ARCH: Finalize Microkernel Decoupling - Move behavioral skills to dynamic user-space

2026-04-13 16:11:09 -04:00
parent 34f59a6e43
commit 19fb888434
74 changed files with 129 additions and 2744 deletions
--- a/skills/org-skill-bouncer.org
+++ b/skills/org-skill-bouncer.org
@@ -23,8 +23,7 @@ While the *Formal Prover* ensures an action is "legal" (e.g., "Yes, you are allo
 *** Secret Exposure Check
 Retrieves all active secrets from the vault and scans the payload for potential leaks.

-#+begin_src lisp :tangle ../src/bouncer.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun bouncer-scan-secrets (text)
  "Returns the name of the secret found in TEXT, or NIL if clean."
  (when (and text (stringp text))
@@ -40,8 +39,7 @@ Retrieves all active secrets from the vault and scans the payload for potential
 *** Network Exfiltration Check
 Inspects shell commands for unwhitelisted domains or IP addresses.

-#+begin_src lisp :tangle ../src/bouncer.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun bouncer-check-network-exfil (cmd)
  "Returns T if the command appears to target an unwhitelisted external host."
  (when (and cmd (stringp cmd))
@@ -58,8 +56,7 @@ Inspects shell commands for unwhitelisted domains or IP addresses.
 ** Runtime Guard (bouncer-check)
 The primary entry point for all high-impact actions.

-#+begin_src lisp :tangle ../src/bouncer.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun bouncer-check (action context)
  "The 5-Vector security gate. Blocks or queues actions based on risk."
  (let* ((target (getf action :target))
@@ -100,8 +97,7 @@ The primary entry point for all high-impact actions.
 #+end_src

 ** Approval Processing
-#+begin_src lisp :tangle ../src/bouncer.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun bouncer-process-approvals ()
  "Scans the object store for APPROVED flight plans and re-injects their actions."
  (let ((approved-nodes (list-objects-with-attribute :TODO "APPROVED"))
@@ -123,8 +119,7 @@ The primary entry point for all high-impact actions.
 #+end_src

 ** Skill Definition
-#+begin_src lisp :tangle ../src/bouncer.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defskill :skill-bouncer
  :priority 100
  :trigger (lambda (ctx) 
--- a/skills/org-skill-chat.org
+++ b/skills/org-skill-chat.org
@@ -49,8 +49,7 @@ Interfaces for conversational event handling and UI integration. Source of truth
 * Phase D: Build (Implementation)

 ** Event Perception
-#+begin_src lisp :tangle ../src/chat-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (defun chat-archive-message (text &key (role :user) channel chat-id)
  "Archives a chat message into the persistent Memory and triggers a snapshot."
@@ -76,7 +75,7 @@ Interfaces for conversational event handling and UI integration. Source of truth
 #+end_src

 ** Deterministic Verification
-#+begin_src lisp :tangle ../src/chat-logic.lisp
+#+begin_src lisp
 (defun verify-skill-chat (proposed-action context)
  (let* ((payload (getf proposed-action :payload))
         (action (or (getf payload :action) (getf proposed-action :action)))
@@ -108,7 +107,7 @@ Interfaces for conversational event handling and UI integration. Source of truth
 ** Neural Response Generation
 The Chat skill acts as the conversational UI. Because the ~org-agent~ kernel evaluates LLM output via ~read-from-string~ (expecting a valid s-expression) and the chat verifier strictly expects an Emacs ~:insert-at-end~ actuation, we must explicitly mandate that the LLM wraps its conversational output in a Common Lisp property list.

-#+begin_src lisp :tangle ../src/chat-logic.lisp
+#+begin_src lisp
 (defun probabilistic-skill-chat (context)
  "Generates a conversational response, stripping system errors from context."
  (let* ((payload (getf context :payload))
@@ -138,7 +137,7 @@ REQUIRED FORMATS:
 #+end_src

 * Registration
-#+begin_src lisp :tangle ../src/chat-logic.lisp
+#+begin_src lisp
 (defskill :skill-chat
  :priority 100
  :trigger #'trigger-skill-chat
--- a/skills/org-skill-consensus.org
+++ b/skills/org-skill-consensus.org
@@ -27,8 +27,7 @@ Enable reliable, cross-instance coordination without a central master.
 * Phase D: Build (Implementation)

 ** Consensus Algorithm (Simplified Raft)
-#+begin_src lisp :tangle ../src/consensus-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun consensus-propose-vote (proposal)
  "Broadcasts a proposal to the peer swarm and collects votes.
   Implements PSF Social Consensus Protocol."
--- a/skills/org-skill-credentials-vault.org
+++ b/skills/org-skill-credentials-vault.org
@@ -61,14 +61,13 @@ Tests in `tests/vault-tests.lisp` will verify:
 * Phase D: Build (Implementation)

 ** Package Context
-#+begin_src lisp :tangle ../src/credentials-vault.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** Vault State
 We maintain an in-memory hash table for secrets, which is hydrated from and persisted to the Memory.

-#+begin_src lisp :tangle ../src/credentials-vault.lisp
+#+begin_src lisp
 (defvar *vault-memory* (make-hash-table :test 'equal)
  "In-memory cache of sensitive credentials.")
 #+end_src
@@ -76,7 +75,7 @@ We maintain an in-memory hash table for secrets, which is hydrated from and pers
 ** Helper: Secret Masking
 The `vault-mask-string` function ensures that diagnostic output never contains the full plaintext of a sensitive token.

-#+begin_src lisp :tangle ../src/credentials-vault.lisp
+#+begin_src lisp
 (defun vault-mask-string (str)
  "Returns a masked version of a sensitive string."
  (if (and str (> (length str) 8))
@@ -87,7 +86,7 @@ The `vault-mask-string` function ensures that diagnostic output never contains t
 ** Retrieval (vault-get-secret)
 This function is the secure getter for all system secrets. It prioritizes the Vault (Memory) and falls back to environment variables for legacy compatibility.

-#+begin_src lisp :tangle ../src/credentials-vault.lisp
+#+begin_src lisp
 (defun vault-get-secret (provider &key (type :api-key))
  "Retrieves a credential. Type can be :api-key or :session."
  (let* ((key (format nil "~a-~a" provider type))
@@ -113,7 +112,7 @@ This function is the secure getter for all system secrets. It prioritizes the Va
 ** Persistence (vault-set-secret)
 When a secret is updated, we immediately snapshot the Memory to ensure the credential change is versioned and durable.

-#+begin_src lisp :tangle ../src/credentials-vault.lisp
+#+begin_src lisp
 (defun vault-set-secret (provider secret &key (type :api-key))
  "Securely stores a secret and triggers a Merkle snapshot."
  (let ((key (format nil "~a-~a" provider type)))
@@ -126,7 +125,7 @@ When a secret is updated, we immediately snapshot the Memory to ensure the crede
 ** Onboarding Logic
 Retained from the legacy Google skill, this provides the instructions for the sovereign cookie handshake.

-#+begin_src lisp :tangle ../src/credentials-vault.lisp
+#+begin_src lisp
 (defun vault-onboard-gemini-web ()
  "Instructions for the Sovereign Cookie Handshake."
  (harness-log "--- GEMINI WEB ONBOARDING ---")
@@ -138,7 +137,7 @@ Retained from the legacy Google skill, this provides the instructions for the so
 #+end_src

 ** Registration
-#+begin_src lisp :tangle ../src/credentials-vault.lisp
+#+begin_src lisp
 (progn
  (defskill :skill-credentials-vault
    :priority 200 ; High priority, foundational
@@ -152,7 +151,7 @@ Retained from the legacy Google skill, this provides the instructions for the so
 * Phase E: Chaos (Verification)

 ** 1. Unit Tests (FiveAM)
-#+begin_src lisp :tangle ../tests/vault-tests.lisp
+#+begin_src lisp
 (defpackage :org-agent-vault-tests
  (:use :cl :fiveam :org-agent))
 (in-package :org-agent-vault-tests)
--- a/skills/org-skill-embedding.org
+++ b/skills/org-skill-embedding.org
@@ -51,8 +51,7 @@ Move heavy neural and mathematical logic out of `core.lisp` and `probabilistic.l
 * Phase D: Build (Implementation)

 ** Vector Operations
-#+begin_src lisp :tangle ../src/embedding-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (defun get-embedding (text)
  "Retrieves a vector representation of text via the configured neural provider."
@@ -104,7 +103,7 @@ Move heavy neural and mathematical logic out of `core.lisp` and `probabilistic.l
 #+end_src

 * Registration
-#+begin_src lisp :tangle ../src/embedding-logic.lisp
+#+begin_src lisp
 (defskill :skill-embedding
  :priority 50
  :trigger (lambda (ctx) (eq (getf (getf ctx :payload) :sensor) :embedding-request))
--- a/skills/org-skill-environment-config.org
+++ b/skills/org-skill-environment-config.org
@@ -34,8 +34,7 @@ Define a standardized `CONFIG` object type in the Memory. Provide getter/setter
 ** 2. Semantic Interfaces

 *** Fleet Configuration
-#+begin_src lisp :tangle ../src/config-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (defun set-llm-model (provider model-id)
  "Registers a preferred model for a provider in the Memory."
--- a/skills/org-skill-event-orchestrator.org
+++ b/skills/org-skill-event-orchestrator.org
@@ -66,14 +66,13 @@ Tests in `tests/orchestrator-tests.lisp` will verify hook execution order, cron-
 * Phase D: Build (Implementation)

 ** Package Context
-#+begin_src lisp :tangle ../src/event-orchestrator.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** Registry State
 We maintain our internal registries in hash-tables, which will be serialized via the State Persistence layer.

-#+begin_src lisp :tangle ../src/event-orchestrator.lisp
+#+begin_src lisp
 (defvar *hook-registry* (make-hash-table :test 'equal)
  "Maps hook-names (symbols) to lists of functions.")

@@ -84,7 +83,7 @@ We maintain our internal registries in hash-tables, which will be serialized via
 ** Hook: Registration
 Allows external skills to register logic at system lifecycle points.

-#+begin_src lisp :tangle ../src/event-orchestrator.lisp
+#+begin_src lisp
 (defun orchestrator-register-hook (hook-name fn)
  "Registers a function for a named hook. Triggers a Merkle snapshot."
  (pushnew fn (gethash hook-name *hook-registry*))
@@ -96,7 +95,7 @@ Allows external skills to register logic at system lifecycle points.
 ** Hook: Triggering
 Executes all functions associated with a specific hook.

-#+begin_src lisp :tangle ../src/event-orchestrator.lisp
+#+begin_src lisp
 (defun orchestrator-trigger-hook (hook-name &rest args)
  "Executes all registered functions for the given hook name."
  (let ((functions (gethash hook-name *hook-registry*)))
@@ -108,7 +107,7 @@ Executes all functions associated with a specific hook.
 ** Cron: Task Scheduling
 Registers a recurring task to be executed during heartbeats.

-#+begin_src lisp :tangle ../src/event-orchestrator.lisp
+#+begin_src lisp
 (defun orchestrator-schedule-task (task-id schedule fn)
  "Schedules a task for execution. Schedule can be an interval (integer seconds) or 'heartbeat'."
  (setf (gethash task-id *cron-registry*) (list :schedule schedule :fn fn :last-run 0))
@@ -120,7 +119,7 @@ Registers a recurring task to be executed during heartbeats.
 ** Cron: Heartbeat Processor
 The internal loop that checks the cron-registry during every system pulse.

-#+begin_src lisp :tangle ../src/event-orchestrator.lisp
+#+begin_src lisp
 (defun orchestrator-process-cron ()
  "Checked by the harness on every heartbeat."
  (let ((now (get-universal-time)))
@@ -139,7 +138,7 @@ The internal loop that checks the cron-registry during every system pulse.
 ** Router: Complexity Classification
 Deterministic logic to classify incoming stimuli into complexity tiers.

-#+begin_src lisp :tangle ../src/event-orchestrator.lisp
+#+begin_src lisp
 (defun orchestrator-classify-complexity (context)
  "Returns the complexity tier (:REFLEX, :COGNITION, :REASONING) for a stimulus."
  (let* ((payload (getf context :payload))
@@ -162,7 +161,7 @@ Deterministic logic to classify incoming stimuli into complexity tiers.
 ** Registration
 We register the orchestrator as a core skill and hot-patch the harness's routing hook to use our classification logic.

-#+begin_src lisp :tangle ../src/event-orchestrator.lisp
+#+begin_src lisp
 (progn
  ;; Hook into kernel routing
  (setf org-agent::*model-selector-fn* #'orchestrator-classify-complexity)
@@ -179,7 +178,7 @@ We register the orchestrator as a core skill and hot-patch the harness's routing
 * Phase E: Chaos (Verification)

 ** 1. Unit Tests (FiveAM)
-#+begin_src lisp :tangle ../tests/orchestrator-tests.lisp
+#+begin_src lisp
 (defpackage :org-agent-orchestrator-tests
  (:use :cl :fiveam :org-agent))
 (in-package :org-agent-orchestrator-tests)
--- a/skills/org-skill-formal-verification.org
+++ b/skills/org-skill-formal-verification.org
@@ -48,20 +48,19 @@ The gate operates as high-priority middleware. It decomposes proposed actions an
 * Phase D: Build (Implementation)

 ** Package Context
-#+begin_src lisp :tangle ../src/verification-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** Invariant Registry
 Global store for all registered security invariants.

-#+begin_src lisp :tangle ../src/verification-logic.lisp
+#+begin_src lisp
 (defvar *formal-invariants* (make-hash-table :test 'equal)
  "Registry of security invariants used by the Formal Verification Gate.")
 #+end_src

 ** Invariant Definition Macro
-#+begin_src lisp :tangle ../src/verification-logic.lisp
+#+begin_src lisp
 (defmacro def-invariant (name action-type (action context) &body body)
  "Defines a formal security invariant. 
   BODY must return T for safe actions and NIL for unsafe ones."
@@ -74,7 +73,7 @@ Global store for all registered security invariants.
 ** Invariant: Path Confinement
 Ensures all file-related operations (including shell calls that touch files) are confined to the memex root.

-#+begin_src lisp :tangle ../src/verification-logic.lisp
+#+begin_src lisp
 (def-invariant path-confinement :all (action context)
  "Forces all path-based operations to reside within the Sovereign Memex."
  (declare (ignore context))
@@ -99,7 +98,7 @@ Ensures all file-related operations (including shell calls that touch files) are
 ** Invariant: No Network Exfiltration
 Blocks common tools and patterns used for data exfiltration via the shell.

-#+begin_src lisp :tangle ../src/verification-logic.lisp
+#+begin_src lisp
 (def-invariant no-network-exfil :shell (action context)
  "Prevents shell commands from establishing unauthorized external connections."
  (declare (ignore context))
@@ -115,7 +114,7 @@ Blocks common tools and patterns used for data exfiltration via the shell.
 ** Verification Engine
 The core prover that applies all relevant invariants to an action.

-#+begin_src lisp :tangle ../src/verification-logic.lisp
+#+begin_src lisp
 (defun verify-action-formally (action context)
  "Deterministically proves that ACTION satisfies all applicable security invariants."
  (let ((action-target (getf action :target))
@@ -137,7 +136,7 @@ The core prover that applies all relevant invariants to an action.
 #+end_src

 ** Registration: Skill
-#+begin_src lisp :tangle ../src/verification-logic.lisp
+#+begin_src lisp
 (defskill :skill-formal-verification
  :priority 95 ; Just below Bouncer
  :trigger (lambda (context) (declare (ignore context)) nil) ; Middleware only
--- a/skills/org-skill-gateway-matrix.org
+++ b/skills/org-skill-gateway-matrix.org
@@ -38,38 +38,37 @@ Autonomous background polling of the Matrix homeserver. Uses `dexador` for HTTP
 * Phase D: Build (Implementation)

 ** Package Context
-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** State: Sync Token
 Tracks the last processed event to ensure we only receive new messages.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defvar *matrix-since-token* nil)
 #+end_src

 ** State: Polling Thread
 Reference to the background thread responsible for sync requests.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defvar *matrix-polling-thread* nil)
 #+end_src

 ** Credential Retrieval: Homeserver
-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defun get-matrix-homeserver () (vault-get-secret :matrix-homeserver))
 #+end_src

 ** Credential Retrieval: Token
-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defun get-matrix-token () (vault-get-secret :matrix-token))
 #+end_src

 ** Actuator: sendMessage
 Sends an `m.room.message` to a Matrix room.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defun execute-matrix-action (action context)
  "Sends a message via Matrix Client API."
  (declare (ignore context))
@@ -94,7 +93,7 @@ Sends an `m.room.message` to a Matrix room.
 ** Sensor: Sync loop & Injection
 Polls the `/sync` endpoint and processes timeline events.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defun matrix-process-sync ()
  "Calls Matrix sync and injects new messages."
  (let* ((hs (get-matrix-homeserver))
@@ -138,7 +137,7 @@ Polls the `/sync` endpoint and processes timeline events.
 ** Start Polling
 Initializes the Matrix background thread.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defun start-matrix-gateway ()
  "Initializes the Matrix background thread."
  (unless (and *matrix-polling-thread* (bt:thread-alive-p *matrix-polling-thread*))
@@ -155,7 +154,7 @@ Initializes the Matrix background thread.
 ** Stop Polling
 Gracefully terminates the background thread.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defun stop-matrix-gateway ()
  (when (and *matrix-polling-thread* (bt:thread-alive-p *matrix-polling-thread*))
    (bt:destroy-thread *matrix-polling-thread*)
@@ -165,14 +164,14 @@ Gracefully terminates the background thread.
 ** Registration: Actuator
 Register the Matrix channel as a physical actuator.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (register-actuator :matrix #'execute-matrix-action)
 #+end_src

 ** Registration: Skill
 Define the passive skill entry for the gateway.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (defskill :skill-gateway-matrix
  :priority 150
  :trigger (lambda (ctx) (declare (ignore ctx)) nil)
@@ -183,6 +182,6 @@ Define the passive skill entry for the gateway.
 ** Initialization
 Trigger the sync loop upon loading.

-#+begin_src lisp :tangle ../src/gateway-matrix.lisp
+#+begin_src lisp
 (start-matrix-gateway)
 #+end_src
--- a/skills/org-skill-gateway-signal.org
+++ b/skills/org-skill-gateway-signal.org
@@ -38,28 +38,27 @@ Wraps the `signal-cli` binary. Polling is done in a background thread to prevent
 * Phase D: Build (Implementation)

 ** Package Context
-#+begin_src lisp :tangle ../src/gateway-signal.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** State: Signal Identity
 Retrieves the Signal account number from the secure vault.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (defun get-signal-account () (vault-get-secret :signal))
 #+end_src

 ** State: Polling Thread
 Reference to the background thread responsible for message reception.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (defvar *signal-polling-thread* nil)
 #+end_src

 ** Actuator: sendMessage
 Executes the `signal-cli send` command.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (defun execute-signal-action (action context)
  "Sends a message via signal-cli."
  (declare (ignore context))
@@ -78,7 +77,7 @@ Executes the `signal-cli send` command.
 ** Sensor: receive & Injection
 Polls for new messages and injects them into the harness.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (defun signal-process-updates ()
  "Polls for new messages via signal-cli and injects them into the harness."
  (let ((account (get-signal-account)))
@@ -108,7 +107,7 @@ Polls for new messages and injects them into the harness.
 ** Start Polling
 Initializes the Signal background thread.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (defun start-signal-gateway ()
  "Initializes the Signal background thread."
  (unless (and *signal-polling-thread* (bt:thread-alive-p *signal-polling-thread*))
@@ -125,7 +124,7 @@ Initializes the Signal background thread.
 ** Stop Polling
 Gracefully terminates the background thread.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (defun stop-signal-gateway ()
  (when (and *signal-polling-thread* (bt:thread-alive-p *signal-polling-thread*))
    (bt:destroy-thread *signal-polling-thread*)
@@ -135,14 +134,14 @@ Gracefully terminates the background thread.
 ** Registration: Actuator
 Register the Signal channel as a physical actuator.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (register-actuator :signal #'execute-signal-action)
 #+end_src

 ** Registration: Skill
 Define the passive skill entry for the gateway.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (defskill :skill-gateway-signal
  :priority 150
  :trigger (lambda (ctx) (declare (ignore ctx)) nil) ;; Passive
@@ -153,6 +152,6 @@ Define the passive skill entry for the gateway.
 ** Initialization
 Trigger the polling loop upon loading.

-#+begin_src lisp :tangle ../src/gateway-signal.lisp
+#+begin_src lisp
 (start-signal-gateway)
 #+end_src
--- a/skills/org-skill-gateway-telegram.org
+++ b/skills/org-skill-gateway-telegram.org
@@ -38,28 +38,27 @@ The gateway operates as an autonomous background service. It uses `dexador` for
 * Phase D: Build (Implementation)

 ** Package Context
-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** State: Update Tracking
 Tracks the last processed message ID to prevent duplicates.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defvar *telegram-last-update-id* 0)
 #+end_src

 ** State: Polling Thread
 Reference to the background thread responsible for message reception.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defvar *telegram-polling-thread* nil)
 #+end_src

 ** State: Authorized Chats
 Whitelist of chat IDs permitted to interact with the agent.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defvar *telegram-authorized-chats* nil 
  "List of chat IDs allowed to interact with the bot. Hydrated from environment.")
 #+end_src
@@ -67,12 +66,12 @@ Whitelist of chat IDs permitted to interact with the agent.
 ** Token Retrieval
 Fetches the Bot API token from the secure vault.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defun get-telegram-token () (vault-get-secret :telegram))
 #+end_src

 ** Actuator: sendMessage
-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defun execute-telegram-action (action context)
  "Sends a message back to Telegram."
  (declare (ignore context))
@@ -92,7 +91,7 @@ Fetches the Bot API token from the secure vault.
 #+end_src

 ** Sensor: getUpdates & Injection
-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defun telegram-process-updates ()
  "Polls for new messages and injects them into the harness."
  (let* ((token (get-telegram-token))
@@ -124,7 +123,7 @@ Fetches the Bot API token from the secure vault.
 ** Start Polling
 Initializes the Telegram background thread.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defun start-telegram-gateway ()
  "Initializes the Telegram background thread."
  (unless (and *telegram-polling-thread* (bt:thread-alive-p *telegram-polling-thread*))
@@ -141,7 +140,7 @@ Initializes the Telegram background thread.
 ** Stop Polling
 Gracefully terminates the background thread.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defun stop-telegram-gateway ()
  (when (and *telegram-polling-thread* (bt:thread-alive-p *telegram-polling-thread*))
    (bt:destroy-thread *telegram-polling-thread*)
@@ -151,14 +150,14 @@ Gracefully terminates the background thread.
 ** Registration: Actuator
 Register the Telegram channel as a physical actuator.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (register-actuator :telegram #'execute-telegram-action)
 #+end_src

 ** Registration: Skill
 Define the passive skill entry for the gateway.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (defskill :skill-gateway-telegram
  :priority 150
  :trigger (lambda (ctx) (declare (ignore ctx)) nil) ;; Passive, handles its own loop
@@ -169,6 +168,6 @@ Define the passive skill entry for the gateway.
 ** Initialization
 Trigger the polling loop upon loading.

-#+begin_src lisp :tangle ../src/gateway-telegram.lisp
+#+begin_src lisp
 (start-telegram-gateway)
 #+end_src
--- a/skills/org-skill-harness-monitor.org
+++ b/skills/org-skill-harness-monitor.org
@@ -12,8 +12,7 @@ The *Harness Monitor* provides tools for inspecting the internal state and healt

 * Implementation

-#+begin_src lisp :tangle ../src/harness-monitor.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (org-agent:def-cognitive-tool :harness-status \"Returns the current operational status of the Org-Agent harness, including loaded skills and telemetry.\"
  nil
--- a/skills/org-skill-homoiconic-memory.org
+++ b/skills/org-skill-homoiconic-memory.org
@@ -60,14 +60,13 @@ Tests in `tests/memory-suite-tests.lisp` will verify the round-trip conversion a
 * Phase D: Build (Implementation)

 ** Package Context
-#+begin_src lisp :tangle ../src/homoiconic-memory.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** Node Structure Definition
 We define the standard `org-node` structure used throughout the harness.

-#+begin_src lisp :tangle ../src/homoiconic-memory.lisp
+#+begin_src lisp
 (defun make-memory-node (headline &key content properties children)
  "Constructor for a normalized Org node alist."
  (list :type :HEADLINE
@@ -79,7 +78,7 @@ We define the standard `org-node` structure used throughout the harness.
 ** ID Generation (org-id-get-create)
 Mandated standard for ID creation. This function ensures that every node in the Memex has a unique, deterministic identifier.

-#+begin_src lisp :tangle ../src/homoiconic-memory.lisp
+#+begin_src lisp
 (defun org-id-get-create ()
  "Generates a new unique ID for an Org node. This is the system-wide standard."
  (format nil "node-~a" (get-universal-time)))
@@ -88,7 +87,7 @@ Mandated standard for ID creation. This function ensures that every node in the
 ** ID Injection (memory-ensure-id)
 Ensures every headline has a unique ID property using the system standard `org-id-get-create`. This is foundational for the Merkle-Tree object store.

-#+begin_src lisp :tangle ../src/homoiconic-memory.lisp
+#+begin_src lisp
 (defun memory-ensure-id (node)
  "Injects a unique ID into an Org node if missing, using the standard org-id-get-create mechanism."
  (let* ((props (getf node :properties))
@@ -104,7 +103,7 @@ Ensures every headline has a unique ID property using the system standard `org-i
 ** Recursive Normalization (memory-normalize-ast)
 Recursively walks the AST to enforce structural rules.

-#+begin_src lisp :tangle ../src/homoiconic-memory.lisp
+#+begin_src lisp
 (defun memory-normalize-ast (ast)
  "Recursively normalizes an Org AST."
  (let ((type (getf ast :type))
@@ -124,7 +123,7 @@ Recursively walks the AST to enforce structural rules.
 ** JSON Bridge: Org-to-JSON
 Utilizes the Emacs bridge (or local parser) to convert text to JSON.

-#+begin_src lisp :tangle ../src/homoiconic-memory.lisp
+#+begin_src lisp
 (defun memory-org-to-json (source-path)
  "Routes to the Emacs-based Org-JSON bridge."
  ;; Future implementation will use the org-json-convert CLI tool
@@ -135,7 +134,7 @@ Utilizes the Emacs bridge (or local parser) to convert text to JSON.
 ** JSON Bridge: JSON-to-Org
 Converts a structured AST back into Org-mode text.

-#+begin_src lisp :tangle ../src/homoiconic-memory.lisp
+#+begin_src lisp
 (defun memory-json-to-org (ast)
  "Materializes a JSON AST into Org-mode text."
  ;; Placeholder for org-element-interpret-data equivalent
@@ -144,7 +143,7 @@ Converts a structured AST back into Org-mode text.
 #+end_src

 ** Registration
-#+begin_src lisp :tangle ../src/homoiconic-memory.lisp
+#+begin_src lisp
 (progn
  (defskill :skill-homoiconic-memory
    :priority 300 ; Core foundational skill
@@ -159,7 +158,7 @@ Converts a structured AST back into Org-mode text.
 * Phase E: Chaos (Verification)

 ** 1. Unit Tests (FiveAM)
-#+begin_src lisp :tangle ../tests/memory-suite-tests.lisp
+#+begin_src lisp
 (defpackage :org-agent-memory-tests
  (:use :cl :fiveam :org-agent))
 (in-package :org-agent-memory-tests)
--- a/skills/org-skill-lisp-repair.org
+++ b/skills/org-skill-lisp-repair.org
@@ -12,8 +12,7 @@ The *Lisp Repair Syntax Gate* asynchronously intercepts `:syntax-error` events e
 * Implementation

 ** Core Repair Logic
-#+begin_src lisp :tangle ../src/lisp-repair.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (defun count-char (char string)
  (let ((count 0))
@@ -46,7 +45,7 @@ MANDATE: Output EXACTLY ONE valid Common Lisp list. Do not explain. Do not use m
 ** Skill Definition
 Reacts to syntax error events and transforms them into repaired requests.

-#+begin_src lisp :tangle ../src/lisp-repair.lisp
+#+begin_src lisp
 (defskill :skill-lisp-repair
  :priority 90
  :trigger (lambda (ctx) (eq (getf (getf ctx :payload) :sensor) :syntax-error))
--- a/skills/org-skill-lisp-validator.org
+++ b/skills/org-skill-lisp-validator.org
@@ -33,12 +33,11 @@ Define a high-integrity, recursive security sandbox for Lisp execution.
 * Implementation

 ** Package
-#+begin_src lisp :tangle ../src/lisp-validator.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** Whitelist Definition
-#+begin_src lisp :tangle ../src/lisp-validator.lisp
+#+begin_src lisp
 (defparameter *lisp-validator-whitelist*
  '(;; Math & Logic
    + - * / = < > <= >= 1+ 1- min max
@@ -84,7 +83,7 @@ Define a high-integrity, recursive security sandbox for Lisp execution.
 ** Dynamic Symbol Registration
 We allow other skills to register safe symbols for the validator.

-#+begin_src lisp :tangle ../src/lisp-validator.lisp
+#+begin_src lisp
 (defvar *lisp-validator-registry* nil
  "List of dynamically registered safe symbols.")

@@ -100,7 +99,7 @@ We allow other skills to register safe symbols for the validator.
 #+end_src

 ** Recursive AST Walker
-#+begin_src lisp :tangle ../src/lisp-validator.lisp
+#+begin_src lisp
 (defun lisp-validator-ast-walk (form)
  "Recursively walks the Lisp AST. Returns T if safe, NIL if unsafe."
  (cond
@@ -125,7 +124,7 @@ We allow other skills to register safe symbols for the validator.
 #+end_src

 ** Cognitive Tools
-#+begin_src lisp :tangle ../src/lisp-validator.lisp
+#+begin_src lisp
 (org-agent:def-cognitive-tool :lisp-validator-status "Returns validator-related telemetry, including blocked actions and harness status."
  nil
  :body (lambda (args)
@@ -140,7 +139,7 @@ We allow other skills to register safe symbols for the validator.
 #+end_src

 ** Skill Definition
-#+begin_src lisp :tangle ../src/lisp-validator.lisp
+#+begin_src lisp
 (org-agent:defskill :skill-lisp-validator
  :priority 900 ; High priority, before most skills
  :trigger (lambda (ctx) 
@@ -157,7 +156,7 @@ We allow other skills to register safe symbols for the validator.


 * Phase E: Chaos (Verification)
-#+begin_src lisp :tangle ../tests/lisp-validator-tests.lisp
+#+begin_src lisp
 (defpackage :org-agent-lisp-validator-tests
  (:use :cl :fiveam :org-agent)
  (:export #:lisp-validator-suite))
--- a/skills/org-skill-llm-gateway.org
+++ b/skills/org-skill-llm-gateway.org
@@ -56,14 +56,13 @@ Verification will occur via `tests/llm-gateway-tests.lisp` using the FiveAM fram
 * Phase D: Build (Implementation)

 ** Package Context
-#+begin_src lisp :tangle ../src/llm-gateway.lisp
-(in-package :org-agent)
+#+begin_src lisp
 #+end_src

 ** Nested Extraction Helper (get-nested)
 A robust utility to navigate deeply nested JSON alists produced by `cl-json`, handling both objects and arrays.

-#+begin_src lisp :tangle ../src/llm-gateway.lisp
+#+begin_src lisp
 (defun get-nested (alist &rest keys)
  "Recursively extracts nested values from an alist, handling both objects and arrays."
  (let ((val alist))
@@ -82,7 +81,7 @@ A robust utility to navigate deeply nested JSON alists produced by `cl-json`, ha
 ** Unified Request Executor (execute-llm-request)
 This is the primary actuator for neural reasoning. It handles the specific JSON payload formats and HTTP headers required by each provider. It retrieves secrets from the [[file:org-skill-credentials-vault.org][Credentials Vault]], ensuring that API keys are masked in all diagnostic output.

-#+begin_src lisp :tangle ../src/llm-gateway.lisp
+#+begin_src lisp
 (defun execute-llm-request (prompt system-prompt &key provider model)
  "Unified entry point for all LLM providers."
  (let ((api-key (vault-get-secret provider :type :api-key))
@@ -144,7 +143,7 @@ The `:ask-llm` tool exposes the gateway's power to Probabilistic Engine, allowin
 ** Registration: Tool
 Register the unified gateway as a cognitive tool.

-#+begin_src lisp :tangle ../src/llm-gateway.lisp
+#+begin_src lisp
 (def-cognitive-tool :ask-llm 
  "Queries an LLM provider via the unified gateway."
  ((:prompt :type :string :description "The user prompt.")
@@ -159,7 +158,7 @@ Register the unified gateway as a cognitive tool.
 #+end_src
 Register each supported provider with the harness's neural registry.

-#+begin_src lisp :tangle ../src/llm-gateway.lisp
+#+begin_src lisp
 (dolist (p '(:anthropic :gemini-api :gemini-web :groq :ollama :openai :openrouter))
  (org-agent:register-probabilistic-backend p (lambda (prompt system-prompt &key model)
                                        (execute-llm-request prompt system-prompt :provider p :model model))))
@@ -168,7 +167,7 @@ Register each supported provider with the harness's neural registry.
 ** Registration: Skill
 Define the foundational skill entry for the gateway.

-#+begin_src lisp :tangle ../src/llm-gateway.lisp
+#+begin_src lisp
 (defskill :skill-llm-gateway
  :priority 150 ; Higher than individual old skills
  :trigger (lambda (context) (declare (ignore context)) nil)
--- a/skills/org-skill-peripheral-vision.org
+++ b/skills/org-skill-peripheral-vision.org
@@ -48,8 +48,7 @@ Move context pruning and rendering logic out of `context.lisp` to allow for more
 * Phase D: Build (Implementation)

 ** Foveal-Peripheral Pruning
-#+begin_src lisp :tangle ../src/context-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (defun context-render-to-org (obj &key (depth 1) (foveal-id nil) (semantic-threshold 0.75) (foveal-vector nil))
  "Recursively renders an org-object and its children to an Org string using a Foveal-Peripheral Hybrid model."
@@ -113,7 +112,7 @@ Move context pruning and rendering logic out of `context.lisp` to allow for more
 #+end_src

 * Registration
-#+begin_src lisp :tangle ../src/context-logic.lisp
+#+begin_src lisp
 (defskill :skill-peripheral-vision
  :priority 90
  :dependencies ("org-skill-embedding")
--- a/skills/org-skill-policy-enforcer.org
+++ b/skills/org-skill-policy-enforcer.org
@@ -19,8 +19,7 @@ Unlike traditional software where a "Kernel" might have hardcoded rules, the Org

 * Implementation

-#+begin_src lisp :tangle ../src/policy-enforcer.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (defskill :skill-policy-enforcer
  :priority 1000 ; Absolute highest priority
--- a/skills/org-skill-self-fix.org
+++ b/skills/org-skill-self-fix.org
@@ -15,8 +15,7 @@ The *Self-Fix Agent* is the system's "Repair Mechanism." It takes failure hypoth
 * Phase D: Build (Implementation)

 ** Repair Logic
-#+begin_src lisp :tangle ../src/self-fix.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (defun self-fix-apply (action context)
  "Applies a surgical code fix and reloads the modified skill."
@@ -64,7 +63,7 @@ The *Self-Fix Agent* is the system's "Repair Mechanism." It takes failure hypoth
 #+end_src

 ** Registration
-#+begin_src lisp :tangle ../src/self-fix.lisp
+#+begin_src lisp
 (def-cognitive-tool :repair-file 
  "Applies a surgical code modification to a file and reloads the skill if applicable."
  ((:file :type :string :description "Path to the target file")
--- a/skills/org-skill-shell-actuator.org
+++ b/skills/org-skill-shell-actuator.org
@@ -78,16 +78,14 @@ Interfaces for secure system calls. State is event-driven via the core kernel bu
 ** Allowed Commands
 Whitelist of permitted host binaries.

-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defparameter *allowed-commands* '("ls" "git" "rg" "grep" "date" "echo" "cat" "node" "python3" "sbcl"))
 #+end_src

 ** Shell Metacharacters
 Dangerous characters that are banned to prevent command injection.

-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defparameter *shell-metacharacters* '(#\; #\& #\| #\> #\< #\$ #\` #\\ #\!)
  "Characters that are banned in shell commands to prevent injection.")
 #+end_src
@@ -95,8 +93,7 @@ Dangerous characters that are banned to prevent command injection.
 ** Safety Check (shell-command-safe-p)
 Predicate to verify a command string is free of metacharacters.

-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun shell-command-safe-p (cmd-string)
  "Returns T if the command string contains no dangerous metacharacters."
  (not (some (lambda (char) (find char cmd-string)) *shell-metacharacters*)))
@@ -105,8 +102,7 @@ Predicate to verify a command string is free of metacharacters.
 ** Shell Execution (execute-shell-safely)
 The primary secure actuator for host system calls.

-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun execute-shell-safely (action context)
  (let* ((cmd-string (getf (getf action :payload) :cmd))
         (executable (car (uiop:split-string (string-trim " " cmd-string) :separator '(#\Space)))))
@@ -136,8 +132,7 @@ The primary secure actuator for host system calls.
 ** Script Synthesis (execute-sandboxed-script)
 Executes a synthesized script (Python/Lisp/JS) in a controlled directory.

-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun execute-sandboxed-script (action context)
  "Executes a synthesized script (Python/Lisp/JS) in a controlled directory.
   This enables SOTA-level Tool Synthesis and Iterative Fixing."
@@ -166,8 +161,7 @@ Executes a synthesized script (Python/Lisp/JS) in a controlled directory.
 ** Infrastructure: MicroVM Provisioning
 Hardware-Level Isolation for future security evolution.

-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun provision-microvm (id &key (cpu 1) (ram 512))
  "Hardware-Level Isolation: Provisions an ephemeral Firecracker MicroVM.
   This is the high-security evolution of directory-based sandboxing."
@@ -177,8 +171,7 @@ Hardware-Level Isolation for future security evolution.
 #+end_src

 ** Feedback Perception
-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun trigger-skill-shell-actuator (context)
  (let ((type (getf context :type))
        (payload (getf context :payload)))
@@ -187,8 +180,7 @@ Hardware-Level Isolation for future security evolution.
 #+end_src

 ** Probabilistic-Cognitive Analysis
-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defun probabilistic-skill-shell-actuator (context)
  (let* ((p (getf context :payload))
         (cmd (getf p :cmd))
@@ -229,16 +221,14 @@ Hardware-Level Isolation for future security evolution.
 ** Registration: Actuator
 Register the shell channel as a physical actuator.

-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (org-agent:register-actuator :shell #'execute-shell-safely)
 #+end_src

 ** Registration: Skill
 Define the skill entry for the shell actuator.

-#+begin_src lisp :tangle ../src/shell-logic.lisp
-(in-package :org-agent)
+#+begin_src lisp
 (defskill :skill-shell-actuator
  :priority 80
  :trigger #'trigger-skill-shell-actuator
--- a/skills/org-skill-state-persistence.org
+++ b/skills/org-skill-state-persistence.org
@@ -90,7 +90,7 @@ Serializes the Merkle history and current pointers to a Lisp file.
    (ensure-directories-exist image-file)
    (harness-log "PERSISTENCE - Dumping local image to ~a..." (uiop:native-namestring image-file))
    (with-open-file (out image-file :direction :output :if-exists :supersede)
-      (format out "(in-package :org-agent)~%")
+      (format out "~%")
      ;; 1. Dump all immutable objects in the history store
      (maphash (lambda (hash obj)
                 (print `(setf (gethash ,hash *history-store*) ,obj) out))
--- a/skills/org-skill-task-integrity.org
+++ b/skills/org-skill-task-integrity.org
@@ -39,8 +39,7 @@ Define automated behaviors for GTD state consistency and dependency verification
 * Implementation

 ** Semantic Mapping
-#+begin_src lisp :tangle ../src/task-integrity.lisp
-(in-package :org-agent)
+#+begin_src lisp

 (defun semantic-mapping (task-state)
  "Maps Org-mode task states to semantic categories."
@@ -51,7 +50,7 @@ Define automated behaviors for GTD state consistency and dependency verification
 #+end_src

 ** Active Children Detection
-#+begin_src lisp :tangle ../src/task-integrity.lisp
+#+begin_src lisp
 (defun detect-active-children (task-id)
  "Checks if a task has any child tasks in an active state."
  (let ((children (list-objects-with-attribute :PARENT task-id)))
@@ -64,7 +63,7 @@ Define automated behaviors for GTD state consistency and dependency verification
 ** Integrity Check (task-integrity-check)
 Enforces high-integrity semantic rules for task management.

-#+begin_src lisp :tangle ../src/task-integrity.lisp
+#+begin_src lisp
 (defun task-integrity-check (action)
  "Enforces semantic GTD integrity rules on proposed actions."
  (let* ((payload (getf action :payload))
@@ -81,7 +80,7 @@ Enforces high-integrity semantic rules for task management.
 #+begin_src

 ** Skill Definition
-#+begin_src lisp :tangle ../src/task-integrity.lisp
+#+begin_src lisp
 (defskill :skill-task-integrity
  :priority 90
  :trigger (lambda (ctx) (declare (ignore ctx)) nil)