@lotargo/memory_plugin 1.6.2 → 1.6.4

package/mcp-server/tools/core/memory_core.js

@@ -76,15 +76,19 @@ export async function rememberFact(
   let supersededInfo = "";
   if (!duplicate) {
     const [date, time] = today().split(" ");
-    const meta = { ttl, tags };
-    if (keep) meta.keep = "1";
-    if (supersedes) {
-      const targetIdx = resolveFactIndex(entries, supersedes);
-      if (targetIdx !== -1) {
-        const newId = nextFactId(entries);
-        const targetId = factMeta(entries[targetIdx]).id || nextFactId(entries);
-        entries[targetIdx] = withMeta(entries[targetIdx], { id: targetId, supersededBy: newId });
-        meta.id = newId;
+    const meta = { ttl, tags };
+    if (keep) meta.keep = "1";
+    if (supersedes) {
+      const targetIdx = resolveFactIndex(entries, supersedes);
+      if (targetIdx !== -1) {
+        let targetId = factMeta(entries[targetIdx]).id;
+        if (!targetId) {
+          targetId = nextFactId(entries);
+          entries[targetIdx] = withMeta(entries[targetIdx], { id: targetId });
+        }
+        const newId = nextFactId(entries);
+        entries[targetIdx] = withMeta(entries[targetIdx], { id: targetId, supersededBy: newId });
+        meta.id = newId;
         meta.supersedes = targetId;
         supersededInfo = ` [superseded: "${factText(entries[targetIdx]).slice(0, 60)}"]`;
       } else {
@@ -129,7 +133,7 @@ async function resolveTargetKey(projectPath) {
 }
 
 export async function recallFacts(
-  { scope, project, query, tags, since, until, mode, offset, limit },
+  { scope, project, query, tags, since, until, mode, offset, limit, includeSuperseded = false },
   ctx = {}
 ) {
   const results = [];
@@ -196,18 +200,26 @@ export async function recallFacts(
   };
 
   const collect = async (entries, key) => {
-    const matched = entries.filter(
-      (e) => matchesQuery(e, query) && matchesTags(e, tags) && inDateRange(e, since, until)
-    );
+    const matched = entries
+      .map((entry, storageIndex) => ({ entry, storageIndex }))
+      .filter(
+        ({ entry }) =>
+          (includeSuperseded || !isSuperseded(entry)) &&
+          matchesQuery(entry, query) &&
+          matchesTags(entry, tags) &&
+          inDateRange(entry, since, until)
+      );
     if (!matched.length) return;
     if (results.length) results.push("");
     results.push(`--- ${key === GLOBAL_KEY ? "Global" : `Project: ${key === target ? label : key}`} ---`);
 
     const hasLimit = limit !== undefined && limit !== null;
-    const targetLimit = hasLimit ? limit : matched.length;
-    const paginated = matched.slice(targetOffset, targetOffset + targetLimit);
-    for (let i = 0; i < paginated.length; i++) {
-      results.push(await formatFactWithLinks(paginated[i], targetOffset + i + 1, key));
+    const targetLimit = hasLimit ? limit : matched.length;
+    const paginated = matched.slice(targetOffset, targetOffset + targetLimit);
+    for (let i = 0; i < paginated.length; i++) {
+      results.push(
+        await formatFactWithLinks(paginated[i].entry, paginated[i].storageIndex + 1, key)
+      );
     }
     if (hasLimit && matched.length > targetLimit) {
       results.push(
@@ -279,11 +291,17 @@ export async function forgetFacts({ query, scope, force }, ctx = {}) {
   if (!indices.length) return "Not found.";
 
   const removable = indices.filter((i) => force || !isKeepFact(entries[i]));
-  const protectedCount = indices.length - removable.length;
-  if (removable.length) {
-    for (const i of removable.sort((a, b) => b - a)) entries.splice(i, 1);
-    await writeMemory(key, entries);
-  }
+  const protectedCount = indices.length - removable.length;
+  if (removable.length) {
+    const removedBodies = removable.map((i) => factBody(entries[i]) || factText(entries[i]));
+    for (const i of removable.sort((a, b) => b - a)) entries.splice(i, 1);
+    await writeMemory(key, entries);
+    try {
+      const { getDatabase } = await import("../../db/database.js");
+      const { deleteLinksForFacts } = await import("../../graph/knowledge_linker.js");
+      await deleteLinksForFacts(await getDatabase(), key, removedBodies);
+    } catch {}
+  }
   let text = removable.length ? "Memory updated" : "Nothing removed.";
   if (protectedCount) text += ` (${protectedCount} protected fact(s) skipped; use force=true to override)`;
   return text;
@@ -312,13 +330,44 @@ export async function updateFactText({ id, newText, title, scope }, ctx = {}) {
 
   let linksUpdated = 0;
   try {
-    const { getDatabase } = await import("../../db/database.js");
-    const db = await getDatabase();
-    const res = await db
-      .prepare("UPDATE knowledge_links SET fact_text = ? WHERE fact_key = ? AND fact_text = ?")
-      .run(finalFact, key, oldBody);
-    linksUpdated = res.changes;
-  } catch {}
+    const { getDatabase } = await import("../../db/database.js");
+    const db = await getDatabase();
+    const linkedRows = await db
+      .prepare("SELECT * FROM knowledge_links WHERE fact_key = ? AND fact_text = ?")
+      .all(key, oldBody);
+    const res = await db
+      .prepare("UPDATE knowledge_links SET fact_text = ? WHERE fact_key = ? AND fact_text = ?")
+      .run(finalFact, key, oldBody);
+    linksUpdated = res.changes;
+    if (linksUpdated) {
+      const { queueDocumentSyncIfNeeded } = await import("../../graph/knowledge_linker.js");
+      const docIds = new Set();
+      for (const link of linkedRows) {
+        const targetSpec = link.start_line
+          ? `${link.doc_id}:L${link.start_line}-${link.end_line || link.start_line}`
+          : link.doc_id;
+        await db.prepare(
+          "DELETE FROM graph_edges WHERE source_id = ? AND target_id = ? AND relation_type = ?"
+        ).run(
+          `fact:${key}:${oldBody.substring(0, 30)}`,
+          targetSpec,
+          link.relation_type || "LINKS_TO"
+        );
+        await db.prepare(`
+          INSERT OR IGNORE INTO graph_edges (source_id, target_id, relation_type, metadata_json, created_at)
+          VALUES (?, ?, ?, ?, ?)
+        `).run(
+          `fact:${key}:${finalFact.substring(0, 30)}`,
+          targetSpec,
+          link.relation_type || "LINKS_TO",
+          link.metadata_json || JSON.stringify({ linkId: link.id }),
+          link.created_at || Date.now()
+        );
+        docIds.add(link.doc_id);
+      }
+      for (const docId of docIds) await queueDocumentSyncIfNeeded(db, docId);
+    }
+  } catch {}
 
   return `Fact updated${linksUpdated ? `, ${linksUpdated} doc link(s) updated` : ""}`;
 }
@@ -327,7 +376,7 @@ export async function memoryInfo(_args = {}, ctx = {}) {
   const dbPath = join(MEMORY_DIR, "storage", "memory.sqlite");
   const activeKey = await projectKey(ctx.worktree ?? null, ctx.directory ?? null);
   const globalFile = storeFilePath(GLOBAL_KEY);
-  const projectFile = storeFilePath(activeKey);
+  const projectFile = activeKey ? storeFilePath(activeKey) : null;
 
   let version = "unknown";
   try {
@@ -358,17 +407,20 @@ export async function memoryInfo(_args = {}, ctx = {}) {
     const { getDatabase } = await import("../../db/database.js");
     const { resolveProjectIdentity, listIdentities } = await import("../../identity.js");
     const db = await getDatabase();
-    const identity = await resolveProjectIdentity(ctx.worktree || ctx.directory || process.cwd());
-    const all = await listIdentities(db);
-    identityLines.push(
-      `Identity: ${identity ? "git" : "no-git"}` +
+    const identity = await resolveProjectIdentity(ctx.worktree || ctx.directory || process.cwd());
+    const all = await listIdentities(db);
+    const registered = identity ? all.find((item) => item.key === identity.key) : null;
+    identityLines.push(
+      `Identity: ${identity ? "git" : "no-git"}` +
         (identity
           ? ` | key: ${identity.key} | name: ${identity.name}${
               identity.primaryRemote ? ` | remote: ${identity.primaryRemote}` : ""
-            }`
-          : ""),
-      `Known identities: ${all.length}`
-    );
+            }`
+          : ""),
+      `Registry: ${identity ? (registered ? "linked" : "unlinked") : "not-applicable"}` +
+        (registered ? ` | aliases: ${registered.aliases.length}` : ""),
+      `Known identities: ${all.length}`
+    );
   } catch (e) {
     identityLines.push(`Identity: unavailable (${e.message})`);
   }
@@ -378,7 +430,7 @@ export async function memoryInfo(_args = {}, ctx = {}) {
     `MEMORY_DIR: ${MEMORY_DIR}`,
     `SQLite DB: ${dbPath}`,
     `Global store: ${globalFile}`,
-    `Project store: ${projectFile}`,
+    `Project store: ${projectFile || "not applicable (outside Git)"}`,
     `Project stores: ${stores.length}`,
     `Facts (global): ${(await readMemoryRaw(GLOBAL_KEY)).length}`,
     `Facts (project): ${(await readMemoryRaw(activeKey)).length}`,

package/mcp-server/tools/identity_tools.js

@@ -1,6 +1,6 @@
 import * as z from "zod/v4";
 import { basename } from "node:path";
-import { scopeKey, canonicalPath, readMemory, writeMemory, storeFilePath } from "../memory.js";
+import { GLOBAL_KEY, scopeKey, canonicalPath, readMemory, writeMemory, storeFilePath } from "../memory.js";
 import { factBody } from "../fact_format.js";
 import { optStr, optNum, defStr, defBool, requireProjectKey } from "./helpers.js";
 
@@ -33,9 +33,18 @@ export function registerIdentityTools(server) {
         if (!factText || !docId) {
           throw new Error("factText and docId are required parameters for link action");
         }
+        const facts = await readMemory(key);
+        const needle = factText.toLowerCase().trim();
+        const matches = facts.filter((entry) => {
+          const body = factBody(entry).toLowerCase();
+          return body === needle || body.includes(needle) || entry.toLowerCase().includes(needle);
+        });
+        if (matches.length === 0) throw new Error(`Notebook fact not found for link: ${factText}`);
+        if (matches.length > 1) throw new Error(`Notebook fact match is ambiguous; use a more specific factText: ${factText}`);
+        const resolvedFactText = factBody(matches[0]);
         const res = await linkFactToDocument({
           factKey: key,
-          factText,
+          factText: resolvedFactText,
           docId,
           startLine,
           endLine,
@@ -48,7 +57,8 @@ export function registerIdentityTools(server) {
 
       if (action === "get_doc_links") {
         if (!docId) throw new Error("docId parameter is required for get_doc_links action");
-        const links = await getLinksForDoc(docId);
+        const allowedScopes = key === GLOBAL_KEY ? [GLOBAL_KEY] : [GLOBAL_KEY, key];
+        const links = await getLinksForDoc(docId, allowedScopes);
         return {
           content: [{ type: "text", text: JSON.stringify(links, null, 2) }],
         };
@@ -130,6 +140,9 @@ export function registerIdentityTools(server) {
           }
         } catch (e) {}
       }
+      const { moveKnowledgeScope } = await import("../graph/knowledge_linker.js");
+      const migratedKnowledge = await moveKnowledgeScope(db, legacyPathKey, key);
+      if (migratedKnowledge.movedLinks > 0 || migratedKnowledge.movedDocuments > 0) migrated = true;
 
       return {
         content: [
@@ -242,8 +255,10 @@ export function registerIdentityTools(server) {
 
       await writeMemory(targetKey, targetFacts);
 
-      await db.prepare("UPDATE project_aliases SET identity_key = ? WHERE identity_key = ?;").run(targetKey, sourceKey);
       await upsertIdentity(db, { key: targetKey, name: sourceIdentity.name, primaryRemote: normalizeRemoteUrl(remote) });
+      await db.prepare("UPDATE project_aliases SET identity_key = ? WHERE identity_key = ?;").run(targetKey, sourceKey);
+      const { moveKnowledgeScope } = await import("../graph/knowledge_linker.js");
+      const movedKnowledge = await moveKnowledgeScope(db, sourceKey, targetKey);
       await removeIdentity(db, sourceKey);
 
       try {
@@ -265,6 +280,8 @@ export function registerIdentityTools(server) {
                 sourceKey,
                 targetKey,
                 mergedFacts: mergedCount,
+                movedKnowledgeLinks: movedKnowledge.movedLinks,
+                movedRagDocuments: movedKnowledge.movedDocuments,
               },
               null,
               2

package/mcp-server/tools/memory_tools.js

@@ -51,7 +51,8 @@ export function registerMemoryTools(server) {
         "Use project: '<directory path>' with scope 'project'/'all' to read facts of a specific project from any working directory. " +
         "query filters by keyword (all space-separated terms must match). " +
         "tags filters by comma-separated tags. since/until filter by date (YYYY-MM-DD, inclusive). " +
-        "Expired facts are shown with [EXPIRED], protected ones with [KEEP]. The response includes the store file paths.",
+        "Superseded facts are excluded by default; pass includeSuperseded=true to inspect history. " +
+        "Expired facts are shown with [EXPIRED], protected ones with [KEEP]. The response includes the store file paths.",
       inputSchema: z.object({
         scope: defStr("all").describe("'project', 'global', 'all', or 'list_projects'"),
         project: optStr().describe("Directory path of the project to read facts from (e.g. 'F:/projects/plugins/memory')"),
@@ -61,7 +62,8 @@ export function registerMemoryTools(server) {
         until: optStr().describe("Optional end date filter, YYYY-MM-DD (inclusive)"),
         mode: z.enum(["headers", "full"]).nullish().transform((v) => v || "full").describe("Result mode: 'full' (with body, default) or 'headers' (title and badges only)"),
         offset: optNum().describe("Pagination offset (optional)"),
-        limit: optNum().describe("Pagination limit (optional)"),
+        limit: optNum().describe("Pagination limit (optional)"),
+        includeSuperseded: defBool(false).describe("Include superseded historical facts (excluded by default)"),
       }),
     },
     async (args) => ({ content: [{ type: "text", text: await recallFacts(args) }] })

package/mcp-server/tools/rag_tools.js

@@ -2,7 +2,8 @@ import * as z from "zod/v4";
 import { optStr, defBool, defNum, optNum } from "./helpers.js";
 import { MEMORY_DIR } from "../memory.js";
 import { registerSnapshotDir } from "../admin/snapshot.js";
-import { ensureExportsDir } from "../ingest/exporter.js";
+import { ensureExportsDir } from "../ingest/exporter.js";
+import { resolveRagScopeKey, resolveRagScopeKeys, resolveManageRagScopeKeys, removeDocumentScopes } from "../rag_scope.js";
 
 export function registerRagTools(server) {
   // Restrict snapshot export/import paths to the plugin's own data directories.
@@ -12,8 +13,8 @@ export function registerRagTools(server) {
   server.registerTool(
     "ingest_document",
     {
-      description:
-        "Ingest a document into the RAG knowledge base. " +
+      description:
+        "Selectively preserve a reliable, reusable source in the RAG knowledge base; do not ingest everything encountered. " +
         "Accepts local file paths, web URLs, or raw Markdown/text content. " +
         "For type='file' the file is read from disk and indexed with a code-block wrapper. " +
         "For type='url' the page is fetched and its content is indexed (not just the URL). " +
@@ -31,18 +32,21 @@ export function registerRagTools(server) {
           .transform((v) => v || "text")
           .describe("Input content type: 'text' (raw content), 'file' (reads from disk, wraps in code block), or 'url' (fetches page content)"),
         title: optStr().describe("Document title"),
-        path: optStr().describe("Original document file path"),
-        generateEmbeddings: defBool(true).describe("Compute dense vector embeddings"),
-      }),
-    },
-    async ({ content, type, title, path, generateEmbeddings }) => {
-      const { ingestDocument } = await import("../ingest/pipeline.js");
-      const result = await ingestDocument({
+        path: optStr().describe("Original document file path"),
+        scope: z.enum(["project", "global"]).nullish().transform((v) => v || "project").describe("RAG visibility: current Git project (default) or global"),
+        generateEmbeddings: defBool(true).describe("Compute dense vector embeddings"),
+      }),
+    },
+    async ({ content, type, title, path, scope, generateEmbeddings }) => {
+      const { ingestDocument } = await import("../ingest/pipeline.js");
+      const projectScope = await resolveRagScopeKey(scope);
+      const result = await ingestDocument({
         content,
         type,
         title: title || null,
         path: path || null,
-        generateEmbeddings,
+        generateEmbeddings,
+        projectScope,
       });
       return {
         content: [
@@ -55,7 +59,8 @@ export function registerRagTools(server) {
                 title: result.title,
                 sectionsCount: result.sectionsCount,
                 microChunksCount: result.microChunksCount,
-                deduplicated: result.deduplicated,
+                deduplicated: result.deduplicated,
+                scope: result.projectScope,
               },
               null,
               2
@@ -69,8 +74,8 @@ export function registerRagTools(server) {
   server.registerTool(
     "query_knowledge_base",
     {
-      description:
-        "Perform hybrid search (RSF/RRF BM25 full-text + dense vector similarity) across the RAG knowledge base. " +
+      description:
+        "Perform project-isolated hybrid search (RSF/RRF BM25 full-text + dense vector similarity) across the RAG knowledge base. " +
         "Returns top-ranked candidate document sections with breadcrumbs, GraphRAG defined code symbols, and relevance scores.",
       inputSchema: z.object({
         query: z.string().describe("Search query in natural language or symbol name"),
@@ -79,19 +84,22 @@ export function registerRagTools(server) {
           "Optional task-specific retrieval instruction shaping embedding focus (e.g. 'Retrieve code snippets', 'Find user preferences'). " +
             "Recommended when using E5/BGE models for domain-specific queries."
         ),
-        generateEmbeddings: defBool(true).describe("Use vector search alongside BM25"),
-      }),
-    },
-    async ({ query, limit, instruction, generateEmbeddings }) => {
+        generateEmbeddings: defBool(true).describe("Use vector search alongside BM25"),
+        scope: z.enum(["all", "project", "global"]).nullish().transform((v) => v || "all").describe("Search global + current project (default), project only, or global only"),
+      }),
+    },
+    async ({ query, limit, instruction, generateEmbeddings, scope }) => {
       const { hybridQuery } = await import("../retrieval/retriever.js");
       const { getConfig } = await import("../config/config_manager.js");
-      const activeConfig = getConfig();
+      const activeConfig = getConfig();
+      const scopeKeys = await resolveRagScopeKeys(scope);
 
       const results = await hybridQuery({
         query,
         limit,
         generateEmbeddings,
-        instruction: instruction || null,
+        instruction: instruction || null,
+        scopeKeys,
       });
 
       if (!results || results.length === 0) {
@@ -128,8 +136,9 @@ export function registerRagTools(server) {
   server.registerTool(
     "batch_query_knowledge_base",
     {
-      description:
-        "Execute multiple hybrid search queries in a single batch call. " +
+      description:
+        "Execute multiple hybrid search queries in a single batch call. " +
+        "Search is isolated to global plus the current project unless another scope is requested. " +
         "More efficient than separate query_knowledge_base calls: all query embeddings computed in one ONNX pass. " +
         "Returns one result set per query, in the same order as input.",
       inputSchema: z.object({
@@ -140,18 +149,21 @@ export function registerRagTools(server) {
         instruction: optStr().describe(
           "Optional task-specific retrieval instruction shaping embedding focus. Applied to all queries."
         ),
-        generateEmbeddings: defBool(true).describe("Use vector search alongside BM25"),
-      }),
-    },
-    async ({ queries, limit, instruction, generateEmbeddings }) => {
+        generateEmbeddings: defBool(true).describe("Use vector search alongside BM25"),
+        scope: z.enum(["all", "project", "global"]).nullish().transform((v) => v || "all").describe("Search global + current project (default), project only, or global only"),
+      }),
+    },
+    async ({ queries, limit, instruction, generateEmbeddings, scope }) => {
       const { batchHybridQuery } = await import("../retrieval/retriever.js");
       const { getConfig } = await import("../config/config_manager.js");
-      const activeConfig = getConfig();
+      const activeConfig = getConfig();
+      const scopeKeys = await resolveRagScopeKeys(scope);
 
       const allResults = await batchHybridQuery(queries, {
         limit,
         generateEmbeddings,
-        instruction: instruction || null,
+        instruction: instruction || null,
+        scopeKeys,
       });
 
       const formatted = allResults
@@ -230,27 +242,48 @@ export function registerRagTools(server) {
   server.registerTool(
     "manage_knowledge_base",
     {
-      description:
-        "Manage the RAG knowledge base: inspect stats, list documents, read full raw document, delete documents, or export/import snapshots.",
+      description:
+        "Manage the project-isolated RAG knowledge base: inspect stats, list documents, read full raw document, unlink/delete documents, or export/import complete snapshots.",
       inputSchema: z.object({
         action: z.enum(["stats", "list", "read_document", "delete", "export_snapshot", "import_snapshot"]).describe("Management action"),
         docId: optStr().describe("Document ID, title, or path (required for read_document and delete)"),
-        snapshotPath: optStr().describe("File path for snapshot export/import"),
-      }),
-    },
-    async ({ action, docId, snapshotPath }) => {
-      const { getDatabase } = await import("../db/database.js");
-      const db = await getDatabase();
-
-      if (action === "stats") {
-        const docCountRow = await db.prepare("SELECT COUNT(*) as cnt FROM documents").get();
-        const docCount = docCountRow ? docCountRow.cnt : 0;
-        const secCountRow = await db.prepare("SELECT COUNT(*) as cnt FROM sections").get();
-        const secCount = secCountRow ? secCountRow.cnt : 0;
-        const chunkCountRow = await db.prepare("SELECT COUNT(*) as cnt FROM micro_chunks").get();
-        const chunkCount = chunkCountRow ? chunkCountRow.cnt : 0;
-        const edgeCountRow = await db.prepare("SELECT COUNT(*) as cnt FROM graph_edges").get();
-        const edgeCount = edgeCountRow ? edgeCountRow.cnt : 0;
+        snapshotPath: optStr().describe("File path for snapshot export/import"),
+        scope: z.enum(["all", "project", "global"]).nullish().describe("For stats/list/read: global + current project by default. Delete defaults to the current project (or global outside Git); pass all/global explicitly for broader removal"),
+      }),
+    },
+    async ({ action, docId, snapshotPath, scope }) => {
+      const { getDatabase } = await import("../db/database.js");
+      const db = await getDatabase();
+      const scopeKeys = ["stats", "list", "read_document", "delete"].includes(action)
+        ? await resolveManageRagScopeKeys(action, scope)
+        : null;
+      const placeholders = scopeKeys ? scopeKeys.map(() => "?").join(",") : "";
+      const visibleDocWhere = scopeKeys
+        ? `EXISTS (SELECT 1 FROM document_scopes ds WHERE ds.doc_id = d.id AND ds.scope_key IN (${placeholders}))`
+        : "1=1";
+
+      if (action === "stats") {
+        const docCountRow = await db.prepare(`SELECT COUNT(*) as cnt FROM documents d WHERE ${visibleDocWhere}`).get(...scopeKeys);
+        const docCount = docCountRow ? docCountRow.cnt : 0;
+        const secCountRow = await db.prepare(`SELECT COUNT(*) as cnt FROM sections s JOIN documents d ON d.id = s.doc_id WHERE ${visibleDocWhere}`).get(...scopeKeys);
+        const secCount = secCountRow ? secCountRow.cnt : 0;
+        const chunkCountRow = await db.prepare(`SELECT COUNT(*) as cnt FROM micro_chunks m JOIN documents d ON d.id = m.doc_id WHERE ${visibleDocWhere}`).get(...scopeKeys);
+        const chunkCount = chunkCountRow ? chunkCountRow.cnt : 0;
+        const visibleDocIds = await db.prepare(`SELECT d.id FROM documents d WHERE ${visibleDocWhere}`).all(...scopeKeys);
+        let edgeCount = 0;
+        if (visibleDocIds.length > 0) {
+          const docIds = visibleDocIds.map((row) => row.id);
+          const docPlaceholders = docIds.map(() => "?").join(",");
+          const ownedRows = await db.prepare(`
+            SELECT id FROM sections WHERE doc_id IN (${docPlaceholders})
+            UNION SELECT id FROM medium_chunks WHERE doc_id IN (${docPlaceholders})
+            UNION SELECT id FROM micro_chunks WHERE doc_id IN (${docPlaceholders})
+          `).all(...docIds, ...docIds, ...docIds);
+          const ownedIds = [...docIds, ...ownedRows.map((row) => row.id)];
+          const edgePlaceholders = ownedIds.map(() => "?").join(",");
+          const edgeCountRow = await db.prepare(`SELECT COUNT(*) as cnt FROM graph_edges WHERE source_id IN (${edgePlaceholders}) OR target_id IN (${edgePlaceholders})`).get(...ownedIds, ...ownedIds);
+          edgeCount = edgeCountRow ? edgeCountRow.cnt : 0;
+        }
         return {
           content: [
             {
@@ -270,8 +303,15 @@ export function registerRagTools(server) {
         };
       }
 
-      if (action === "list") {
-        const docs = await db.prepare("SELECT id, title, path, blob_hash, created_at FROM documents ORDER BY created_at DESC").all();
+      if (action === "list") {
+        const docs = await db.prepare(`
+          SELECT d.id, d.title, d.path, d.blob_hash, d.created_at,
+                 GROUP_CONCAT(ds.scope_key) AS scopes
+          FROM documents d
+          JOIN document_scopes ds ON ds.doc_id = d.id AND ds.scope_key IN (${placeholders})
+          GROUP BY d.id, d.title, d.path, d.blob_hash, d.created_at
+          ORDER BY d.created_at DESC
+        `).all(...scopeKeys);
         return {
           content: [{ type: "text", text: JSON.stringify(docs, null, 2) }],
         };
@@ -279,9 +319,9 @@ export function registerRagTools(server) {
 
       if (action === "read_document") {
         if (!docId) throw new Error("docId parameter is required for read_document action");
-        const doc = await db
-          .prepare("SELECT id, title, path, blob_hash, created_at FROM documents WHERE id = ? OR path = ? OR title = ?")
-          .get(docId, docId, docId);
+        const doc = await db
+          .prepare(`SELECT d.id, d.title, d.path, d.blob_hash, d.created_at FROM documents d WHERE (d.id = ? OR d.path = ? OR d.title = ?) AND ${visibleDocWhere}`)
+          .get(docId, docId, docId, ...scopeKeys);
         if (!doc) {
           throw new Error(`Document not found in knowledge base for docId: ${docId}`);
         }
@@ -307,10 +347,29 @@ export function registerRagTools(server) {
         };
       }
 
-      if (action === "delete") {
-        if (!docId) throw new Error("docId parameter is required for delete action");
-        const { deleteDocument } = await import("../ingest/pipeline.js");
-        const result = await deleteDocument(docId, db);
+      if (action === "delete") {
+        if (!docId) throw new Error("docId parameter is required for delete action");
+        const visible = await db
+          .prepare(`SELECT d.id FROM documents d WHERE (d.id = ? OR d.path = ? OR d.title = ?) AND ${visibleDocWhere}`)
+          .get(docId, docId, docId, ...scopeKeys);
+        if (!visible) throw new Error(`Document not found in the selected RAG scope for docId: ${docId}`);
+        const scopeRemoval = await removeDocumentScopes(db, visible.id, scopeKeys);
+        if (scopeRemoval.remainingScopes > 0) {
+          return {
+            content: [{
+              type: "text",
+              text: JSON.stringify({
+                deleted: false,
+                unlinked: true,
+                docId: visible.id,
+                removedScopes: scopeRemoval.removedScopes,
+                remainingScopes: scopeRemoval.remainingScopes,
+              }, null, 2),
+            }],
+          };
+        }
+        const { deleteDocument } = await import("../ingest/pipeline.js");
+        const result = await deleteDocument(visible.id, db);
         return {
           content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
         };