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fix(chaos): force absolute-relative tangle paths in harness

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Amr Gharbeia
2026-04-28 18:00:49 -04:00
parent 75cc9e3629
commit d15225a453
13 changed files with 54 additions and 54 deletions
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4
harness/act.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/act.lisp" (expand-file-name "")) #+PROPERTY: header-args:lisp :tangle (expand-file-name "harness/act.lisp" (expand-file-name "harness/"))
#+TITLE: Stage 3: Act (act.lisp) #+TITLE: Stage 3: Act (act.lisp)
#+AUTHOR: Amr #+AUTHOR: Amr
#+FILETAGS: :harness:act: #+FILETAGS: :harness:act:
@@ -393,7 +393,7 @@ Example feedback chain:
These tests verify the Act pipeline. Run with: These tests verify the Act pipeline. Run with:
~(fiveam:run! 'pipeline-act-suite)~ ~(fiveam:run! 'pipeline-act-suite)~
#+begin_src lisp :tangle (expand-file-name "pipeline-act-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/pipeline-act-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(defpackage :opencortex-pipeline-act-tests (defpackage :opencortex-pipeline-act-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:pipeline-act-suite)) (:export #:pipeline-act-suite))

6
harness/communication.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/communication.lisp" (expand-file-name "")) #+PROPERTY: header-args:lisp :tangle (expand-file-name "harness/communication.lisp" (expand-file-name "harness/"))
#+TITLE: Communication Protocol (communication.lisp) #+TITLE: Communication Protocol (communication.lisp)
#+AUTHOR: Amr #+AUTHOR: Amr
#+FILETAGS: :harness:protocol: #+FILETAGS: :harness:protocol:
@@ -79,7 +79,7 @@ The ~communication.lisp~ module defines the low-level transport and framing logi
** Structural Validation (communication-validator.lisp) ** Structural Validation (communication-validator.lisp)
The validator ensures that incoming messages adhere to the strict property list schema of the communication protocol. The validator ensures that incoming messages adhere to the strict property list schema of the communication protocol.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/communication-validator.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/communication-validator.lisp" (expand-file-name "harness/"))
(in-package :opencortex) (in-package :opencortex)
(defun validate-communication-protocol-schema (msg) (defun validate-communication-protocol-schema (msg)
@@ -154,7 +154,7 @@ Frames a message with a hex length prefix and ensures all data is serializable.
These tests verify the communication protocol functions. Run with: These tests verify the communication protocol functions. Run with:
~(fiveam:run! 'communication-protocol-suite)~ ~(fiveam:run! 'communication-protocol-suite)~
#+begin_src lisp :tangle (expand-file-name "communication-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/communication-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(defpackage :opencortex-communication-tests (defpackage :opencortex-communication-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:communication-protocol-suite)) (:export #:communication-protocol-suite))

8
harness/context.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/context.lisp" (expand-file-name "")) #+PROPERTY: header-args:lisp :tangle (expand-file-name "harness/context.lisp" (expand-file-name "harness/"))
#+TITLE: Peripheral Vision (context.lisp) #+TITLE: Peripheral Vision (context.lisp)
#+AUTHOR: Amr #+AUTHOR: Amr
#+FILETAGS: :harness:context: #+FILETAGS: :harness:context:
@@ -217,7 +217,7 @@ The primary entry point for context generation. This function identifies active
Following the Engineering Standards, the peripheral vision extraction and rendering logic must be empirically verified. Following the Engineering Standards, the peripheral vision extraction and rendering logic must be empirically verified.
** Test Suite Context ** Test Suite Context
#+begin_src lisp :tangle (expand-file-name "peripheral-vision-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/peripheral-vision-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(defpackage :opencortex-peripheral-vision-tests (defpackage :opencortex-peripheral-vision-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:vision-suite)) (:export #:vision-suite))
@@ -231,7 +231,7 @@ Following the Engineering Standards, the peripheral vision extraction and render
** Foveal Rendering Test ** Foveal Rendering Test
Verify that the foveal target is rendered with content, while siblings are skeletal. Verify that the foveal target is rendered with content, while siblings are skeletal.
#+begin_src lisp :tangle (expand-file-name "peripheral-vision-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/peripheral-vision-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(test test-foveal-rendering (test test-foveal-rendering
"Verify that the foveal target is rendered with content, while siblings are skeletal." "Verify that the foveal target is rendered with content, while siblings are skeletal."
(clrhash opencortex::*memory*) (clrhash opencortex::*memory*)
@@ -251,7 +251,7 @@ Verify that the foveal target is rendered with content, while siblings are skele
** Awareness Budget Test ** Awareness Budget Test
Verify that context-assemble-global-awareness handles multiple projects correctly. Verify that context-assemble-global-awareness handles multiple projects correctly.
#+begin_src lisp :tangle (expand-file-name "peripheral-vision-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/peripheral-vision-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(test test-awareness-budget (test test-awareness-budget
"Verify that context-assemble-global-awareness handles multiple projects." "Verify that context-assemble-global-awareness handles multiple projects."
(clrhash opencortex::*memory*) (clrhash opencortex::*memory*)

26
harness/doctor.org
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@@ -23,26 +23,26 @@ Common Lisp's `getenv` is strictly typed in SBCL. The Doctor must ensure that mi
* Phase B: Protocol (Success Criteria) * Phase B: Protocol (Success Criteria)
** Package Context ** Package Context
#+begin_src lisp :tangle (expand-file-name "doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(defpackage :opencortex-doctor-tests (defpackage :opencortex-doctor-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:doctor-suite)) (:export #:doctor-suite))
#+end_src #+end_src
#+begin_src lisp :tangle (expand-file-name "doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(in-package :opencortex-doctor-tests) (in-package :opencortex-doctor-tests)
#+end_src #+end_src
#+begin_src lisp :tangle (expand-file-name "doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(def-suite doctor-suite :description "Verification of the System Doctor diagnostic logic") (def-suite doctor-suite :description "Verification of the System Doctor diagnostic logic")
#+end_src #+end_src
#+begin_src lisp :tangle (expand-file-name "doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(in-suite doctor-suite) (in-suite doctor-suite)
#+end_src #+end_src
** Dependency Tests ** Dependency Tests
#+begin_src lisp :tangle (expand-file-name "doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(test test-dependency-check-fail (test test-dependency-check-fail
"Verify that missing binaries are correctly identified as failures." "Verify that missing binaries are correctly identified as failures."
(let ((opencortex::*doctor-required-binaries* '("non-existent-binary-123"))) (let ((opencortex::*doctor-required-binaries* '("non-existent-binary-123")))
@@ -50,7 +50,7 @@ Common Lisp's `getenv` is strictly typed in SBCL. The Doctor must ensure that mi
#+end_src #+end_src
** Environment Tests ** Environment Tests
#+begin_src lisp :tangle (expand-file-name "doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/doctor-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(test test-env-validation-fail (test test-env-validation-fail
"Verify that an invalid MEMEX_DIR triggers a critical failure." "Verify that an invalid MEMEX_DIR triggers a critical failure."
(let ((old-m (getenv "MEMEX_DIR")) (let ((old-m (getenv "MEMEX_DIR"))
@@ -66,18 +66,18 @@ Common Lisp's `getenv` is strictly typed in SBCL. The Doctor must ensure that mi
* Phase C: Implementation (Build) * Phase C: Implementation (Build)
** Package Context ** Package Context
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/doctor.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/doctor.lisp" (expand-file-name "harness/"))
(in-package :opencortex) (in-package :opencortex)
#+end_src #+end_src
** Global Configuration ** Global Configuration
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/doctor.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/doctor.lisp" (expand-file-name "harness/"))
(defvar *doctor-required-binaries* '("sbcl" "emacs" "git" "socat" "nc") (defvar *doctor-required-binaries* '("sbcl" "emacs" "git" "socat" "nc")
"List of external binaries required for full system operation.") "List of external binaries required for full system operation.")
#+end_src #+end_src
** Dependency Verification ** Dependency Verification
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/doctor.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/doctor.lisp" (expand-file-name "harness/"))
(defun doctor-check-dependencies () (defun doctor-check-dependencies ()
"Verifies that required external binaries are available in the PATH via a shell probe." "Verifies that required external binaries are available in the PATH via a shell probe."
(let ((all-ok t)) (let ((all-ok t))
@@ -95,7 +95,7 @@ Common Lisp's `getenv` is strictly typed in SBCL. The Doctor must ensure that mi
#+end_src #+end_src
** Environment & XDG Validation ** Environment & XDG Validation
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/doctor.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/doctor.lisp" (expand-file-name "harness/"))
(defun doctor-check-env () (defun doctor-check-env ()
"Validates XDG directories and environment configuration against the POSIX standard." "Validates XDG directories and environment configuration against the POSIX standard."
(harness-log "DOCTOR: Checking XDG environment...") (harness-log "DOCTOR: Checking XDG environment...")
@@ -124,7 +124,7 @@ Common Lisp's `getenv` is strictly typed in SBCL. The Doctor must ensure that mi
#+end_src #+end_src
** LLM Connectivity ** LLM Connectivity
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/doctor.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/doctor.lisp" (expand-file-name "harness/"))
(defun doctor-check-llm () (defun doctor-check-llm ()
"Tests connectivity to primary LLM providers. Non-critical fallback allowed." "Tests connectivity to primary LLM providers. Non-critical fallback allowed."
(harness-log "DOCTOR: Checking LLM connectivity...") (harness-log "DOCTOR: Checking LLM connectivity...")
@@ -139,7 +139,7 @@ Common Lisp's `getenv` is strictly typed in SBCL. The Doctor must ensure that mi
#+end_src #+end_src
** Orchestration ** Orchestration
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/doctor.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/doctor.lisp" (expand-file-name "harness/"))
(defun doctor-run-all () (defun doctor-run-all ()
"Executes the full diagnostic suite and returns T if system is healthy." "Executes the full diagnostic suite and returns T if system is healthy."
(harness-log "==================================================") (harness-log "==================================================")
@@ -159,7 +159,7 @@ Common Lisp's `getenv` is strictly typed in SBCL. The Doctor must ensure that mi
#+end_src #+end_src
** CLI Entry Point ** CLI Entry Point
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/doctor.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/doctor.lisp" (expand-file-name "harness/"))
(defun doctor-main () (defun doctor-main ()
"Entry point for the 'doctor' CLI command." "Entry point for the 'doctor' CLI command."
(if (doctor-run-all) (if (doctor-run-all)

4
harness/loop.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/loop.lisp" (expand-file-name "")) #+PROPERTY: header-args:lisp :tangle (expand-file-name "harness/loop.lisp" (expand-file-name "harness/"))
#+TITLE: The Metabolic Loop (loop.lisp) #+TITLE: The Metabolic Loop (loop.lisp)
#+AUTHOR: Amr #+AUTHOR: Amr
#+FILETAGS: :harness:loop: #+FILETAGS: :harness:loop:
@@ -324,7 +324,7 @@ The main function orchestrates system startup:
These tests verify the metabolic loop and error recovery. Run with: These tests verify the metabolic loop and error recovery. Run with:
~(fiveam:run! 'immune-suite)~ ~(fiveam:run! 'immune-suite)~
#+begin_src lisp :tangle (expand-file-name "immune-system-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/immune-system-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(defpackage :opencortex-immune-system-tests (defpackage :opencortex-immune-system-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:immune-suite)) (:export #:immune-suite))

8
harness/manifest.org
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@@ -9,7 +9,7 @@ The *System Manifest* defines the structural components of the OpenCortex. It se
* Implementation * Implementation
** Main System ** Main System
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/opencortex.asd") #+begin_src lisp :tangle (expand-file-name "opencortex.asd")
(defsystem :opencortex (defsystem :opencortex
:name "opencortex" :name "opencortex"
:author "Amr Gharbeia" :author "Amr Gharbeia"
@@ -31,7 +31,7 @@ The *System Manifest* defines the structural components of the OpenCortex. It se
#+end_src #+end_src
** Test System ** Test System
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/opencortex.asd") #+begin_src lisp :tangle (expand-file-name "opencortex.asd")
(defsystem :opencortex/tests (defsystem :opencortex/tests
:depends-on (:opencortex :fiveam) :depends-on (:opencortex :fiveam)
:components ((:file "tests/pipeline-act-tests") :components ((:file "tests/pipeline-act-tests")
@@ -55,14 +55,14 @@ The *System Manifest* defines the structural components of the OpenCortex. It se
#+end_src #+end_src
** TUI System ** TUI System
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/opencortex.asd") #+begin_src lisp :tangle (expand-file-name "opencortex.asd")
(defsystem :opencortex/tui (defsystem :opencortex/tui
:depends-on (:opencortex :croatoan :usocket :bordeaux-threads) :depends-on (:opencortex :croatoan :usocket :bordeaux-threads)
:components ((:file "harness/tui-client"))) :components ((:file "harness/tui-client")))
#+end_src #+end_src
** Test Orchestrator ** Test Orchestrator
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/run-all-tests.lisp") #+begin_src lisp :tangle (expand-file-name "run-all-tests.lisp")
(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname))) (load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))
(let ((oc-dir (or (getenv "OC_DATA_DIR") (let ((oc-dir (or (getenv "OC_DATA_DIR")

28
harness/memory.org
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@@ -31,14 +31,14 @@ flowchart TD
#+end_src #+end_src
** Package Context ** Package Context
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(in-package :opencortex) (in-package :opencortex)
#+end_src #+end_src
** The Object Repository ** The Object Repository
The `*memory*` is the global hash table that holds every Org element by its unique ID. This is the "live RAM" of the agent's memory. The `*memory*` is the global hash table that holds every Org element by its unique ID. This is the "live RAM" of the agent's memory.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defvar *memory* (make-hash-table :test 'equal)) (defvar *memory* (make-hash-table :test 'equal))
(defvar *history-store* (make-hash-table :test 'equal) (defvar *history-store* (make-hash-table :test 'equal)
@@ -48,7 +48,7 @@ The `*memory*` is the global hash table that holds every Org element by its uniq
** The Data Structure (org-object) ** The Data Structure (org-object)
Every element in the Memex (headlines, paragraphs, etc.) is represented by an `org-object` structure. It contains both semantic metadata (attributes, content) and structural metadata (parent/child pointers, Merkle hashes). Every element in the Memex (headlines, paragraphs, etc.) is represented by an `org-object` structure. It contains both semantic metadata (attributes, content) and structural metadata (parent/child pointers, Merkle hashes).
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defstruct org-object (defstruct org-object
id type attributes content vector parent-id children version last-sync hash) id type attributes content vector parent-id children version last-sync hash)
@@ -60,7 +60,7 @@ Every element in the Memex (headlines, paragraphs, etc.) is represented by an `o
** Merkle Tree Integrity (compute-merkle-hash) ** Merkle Tree Integrity (compute-merkle-hash)
The `compute-merkle-hash` function ensures the cryptographic integrity of the knowledge graph. A node's hash depends on its own properties and the hashes of all its children. This creates a recursive fingerprint where any change to a single note propagates up to the root hash. The `compute-merkle-hash` function ensures the cryptographic integrity of the knowledge graph. A node's hash depends on its own properties and the hashes of all its children. This creates a recursive fingerprint where any change to a single note propagates up to the root hash.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defun compute-merkle-hash (id type attributes content child-hashes) (defun compute-merkle-hash (id type attributes content child-hashes)
"Computes a SHA-256 Merkle hash for a node based on its core properties and children's hashes." "Computes a SHA-256 Merkle hash for a node based on its core properties and children's hashes."
(let* ((alist (loop for (k v) on attributes by #'cddr collect (cons k v))) (let* ((alist (loop for (k v) on attributes by #'cddr collect (cons k v)))
@@ -77,7 +77,7 @@ The `compute-merkle-hash` function ensures the cryptographic integrity of the kn
** Ingesting the AST (ingest-ast) ** Ingesting the AST (ingest-ast)
The `ingest-ast` function is the primary bridge between the external world (Emacs/JSON) and the internal Lisp machine. It recursively parses an Org-mode Abstract Syntax Tree (AST) into `org-object` structures and registers them in the store. The `ingest-ast` function is the primary bridge between the external world (Emacs/JSON) and the internal Lisp machine. It recursively parses an Org-mode Abstract Syntax Tree (AST) into `org-object` structures and registers them in the store.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defun ingest-ast (ast &optional parent-id) (defun ingest-ast (ast &optional parent-id)
"Parses an Org AST into the recursive Lisp Memory with Merkle hashing." "Parses an Org AST into the recursive Lisp Memory with Merkle hashing."
(let* ((type (getf ast :type)) (let* ((type (getf ast :type))
@@ -116,7 +116,7 @@ The `ingest-ast` function is the primary bridge between the external world (Emac
** Memory Snapshots (snapshot-memory) ** Memory Snapshots (snapshot-memory)
Because objects are stored immutably in the `*history-store*`, a snapshot is a lightweight shallow copy of the active `*memory*` pointers. The system maintains a rolling buffer of 20 snapshots, allowing for near-instant, zero-cost rollback. Because objects are stored immutably in the `*history-store*`, a snapshot is a lightweight shallow copy of the active `*memory*` pointers. The system maintains a rolling buffer of 20 snapshots, allowing for near-instant, zero-cost rollback.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defvar *object-store-snapshots* nil) (defvar *object-store-snapshots* nil)
(defun copy-hash-table (hash-table) (defun copy-hash-table (hash-table)
@@ -143,7 +143,7 @@ Because objects are stored immutably in the `*history-store*`, a snapshot is a l
** Memory Rollback (rollback-memory) ** Memory Rollback (rollback-memory)
Restores the state of the Memex from one of the previous snapshots. Restores the state of the Memex from one of the previous snapshots.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defun rollback-memory (&optional (index 0)) (defun rollback-memory (&optional (index 0))
"Restores the Memory to a previously captured snapshot using immutable history pointers." "Restores the Memory to a previously captured snapshot using immutable history pointers."
(let ((snapshot (nth index *object-store-snapshots*))) (let ((snapshot (nth index *object-store-snapshots*)))
@@ -156,7 +156,7 @@ Restores the state of the Memex from one of the previous snapshots.
** Disk Persistence (save-memory / load-memory) ** Disk Persistence (save-memory / load-memory)
Essential for surviving crashes. Saves the in-memory hash tables to disk and loads them back on restart. Essential for surviving crashes. Saves the in-memory hash tables to disk and loads them back on restart.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defvar *memory-snapshot-path* nil (defvar *memory-snapshot-path* nil
"Path to the memory snapshot file. Set from MEMORY_SNAPSHOT_PATH env or default.") "Path to the memory snapshot file. Set from MEMORY_SNAPSHOT_PATH env or default.")
@@ -209,7 +209,7 @@ Reconstitutes alists into hash tables."
** Semantic Search (get-embedding, semantic-search) ** Semantic Search (get-embedding, semantic-search)
Support for vector embeddings via Ollama and semantic search with cosine similarity. Support for vector embeddings via Ollama and semantic search with cosine similarity.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defvar *embedding-cache* (make-hash-table :test 'equal) (defvar *embedding-cache* (make-hash-table :test 'equal)
"Cache for embeddings to avoid redundant API calls.") "Cache for embeddings to avoid redundant API calls.")
@@ -258,7 +258,7 @@ Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similar
#+end_src #+end_src
** Cognitive Tool: Semantic Search ** Cognitive Tool: Semantic Search
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(def-cognitive-tool :semantic-search (def-cognitive-tool :semantic-search
"Searches memory for objects semantically similar to a query." "Searches memory for objects semantically similar to a query."
((:query :type :string :description "The search query.") ((:query :type :string :description "The search query.")
@@ -271,7 +271,7 @@ Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similar
#+end_src #+end_src
** Cognitive Tool: Generate Embeddings ** Cognitive Tool: Generate Embeddings
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(def-cognitive-tool :generate-embeddings (def-cognitive-tool :generate-embeddings
"Generates vector embeddings for given text via the configured embedding backend (Ollama)." "Generates vector embeddings for given text via the configured embedding backend (Ollama)."
((:texts :type :list :description "List of text strings to embed.")) ((:texts :type :list :description "List of text strings to embed."))
@@ -294,7 +294,7 @@ Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similar
** Lookup Utilities ** Lookup Utilities
Basic functions for retrieving objects by ID or type. Basic functions for retrieving objects by ID or type.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defun org-id-new () (defun org-id-new ()
"Generates a new UUID string for Org-mode identification." "Generates a new UUID string for Org-mode identification."
(string-downcase (format nil "~a" (uuid:make-v4-uuid)))) (string-downcase (format nil "~a" (uuid:make-v4-uuid))))
@@ -324,7 +324,7 @@ Basic functions for retrieving objects by ID or type.
** Structural Helpers ** Structural Helpers
Utility functions for AST traversal and path resolution. Utility functions for AST traversal and path resolution.
#+begin_src lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/memory.lisp" (expand-file-name "")) #+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
(defun find-headline-missing-id (ast) (defun find-headline-missing-id (ast)
"Traverses an AST to find headlines that lack an :ID: property." "Traverses an AST to find headlines that lack an :ID: property."
(when (listp ast) (when (listp ast)
@@ -339,7 +339,7 @@ Utility functions for AST traversal and path resolution.
* Test Suite * Test Suite
#+begin_src lisp :tangle (expand-file-name "memory-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/memory-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(defpackage :opencortex-memory-tests (defpackage :opencortex-memory-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:memory-suite)) (:export #:memory-suite))

2
harness/package.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/package.lisp") #+PROPERTY: header-args:lisp :tangle (expand-file-name "harness/package.lisp")
#+TITLE: System Interface (package.lisp) #+TITLE: System Interface (package.lisp)
#+AUTHOR: Amr #+AUTHOR: Amr
#+FILETAGS: :harness:interface: #+FILETAGS: :harness:interface:

4
harness/perceive.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/perceive.lisp" (expand-file-name "")) #+PROPERTY: header-args:lisp :tangle (expand-file-name "harness/perceive.lisp" (expand-file-name "harness/"))
#+TITLE: Stage 1: Perceive (perceive.lisp) #+TITLE: Stage 1: Perceive (perceive.lisp)
#+AUTHOR: Amr #+AUTHOR: Amr
#+FILETAGS: :harness:perceive: #+FILETAGS: :harness:perceive:
@@ -227,7 +227,7 @@ Other sensors (heartbeats, interrupts) are processed synchronously to maintain o
These tests verify the Perceive pipeline. Run with: These tests verify the Perceive pipeline. Run with:
~(fiveam:run! 'pipeline-perceive-suite)~ ~(fiveam:run! 'pipeline-perceive-suite)~
#+begin_src lisp :tangle (expand-file-name "pipeline-perceive-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/pipeline-perceive-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(defpackage :opencortex-pipeline-perceive-tests (defpackage :opencortex-pipeline-perceive-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:pipeline-perceive-suite)) (:export #:pipeline-perceive-suite))

4
harness/reason.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (concat (getenv "INSTALL_DIR") "/harness/reason.lisp" (expand-file-name "")) #+PROPERTY: header-args:lisp :tangle (expand-file-name "harness/reason.lisp" (expand-file-name "harness/"))
#+TITLE: Stage 2: Reason (reason.lisp) #+TITLE: Stage 2: Reason (reason.lisp)
#+AUTHOR: Amr #+AUTHOR: Amr
#+FILETAGS: :harness:reason: #+FILETAGS: :harness:reason:
@@ -472,7 +472,7 @@ The deterministic engine runs all registered skills' verification functions. Thi
These tests verify the Reason (cognitive) pipeline. Run with: These tests verify the Reason (cognitive) pipeline. Run with:
~(fiveam:run! 'pipeline-reason-suite)~ ~(fiveam:run! 'pipeline-reason-suite)~
#+begin_src lisp :tangle (expand-file-name "pipeline-reason-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests")) #+begin_src lisp :tangle (expand-file-name "harness/pipeline-reason-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
(defpackage :opencortex-pipeline-reason-tests (defpackage :opencortex-pipeline-reason-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:pipeline-reason-suite)) (:export #:pipeline-reason-suite))

2
harness/setup.org
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@@ -23,7 +23,7 @@ To maintain sovereignty, the harness must remain a "dumb" bus. It should not kno
** The Installer Script (opencortex.sh) ** The Installer Script (opencortex.sh)
The shell script is the primary entry point. It handles the initial git clone, dependency installation, and literate tangle. The shell script is the primary entry point. It handles the initial git clone, dependency installation, and literate tangle.
#+begin_src bash :tangle (concat (getenv "INSTALL_DIR") "/harness/../opencortex.sh") #+begin_src bash :tangle (expand-file-name "harness/../opencortex.sh")
#!/bin/bash #!/bin/bash
# (The content here is a duplicate of the main opencortex.sh for literate consistency) # (The content here is a duplicate of the main opencortex.sh for literate consistency)
# [Note: Implementation is already verified in the top-level script] # [Note: Implementation is already verified in the top-level script]

2
harness/skills.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (expand-file-name "skills.lisp") #+PROPERTY: header-args:lisp :tangle (expand-file-name "harness/skills.lisp")
#+TITLE: The Skill Engine (skills.lisp) #+TITLE: The Skill Engine (skills.lisp)
#+AUTHOR: Amr #+AUTHOR: Amr
#+FILETAGS: :harness:skills: #+FILETAGS: :harness:skills:

10
harness/tui-client.org
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@@ -22,26 +22,26 @@ A simple MVP console is insufficient for a Lisp Machine. To reach v0.2.0, the TU
* Phase B: Protocol (Success Criteria) * Phase B: Protocol (Success Criteria)
** Test Suite Context ** Test Suite Context
#+begin_src lisp :tangle ((concat (getenv "INSTALL_DIR") "/tests/tui-tests.lisp")) #+begin_src lisp :tangle ((expand-file-name "tui-tests.lisp"))
(defpackage :opencortex-tui-tests (defpackage :opencortex-tui-tests
(:use :cl :fiveam :opencortex) (:use :cl :fiveam :opencortex)
(:export #:tui-suite)) (:export #:tui-suite))
#+end_src #+end_src
#+begin_src lisp :tangle ((concat (getenv "INSTALL_DIR") "/tests/tui-tests.lisp")) #+begin_src lisp :tangle ((expand-file-name "tui-tests.lisp"))
(in-package :opencortex-tui-tests) (in-package :opencortex-tui-tests)
#+end_src #+end_src
#+begin_src lisp :tangle ((concat (getenv "INSTALL_DIR") "/tests/tui-tests.lisp")) #+begin_src lisp :tangle ((expand-file-name "tui-tests.lisp"))
(def-suite tui-suite :description "Verification of the TUI parsing and styling logic") (def-suite tui-suite :description "Verification of the TUI parsing and styling logic")
#+end_src #+end_src
#+begin_src lisp :tangle ((concat (getenv "INSTALL_DIR") "/tests/tui-tests.lisp")) #+begin_src lisp :tangle ((expand-file-name "tui-tests.lisp"))
(in-suite tui-suite) (in-suite tui-suite)
#+end_src #+end_src
** Command Parsing Tests ** Command Parsing Tests
#+begin_src lisp :tangle ((concat (getenv "INSTALL_DIR") "/tests/tui-tests.lisp")) #+begin_src lisp :tangle ((expand-file-name "tui-tests.lisp"))
(test test-tui-connection-drop (test test-tui-connection-drop
"Tier 2 Chaos: Verify that handle-return degrades gracefully when the daemon connection is lost." "Tier 2 Chaos: Verify that handle-return degrades gracefully when the daemon connection is lost."
(let ((opencortex.tui::*incoming-msgs* nil) (let ((opencortex.tui::*incoming-msgs* nil)