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fix(chaos): use robust (or INSTALL_DIR buffer-dir) for tangle paths

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Amr Gharbeia
2026-04-28 17:55:08 -04:00
parent 635db05d17
commit d6a7e83de4
35 changed files with 143 additions and 143 deletions
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harness/memory.org
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@@ -31,14 +31,14 @@ flowchart TD
#+end_src
** Package Context
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(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 (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(defvar *memory* (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)
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 (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(defstruct org-object
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)
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 (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(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)))
@@ -77,7 +77,7 @@ 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 (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(defun ingest-ast (ast &optional parent-id)
"Parses an Org AST into the recursive Lisp Memory with Merkle hashing."
(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)
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 (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(defvar *object-store-snapshots* nil)
(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)
Restores the state of the Memex from one of the previous snapshots.
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(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*)))
@@ -156,7 +156,7 @@ 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 (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(defvar *memory-snapshot-path* nil
"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)
Support for vector embeddings via Ollama and semantic search with cosine similarity.
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(defvar *embedding-cache* (make-hash-table :test 'equal)
"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
** Cognitive Tool: Semantic Search
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(def-cognitive-tool :semantic-search
"Searches memory for objects semantically similar to a 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
** Cognitive Tool: Generate Embeddings
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(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."))
@@ -294,7 +294,7 @@ Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similar
** Lookup Utilities
Basic functions for retrieving objects by ID or type.
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(defun org-id-new ()
"Generates a new UUID string for Org-mode identification."
(string-downcase (format nil "~a" (uuid:make-v4-uuid))))
@@ -324,7 +324,7 @@ Basic functions for retrieving objects by ID or type.
** Structural Helpers
Utility functions for AST traversal and path resolution.
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/harness"))
#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
(defun find-headline-missing-id (ast)
"Traverses an AST to find headlines that lack an :ID: property."
(when (listp ast)