fix(v0.2.0): resolve macro conflicts, sync load order, and fix skill packaging

- Standardized def-cognitive-tool to 5-argument signature.
- Consolidated *cognitive-tools* as a hash table in package.lisp.
- Removed skills from opencortex.asd to enforce dynamic Skill Engine loading.
- Added missing (in-package :opencortex) to various skill files.
- Fixed let/let* sequential binding issues in emacs-edit and self-edit.
- Updated opencortex.sh to initialize skills before running doctor.
- Fixed uiop:user-homedir-pathname usage in config-manager.

harness/skills.org

@@ -400,18 +400,8 @@ EXAMPLES:
 #+begin_src lisp
 ** Cognitive Tool Registration
 #+begin_src lisp :tangle (expand-file-name "skills.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
-(defvar *cognitive-tools* nil "Registry of available Agent capabilities.")
+;; Cognitive tools are registered in *cognitive-tools* (defined in package.lisp)
-
+;; using the def-cognitive-tool macro.
-(defmacro def-cognitive-tool (name arg-list &body body)
-  "Registers a new cognitive tool (capability) into the global registry."
-  `(setf (getf *cognitive-tools* ,name)
-         (list :args ',arg-list
-               :executor (lambda (args)
-                           (let ,(mapcar (lambda (arg)
-                                           (let ((arg-name (if (listp arg) (first arg) arg)))
-                                             `(,arg-name (getf args ,(intern (string arg-name) :keyword)))))
-                                         arg-list)
-                             ,@body)))))
 #+end_src
 
 (def-cognitive-tool :eval "Evaluates raw Common Lisp code in the harness image. Use this for complex calculations or internal state inspection."

opencortex.asd

@@ -18,23 +18,7 @@
                 (:file "harness/perceive")
                 (:file "harness/reason")
                 (:file "harness/act")
-                (:file "harness/loop")
+                (:file "harness/loop"))
-
-                (:file "skills/org-skill-policy")
-                (:file "skills/org-skill-bouncer")
-                (:file "skills/org-skill-scribe")
-                (:file "skills/org-skill-gardener")
-                (:file "skills/org-skill-lisp-utils")
-                (:file "skills/org-skill-literate-programming")
-                (:file "skills/org-skill-engineering-standards")
-                (:file "skills/org-skill-self-edit")
-                (:file "skills/org-skill-emacs-edit")
-                (:file "skills/org-skill-tool-permissions")
-                (:file "skills/org-skill-self-fix")
-                (:file "skills/org-skill-peripheral-vision")
-                (:file "skills/org-skill-gateway-manager")
-                (:file "skills/org-skill-diagnostics")
-                (:file "skills/org-skill-config-manager"))
 
   :build-operation "program-op"
   :build-pathname "opencortex-server"

opencortex.sh

@@ -99,6 +99,7 @@ case "$COMMAND" in
              --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
              --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
              --eval '(ql:quickload :opencortex)' \
+             --eval '(opencortex:initialize-all-skills)' \
              --eval '(opencortex:doctor-main)'
         ;;
 

skills/org-skill-cli-gateway.org

@@ -13,6 +13,7 @@ The *CLI Gateway* is the primary sensory and actuating interface for human inter
 * Implementation
 
 #+begin_src lisp
+(in-package :opencortex)
 
 (defvar *cli-port* 9105)
 (defvar *cli-server-socket* nil)

skills/org-skill-config-manager.org

@@ -75,15 +75,38 @@ Secrets are appended to `~/.config/opencortex/.env`, while structural metadata i
 ** Registry Persistence
 #+begin_src lisp :tangle (expand-file-name "org-skill-config-manager.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/skills"))
 (defvar *providers* nil "Global registry of configured LLM providers.")
-#+end_src
 
-#+begin_src lisp :tangle (expand-file-name "org-skill-config-manager.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/skills"))
+(defun get-oc-config-dir ()
+  "Returns the XDG-compliant config directory for OpenCortex."
+  (let ((env (uiop:getenv "OC_CONFIG_DIR")))
+    (if (and env (> (length env) 0))
+        (uiop:ensure-directory-pathname env)
+        (uiop:merge-pathnames* ".config/opencortex/" (user-homedir-pathname)))))
+
 (defun save-providers ()
   "Persist provider configuration to XDG config directory."
   (let ((path (merge-pathnames "providers.lisp" (get-oc-config-dir))))
     (ensure-directories-exist path)
     (with-open-file (s path :direction :output :if-exists :supersede)
       (format s ";;; OpenCortex Provider Metadata~%~s~%" *providers*))))
+
+(defun prompt-for (label &optional default)
+  "Prompts the user for input on the CLI."
+  (format t "~a~@[ [~a]~]: " label default)
+  (finish-output)
+  (let ((input (read-line)))
+    (if (string= input "")
+        (or default "")
+        input)))
+
+(defun save-secret (provider field val)
+  "Appends a secret to the XDG .env file."
+  (let ((env-file (merge-pathnames ".env" (get-oc-config-dir)))
+        (var-name (format nil "~:@(~a_~a~)" provider field)))
+    (ensure-directories-exist env-file)
+    (with-open-file (out env-file :direction :output :if-exists :append :if-does-not-exist :create)
+      (format out "~a=~a~%" var-name val))
+    (setf (uiop:getenv var-name) val)))
 #+end_src
 
 ** Registry API

skills/org-skill-emacs-edit.org

@@ -89,10 +89,10 @@ Converts AST back to org format, preserving structure.
 (defun emacs-edit-print-headline (ast &key indent-level)
   "Converts a HEADLINE AST node to org text.
 INDENT-LEVEL is number of leading asterisks."
-  (let ((level (or indent-level 1))
+  (let* ((level (or indent-level 1))
-        (stars (make-string level :initial-element #\*))
+         (stars (make-string level :initial-element #\*))
-        (title (or (getf (getf ast :properties) :TITLE) ""))
+         (title (or (getf (getf ast :properties) :TITLE) ""))
-        (todo (getf (getf ast :properties) :TODO)))
+         (todo (getf (getf ast :properties) :TODO)))
     (format nil "~a ~a~%~a"
             stars
             (if todo (format nil "[~a] " (string-upcase todo)) "")
@@ -200,17 +200,17 @@ Add a new headline to an existing AST.
 (defun emacs-edit-add-headline (ast title &key todo properties)
   "Adds a new headline to AST.
 Returns modified AST."
-  (let ((new-id (emacs-edit-generate-id))
+  (let* ((new-id (emacs-edit-generate-id))
-        (new-props (list :ID new-id
+         (new-props (list :ID new-id
-                        :TITLE title
+                         :TITLE title
-                        :TODO (or todo "TODO")
+                         :TODO (or todo "TODO")
-                        :CREATED (format nil "[~a]" 
+                         :CREATED (format nil "[~a]" 
-                                       (multiple-value-bind (s mi h d mo y)
+                                        (multiple-value-bind (s mi h d mo y)
-                                           (decode-universal-time (get-universal-time))
+                                            (decode-universal-time (get-universal-time))
-                                         (format nil "~a-~a-~a ~a:~a"
+                                          (format nil "~a-~a-~a ~a:~a"
-                                                  y mo d h mi)))))
+                                                   y mo d h mi)))))
-        (merged-props (loop for (k v) on properties by #'cddr
+         (merged-props (loop for (k v) on properties by #'cddr
-                           collect k collect v)))
+                            collect k collect v)))
     
     (setf merged-props (append merged-props new-props))
     

skills/org-skill-homoiconic-memory.org

@@ -13,6 +13,7 @@ The *Homoiconic Memory* skill provides the core persistence layer for OpenCortex
 * Implementation
 
 #+begin_src lisp
+(in-package :opencortex)
 
 (defun memory-org-to-json (source)
   "Converts Org-mode source to JSON AST."

skills/org-skill-llm-gateway.org

@@ -49,23 +49,33 @@ The *LLM Gateway* skill provides a unified interface for interacting with multip
 
 ** Cognitive Tools
 #+begin_src lisp :tangle (expand-file-name "org-skill-llm-gateway.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/skills"))
-(def-cognitive-tool :get-ollama-embedding (text)
+(def-cognitive-tool :get-ollama-embedding 
-  (let* ((host (or (uiop:getenv "OLLAMA_HOST") "localhost:11434"))
+  "Generates vector embeddings via Ollama API."
-         (url (format nil "http://~a/api/embeddings" host))
+  ((:text :type :string :description "Text to embed."))
-         (body (cl-json:encode-json-to-string `((model . "nomic-embed-text") (prompt . ,text)))))
+  :body (lambda (args)
-    (handler-case
+          (let ((text (getf args :text)))
-        (let* ((response (dex:post url :headers '(("Content-Type" . "application/json")) :content body))
+            (let* ((host (or (uiop:getenv "OLLAMA_HOST") "localhost:11434"))
-               (json (cl-json:decode-json-from-string response)))
+                   (url (format nil "http://~a/api/embeddings" host))
-          (cdr (assoc :embedding json)))
+                   (body (cl-json:encode-json-to-string `((model . "nomic-embed-text") (prompt . ,text)))))
-      (error (c) (harness-log "OLLAMA EMBED ERROR: ~a" c) nil))))
+              (handler-case
+                  (let* ((response (dex:post url :headers '(("Content-Type" . "application/json")) :content body))
+                         (json (cl-json:decode-json-from-string response)))
+                    (cdr (assoc :embedding json)))
+                (error (c) (harness-log "OLLAMA EMBED ERROR: ~a" c) nil))))))
 #+end_src
 
 #+begin_src lisp :tangle (expand-file-name "org-skill-llm-gateway.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/skills"))
-(def-cognitive-tool :ask-llm (prompt system-prompt provider model)
+(def-cognitive-tool :ask-llm 
-  (execute-llm-request :prompt prompt 
+  "Unified interface for interacting with LLM providers."
-                       :system-prompt system-prompt 
+  ((:prompt :type :string :description "The user prompt")
-                       :provider provider 
+   (:system-prompt :type :string :description "The system prompt (optional)")
-                       :model model))
+   (:provider :type :keyword :description "The provider (e.g., :ollama, :openai)")
+   (:model :type :string :description "The model name"))
+  :body (lambda (args)
+          (execute-llm-request :prompt (getf args :prompt)
+                               :system-prompt (getf args :system-prompt)
+                               :provider (getf args :provider)
+                               :model (getf args :model))))
 #+end_src
 
 ** Skill Registration

skills/org-skill-self-edit.org

@@ -37,6 +37,13 @@ Fast paren balancing for syntax errors.
        (concatenate 'string code (make-string (- opens closes) :initial-element #\))))
       ((> closes opens)
        (concatenate 'string (make-string (- closes opens) :initial-element #\() code)))))
+
+(defun copy-hash-table (table)
+  "Returns a shallow copy of a hash table."
+  (let ((new-table (make-hash-table :test (hash-table-test table)
+                                    :size (hash-table-count table))))
+    (maphash (lambda (k v) (setf (gethash k new-table) v)) table)
+    new-table))
 #+end_src
 
 ** Parse Target Location
@@ -152,8 +159,8 @@ Provide a fixed version of the code as a lisp form.")
   "Balances parentheses in a code string."
   ((:code :type :string :description "The code to balance"))
   :body (lambda (args)
-          (let ((code (getf args :code))
+          (let* ((code (getf args :code))
-                (balanced (self-edit-balance-parens code)))
+                 (balanced (self-edit-balance-parens code)))
             (handler-case
                 (progn
                   (read-from-string balanced)

skills/org-skill-shell-actuator.org

@@ -12,7 +12,8 @@ The *Shell Actuator* provides a controlled interface for the OpenCortex to execu
 
 * Implementation
 
-#+begin_src lisp
+#+begin_src lisp :tangle (expand-file-name "org-skill-shell-actuator.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/skills"))
+(in-package :opencortex)
 
 (defparameter *allowed-commands* '("ls" "git" "rg" "grep" "date" "echo" "cat" "node" "python3" "sbcl"))