feat(v0.2.0): finalize autonomous self-editing foundation

- Hardened actuators: Fixed path-traversal vulnerabilities in file I/O tools and blocked .org files from regex replacements to force AST usage. Enforced Merkle snapshots on AST edits.
- Implemented Reflection Loops: Injected rejection traces from deterministic gates back into the LLM context to enable autonomous self-correction.
- Finalized tool permission tiers (ask/allow/deny) with proper LLM prompt filtering.

harness/package.org

@@ -225,3 +225,56 @@ Centralized logging function. It simultaneously writes to standard output and th
     (format t "~a~%" formatted-msg)
     (finish-output)))
 #+end_src
+* Global Test Runner
+#+begin_src lisp :tangle (expand-file-name "tests/run-all-tests.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
+(load "~/quicklisp/setup.lisp")
+
+(push #p"./" asdf:*central-registry*)
+
+(ql:quickload '(:usocket :bordeaux-threads :cl-postgres :split-sequence
+                :dexador :jonathan :cl-dotenv :hunchentoot
+                :trivial-garbage :s-sql :str :uuid :cl-json :uiop :fiveam))
+
+(asdf:load-system :opencortex)
+(asdf:load-system :opencortex/tests)
+
+(format t "~%=== Running ALL Test Suites ===~%")
+
+;; Engineering Standards tests
+(when (find-package :OPENCORTEX-ENGINEERING-STANDARDS-TESTS)
+  (fiveam:run! 'OPENCORTEX-ENGINEERING-STANDARDS-TESTS::ENGINEERING-STANDARDS-SUITE))
+
+;; Literate Programming tests
+(when (find-package :OPENCORTEX-LITERATE-PROGRAMMING-TESTS)
+  (fiveam:run! 'OPENCORTEX-LITERATE-PROGRAMMING-TESTS::LITERATE-PROGRAMMING-SUITE))
+
+;; Communication tests
+(when (find-package :OPENCORTEX-TESTS)
+  (fiveam:run! 'OPENCORTEX-TESTS::COMMUNICATION-PROTOCOL-SUITE))
+
+;; Pipeline tests
+(when (find-package :OPENCORTEX-PIPELINE-TESTS)
+  (fiveam:run! 'OPENCORTEX-PIPELINE-TESTS::PIPELINE-SUITE))
+
+;; Boot sequence tests
+(when (find-package :OPENCORTEX-BOOT-TESTS)
+  (fiveam:run! 'OPENCORTEX-BOOT-TESTS::BOOT-SUITE))
+
+;; Memory tests
+(when (find-package :OPENCORTEX-MEMORY-TESTS)
+  (fiveam:run! 'OPENCORTEX-MEMORY-TESTS::MEMORY-SUITE))
+
+;; Immune system tests
+(when (find-package :OPENCORTEX-IMMUNE-SYSTEM-TESTS)
+  (fiveam:run! 'OPENCORTEX-IMMUNE-SYSTEM-TESTS::IMMUNE-SUITE))
+
+;; Emacs edit tests
+(when (find-package :OPENCORTEX-EMACS-EDIT-TESTS)
+  (fiveam:run! 'OPENCORTEX-EMACS-EDIT-TESTS::EMACS-EDIT-SUITE))
+
+;; Lisp utils tests
+(when (find-package :OPENCORTEX-LISP-UTILS-TESTS)
+  (fiveam:run! 'OPENCORTEX-LISP-UTILS-TESTS::LISP-UTILS-SUITE))
+
+(format t "~%=== ALL TESTS COMPLETE ===~%")
+#+end_src

harness/reason.org

@@ -199,7 +199,8 @@ The `think` function is the heart of the probabilistic engine. It constructs a p
          (tool-belt (generate-tool-belt-prompt))
          (global-context (context-assemble-global-awareness))
          (system-logs (context-get-system-logs))
-         (assistant-name (or (uiop:getenv "MEMEX_ASSISTANT") "Agent")))
+         (assistant-name (or (uiop:getenv "MEMEX_ASSISTANT") "Agent"))
+         (rejection-trace (proto-get (proto-get context :payload) :rejection-trace)))
 
     ;; Generate prompt from skill or raw text
     (let* ((prompt-generator (when active-skill
@@ -211,8 +212,14 @@ The `think` function is the heart of the probabilistic engine. It constructs a p
                              (if (and p (stringp p))
                                  p
                                  "Maintain metabolic stasis."))))
+           
+           ;; Inject Reflection Loop feedback if a previous proposal was rejected
+           (reflection-feedback (if rejection-trace
+                                    (format nil "~%~%PREVIOUS PROPOSAL REJECTED:~%Your previous proposal was rejected by the deterministic safety gates.~%Rejection Trace: ~a~%You MUST fix the syntax or logic error described above and try again." rejection-trace)
+                                    ""))
+
            (system-prompt (format nil
-                                   "IDENTITY: ~a
+                                   "IDENTITY: ~a~a
 
 You are a component of the OpenCortex neurosymbolic AI agent.
 Your task is to generate exactly ONE valid Lisp plist response.
@@ -243,6 +250,7 @@ GLOBAL CONTEXT:
 RECENT LOGS:
 ~a"
                                    assistant-name
+                                   reflection-feedback
                                    tool-belt
                                    global-context
                                    system-logs)))
@@ -417,30 +425,45 @@ The deterministic engine runs all registered skills' verification functions. Thi
                 (member sensor '(:user-input :chat-message)))
       (return-from reason-gate signal))
 
-    ;; Generate proposal via LLM
+    ;; Reflection Loop: Retry up to 3 times if deterministic gates reject
-    (let ((candidate (think signal)))
+    (let ((retries 3)
+          (current-signal (copy-tree signal))
+          (last-rejection nil))
+      (loop
+        (when (<= retries 0)
+          (harness-log "REASON: Reflection loop exhausted. Final rejection.")
+          (setf (getf signal :approved-action) last-rejection)
+          (setf (getf signal :status) :reasoned)
+          (return signal))
 
+        (when last-rejection
+          (setf (getf (getf current-signal :payload) :rejection-trace) last-rejection))
+
+        (let ((candidate (think current-signal)))
           (harness-log "REASON: candidate type = ~a" (type-of candidate))
 
-      ;; Validate candidate is a proper plist (not an error string or symbol)
           (if (and candidate
                    (listp candidate)
                    (or (keywordp (car candidate))
                        (eq (car candidate) 'TYPE)
                        (eq (car candidate) 'type)))
 
-          ;; Valid proposal - run through deterministic verification
+              (let ((verified (deterministic-verify candidate current-signal)))
-          (setf (getf signal :approved-action)
+                (if (member (getf verified :type) '(:LOG :EVENT :log :event))
-                (deterministic-verify candidate signal))
-
-          ;; Invalid response - log and drop
                     (progn
-            (harness-log "REASON: Invalid candidate type ~a, dropping"
+                      (harness-log "REASON: Proposal rejected by gate. Retrying (~a left)." (1- retries))
-                         (type-of candidate))
+                      (decf retries)
-            (setf (getf signal :approved-action) nil)))
+                      (setf last-rejection verified))
-
+                    (progn
+                      (setf (getf signal :approved-action) verified)
                       (setf (getf signal :status) :reasoned)
-      signal)))
+                      (return signal))))
+
+              (progn
+                (harness-log "REASON: Invalid candidate type ~a, dropping" (type-of candidate))
+                (setf (getf signal :approved-action) nil)
+                (setf (getf signal :status) :reasoned)
+                (return signal))))))))
 #+end_src
 
 * Test Suite

harness/skills.org

@@ -363,11 +363,13 @@ EXAMPLES:
 ---
 " )))
     (maphash (lambda (name tool)
+               (let ((perm (ignore-errors (uiop:symbol-call :opencortex.skills.org-skill-tool-permissions :get-tool-permission name))))
+                 (unless (eq perm :deny)
                    (setf output (concatenate 'string output
                                              (format nil "- ~a: ~a~%  Parameters: ~s~%~%"
                                                      name
                                                      (cognitive-tool-description tool)
-                                                 (cognitive-tool-parameters tool)))))
+                                                     (cognitive-tool-parameters tool)))))))
              *cognitive-tools*)
     output))
 #+end_src
@@ -462,9 +464,9 @@ EXAMPLES:
            (declare (ignore context))
            (let* ((file (getf args :file))
                   (memex-root (or (uiop:getenv "MEMEX_DIR") "/home/user/memex"))
-                  (truename (ignore-errors (namestring (truename file)))))
+                  (abs-path (namestring (uiop:ensure-absolute-pathname file (uiop:getcwd)))))
-             (or (null truename)
+             (and (str:starts-with-p memex-root abs-path)
-                 (str:starts-with-p memex-root truename))))
+                  (not (search ".." abs-path)))))
   :body (lambda (args)
           (let ((file (getf args :file)))
             (handler-case
@@ -483,9 +485,10 @@ EXAMPLES:
            (declare (ignore context))
            (let* ((file (getf args :file))
                   (memex-root (or (uiop:getenv "MEMEX_DIR") "/home/user/memex"))
-                  (truename (ignore-errors (namestring (truename file)))))
+                  (abs-path (namestring (uiop:ensure-absolute-pathname file (uiop:getcwd)))))
-             (or (null truename)
+             (and (str:starts-with-p memex-root abs-path)
-                 (str:starts-with-p memex-root truename))))
+                  (not (search ".." abs-path))
+                  (not (str:ends-with-p ".org" abs-path))))) ;; Force AST tools for .org files
   :body (lambda (args)
           (let ((file (getf args :file))
                 (content (getf args :content))
@@ -515,9 +518,10 @@ EXAMPLES:
            (declare (ignore context))
            (let* ((file (getf args :file))
                   (memex-root (or (uiop:getenv "MEMEX_DIR") "/home/user/memex"))
-                  (truename (ignore-errors (namestring (truename file)))))
+                  (abs-path (namestring (uiop:ensure-absolute-pathname file (uiop:getcwd)))))
-             (or (null truename)
+             (and (str:starts-with-p memex-root abs-path)
-                 (str:starts-with-p memex-root truename))))
+                  (not (search ".." abs-path))
+                  (not (str:ends-with-p ".org" abs-path))))) ;; Force AST tools for .org files
   :body (lambda (args)
           (let ((file (getf args :file))
                 (old (getf args :old))

skills/org-skill-emacs-edit.org

@@ -184,6 +184,7 @@ Write AST back to file preserving structure.
 (defun emacs-edit-write-file (file-path ast)
   "Writes AST back to FILE-PATH, preserving org structure.
 Clears cache after write."
+  (opencortex::snapshot-memory)
   (let ((org-text (emacs-edit-ast-to-org ast)))
     (with-open-file (out file-path :direction :output :if-exists :supersede)
       (write-string org-text out)))

skills/org-skill-tool-permissions.org

@@ -47,7 +47,7 @@ Tool permissions and embedding generation via multiple providers.
     (case perm
       (:allow :allow)
       (:deny :deny)
-      (:ask (list :ask tool-name context))
+      (:ask (list :ask tool-name))
       (t :allow))))
 
 (def-cognitive-tool :get-embedding
@@ -111,10 +111,22 @@ Tool permissions and embedding generation via multiple providers.
 
 (defskill :skill-tool-permissions
   :priority 600
-  :trigger (lambda (c) (declare (ignore c)) nil)
+  ;; Trigger whenever there's a tool call
+  :trigger (lambda (c) 
+             (let* ((action (getf c :candidate))
+                    (target (getf action :target)))
+               (or (eq target :TOOL) (eq target :tool))))
   :deterministic (lambda (a c)
     (let ((tool (getf (getf a :payload) :tool)))
-      (when tool (check-tool-permission-gate tool c)))))
+      (if tool
+          (let ((perm (check-tool-permission-gate tool c)))
+            (cond
+              ((eq perm :deny)
+               (list :type :LOG :payload (list :text (format nil "Tool '~a' execution denied by permission tiers." tool))))
+              ((and (listp perm) (eq (car perm) :ask))
+               (list :type :EVENT :status :suspended :reason :ask-permission :payload (list :tool tool :action a)))
+              (t a)))
+          a))))
 #+end_src
 
 * Test Suite