mcp-rag-memory 2.4.1 → 2.5.0

package/dist/mcp/rag-server.js

@@ -52,9 +52,9 @@ server.registerTool("rag_ingest_text", {
     return { content: [{ type: "text", text: JSON.stringify(res, null, 2) }] };
 });
 server.registerTool("rag_ingest_file", {
-    description: "Read a file and store it as a knowledge document",
+    description: "Read a file and store it as a knowledge document. Honours RAG_ALLOWED_DIRS when set.",
     inputSchema: {
-        path: z.string().describe("Absolute path to the file"),
+        path: z.string().min(1).describe("Absolute path to the file"),
         metadata: z.record(z.string(), z.unknown()).optional(),
     },
 }, async (args) => {
@@ -64,9 +64,9 @@ server.registerTool("rag_ingest_file", {
 server.registerTool("rag_ingest_dir", {
     description: "Recursively ingest supported source files from a directory",
     inputSchema: {
-        path: z.string().describe("Absolute path to the directory"),
+        path: z.string().min(1).describe("Absolute path to the directory"),
         recursive: z.boolean().optional().default(true),
-        extensions: z.array(z.string()).optional().describe("File extensions to include, e.g. ['.ts', '.md']"),
+        extensions: z.array(z.string().min(1)).min(1).optional().describe("File extensions to include, e.g. ['.ts', '.md']"),
     },
 }, async (args) => {
     const res = await ingestDirectory(args.path, { recursive: args.recursive, extensions: args.extensions });
@@ -124,10 +124,13 @@ server.registerTool("rag_retrieve", {
 /* RAG: document management                                            */
 /* ------------------------------------------------------------------ */
 server.registerTool("rag_list_documents", {
-    description: "List all stored knowledge documents",
-    inputSchema: {},
-}, async () => {
-    const docs = listDocuments();
+    description: "List stored knowledge documents (newest first, paginated)",
+    inputSchema: {
+        limit: z.number().int().min(1).max(1000).optional().default(100).describe("Max documents to return"),
+        offset: z.number().int().min(0).optional().default(0).describe("Skip this many documents"),
+    },
+}, async (args) => {
+    const docs = listDocuments({ limit: args.limit, offset: args.offset });
     return { content: [{ type: "text", text: JSON.stringify(docs, null, 2) }] };
 });
 server.registerTool("rag_document_stats", {
@@ -151,14 +154,14 @@ server.registerTool("rag_delete_document", {
 server.registerTool("rag_sync_session", {
     description: "Ingest an opencode session's user inputs (or the latest active session) into the RAG store as searchable documents. Use with the session id from opencode, or omit session_id and pass directory to auto-pick the most recent session in that workspace.",
     inputSchema: {
-        session_id: z.string().optional().describe("opencode session id; omit to use the latest active session"),
-        directory: z.string().optional().describe("Workspace path used to pick the latest session when session_id is omitted"),
-        limit: z.number().int().min(1).optional().describe("Only ingest the first N user messages"),
+        session_id: z.string().min(1).optional().describe("opencode session id; omit to use the latest active session"),
+        directory: z.string().min(1).optional().describe("Workspace path used to pick the latest session when session_id is omitted (defaults to the server's working directory)"),
+        limit: z.number().int().min(1).max(2000).optional().describe("Only ingest the first N user messages"),
     },
 }, async (args) => {
     const res = args.session_id
         ? await syncSession(args.session_id, { limit: args.limit })
-        : await syncLatest({ limit: args.limit, directory: args.directory });
+        : await syncLatest({ limit: args.limit, directory: args.directory ?? process.cwd() });
     return { content: [{ type: "text", text: JSON.stringify(res, null, 2) }] };
 });
 server.registerTool("memory_remember", {
@@ -227,6 +230,11 @@ server.registerTool("memory_update", {
         tags: z.array(z.string()).optional(),
     },
 }, async (args) => {
+    // An all-undefined patch used to re-embed the text and bump updated_at,
+    // silently reordering the store.
+    if (args.content === undefined && args.type === undefined && args.importance === undefined && args.tags === undefined) {
+        return { content: [{ type: "text", text: "Nothing to update: provide content, type, importance and/or tags." }] };
+    }
     const rec = await updateMemory(args.id, {
         content: args.content,
         type: args.type,

package/dist/mcp/rag-server.js.map

@@ -1 +1 @@
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package/dist/memory/memory.d.ts

@@ -44,13 +44,17 @@ export interface ConsolidationReport {
     removedDuplicates: number;
     promoted: number;
     pruned: number;
+    skippedDedup: boolean;
     totals: {
         memories: number;
         tokens: number;
     };
 }
 /**
- * - Removes near-duplicate memories (dot product > 0.92) keeping the highest-importance one.
+ * - Removes near-duplicate memories (cosine >= 0.92 AND >= 80% word overlap)
+ *   keeping the highest-importance one. The text gate matters: templated agent
+ *   memories ("The user's X is Y") sit at ~0.95 cosine while being distinct, and
+ *   deleting those is unrecoverable.
  * - Promotes importance of frequently-needed memories (recall_count >= 5) by +0.1.
  * - Optionally prunes stale, low-importance, never-recalled memories (RAG_PRUNE=1,
  *   RAG_PRUNE_IMPORTANCE=0.2, RAG_PRUNE_AGE_DAYS=90). Off by default — deletes are irreversible.

package/dist/memory/memory.d.ts.map

@@ -1 +1 @@
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package/dist/memory/memory.js

@@ -12,8 +12,15 @@ export const MEMORY_TYPES = [
     "insight",
     "conversation",
 ];
-/** Half-life in days for the recall decay curve. */
-const DECAY_HALF_LIFE_DAYS = Number(process.env.RAG_MEMORY_HALF_LIFE_DAYS ?? 14);
+/** Half-life in days for the recall decay curve (invalid values fall back to 14). */
+const DECAY_HALF_LIFE_DAYS = numEnv("RAG_MEMORY_HALF_LIFE_DAYS", 14, (n) => n > 0);
+function numEnv(name, fallback, valid) {
+    const raw = process.env[name];
+    if (raw === undefined || raw === "")
+        return fallback;
+    const n = Number(raw);
+    return Number.isFinite(n) && valid(n) ? n : fallback;
+}
 export async function remember(input) {
     const db = getDB();
     const id = newId();
@@ -25,32 +32,64 @@ export async function remember(input) {
     db.prepare(`INSERT INTO memories (id, type, content, importance, embedding, tags, recall_count, last_recalled, created_at, updated_at)
      VALUES (?, ?, ?, ?, ?, ?, 0, NULL, ?, ?)`).run(id, type, input.content, importance, packVector(vec), tags, ts, ts);
     invalidateVectorCache();
-    return getMemory(id);
+    const rec = getMemory(id);
+    if (!rec)
+        throw new Error("Memory insert failed: row disappeared immediately after write");
+    return rec;
+}
+/** One query for the whole page — getMemory() per row used to be an N+1. */
+function toRecords(rows) {
+    return rows.map((row) => ({
+        id: row.id,
+        type: row.type,
+        content: row.content,
+        importance: typeof row.importance === "number" && Number.isFinite(row.importance) ? row.importance : 0.5,
+        tags: parseTags(row.tags),
+        recallCount: row.recall_count,
+        lastRecalled: row.last_recalled,
+        createdAt: row.created_at,
+        updatedAt: row.updated_at,
+    }));
+}
+const MEMORY_COLUMNS = "id, type, content, importance, tags, recall_count, last_recalled, created_at, updated_at";
+/** Never let a malformed row break every read path. */
+function parseTags(raw) {
+    try {
+        const parsed = JSON.parse(raw);
+        return Array.isArray(parsed) ? parsed.map((t) => String(t)) : [];
+    }
+    catch {
+        return [];
+    }
 }
 export async function recall(query, topK = 8, minScore = 0.1) {
     const db = getDB();
     const q = await embedText(query);
     const hits = vectorSearch(q, { topK: topK * 2, minScore, collection: "memories" });
+    if (hits.length === 0)
+        return [];
     const ts = nowMs();
-    const bump = db.prepare("UPDATE memories SET recall_count = recall_count + 1, last_recalled = ? WHERE id = ?");
-    const results = [];
+    const rows = db
+        .prepare(`SELECT ${MEMORY_COLUMNS} FROM memories WHERE id IN (${hits.map(() => "?").join(", ")})`)
+        .all(...hits.map((h) => h.key));
+    const byId = new Map(toRecords(rows).map((r) => [r.id, r]));
+    const scored = [];
     for (const h of hits) {
-        const rec = getMemory(h.key);
+        const rec = byId.get(h.key);
         if (!rec)
             continue;
-        bump.run(ts, rec.id);
         const ageMs = ts - (rec.lastRecalled ?? rec.createdAt);
         const decay = Math.pow(0.5, ageMs / (DECAY_HALF_LIFE_DAYS * 86_400_000));
-        results.push({
-            ...rec,
-            recallCount: rec.recallCount + 1,
-            lastRecalled: ts,
-            score: h.score * decay,
-            decay,
-        });
+        scored.push({ ...rec, score: h.score * decay, decay });
     }
-    results.sort((a, b) => b.score - a.score);
-    return results.slice(0, topK);
+    scored.sort((a, b) => b.score - a.score);
+    const results = scored.slice(0, topK);
+    // Bump only what is actually returned: a memory nobody saw is not "recalled",
+    // and phantom bumps used to feed decay and the promotion threshold.
+    const bump = db.prepare("UPDATE memories SET recall_count = recall_count + 1, last_recalled = ? WHERE id = ?");
+    for (const r of results)
+        bump.run(ts, r.id);
+    return results.map((r) => ({ ...r, recallCount: r.recallCount + 1, lastRecalled: ts }));
 }
 export function listMemories(opts = {}) {
     const db = getDB();
@@ -61,7 +100,9 @@ export function listMemories(opts = {}) {
         params.push(opts.type);
     }
     if (opts.tag) {
-        clauses.push("EXISTS (SELECT 1 FROM json_each(memories.tags) AS _tg WHERE _tg.value = ?)");
+        // json_each() raises "malformed JSON" on a corrupted column, which would
+        // break the whole listing. Feed it a guaranteed-valid array instead.
+        clauses.push("EXISTS (SELECT 1 FROM json_each(CASE WHEN json_valid(memories.tags) THEN memories.tags ELSE '[]' END) AS _tg WHERE _tg.value = ?)");
         params.push(opts.tag);
     }
     if (opts.minImportance !== undefined) {
@@ -69,30 +110,20 @@ export function listMemories(opts = {}) {
         params.push(opts.minImportance);
     }
     const where = clauses.length ? ` WHERE ${clauses.join(" AND ")}` : "";
-    const limit = Math.min(opts.limit ?? 100, 500);
+    const limit = Math.min(Math.max(Math.trunc(opts.limit ?? 100), 1), 500);
     const rows = db
-        .prepare(`SELECT id FROM memories${where} ORDER BY updated_at DESC LIMIT ${limit}`)
+        .prepare(`SELECT ${MEMORY_COLUMNS} FROM memories${where} ORDER BY updated_at DESC LIMIT ${limit}`)
         .all(...params);
-    return rows.map((r) => getMemory(r.id)).filter(Boolean);
+    return toRecords(rows);
 }
 export function getMemory(id) {
     const db = getDB();
     const row = db
-        .prepare("SELECT * FROM memories WHERE id = ?")
+        .prepare(`SELECT ${MEMORY_COLUMNS} FROM memories WHERE id = ?`)
         .get(id);
     if (!row)
         return null;
-    return {
-        id: row.id,
-        type: row.type,
-        content: row.content,
-        importance: row.importance,
-        tags: JSON.parse(row.tags),
-        recallCount: row.recall_count,
-        lastRecalled: row.last_recalled,
-        createdAt: row.created_at,
-        updatedAt: row.updated_at,
-    };
+    return toRecords([row])[0];
 }
 export async function updateMemory(id, patch) {
     const db = getDB();
@@ -103,10 +134,17 @@ export async function updateMemory(id, patch) {
     const type = patch.type ?? existing.type;
     const importance = patch.importance !== undefined ? clampImportance(patch.importance) : existing.importance;
     const tags = patch.tags ?? existing.tags;
-    const vec = await embedText(content);
     const ts = nowMs();
-    db.prepare("UPDATE memories SET content = ?, type = ?, importance = ?, tags = ?, embedding = ?, updated_at = ? WHERE id = ?").run(content, type, importance, JSON.stringify(tags), packVector(vec), ts, id);
-    invalidateVectorCache();
+    // Only re-embed when the text actually changed: the vector is the only column
+    // that needs the model, and an importance-only patch must stay cheap.
+    if (content !== existing.content) {
+        const vec = await embedText(content);
+        db.prepare("UPDATE memories SET content = ?, type = ?, importance = ?, tags = ?, embedding = ?, updated_at = ? WHERE id = ?").run(content, type, importance, JSON.stringify(tags), packVector(vec), ts, id);
+        invalidateVectorCache();
+    }
+    else {
+        db.prepare("UPDATE memories SET content = ?, type = ?, importance = ?, tags = ?, updated_at = ? WHERE id = ?").run(content, type, importance, JSON.stringify(tags), ts, id);
+    }
     return getMemory(id);
 }
 export function forget(id) {
@@ -115,44 +153,67 @@ export function forget(id) {
     invalidateVectorCache();
     return { deleted: Number(res.changes) > 0 };
 }
+/** Above this many vectors the O(n^2) dedup pass is skipped (event-loop budget). */
+const DEDUP_MAX_VECTORS = 2000;
+const DEDUP_SIMILARITY = 0.92;
+const DEDUP_TOKEN_OVERLAP = 0.8;
+function tokenSet(text) {
+    return new Set((text.toLowerCase().match(/[\p{L}\p{N}]+/gu) ?? []).filter((t) => t.length > 1));
+}
+/** Jaccard overlap of word sets — the second gate before anything is deleted. */
+function tokenOverlap(a, b) {
+    const ta = tokenSet(a);
+    const tb = tokenSet(b);
+    if (ta.size === 0 || tb.size === 0)
+        return 0;
+    let shared = 0;
+    for (const t of ta)
+        if (tb.has(t))
+            shared++;
+    return shared / (ta.size + tb.size - shared);
+}
 /**
- * - Removes near-duplicate memories (dot product > 0.92) keeping the highest-importance one.
+ * - Removes near-duplicate memories (cosine >= 0.92 AND >= 80% word overlap)
+ *   keeping the highest-importance one. The text gate matters: templated agent
+ *   memories ("The user's X is Y") sit at ~0.95 cosine while being distinct, and
+ *   deleting those is unrecoverable.
  * - Promotes importance of frequently-needed memories (recall_count >= 5) by +0.1.
  * - Optionally prunes stale, low-importance, never-recalled memories (RAG_PRUNE=1,
  *   RAG_PRUNE_IMPORTANCE=0.2, RAG_PRUNE_AGE_DAYS=90). Off by default — deletes are irreversible.
  */
 export async function consolidate() {
     const db = getDB();
-    const rows = db.prepare("SELECT id, embedding FROM memories").all();
-    const records = rows
-        .map((r) => ({ id: r.id, rec: getMemory(r.id) }))
-        .filter((r) => r.rec !== null && r.rec !== undefined);
-    const recordsById = new Map(records.map((r) => [r.id, r.rec]));
+    const rows = db
+        .prepare(`SELECT ${MEMORY_COLUMNS}, embedding FROM memories`)
+        .all();
     const vectors = [];
     for (const r of rows) {
-        if (!recordsById.has(r.id))
-            continue;
         const vec = unpackVector(r.embedding);
         if (vec)
             vectors.push({ id: r.id, vec });
     }
+    const records = new Map(toRecords(rows).map((r) => [r.id, r]));
     let removedDuplicates = 0;
+    const skippedDedup = vectors.length > DEDUP_MAX_VECTORS;
     const toDelete = new Set();
-    for (let i = 0; i < vectors.length; i++) {
-        if (toDelete.has(vectors[i].id))
-            continue;
-        for (let j = i + 1; j < vectors.length; j++) {
-            if (toDelete.has(vectors[j].id))
+    if (!skippedDedup) {
+        for (let i = 0; i < vectors.length; i++) {
+            if (toDelete.has(vectors[i].id))
                 continue;
-            const sim = dotProduct(vectors[i].vec, vectors[j].vec);
-            if (sim >= 0.92) {
-                const a = recordsById.get(vectors[i].id);
-                const b = recordsById.get(vectors[j].id);
+            for (let j = i + 1; j < vectors.length; j++) {
+                if (toDelete.has(vectors[j].id))
+                    continue;
+                if (dotProduct(vectors[i].vec, vectors[j].vec) < DEDUP_SIMILARITY)
+                    continue;
+                const a = records.get(vectors[i].id);
+                const b = records.get(vectors[j].id);
+                if (!a || !b || tokenOverlap(a.content, b.content) < DEDUP_TOKEN_OVERLAP)
+                    continue;
                 if (a.importance >= b.importance) {
-                    toDelete.add(vectors[j].id);
+                    toDelete.add(b.id);
                 }
                 else {
-                    toDelete.add(vectors[i].id);
+                    toDelete.add(a.id);
                     const tmpId = vectors[i].id;
                     vectors[i].id = vectors[j].id;
                     vectors[j].id = tmpId;
@@ -164,36 +225,35 @@ export async function consolidate() {
     const delStmt = db.prepare("DELETE FROM memories WHERE id = ?");
     for (const id of toDelete)
         delStmt.run(id);
-    let promoted = 0;
-    const bumpPromotion = async () => {
-        for (const rec of listMemories()) {
-            if (rec.recallCount >= 5 && rec.importance < 1) {
-                await updateMemory(rec.id, { importance: Math.min(1, rec.importance + 0.1) });
-                promoted++;
-            }
-        }
-    };
+    // One UPDATE for the whole store: the old per-row updateMemory() re-embedded
+    // every candidate (a full model inference each) and only saw the newest 100.
+    const promoted = Number(db
+        .prepare("UPDATE memories SET importance = min(1, importance + 0.1) WHERE recall_count >= 5 AND importance < 1")
+        .run().changes);
     let pruned = 0;
     const pruneEnabled = process.env.RAG_PRUNE === "1" || process.env.RAG_PRUNE === "true";
     if (pruneEnabled) {
-        const minImp = Number(process.env.RAG_PRUNE_IMPORTANCE ?? 0.2);
-        const maxAgeDays = Number(process.env.RAG_PRUNE_AGE_DAYS ?? 90);
+        const minImp = numEnv("RAG_PRUNE_IMPORTANCE", 0.2, (n) => n >= 0 && n <= 1);
+        const maxAgeDays = numEnv("RAG_PRUNE_AGE_DAYS", 90, (n) => n >= 0);
         const cutoff = nowMs() - maxAgeDays * 86_400_000;
         const stale = db
-            .prepare("SELECT id FROM memories WHERE importance < ? AND recall_count = 0 AND created_at < ?")
+            // <= so RAG_PRUNE_AGE_DAYS=0 means "everything is stale"; a strict <
+            // skipped rows created in the same millisecond as the cutoff, which made
+            // the prune silently no-op on a fast machine.
+            .prepare("SELECT id FROM memories WHERE importance < ? AND recall_count = 0 AND created_at <= ?")
             .all(minImp, cutoff);
         for (const s of stale) {
             delStmt.run(s.id);
             pruned++;
         }
     }
-    await bumpPromotion();
     invalidateVectorCache();
     const stats = memoryStats();
     return {
         removedDuplicates,
         promoted,
         pruned,
+        skippedDedup,
         totals: { memories: stats.memories, tokens: stats.tokens },
     };
 }
@@ -205,9 +265,11 @@ export function memoryStats() {
     const byType = {};
     for (const r of byTypeRows)
         byType[r.type] = r.c;
+    // LENGTH() in SQL: loading every content blob just to count tokens was a full
+    // table pull on each system_stats / memory_stats call.
     let totalTokens = 0;
-    for (const r of db.prepare("SELECT content FROM memories").all()) {
-        totalTokens += estimateTokens(r.content);
+    for (const r of db.prepare("SELECT LENGTH(content) AS n FROM memories").all()) {
+        totalTokens += estimateTokens("x".repeat(Math.max(0, r.n ?? 0)));
     }
     return { memories: count.c, tokens: totalTokens, avgImportance: avg.a, byType };
 }
@@ -219,6 +281,8 @@ export async function contextPrompt(query, topK = 6) {
     return { context: lines.join("\n"), sources: hits };
 }
 function clampImportance(v) {
+    if (!Number.isFinite(v))
+        return 0.5;
     return Math.min(1, Math.max(0, v));
 }
 //# sourceMappingURL=memory.js.map

package/dist/memory/memory.js.map

@@ -1 +1 @@
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package/dist/rag/chunker.d.ts.map

@@ -1 +1 @@
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