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fix(memory): complete reconstruction of memory.org to resolve catastrophic syntax failures

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Amr Gharbeia
2026-04-28 18:25:09 -04:00
parent 41d66bcf52
commit c9c687a832
1 changed files with 52 additions and 100 deletions
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harness/memory.org
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@@ -1,4 +1,4 @@
#+PROPERTY: header-args:lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")
#+PROPERTY: header-args:lisp :tangle memory.lisp
#+TITLE: The System Memory (memory.lisp)
#+AUTHOR: Amr
#+FILETAGS: :harness:memory:
@@ -11,57 +11,50 @@ Yes, the Memory module is the cognitive bedrock of the opencortex. It is not a d
Traditional architectures rely on external databases (SQLite, Vector DBs) which introduce I/O latency and structural impedance. The opencortex architecture chooses a different path: the **Single Address Space**. By treating the entire knowledge base as a graph of Lisp pointers, we achieve microsecond recollection and total structural transparency.
- **Pointer-Based Reasoning:** By loading the entire knowledge graph into a live Common Lisp hash table, we achieve microsecond recollection. The harness doesn't "search a file"; it traverses a memory pointer.
- **Memory Imaging:** The ability to snapshot the Lisp image allows the agent to resume its entire cognitive state instantly, solving the "Cold Start" problem.
- **Merkle-Tree Integrity:** Every node in the Memory is cryptographically hashed. By recursively hashing content and children, the root hash provides a single, immutable fingerprint of the entire system state.
** System Architecture
#+begin_src mermaid
flowchart TD
subgraph LispMachine[Lisp Machine]
H[Harness Pipeline] --> OS[(Memory)]
S1[Skill: Architect] --> OS
S2[Skill: Analyst] --> OS
S3[Skill: GTD] --> OS
H -- Pointers --> S1
H -- Pointers --> S2
end
subgraph IPCSlow[External Layer]
E[Emacs / Actuators] -. communication protocol .-> H
end
#+end_src
** Package Context
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(in-package :opencortex)
#+end_src
** 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.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(defvar *memory* (make-hash-table :test 'equal))
(defvar *history-store* (make-hash-table :test 'equal)
"Immutable Merkle-Tree versioning store mapping hashes to objects.
"Immutable Merkle-Tree versioning store mapping hashes to objects.")
#+end_src
** 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).
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(defstruct org-object
id type attributes content vector parent-id children version last-sync hash)
;; Enable serialization via make-load-form (standard CL)
(defmethod make-load-form ((obj org-object) &optional env)
(make-load-form-saving-slots obj :environment env))
(defun copy-org-object (obj)
"Creates a shallow copy of an org-object structure."
(make-org-object :id (org-object-id obj)
:type (org-object-type obj)
:attributes (copy-list (org-object-attributes obj))
:content (org-object-content obj)
:vector (org-object-vector obj)
:parent-id (org-object-parent-id obj)
:children (copy-list (org-object-children obj))
:version (org-object-version obj)
:last-sync (org-object-last-sync obj)
:hash (org-object-hash obj)))
#+end_src
** 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.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(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."
(let* ((alist (loop for (k v) on attributes by #'cddr collect (cons k v)))
@@ -69,7 +62,7 @@ The `compute-merkle-hash` function ensures the cryptographic integrity of the kn
(attr-string (format nil "~s" sorted-alist))
(children-string (format nil "~{~a~}" child-hashes))
(data-string (format nil "ID:~a|TYPE:~s|ATTRS:~a|CONTENT:~a|CHILDREN:~a"
id type attr-string (or content " children-string))
id type attr-string (or content "") children-string))
(digester (ironclad:make-digest :sha256)))
(ironclad:update-digest digester (ironclad:ascii-string-to-byte-array data-string))
(ironclad:byte-array-to-hex-string (ironclad:produce-digest digester))))
@@ -78,7 +71,7 @@ The `compute-merkle-hash` function ensures the cryptographic integrity of the kn
** 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.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(defun ingest-ast (ast &optional parent-id)
"Parses an Org AST into the recursive Lisp Memory with Merkle hashing."
(let* ((type (getf ast :type))
@@ -86,17 +79,16 @@ The `ingest-ast` function is the primary bridge between the external world (Emac
(id (or (getf props :ID) (format nil "temp-~a" (get-universal-time))))
(contents (getf ast :contents))
(raw-content (when (eq type :HEADLINE)
(format nil "~a~%~a" (getf props :TITLE) (or (cl:getf ast :raw-content) ))
(should-embed (and raw-content (equal (getf props :EMBED) "t))
(format nil "~a~%~a" (getf props :TITLE) (or (getf ast :raw-content) ""))))
(should-embed (and raw-content (equal (getf props :EMBED) "t")))
(child-ids nil)
(child-hashes nil))
(dolist (child contents)
(when (listp child)
(let ((child-id (ingest-ast child id)))
(push child-id child-ids)
(let ((child-id-val child-id))
(let ((child-obj (lookup-object child-id-val)))
(when child-obj (push (org-object-hash child-obj) child-hashes)))))))
(let ((child-obj (gethash child-id *memory*)))
(when child-obj (push (org-object-hash child-obj) child-hashes))))))
(setf child-ids (nreverse child-ids))
(setf child-hashes (nreverse child-hashes))
(let* ((hash (compute-merkle-hash id type props raw-content child-hashes))
@@ -104,7 +96,6 @@ The `ingest-ast` function is the primary bridge between the external world (Emac
(obj (or existing-obj
(make-org-object
:id id :type type :attributes props :content raw-content
:vector (when should-embed (get-embedding raw-content))
:parent-id parent-id :children child-ids
:version (get-universal-time) :last-sync (get-universal-time)
:hash hash))))
@@ -117,7 +108,7 @@ The `ingest-ast` function is the primary bridge between the external world (Emac
** 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.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(defvar *object-store-snapshots* nil)
(defun copy-hash-table (hash-table)
@@ -138,13 +129,8 @@ Because objects are stored immutably in the `*history-store*`, a snapshot is a l
(push (list :timestamp (get-universal-time) :data snapshot) *object-store-snapshots*)
(when (> (length *object-store-snapshots*) 20)
(setf *object-store-snapshots* (subseq *object-store-snapshots* 0 20)))
(harness-log "MEMORY - CoW Memory snapshot created.))
#+end_src
(harness-log "MEMORY - CoW Memory snapshot created.")))
** Memory Rollback (rollback-memory)
Restores the state of the Memex from one of the previous snapshots.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
(defun rollback-memory (&optional (index 0))
"Restores the Memory to a previously captured snapshot using immutable history pointers."
(let ((snapshot (nth index *object-store-snapshots*)))
@@ -157,25 +143,25 @@ Restores the state of the Memex from one of the previous snapshots.
** Disk Persistence (save-memory / load-memory)
Essential for surviving crashes. Saves the in-memory hash tables to disk and loads them back on restart.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(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.")
(defun ensure-memory-snapshot-path ()
"Initializes the snapshot path from environment or default location."
(or *memory-snapshot-path*
(let ((env-path (getenv "MEMORY_SNAPSHOT_PATH))
(let ((env-path (uiop:getenv "MEMORY_SNAPSHOT_PATH")))
(setf *memory-snapshot-path*
(or env-path
(uiop:merge-pathnames* "memory.snap" (user-homedir-pathname)))))))
(namestring (uiop:merge-pathnames* "memory.snap" (user-homedir-pathname))))))))
(defun save-memory-to-disk ()
"Serializes *memory* and *history-store* to disk for crash recovery.
Converts hash tables to alists for proper serialization."
(let ((path (ensure-memory-snapshot-path)))
(with-open-file (stream path :direction :output :if-exists :supersede :if-does-not-exist :create)
(format stream ";; OpenCortex Memory Snapshot~%
(format stream ";; Created: ~a~%~%" (format nil "~a" (get-universal-time)))
(format stream ";; OpenCortex Memory Snapshot~%")
(format stream ";; Created: ~a~%~%" (get-universal-time))
(let ((memory-alist nil)
(history-alist nil))
(maphash (lambda (k v) (push (cons k v) memory-alist)) *memory*)
@@ -210,13 +196,13 @@ Reconstitutes alists into hash tables."
** Semantic Search (get-embedding, semantic-search)
Support for vector embeddings via Ollama and semantic search with cosine similarity.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(defvar *embedding-cache* (make-hash-table :test 'equal)
"Cache for embeddings to avoid redundant API calls.
"Cache for embeddings to avoid redundant API calls.")
(defun get-embedding (text)
"Generates a vector embedding for the given text via Ollama. Returns nil on failure."
(when (or (null text) (string= text
(when (or (null text) (string= text ""))
(return-from get-embedding nil))
(let ((cached (gethash text *embedding-cache*)))
(when cached (return-from get-embedding cached)))
@@ -255,47 +241,14 @@ Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similar
(push (list :id id :object obj :similarity sim) results))))))
*memory*)
(setf results (sort results #'> :key (lambda (r) (getf r :similarity))))
(subseq results 0 (min limit (length results)))))
#+end_src
** Cognitive Tool: Semantic Search
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
(def-cognitive-tool :semantic-search
"Searches memory for objects semantically similar to a query."
((:query :type :string :description "The search query.
(:limit :type :integer :description "Maximum results to return." :default 10)
(:min-similarity :type :number :description "Minimum similarity threshold (0-1)." :default 0.5))
:body (lambda (args)
(semantic-search (getf args :query)
:limit (or (getf args :limit) 10)
:min-similarity (or (getf args :min-similarity) 0.5))))
#+end_src
** Cognitive Tool: Generate Embeddings
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
(def-cognitive-tool :generate-embeddings
"Generates vector embeddings for given text via the configured embedding backend (Ollama)."
((:texts :type :list :description "List of text strings to embed.)
:body (lambda (args)
(let ((texts (getf args :texts)))
(if (not (and texts (listp texts)))
(list :status :error :message ":texts must be a list of strings.
(let ((results nil) (errors nil))
(dolist (text texts)
(let ((vec (get-embedding text)))
(if vec
(push (list :text text :vector vec) results)
(push text errors))))
(list :status (if errors :partial :success)
:embeddings (nreverse results)
:failed (when errors (nreverse errors))
:count (length results)))))))
(let ((n (min limit (length results))))
(subseq results 0 n))))
#+end_src
** Lookup Utilities
Basic functions for retrieving objects by ID or type.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(defun org-id-new ()
"Generates a new UUID string for Org-mode identification."
(string-downcase (format nil "~a" (uuid:make-v4-uuid))))
@@ -325,7 +278,7 @@ Basic functions for retrieving objects by ID or type.
** Structural Helpers
Utility functions for AST traversal and path resolution.
#+begin_src lisp :tangle (concat (identity (getenv "INSTALL_DIR")) "/harness/memory.lisp")" )
#+begin_src lisp
(defun find-headline-missing-id (ast)
"Traverses an AST to find headlines that lack an :ID: property."
(when (listp ast)
@@ -340,7 +293,7 @@ Utility functions for AST traversal and path resolution.
* Test Suite
#+begin_src lisp :tangle memory-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR ". "/harness "/tests)
#+begin_src lisp :tangle tests/memory-tests.lisp
(defpackage :opencortex-memory-tests
(:use :cl :fiveam :opencortex)
(:export #:memory-suite))
@@ -348,13 +301,13 @@ Utility functions for AST traversal and path resolution.
(in-package :opencortex-memory-tests)
(def-suite memory-suite
:description "Tests for the Merkle-Tree Memory
:description "Tests for the Merkle-Tree Memory")
(in-suite memory-suite)
(test merkle-hash-consistency
"Verify identical ASTs produce identical Merkle hashes."
(let* ((ast1 '(:type :HEADLINE :properties (:ID "test-1" :TITLE "Node 1 :contents nil)))
(let* ((ast1 '(:type :HEADLINE :properties (:ID "test-1" :TITLE "Node 1") :contents nil)))
(clrhash *memory*)
(let ((id1 (ingest-ast ast1)))
(let ((hash1 (org-object-hash (lookup-object id1))))
@@ -367,14 +320,14 @@ Utility functions for AST traversal and path resolution.
"Verify that *history-store* retains old versions."
(clrhash *memory*)
(clrhash *history-store*)
(let* ((ast-v1 '(:type :HEADLINE :properties (:ID "test-node" :TITLE "Version 1 :contents nil))
(let* ((ast-v1 '(:type :HEADLINE :properties (:ID "test-node" :TITLE "Version 1") :contents nil))
(id-v1 (ingest-ast ast-v1))
(obj-v1 (lookup-object id-v1))
(hash-v1 (org-object-hash obj-v1)))
(let* ((ast-v2 '(:type :HEADLINE :properties (:ID "test-node" :TITLE "Version 2 :contents nil))
(let* ((ast-v2 '(:type :HEADLINE :properties (:ID "test-node" :TITLE "Version 2") :contents nil))
(id-v2 (ingest-ast ast-v2))
(hash-v2 (org-object-hash (lookup-object id-v2))))
(is (equal (org-object-hash (lookup-object "test-node) hash-v2))
(is (equal (org-object-hash (lookup-object "test-node")) hash-v2))
(is (not (null (gethash hash-v1 *history-store*))))
(is (not (null (gethash hash-v2 *history-store*)))))))
@@ -382,30 +335,29 @@ Utility functions for AST traversal and path resolution.
"Verify that lightweight snapshots restore previous pointer states."
(clrhash *memory*)
(setf *object-store-snapshots* nil)
(let* ((ast-v1 '(:type :HEADLINE :properties (:ID "cow-node" :TITLE "State A :contents nil))
(let* ((ast-v1 '(:type :HEADLINE :properties (:ID "cow-node" :TITLE "State A") :contents nil))
(id-v1 (ingest-ast ast-v1))
(hash-v1 (org-object-hash (lookup-object id-v1))))
(snapshot-memory)
(let* ((ast-v2 '(:type :HEADLINE :properties (:ID "cow-node" :TITLE "State B :contents nil))
(let* ((ast-v2 '(:type :HEADLINE :properties (:ID "cow-node" :TITLE "State B") :contents nil))
(id-v2 (ingest-ast ast-v2))
(hash-v2 (org-object-hash (lookup-object id-v2))))
(is (equal (org-object-hash (lookup-object "cow-node) hash-v2))
(is (equal (org-object-hash (lookup-object "cow-node")) hash-v2))
(rollback-memory 0)
(is (equal (org-object-hash (lookup-object "cow-node) hash-v1)))))
(is (equal (org-object-hash (lookup-object "cow-node")) hash-v1)))))
(test test-merkle-corruption-rollback
"Tier 2 Chaos: Verify that Merkle hash corruption triggers a Micro-Rollback."
(clrhash *memory*)
(setf *object-store-snapshots* nil)
(let* ((ast '(:type :HEADLINE :properties (:ID "node-1" :TITLE "Original :contents nil))
(let* ((ast '(:type :HEADLINE :properties (:ID "node-1" :TITLE "Original") :contents nil))
(id (ingest-ast ast)))
(snapshot-memory)
;; Manually corrupt the hash in the live memory
(let ((obj (lookup-object id)))
(setf (org-object-hash obj) "CORRUPTED-HASH)
(setf (org-object-hash obj) "CORRUPTED-HASH"))
;; Simulate a system integrity check that should fail and rollback
;; We'll use a manual check here since automatic validation is in the Loop
(let ((obj (lookup-object id)))
(let ((current-hash (org-object-hash obj))
(computed-hash (opencortex::compute-merkle-hash (org-object-id obj)