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