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.

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"))