ARCH: Finalize semantic reorganization, skill jailing, and unified CLI

harness/loop.org

@@ -13,7 +13,7 @@ The Metabolic Loop is the high-level coordinator of the OpenCortex. It orchestra
 ** Package and Variables
 The loop requires thread-safe interrupt handling to ensure that the agent can be stopped gracefully without leaving the Lisp image in an inconsistent state.
 
-#+begin_src lisp :tangle ../src/loop.lisp
+#+begin_src lisp :tangle ../library/loop.lisp
 (in-package :opencortex)
 
 (defvar *interrupt-flag* nil)
@@ -24,7 +24,7 @@ The loop requires thread-safe interrupt handling to ensure that the agent can be
 ** The Metabolic Pipeline
 The `process-signal` function is the core metabolic processor. It iterates through the Perceive-Reason-Act gates until the signal is fully processed or an error state is reached. We have refined the error handling to ensure that memory rollbacks only occur on critical system failures, preventing transient tool errors from wiping short-term cognitive state.
 
-#+begin_src lisp :tangle ../src/loop.lisp
+#+begin_src lisp :tangle ../library/loop.lisp
 (defun process-signal (signal)
   "The entry point to the Metabolic Pipeline: Perceive -> Reason -> Act."
   (let ((current-signal signal))
@@ -64,7 +64,7 @@ The `process-signal` function is the core metabolic processor. It iterates throu
 ** Heartbeat Mechanism
 The heartbeat ensures the agent remains "alive" even in the absence of external stimuli, allowing for latent reflection and periodic maintenance. The interval is externalized to the `HEARTBEAT_INTERVAL` environment variable.
 
-#+begin_src lisp :tangle ../src/loop.lisp
+#+begin_src lisp :tangle ../library/loop.lisp
 (defun start-heartbeat ()
   "Starts the background heartbeat thread. Interval is loaded from HEARTBEAT_INTERVAL."
   (let ((interval (or (ignore-errors (parse-integer (uiop:getenv "HEARTBEAT_INTERVAL"))) 60)))
@@ -81,7 +81,7 @@ The heartbeat ensures the agent remains "alive" even in the absence of external
 ** Main Entry Point
 The `main` function initializes the environment, loads skills, and starts the heartbeat. It now includes a graceful shutdown handler for `SIGINT` (Ctrl+C) and uses `DAEMON_SLEEP_INTERVAL` to control its idle rhythm.
 
-#+begin_src lisp :tangle ../src/loop.lisp
+#+begin_src lisp :tangle ../library/loop.lisp
 (defun main ()
   "Entry point for the Skeleton MVP. Handles initialization and graceful shutdown."
   (let* ((home (uiop:getenv "HOME"))