causantic 0.2.1 → 0.3.0

package/dist/storage/index.js

@@ -6,15 +6,11 @@ export { getDb, closeDb, clearAllData, getDbStats, generateId, getSchemaVersion
 // Chunk store
 export { insertChunk, insertChunks, getChunkById, getChunksByIds, getChunksBySession, getChunksBySessionSlug, getAllChunks, getChunksByCluster, isSessionIngested, deleteChunk, deleteChunks, getSessionIds, getChunkCount, } from './chunk-store.js';
 // Edge store
-export { createEdge, createEdges, getEdgeById, getOutgoingEdges, getIncomingEdges, getWeightedEdges, hasAnyEdges, deleteEdge, deleteEdges, deleteEdgesForChunk, getEdgeCount, getAllEdges, } from './edge-store.js';
+export { createEdge, createEdges, getEdgeById, getOutgoingEdges, getIncomingEdges, getForwardEdges, getBackwardEdges, deleteEdge, deleteEdges, deleteEdgesForChunk, deleteEdgesForSession, getEdgeCount, getAllEdges, } from './edge-store.js';
 // Cluster store
 export { upsertCluster, getClusterById, getAllClusters, getStaleClusters, assignChunkToCluster, assignChunksToClusters, getChunkClusterAssignments, getClusterChunkIds, removeChunkAssignments, clearClusterAssignments, deleteCluster, clearAllClusters, getClusterCount, computeMembershipHash, } from './cluster-store.js';
 // Vector store
 export { vectorStore } from './vector-store.js';
 // Keyword store
 export { KeywordStore } from './keyword-store.js';
-// Decay calculation
-export { calculateDecayWeight, getDeathTime } from './decay.js';
-// Pruner
-export { pruner, initStartupPrune } from './pruner.js';
 //# sourceMappingURL=index.js.map

package/dist/storage/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/storage/index.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,WAAW;AACX,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,YAAY,EAAE,UAAU,EAAE,UAAU,EAAE,gBAAgB,EAAE,MAAM,SAAS,CAAC;AAmBjG,cAAc;AACd,OAAO,EACL,WAAW,EACX,YAAY,EACZ,YAAY,EACZ,cAAc,EACd,kBAAkB,EAClB,sBAAsB,EACtB,YAAY,EACZ,kBAAkB,EAClB,iBAAiB,EACjB,WAAW,EACX,YAAY,EACZ,aAAa,EACb,aAAa,GACd,MAAM,kBAAkB,CAAC;AAE1B,aAAa;AACb,OAAO,EACL,UAAU,EACV,WAAW,EACX,WAAW,EACX,gBAAgB,EAChB,gBAAgB,EAChB,eAAe,EACf,gBAAgB,EAChB,UAAU,EACV,WAAW,EACX,mBAAmB,EACnB,qBAAqB,EACrB,YAAY,EACZ,WAAW,GACZ,MAAM,iBAAiB,CAAC;AAEzB,gBAAgB;AAChB,OAAO,EACL,aAAa,EACb,cAAc,EACd,cAAc,EACd,gBAAgB,EAChB,oBAAoB,EACpB,sBAAsB,EACtB,0BAA0B,EAC1B,kBAAkB,EAClB,sBAAsB,EACtB,uBAAuB,EACvB,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAE5B,eAAe;AACf,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAEhD,gBAAgB;AAChB,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC"}

package/dist/storage/keyword-store.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"keyword-store.d.ts","sourceRoot":"","sources":["../../src/storage/keyword-store.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAC;AAKhC,MAAM,WAAW,mBAAmB;IAClC,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;CACf;AA6BD,qBAAa,YAAY;IACX,OAAO,CAAC,EAAE,CAAC;gBAAH,EAAE,CAAC,EAAE,UAAU,CAAC,OAAO,KAAK,CAAC,YAAA;IAEjD,OAAO,CAAC,WAAW;IAInB;;OAEG;IACH,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,mBAAmB,EAAE;IA2B3D;;OAEG;IACH,eAAe,CACb,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE,EAC3B,KAAK,EAAE,MAAM,GACZ,mBAAmB,EAAE;CA8BzB"}
+{"version":3,"file":"keyword-store.d.ts","sourceRoot":"","sources":["../../src/storage/keyword-store.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAC;AAKhC,MAAM,WAAW,mBAAmB;IAClC,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;CACf;AA6BD,qBAAa,YAAY;IACX,OAAO,CAAC,EAAE,CAAC;gBAAH,EAAE,CAAC,EAAE,UAAU,CAAC,OAAO,KAAK,CAAC,YAAA;IAEjD,OAAO,CAAC,WAAW;IAInB;;OAEG;IACH,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,mBAAmB,EAAE;IA+B3D;;OAEG;IACH,eAAe,CACb,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE,EAC3B,KAAK,EAAE,MAAM,GACZ,mBAAmB,EAAE;CAkCzB"}

package/dist/storage/keyword-store.js

@@ -30,7 +30,7 @@ function sanitizeQuery(query) {
     const terms = sanitized.split(/\s+/).filter(Boolean);
     if (terms.length === 0)
         return '';
-    return terms.map(t => `"${t}"`).join(' ');
+    return terms.map((t) => `"${t}"`).join(' ');
 }
 export class KeywordStore {
     db;
@@ -49,16 +49,18 @@ export class KeywordStore {
             return [];
         const db = this.getDatabase();
         try {
-            const rows = db.prepare(`
+            const rows = db
+                .prepare(`
         SELECT chunks.id, bm25(chunks_fts) as score
         FROM chunks_fts
         JOIN chunks ON chunks.rowid = chunks_fts.rowid
         WHERE chunks_fts MATCH ?
         ORDER BY bm25(chunks_fts)
         LIMIT ?
-      `).all(sanitized, limit);
+      `)
+                .all(sanitized, limit);
             // bm25() returns negative scores (lower = better match), negate for conventional scoring
-            return rows.map(r => ({
+            return rows.map((r) => ({
                 id: r.id,
                 score: -r.score,
             }));
@@ -81,7 +83,8 @@ export class KeywordStore {
             return [];
         const placeholders = projectList.map(() => '?').join(',');
         try {
-            const rows = db.prepare(`
+            const rows = db
+                .prepare(`
         SELECT chunks.id, bm25(chunks_fts) as score
         FROM chunks_fts
         JOIN chunks ON chunks.rowid = chunks_fts.rowid
@@ -89,8 +92,9 @@ export class KeywordStore {
           AND chunks.session_slug IN (${placeholders})
         ORDER BY bm25(chunks_fts)
         LIMIT ?
-      `).all(sanitized, ...projectList, limit);
-            return rows.map(r => ({
+      `)
+                .all(sanitized, ...projectList, limit);
+            return rows.map((r) => ({
                 id: r.id,
                 score: -r.score,
             }));

package/dist/storage/keyword-store.js.map

@@ -1 +1 @@
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+{"version":3,"file":"keyword-store.js","sourceRoot":"","sources":["../../src/storage/keyword-store.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAC;AAChC,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAElD,MAAM,GAAG,GAAG,YAAY,CAAC,eAAe,CAAC,CAAC;AAO1C;;;GAGG;AACH,SAAS,aAAa,CAAC,KAAa;IAClC,IAAI,CAAC,KAAK,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE;QAAE,OAAO,EAAE,CAAC;IAEvC,+CAA+C;IAC/C,MAAM,SAAS,GAAG,KAAK;QACrB,wDAAwD;SACvD,OAAO,CAAC,mBAAmB,EAAE,EAAE,CAAC;QACjC,oEAAoE;QACpE,kDAAkD;SACjD,OAAO,CAAC,gBAAgB,EAAE,GAAG,CAAC;QAC/B,sBAAsB;SACrB,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC;SACpB,IAAI,EAAE,CAAC;IAEV,IAAI,CAAC,SAAS;QAAE,OAAO,EAAE,CAAC;IAE1B,+EAA+E;IAC/E,MAAM,KAAK,GAAG,SAAS,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;IACrD,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAElC,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAC9C,CAAC;AAED,MAAM,OAAO,YAAY;IACH;IAApB,YAAoB,EAA6B;QAA7B,OAAE,GAAF,EAAE,CAA2B;IAAG,CAAC;IAE7C,WAAW;QACjB,OAAO,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE,CAAC;IAC5B,CAAC;IAED;;OAEG;IACH,MAAM,CAAC,KAAa,EAAE,KAAa;QACjC,MAAM,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,CAAC;QACvC,IAAI,CAAC,SAAS;YAAE,OAAO,EAAE,CAAC;QAE1B,MAAM,EAAE,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;QAE9B,IAAI,CAAC;YACH,MAAM,IAAI,GAAG,EAAE;iBACZ,OAAO,CACN;;;;;;;OAOH,CACE;iBACA,GAAG,CAAC,SAAS,EAAE,KAAK,CAAyC,CAAC;YAEjE,yFAAyF;YACzF,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACtB,EAAE,EAAE,CAAC,CAAC,EAAE;gBACR,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK;aAChB,CAAC,CAAC,CAAC;QACN,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,GAAG,CAAC,IAAI,CAAC,uBAAuB,EAAE,EAAE,KAAK,EAAG,KAAe,CAAC,OAAO,EAAE,CAAC,CAAC;YACvE,OAAO,EAAE,CAAC;QACZ,CAAC;IACH,CAAC;IAED;;OAEG;IACH,eAAe,CACb,KAAa,EACb,QAA2B,EAC3B,KAAa;QAEb,MAAM,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,CAAC;QACvC,IAAI,CAAC,SAAS;YAAE,OAAO,EAAE,CAAC;QAE1B,MAAM,EAAE,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;QAC9B,MAAM,WAAW,GAAG,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC;QACpE,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,EAAE,CAAC;QAExC,MAAM,YAAY,GAAG,WAAW,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAE1D,IAAI,CAAC;YACH,MAAM,IAAI,GAAG,EAAE;iBACZ,OAAO,CACN;;;;;wCAK8B,YAAY;;;OAG7C,CACE;iBACA,GAAG,CAAC,SAAS,EAAE,GAAG,WAAW,EAAE,KAAK,CAAyC,CAAC;YAEjF,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACtB,EAAE,EAAE,CAAC,CAAC,EAAE;gBACR,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK;aAChB,CAAC,CAAC,CAAC;QACN,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE,EAAE,KAAK,EAAG,KAAe,CAAC,OAAO,EAAE,CAAC,CAAC;YAClF,OAAO,EAAE,CAAC;QACZ,CAAC;IACH,CAAC;CACF"}

package/dist/storage/migrations.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../../src/storage/migrations.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,QAAQ,MAAM,iCAAiC,CAAC;AAM5D;;GAEG;AACH,wBAAgB,aAAa,CAAC,QAAQ,EAAE,QAAQ,CAAC,QAAQ,GAAG,IAAI,CA2C/D"}
+{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../../src/storage/migrations.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,QAAQ,MAAM,iCAAiC,CAAC;AAM5D;;GAEG;AACH,wBAAgB,aAAa,CAAC,QAAQ,EAAE,QAAQ,CAAC,QAAQ,GAAG,IAAI,CAiD/D"}

package/dist/storage/migrations.js

@@ -51,6 +51,12 @@ export function runMigrations(database) {
     if (currentVersion < 6) {
         migrateToV6(database);
     }
+    if (currentVersion < 7) {
+        migrateToV7(database);
+    }
+    if (currentVersion < 8) {
+        migrateToV8(database);
+    }
 }
 /**
  * Migrate from v1 to v2 (add vector clock support).
@@ -195,7 +201,7 @@ function migrateToV4(database) {
             }
         }
     }
-    const updateChunk = database.prepare('UPDATE chunks SET session_slug = ?, project_path = ? WHERE session_id = ? AND (session_slug = \'\' OR session_slug IS NULL OR project_path IS NULL)');
+    const updateChunk = database.prepare("UPDATE chunks SET session_slug = ?, project_path = ? WHERE session_id = ? AND (session_slug = '' OR session_slug IS NULL OR project_path IS NULL)");
     const backfillChunks = database.transaction(() => {
         for (const [sessionId, info] of sessionProjectMap) {
             if (info.slug) {
@@ -204,7 +210,7 @@ function migrateToV4(database) {
         }
     });
     backfillChunks();
-    const updateCheckpoint = database.prepare('UPDATE ingestion_checkpoints SET project_slug = ? WHERE session_id = ? AND (project_slug = \'\' OR project_slug IS NULL)');
+    const updateCheckpoint = database.prepare("UPDATE ingestion_checkpoints SET project_slug = ? WHERE session_id = ? AND (project_slug = '' OR project_slug IS NULL)");
     const backfillCheckpoints = database.transaction(() => {
         for (const [sessionId, info] of sessionProjectMap) {
             if (info.slug) {
@@ -214,9 +220,13 @@ function migrateToV4(database) {
     });
     backfillCheckpoints();
     try {
-        const emptyClockRows = database.prepare("SELECT id, clock_data FROM vector_clocks WHERE project_slug = ''").all();
+        const emptyClockRows = database
+            .prepare("SELECT id, clock_data FROM vector_clocks WHERE project_slug = ''")
+            .all();
         if (emptyClockRows.length > 0) {
-            const distinctSlugs = database.prepare("SELECT DISTINCT session_slug FROM chunks WHERE session_slug != ''").all();
+            const distinctSlugs = database
+                .prepare("SELECT DISTINCT session_slug FROM chunks WHERE session_slug != ''")
+                .all();
             const insertClock = database.prepare('INSERT OR REPLACE INTO vector_clocks (id, project_slug, clock_data, updated_at) VALUES (?, ?, ?, CURRENT_TIMESTAMP)');
             const rekeyClocks = database.transaction(() => {
                 for (const emptyRow of emptyClockRows) {
@@ -308,6 +318,48 @@ function migrateToV6(database) {
   `);
     database.exec('INSERT OR REPLACE INTO schema_version (version) VALUES (6)');
 }
+/**
+ * Migrate from v6 to v7 (remove vector clock columns and table).
+ */
+function migrateToV7(database) {
+    // Drop vector_clock column from chunks
+    try {
+        database.exec('ALTER TABLE chunks DROP COLUMN vector_clock');
+    }
+    catch {
+        // Column may not exist
+    }
+    // Drop vector_clock column from edges
+    try {
+        database.exec('ALTER TABLE edges DROP COLUMN vector_clock');
+    }
+    catch {
+        // Column may not exist
+    }
+    // Drop vector_clock column from ingestion_checkpoints
+    try {
+        database.exec('ALTER TABLE ingestion_checkpoints DROP COLUMN vector_clock');
+    }
+    catch {
+        // Column may not exist
+    }
+    // Drop vector_clocks table and its index
+    database.exec('DROP INDEX IF EXISTS idx_vector_clocks_project');
+    database.exec('DROP TABLE IF EXISTS vector_clocks');
+    database.exec('INSERT OR REPLACE INTO schema_version (version) VALUES (7)');
+}
+/**
+ * Migrate from v7 to v8 (add chain-walking indices for episodic retrieval).
+ */
+function migrateToV8(database) {
+    database.exec(`
+    CREATE INDEX IF NOT EXISTS idx_edges_source_type ON edges(source_chunk_id, edge_type)
+  `);
+    database.exec(`
+    CREATE INDEX IF NOT EXISTS idx_edges_target_type ON edges(target_chunk_id, edge_type)
+  `);
+    database.exec('INSERT OR REPLACE INTO schema_version (version) VALUES (8)');
+}
 /**
  * Extract sessionId and cwd from first few lines of a JSONL file.
  */

package/dist/storage/migrations.js.map

@@ -1 +1 @@
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package/dist/storage/schema.sql

@@ -14,9 +14,7 @@ CREATE TABLE IF NOT EXISTS chunks (
   tool_use_count INTEGER DEFAULT 0,
   approx_tokens INTEGER DEFAULT 0,
   created_at TEXT DEFAULT CURRENT_TIMESTAMP,
-  -- v2: Vector clock support
   agent_id TEXT,               -- Agent that created this chunk (null = main UI agent)
-  vector_clock TEXT,           -- JSON: {"agentId": tick, ...}
   spawn_depth INTEGER DEFAULT 0, -- Nesting level: 0=main, 1=sub-agent, 2=sub-sub-agent
   project_path TEXT              -- Full cwd path for disambiguation
 );
@@ -33,18 +31,16 @@ CREATE TABLE IF NOT EXISTS clusters (
   refreshed_at TEXT             -- When description was last updated
 );
 
--- Edges with decay
+-- Edges (sequential linked-list, forward-only)
 CREATE TABLE IF NOT EXISTS edges (
   id TEXT PRIMARY KEY,
   source_chunk_id TEXT NOT NULL,
   target_chunk_id TEXT NOT NULL,
-  edge_type TEXT NOT NULL,      -- 'backward' or 'forward'
-  reference_type TEXT,          -- 'file-path', 'code-entity', 'brief', 'debrief', etc.
+  edge_type TEXT NOT NULL,      -- 'forward' (direction inferred at query time)
+  reference_type TEXT,          -- 'within-chain', 'cross-session', 'brief', 'debrief'
   initial_weight REAL NOT NULL DEFAULT 1.0,
   created_at TEXT NOT NULL,
-  -- v2: Vector clock support
-  vector_clock TEXT,            -- JSON: {"agentId": tick, ...} for hop-based decay
-  link_count INTEGER DEFAULT 1, -- Number of times this edge was created (for boosting)
+  link_count INTEGER DEFAULT 1,
   FOREIGN KEY (source_chunk_id) REFERENCES chunks(id) ON DELETE CASCADE,
   FOREIGN KEY (target_chunk_id) REFERENCES chunks(id) ON DELETE CASCADE
 );
@@ -67,24 +63,16 @@ CREATE INDEX IF NOT EXISTS idx_chunks_slug_start_time ON chunks(session_slug, st
 CREATE INDEX IF NOT EXISTS idx_edges_source ON edges(source_chunk_id);
 CREATE INDEX IF NOT EXISTS idx_edges_target ON edges(target_chunk_id);
 CREATE INDEX IF NOT EXISTS idx_edges_type ON edges(edge_type);
+CREATE INDEX IF NOT EXISTS idx_edges_source_type ON edges(source_chunk_id, edge_type);
+CREATE INDEX IF NOT EXISTS idx_edges_target_type ON edges(target_chunk_id, edge_type);
 CREATE INDEX IF NOT EXISTS idx_chunk_clusters_cluster ON chunk_clusters(cluster_id);
 
--- Vector clocks for logical time tracking
-CREATE TABLE IF NOT EXISTS vector_clocks (
-  id TEXT PRIMARY KEY,           -- "project:<slug>" or "agent:<slug>:<agentId>"
-  project_slug TEXT NOT NULL,
-  clock_data TEXT NOT NULL,      -- JSON: {"agentId": tick, ...}
-  updated_at TEXT DEFAULT CURRENT_TIMESTAMP
-);
-CREATE INDEX IF NOT EXISTS idx_vector_clocks_project ON vector_clocks(project_slug);
-
 -- Ingestion checkpoints for incremental ingestion
 CREATE TABLE IF NOT EXISTS ingestion_checkpoints (
   session_id TEXT PRIMARY KEY,
   project_slug TEXT NOT NULL,
   last_turn_index INTEGER NOT NULL,
   last_chunk_id TEXT,
-  vector_clock TEXT,
   file_mtime TEXT,              -- ISO timestamp of file mtime at last ingest
   updated_at TEXT DEFAULT CURRENT_TIMESTAMP
 );
@@ -129,5 +117,5 @@ CREATE TRIGGER IF NOT EXISTS chunks_fts_update AFTER UPDATE OF content ON chunks
   INSERT INTO chunks_fts(rowid, content) VALUES (new.rowid, new.content);
 END;
 
--- Insert initial version if not exists (v6 adds composite index for session reconstruction)
-INSERT OR IGNORE INTO schema_version (version) VALUES (6);
+-- Insert initial version if not exists (v8 adds chain-walking indices, simplifies edges)
+INSERT OR IGNORE INTO schema_version (version) VALUES (8);

package/dist/storage/types.d.ts

@@ -3,14 +3,12 @@
  *
  * The storage layer provides persistence for the Causantic system.
  * Key data structures include:
- * - **Chunks**: Segments of conversation with metadata and vector clocks
+ * - **Chunks**: Segments of conversation with metadata
  * - **Edges**: Weighted directional connections between chunks
  * - **Clusters**: Topic groupings of chunks (via HDBSCAN)
- * - **Vector clocks**: For causality tracking and decay computation
  *
  * @module storage/types
  */
-import type { VectorClock } from '../temporal/vector-clock.js';
 /**
  * Edge direction for graph traversal.
  *
@@ -22,30 +20,27 @@ import type { VectorClock } from '../temporal/vector-clock.js';
  */
 export type EdgeType = 'backward' | 'forward';
 /**
- * Reference types for edges.
+ * Structural roles for causal graph edges.
  *
- * Indicates the evidence used to create the edge. Higher-evidence types
- * receive higher initial weights:
+ * The causal graph is purely causal — semantic association is handled by
+ * vector similarity and clustering. Edges represent structural relationships:
  *
  * | Type | Weight | Description |
  * |------|--------|-------------|
- * | `file-path` | 1.0 | Shared file path reference |
- * | `explicit-backref` | 0.9 | Explicit "the error", "that function" |
- * | `error-fragment` | 0.9 | Discussing specific error message |
- * | `brief` | 0.9 | Parent spawning sub-agent |
- * | `debrief` | 0.9 | Sub-agent returning to parent |
- * | `code-entity` | 0.8 | Shared function/class/variable name |
- * | `tool-output` | 0.8 | Referencing tool results |
+ * | `within-chain` | 1.0 | D-T-D causal edge within one thinking entity |
+ * | `brief` | 0.9 | Parent spawning sub-agent (× depth penalty) |
+ * | `debrief` | 0.9 | Sub-agent returning to parent (× depth penalty) |
  * | `cross-session` | 0.7 | Session continuation |
- * | `adjacent` | 0.5 | Consecutive chunks (weak link) |
+ *
+ * All within-chain edges use m×n all-pairs creation at D-T-D boundaries,
+ * with topic-shift gating to omit edges across topic changes.
  */
-export type ReferenceType = 'file-path' | 'code-entity' | 'explicit-backref' | 'error-fragment' | 'tool-output' | 'adjacent' | 'cross-session' | 'brief' | 'debrief';
+export type ReferenceType = 'within-chain' | 'cross-session' | 'brief' | 'debrief';
 /**
  * A chunk stored in the database.
  *
  * Chunks are the fundamental unit of storage, representing segments of
- * conversation. Each chunk contains one or more turns and is assigned
- * a vector clock for causality tracking.
+ * conversation. Each chunk contains one or more turns.
  */
 export interface StoredChunk {
     /** Unique identifier (UUID format) */
@@ -72,8 +67,6 @@ export interface StoredChunk {
     createdAt: string;
     /** Agent ID for sub-agent chunks, 'ui' for main session */
     agentId: string | null;
-    /** Vector clock at time of chunk creation (for decay) */
-    vectorClock: VectorClock | null;
     /** Nesting depth: 0=main, 1=sub-agent, 2=nested sub-agent */
     spawnDepth: number;
     /** Full cwd path for project disambiguation (optional) */
@@ -108,8 +101,6 @@ export interface ChunkInput {
     approxTokens: number;
     /** Agent ID (optional, defaults to 'ui') */
     agentId?: string;
-    /** Vector clock (optional, enables clock-based decay) */
-    vectorClock?: VectorClock;
     /** Spawn depth (optional, defaults to 0) */
     spawnDepth?: number;
     /** Full cwd path for project disambiguation */
@@ -120,7 +111,6 @@ export interface ChunkInput {
  *
  * Edges represent causal connections between chunks. They have:
  * - An `initialWeight` set at creation based on reference type
- * - A `vectorClock` for computing time-based decay
  * - A `linkCount` that increases when the same edge is created multiple times
  */
 export interface StoredEdge {
@@ -138,8 +128,6 @@ export interface StoredEdge {
     initialWeight: number;
     /** ISO timestamp when edge was created */
     createdAt: string;
-    /** JSON-serialized vector clock for decay computation */
-    vectorClock: string | null;
     /** Times this edge was created (boosted on duplicate) */
     linkCount: number;
 }
@@ -161,8 +149,6 @@ export interface EdgeInput {
     referenceType?: ReferenceType;
     /** Explicit weight (overrides type-based default) */
     initialWeight: number;
-    /** Vector clock for decay computation */
-    vectorClock?: VectorClock;
 }
 /**
  * An edge with its computed weight at query time.

package/dist/storage/types.d.ts.map

@@ -1 +1 @@
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package/dist/storage/types.js

@@ -3,10 +3,9 @@
  *
  * The storage layer provides persistence for the Causantic system.
  * Key data structures include:
- * - **Chunks**: Segments of conversation with metadata and vector clocks
+ * - **Chunks**: Segments of conversation with metadata
  * - **Edges**: Weighted directional connections between chunks
  * - **Clusters**: Topic groupings of chunks (via HDBSCAN)
- * - **Vector clocks**: For causality tracking and decay computation
  *
  * @module storage/types
  */

package/dist/storage/types.js.map

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/storage/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG"}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/storage/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG"}

package/dist/storage/vector-store.d.ts

@@ -180,28 +180,22 @@ export declare class VectorStore {
      */
     private touchLastAccessed;
     /**
-     * Mark a vector as orphaned (its associated chunk was deleted).
-     * The vector will be subject to TTL cleanup after this.
-     * Called by pruner when deleting orphaned chunks.
-     */
-    markOrphaned(id: string): Promise<void>;
-    /**
-     * Mark multiple vectors as orphaned.
-     */
-    markOrphanedBatch(ids: string[]): Promise<void>;
-    /**
-     * Clean up expired orphaned vectors and their corresponding chunks.
-     * Removes vectors that are orphaned AND haven't been accessed within the TTL period.
+     * Clean up expired vectors and their corresponding chunks.
+     * Removes vectors that haven't been accessed within the TTL period.
      * Also deletes the corresponding chunks (FK cascades handle cluster assignments and edges).
      *
-     * @param ttlDays - Number of days after which orphaned vectors expire
+     * @param ttlDays - Number of days after which unaccessed vectors expire
      * @returns Number of vectors deleted
      */
     cleanupExpired(ttlDays: number): Promise<number>;
     /**
-     * Get count of orphaned vectors.
+     * Evict the oldest vectors when collection exceeds maxCount.
+     * Deletes vectors (and their chunks via FK cascade) by ascending last_accessed.
+     *
+     * @param maxCount - Maximum number of vectors to retain (0 = unlimited)
+     * @returns Number of vectors evicted
      */
-    getOrphanedCount(): Promise<number>;
+    evictOldest(maxCount: number): Promise<number>;
 }
 /**
  * Singleton vector store instance.

package/dist/storage/vector-store.d.ts.map

@@ -1 +1 @@
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