fix(v0.2.0): finalize structural integrity and clean boot

- Fixed memory.org source blocks to ensure persistence functions are tangled.
- Improved extract-tangle-target to handle complex Elisp expressions.
- Corrected opencortex.sh initialization paths to prevent setup loops.
- Reordered variable definitions in policy and standards skills to eliminate forward-reference warnings.

harness/loop.org

@@ -1,3 +1,4 @@
+#+PROPERTY: header-args:lisp :tangle (expand-file-name "loop.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
 #+TITLE: The Metabolic Loop (loop.lisp)
 #+AUTHOR: Amr
 #+FILETAGS: :harness:loop:
@@ -67,7 +68,7 @@ The loop operates in a multi-threaded environment:
 
 * Package and Thread-Safe Variables
 
-#+begin_src lisp :tangle (expand-file-name "loop.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
+#+begin_src lisp
 (in-package :opencortex)
 
 (defvar *interrupt-flag* nil
@@ -90,7 +91,7 @@ This function implements the Perceive-Reason-Act pipeline. It processes a signal
 
 The depth counter prevents infinite recursion—a signal that generates another signal that generates another, etc. By limiting to depth 10, we ensure the system eventually converges or gracefully terminates.
 
-#+begin_src lisp :tangle (expand-file-name "loop.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
+#+begin_src lisp
 (defun process-signal (signal)
   "The entry point to the Metabolic Pipeline: Perceive -> Reason -> Act.
 
@@ -184,7 +185,7 @@ The heartbeat thread ensures the agent remains alive even without external input
 
 ** Heartbeat Configuration Variables
 
-#+begin_src lisp :tangle (expand-file-name "loop.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
+#+begin_src lisp
 (defvar *auto-save-interval* 300
   "Interval in seconds between automatic memory saves.
   Defaults to 300 seconds (5 minutes). Set via MEMORY_AUTO_SAVE_INTERVAL env var.")
@@ -195,7 +196,7 @@ The heartbeat thread ensures the agent remains alive even without external input
 
 ** start-heartbeat: The Pulsing Heart
 
-#+begin_src lisp :tangle (expand-file-name "loop.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
+#+begin_src lisp
 (defun start-heartbeat ()
   "Starts the background heartbeat thread.
 
@@ -241,7 +242,7 @@ The heartbeat thread ensures the agent remains alive even without external input
 
 ** Shutdown Configuration
 
-#+begin_src lisp :tangle (expand-file-name "loop.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
+#+begin_src lisp
 (defvar *shutdown-save-enabled* t
   "When T, save memory to disk on graceful shutdown.
   Disable for testing or when memory persistence is handled externally.")
@@ -258,7 +259,7 @@ The main function orchestrates system startup:
 5. Register SIGINT handler for graceful Ctrl+C shutdown
 6. Enter idle loop (sleeping in 1-hour increments)
 
-#+begin_src lisp :tangle (expand-file-name "loop.lisp" (concat (or (getenv "INSTALL_DIR") ".") "/harness"))
+#+begin_src lisp
 (defun main ()
   "Entry point for OpenCortex. Initializes the system and enters idle loop.