search tool for LLM queries

- Tool permission tiers: security gating for cognitive tools
  - Three tiers: :allow, :deny, :ask
  - Gate in execute-tool-action before tool runs
  - Defaults: :deny for shell/delete-file, :ask for eval/write-file
  - :tool-permissions cognitive tool for management

- Embedding provider support: Ollama AND llama.cpp
  - EMBEDDING_PROVIDER env var
  - EMBEDDING_MODEL env var
  - LLAMA_HOST for llama.cpp server

- .env.example: Add embedding config variables
- Fix parse-message in communication.lisp

- Update ASDF: add test files, tool-permissions skill

All 60 tests pass (6 suites x 100%)

library/memory.lisp

@@ -161,3 +161,58 @@ Reconstitutes alists into hash tables."
 (defun file-name-nondirectory (path)
   "Extracts the filename from a full path string."
   (let ((pos (position #\/ path :from-end t))) (if pos (subseq path (1+ pos)) path)))
+
+(defvar *embedding-cache* (make-hash-table :test 'equal)
+  "Cache for embeddings to avoid redundant API calls.")
+
+(defun get-embedding (text)
+  "Generates a vector embedding for the given text via Ollama. Returns nil on failure."
+  (when (or (null text) (string= text ""))
+    (return-from get-embedding nil))
+  (let ((cached (gethash text *embedding-cache*)))
+    (when cached (return-from get-embedding cached)))
+  (let ((result (funcall (get-cognitive-tool-body :get-ollama-embedding) (list :text text))))
+    (when (eq (getf result :status) :success)
+      (let ((vec (getf result :vector)))
+        (setf (gethash text *embedding-cache*) vec)
+        vec))))
+
+(defun cosine-similarity (vec-a vec-b)
+  "Computes cosine similarity between two vectors. Both should be sequences of numbers."
+  (when (or (null vec-a) (null vec-b) (zerop (length vec-a)) (zerop (length vec-b)))
+    (return-from cosine-similarity 0.0))
+  (let ((dot-product (loop for a across vec-a
+                          for b across vec-b
+                          sum (* a b)))
+        (norm-a (sqrt (loop for a across vec-a sum (* a a))))
+        (norm-b (sqrt (loop for b across vec-b sum (* b b)))))
+    (if (or (zerop norm-a) (zerop norm-b))
+        0.0
+        (/ dot-product (* norm-a norm-b)))))
+
+(defun semantic-search (query &key (limit 10) (min-similarity 0.5))
+  "Searches memory for objects semantically similar to the query."
+  (let* ((query-vec (get-embedding query))
+         (results nil))
+    (unless query-vec
+      (harness-log "EMBEDDING: Failed to generate embedding for query: ~a" query)
+      (return-from semantic-search nil))
+    (maphash (lambda (id obj)
+               (let ((obj-vec (org-object-vector obj)))
+                 (when obj-vec
+                   (let ((sim (cosine-similarity query-vec obj-vec)))
+                     (when (>= sim min-similarity)
+                       (push (list :id id :object obj :similarity sim) results))))))
+             *memory*)
+    (setf results (sort results #'> :key (lambda (r) (getf r :similarity))))
+    (subseq results 0 (min limit (length results)))))
+
+(def-cognitive-tool :semantic-search
+  "Searches memory for objects semantically similar to a query."
+  ((:query :type :string :description "The search query.")
+   (:limit :type :integer :description "Maximum results to return." :default 10)
+   (:min-similarity :type :number :description "Minimum similarity threshold (0-1)." :default 0.5))
+  :body (lambda (args)
+          (semantic-search (getf args :query)
+                        :limit (or (getf args :limit) 10)
+                        :min-similarity (or (getf args :min-similarity) 0.5))))