@lotargo/memory_plugin 1.6.3 → 1.6.5

package/mcp-server/ingest/pipeline.js

@@ -8,8 +8,10 @@ import { buildTripleHierarchy } from "./chunker.js";
 import { embedBatch, vectorToBuffer } from "../ml/model_manager.js";
 import { buildGraphEdges, saveGraphEdges } from "../graph/graph_extractor.js";
 import { getConfig } from "../config/config_manager.js";
-import { assertIngestPathAllowed } from "../security/path_guard.js";
-import { logger } from "../logger.js";
+import { assertIngestPathAllowed } from "../security/path_guard.js";
+import { logger } from "../logger.js";
+import { GLOBAL_KEY } from "../memory.js";
+import { addDocumentScope } from "../rag_scope.js";
 
 export async function ingestDocument({
   content,
@@ -17,9 +19,10 @@ export async function ingestDocument({
   path = null,
   title = null,
   customDb = null,
-  customBlobDir = BLOBS_DIR,
-  generateEmbeddings = true,
-}) {
+  customBlobDir = BLOBS_DIR,
+  generateEmbeddings = true,
+  projectScope = GLOBAL_KEY,
+}) {
   const db = customDb || await getDatabase();
 
   let effectiveType = type;
@@ -47,14 +50,58 @@ export async function ingestDocument({
   const { markdown, title: docTitle, metadata } = await normalizeContent({ content, type: effectiveType, path: effectivePath, title: effectiveTitle });
   if (type === "url") metadata.source_type = "url";
 
-  const blobRes = await saveBlob(markdown, customBlobDir);
-  const blobHash = blobRes.hash;
-
-  const docId = `doc_${randomUUID().replace(/-/g, "").substring(0, 12)}`;
-  const docPath = effectivePath || `virtual://${type}/${docId}`;
-  const now = Date.now();
-
-  const hierarchy = buildTripleHierarchy(markdown, docId, docTitle);
+  const blobRes = await saveBlob(markdown, customBlobDir);
+  const blobHash = blobRes.hash;
+
+  const generatedDocId = `doc_${randomUUID().replace(/-/g, "").substring(0, 12)}`;
+  const docPath = effectivePath || `virtual://${type}/${generatedDocId}`;
+  const existingDoc = await db.prepare("SELECT * FROM documents WHERE path = ?").get(docPath);
+  const docId = existingDoc?.id || generatedDocId;
+  const now = Date.now();
+
+  // Identical re-ingestion only adds the new project/global scope. Keeping the
+  // existing document id preserves every Notebook link and avoids recomputing vectors.
+  if (existingDoc && existingDoc.checksum === blobHash) {
+    await db.exec("BEGIN IMMEDIATE;");
+    try {
+      await db
+        .prepare("UPDATE documents SET title = ?, metadata_json = ?, updated_at = ? WHERE id = ?;")
+        .run(docTitle, JSON.stringify(metadata), now, docId);
+      const assignedScope = await addDocumentScope(db, docId, projectScope);
+      await db.exec("COMMIT;");
+
+      const sectionsRow = await db.prepare("SELECT COUNT(*) AS cnt FROM sections WHERE doc_id = ?").get(docId);
+      const chunksRow = await db.prepare("SELECT COUNT(*) AS cnt FROM micro_chunks WHERE doc_id = ?").get(docId);
+      if (getConfig().mode === "hybrid-sync") {
+        try {
+          const { exportDocumentData } = await import("./exporter.js");
+          const { enqueueSyncTask } = await import("../db/sync_queue.js");
+          await enqueueSyncTask("ingest_document", docId, await exportDocumentData(docId, db));
+        } catch (err) {
+          logger.error("Failed to queue document scope sync task:", err.message);
+        }
+      }
+      return {
+        docId,
+        doc_id: docId,
+        path: docPath,
+        blobHash,
+        blob_hash: blobHash,
+        title: docTitle,
+        sectionsCount: sectionsRow?.cnt || 0,
+        sections_count: sectionsRow?.cnt || 0,
+        microChunksCount: chunksRow?.cnt || 0,
+        micro_chunks_count: chunksRow?.cnt || 0,
+        deduplicated: true,
+        projectScope: assignedScope,
+      };
+    } catch (err) {
+      await db.exec("ROLLBACK;");
+      throw new Error(`Ingestion scope transaction failed: ${err.message}`);
+    }
+  }
+
+  const hierarchy = buildTripleHierarchy(markdown, docId, docTitle);
 
   if (generateEmbeddings && hierarchy.microChunks.length > 0) {
     const BATCH_SIZE = getConfig().batchSize || 12;
@@ -84,31 +131,49 @@ export async function ingestDocument({
     }
   }
 
-  await db.exec("BEGIN IMMEDIATE;");
-  try {
-    const existingDoc = await db.prepare("SELECT id FROM documents WHERE path = ?").get(docPath);
-    if (existingDoc) {
-      try {
-        await db.prepare("DELETE FROM micro_chunks_fts WHERE id IN (SELECT id FROM micro_chunks WHERE doc_id = ?);").run(existingDoc.id);
-      } catch {}
-      await db.prepare("DELETE FROM graph_edges WHERE source_id = ? OR target_id = ?").run(existingDoc.id, existingDoc.id);
-      await db.prepare("DELETE FROM documents WHERE id = ?").run(existingDoc.id);
-    }
-
-    await db.prepare(`
-      INSERT INTO documents (id, path, blob_hash, title, checksum, toc_json, metadata_json, created_at, updated_at)
-      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?);
-    `).run(
-      docId,
-      docPath,
-      blobHash,
-      docTitle,
-      blobHash,
-      hierarchy.toc,
-      JSON.stringify(metadata),
-      now,
-      now
-    );
+  await db.exec("BEGIN IMMEDIATE;");
+  try {
+    if (existingDoc) {
+      const ownedRows = await db.prepare(`
+        SELECT id FROM sections WHERE doc_id = ?
+        UNION SELECT id FROM medium_chunks WHERE doc_id = ?
+        UNION SELECT id FROM micro_chunks WHERE doc_id = ?;
+      `).all(docId, docId, docId);
+      const ownedIds = [docId, ...ownedRows.map((row) => row.id)];
+      try {
+        await db.prepare("DELETE FROM micro_chunks_fts WHERE id IN (SELECT id FROM micro_chunks WHERE doc_id = ?);").run(docId);
+      } catch {}
+      if (ownedIds.length > 0) {
+        const placeholders = ownedIds.map(() => "?").join(",");
+        await db
+          .prepare(`DELETE FROM graph_edges WHERE source_id IN (${placeholders}) OR target_id IN (${placeholders});`)
+          .run(...ownedIds, ...ownedIds);
+      }
+      await db.prepare("DELETE FROM micro_chunks WHERE doc_id = ?;").run(docId);
+      await db.prepare("DELETE FROM medium_chunks WHERE doc_id = ?;").run(docId);
+      await db.prepare("DELETE FROM sections WHERE doc_id = ?;").run(docId);
+      await db.prepare(`
+        UPDATE documents
+        SET blob_hash = ?, title = ?, checksum = ?, toc_json = ?, metadata_json = ?, updated_at = ?
+        WHERE id = ?;
+      `).run(blobHash, docTitle, blobHash, hierarchy.toc, JSON.stringify(metadata), now, docId);
+    } else {
+      await db.prepare(`
+        INSERT INTO documents (id, path, blob_hash, title, checksum, toc_json, metadata_json, created_at, updated_at)
+        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?);
+      `).run(
+        docId,
+        docPath,
+        blobHash,
+        docTitle,
+        blobHash,
+        hierarchy.toc,
+        JSON.stringify(metadata),
+        now,
+        now
+      );
+    }
+    const assignedScope = await addDocumentScope(db, docId, projectScope);
 
     const insertSectionStmt = db.prepare(`
       INSERT INTO sections (id, doc_id, heading, breadcrumbs, content, token_count)
@@ -142,14 +207,46 @@ export async function ingestDocument({
       await insertFtsStmt.run(micro.id, micro.content, micro.breadcrumbs);
     }
 
-    const edges = buildGraphEdges(docId, hierarchy);
-    await saveGraphEdges(db, edges);
-
-    await db.exec("COMMIT;");
+    const edges = buildGraphEdges(docId, hierarchy);
+    await saveGraphEdges(db, edges);
+
+    // Recreate graph projections for preserved Notebook links after replacing
+    // the document's structural chunks. The knowledge_links rows themselves
+    // remain stable because the document id remains stable.
+    if (existingDoc) {
+      const links = await db.prepare("SELECT * FROM knowledge_links WHERE doc_id = ?").all(docId);
+      const insertLinkEdge = db.prepare(`
+        INSERT OR IGNORE INTO graph_edges (source_id, target_id, relation_type, metadata_json, created_at)
+        VALUES (?, ?, ?, ?, ?);
+      `);
+      for (const link of links) {
+        const targetSpec = link.start_line
+          ? `${docId}:L${link.start_line}-${link.end_line || link.start_line}`
+          : docId;
+        await insertLinkEdge.run(
+          `fact:${link.fact_key}:${link.fact_text.substring(0, 30)}`,
+          targetSpec,
+          link.relation_type || "LINKS_TO",
+          JSON.stringify({ linkId: link.id }),
+          link.created_at || now
+        );
+      }
+    }
+
+    await db.exec("COMMIT;");
   } catch (err) {
     await db.exec("ROLLBACK;");
     throw new Error(`Ingestion transaction failed: ${err.message}`);
-  }
+  }
+
+  if (existingDoc?.blob_hash && existingDoc.blob_hash !== blobHash) {
+    const refs = await db.prepare("SELECT COUNT(*) AS cnt FROM documents WHERE blob_hash = ?").get(existingDoc.blob_hash);
+    if (!refs?.cnt) {
+      try {
+        await deleteBlob(existingDoc.blob_hash, customBlobDir);
+      } catch {}
+    }
+  }
 
   if (getConfig().mode === "hybrid-sync") {
     try {
@@ -172,14 +269,15 @@ export async function ingestDocument({
     sectionsCount: hierarchy.sections.length,
     sections_count: hierarchy.sections.length,
     microChunksCount: hierarchy.microChunks.length,
-    micro_chunks_count: hierarchy.microChunks.length,
-    deduplicated: blobRes.deduplicated,
-  };
-}
+    micro_chunks_count: hierarchy.microChunks.length,
+    deduplicated: blobRes.deduplicated,
+    projectScope: projectScope || GLOBAL_KEY,
+  };
+}
 
 export async function deleteDocument(docIdOrPath, customDb = null, customBlobDir = BLOBS_DIR) {
   const db = customDb || await getDatabase();
-  const doc = await db.prepare("SELECT * FROM documents WHERE id = ? OR path = ?").get(docIdOrPath, docIdOrPath);
+  const doc = await db.prepare("SELECT * FROM documents WHERE id = ? OR path = ? OR title = ?").get(docIdOrPath, docIdOrPath, docIdOrPath);
   if (!doc) {
     return { deleted: false, reason: "Document not found" };
   }

package/mcp-server/memory.js

@@ -48,8 +48,18 @@ export function ensureDirSync() {
   if (!existsSync(exportsDir)) mkdirSync(exportsDir, { recursive: true });
 }
 
+export function getActiveWorkspaceDir() {
+  return (
+    process.env.WORKSPACE_DIR ||
+    process.env.PROJECT_DIR ||
+    process.env.OPENCODE_WORKSPACE ||
+    process.env.IDE_WORKSPACE ||
+    null
+  );
+}
+
 export function canonicalPath(dir) {
-  let p = resolve(dir || process.cwd());
+  let p = resolve(dir || getActiveWorkspaceDir() || process.cwd());
   if (process.platform === "win32") {
     p = p.replace(/\\/g, "/").replace(/^([a-zA-Z]):/, (_, d) => `${d.toLowerCase()}:`);
   }
@@ -57,13 +67,13 @@ export function canonicalPath(dir) {
 }
 
 export async function projectKey(worktree, directory) {
-  const dir = worktree || directory || process.cwd();
+  const dir = worktree || directory || getActiveWorkspaceDir() || process.cwd();
   const identity = await resolveProjectIdentity(dir);
   return identity ? identity.key : null;
 }
 
 export async function projectName(worktree, directory) {
-  const dir = worktree || directory || process.cwd();
+  const dir = worktree || directory || getActiveWorkspaceDir() || process.cwd();
   const identity = await resolveProjectIdentity(dir);
   return identity ? identity.name : (dir ? basename(resolve(dir)) : "default");
 }

package/mcp-server/prompt_manager.js

@@ -10,10 +10,12 @@ const END_MARKER = "<!-- END MEMORY AGENT PROMPT -->";
 export const PROMPT_BLOCK = `${START_MARKER}
 [SYSTEM INSTRUCTION: PERSONAL CONTEXT & MEMORY AGENT]
 1. MANDATORY FIRST STEP (SESSION INITIALIZATION): At the very start of every session or conversation, your VERY FIRST ACTION MUST BE to execute \`recall\` from \`memory-agent\` with \`scope: "all"\` (or without restrictive query filters) to load ALL saved global facts, user preferences, personal context, and project guidelines BEFORE performing any other tasks or reading code. Do NOT filter or restrict the initial \`recall\` call with specific query keywords or scoped parameters, so that no global facts are missed.
-2. PROACTIVE SAVING DIRECTIVE: You MUST automatically and proactively call \`remember\` from \`memory-agent\` whenever the user shares durable facts, personal preferences, coding guidelines, technology choices, or project architecture decisions. Do NOT wait for explicit user commands like "remember this".
-3. SIGNAL FILTER: Save only high-signal facts (name, language, roles, constraints, tech stack preferences, architecture decisions, conventions). Translate facts into clear, concise English when saving. Do NOT save transient details or one-off conversation turns.
-4. QUERY OPTIMIZATION: When using \`query_knowledge_base\` from \`memory-agent\`, transform the user's natural language question into concept-dense search queries. Do NOT send raw conversational questions ("как мне сделать X?", "что такое Y?"). Instead, extract key terms and use concise factual phrases. For multi-part queries or comparisons, use \`batch_query_knowledge_base\` with multiple targeted queries — this is more efficient (single API call, single ONNX inference pass) and yields higher retrieval quality than separate calls.
-5. POLICY EXPANSION: The knowledge base automatically expands table summaries and code signatures for better recall (config \`policyExpansion\`, default: ON). If you need raw micro_chunk precision without expansion, pass \`policyExpansion: false\` per-call or set via config.${END_MARKER}`;
+2. PROJECT IDENTITY INITIALIZATION: After the initial recall, call \`memory_info\` for the current workspace. If it reports a Git identity with \`Registry: unlinked\`, immediately call \`link_project_memory\` for the current directory. If linking migrated legacy facts, repeat \`recall(scope: "all")\`. Outside a Git repository, do not create project memory; use global memory only.
+3. PROACTIVE SAVING DIRECTIVE: You MUST automatically and proactively call \`remember\` from \`memory-agent\` whenever the user shares durable facts, personal preferences, coding guidelines, technology choices, or project architecture decisions. Do NOT wait for explicit user commands like "remember this".
+4. SIGNAL FILTER: Save only high-signal facts (name, language, roles, constraints, tech stack preferences, architecture decisions, conventions). Translate facts into clear, concise English when saving. Do NOT save transient details or one-off conversation turns.
+5. QUERY OPTIMIZATION: When using \`query_knowledge_base\` from \`memory-agent\`, transform the user's natural language question into concept-dense search queries. Do NOT send raw conversational questions ("как мне сделать X?", "что такое Y?"). Instead, extract key terms and use concise factual phrases. For multi-part queries or comparisons, use \`batch_query_knowledge_base\` with multiple targeted queries — this is more efficient (single API call, single ONNX inference pass) and yields higher retrieval quality than separate calls.
+6. SELECTIVE RAG CURATION: When web research or current technical documentation yields reliable project knowledge likely to be needed again, ingest the relevant source or excerpt with project scope and link it to the project-scoped Notebook fact it supports. Use global RAG scope only for sources intentionally reusable across projects. Prioritize authoritative documentation and knowledge newer than model training. Do not ingest everything encountered, transient output, or duplicate low-value content.
+7. POLICY EXPANSION: The knowledge base automatically expands table summaries and code signatures for better recall (config \`policyExpansion\`, default: ON). If you need raw micro_chunk precision without expansion, pass \`policyExpansion: false\` per-call or set via config.${END_MARKER}`;
 
 // Plugin-owned files live here so we never destroy user-owned config content.
 const AGENT_CONFIG_DIR = join(homedir(), ".config", "memory-agent");
@@ -115,9 +117,10 @@ export function upsertPromptBlock(content, block = PROMPT_BLOCK) {
   return clean ? `${clean}\n\n${block}\n` : `${block}\n`;
 }
 
-export async function enableGlobalPrompt() {
-  const promptFile = await syncPromptFile();
-  const targets = getGlobalPromptTargets();
+export async function enableGlobalPrompt(targetNames = null) {
+  const promptFile = await syncPromptFile();
+  const requested = Array.isArray(targetNames) ? new Set(targetNames) : null;
+  const targets = getGlobalPromptTargets().filter((target) => !requested || requested.has(target.name));
   const state = await loadState();
   const results = [];
 

package/mcp-server/retrieval/retriever.js

@@ -10,19 +10,29 @@ export function sanitizeFtsQuery(query) {
   return words.join(" OR ");
 }
 
-export async function bm25Search(db, query, limit = 30) {
-  const ftsQuery = sanitizeFtsQuery(query);
-  if (!ftsQuery) return [];
-
-  try {
-    const stmt = db.prepare(`
-      SELECT id, content, breadcrumbs, rank
-      FROM micro_chunks_fts
-      WHERE micro_chunks_fts MATCH ?
-      ORDER BY rank
-      LIMIT ?;
-    `);
-    const rows = await stmt.all(ftsQuery, limit);
+export async function bm25Search(db, query, limit = 30, scopeKeys = null) {
+  const ftsQuery = sanitizeFtsQuery(query);
+  if (!ftsQuery) return [];
+
+  try {
+    const scoped = Array.isArray(scopeKeys) && scopeKeys.length > 0;
+    const scopeClause = scoped
+      ? `AND EXISTS (
+          SELECT 1 FROM micro_chunks scoped_m
+          JOIN document_scopes scoped_ds ON scoped_ds.doc_id = scoped_m.doc_id
+          WHERE scoped_m.id = micro_chunks_fts.id
+            AND scoped_ds.scope_key IN (${scopeKeys.map(() => "?").join(",")})
+        )`
+      : "";
+    const stmt = db.prepare(`
+      SELECT id, content, breadcrumbs, rank
+      FROM micro_chunks_fts
+      WHERE micro_chunks_fts MATCH ?
+      ${scopeClause}
+      ORDER BY rank
+      LIMIT ?;
+    `);
+    const rows = await stmt.all(ftsQuery, ...(scoped ? scopeKeys : []), limit);
     return rows.map((r, i) => ({
       id: r.id,
       content: r.content,
@@ -50,7 +60,7 @@ export function toVectorBytes(value) {
   return null;
 }
 
-export async function vectorSearch(db, queryVector, limit = 30, minSim = 0.25) {
+export async function vectorSearch(db, queryVector, limit = 30, minSim = 0.25, scopeKeys = null) {
   if (!queryVector || queryVector.length === 0) return [];
 
   const vectorDim = queryVector.length;
@@ -59,21 +69,32 @@ export async function vectorSearch(db, queryVector, limit = 30, minSim = 0.25) {
   const tempVec = new Float32Array(tempBuf);
 
   const scanLimit = Number(getConfig().vectorScanLimit) || 0;
-  const scanSql = scanLimit > 0
-    ? `
-      SELECT m.id, m.section_id, m.doc_id, m.content, m.vector, s.breadcrumbs
-      FROM micro_chunks m
-      JOIN sections s ON m.section_id = s.id
-      LIMIT ?;
-    `
-    : `
-      SELECT m.id, m.section_id, m.doc_id, m.content, m.vector, s.breadcrumbs
-      FROM micro_chunks m
-      JOIN sections s ON m.section_id = s.id;
-    `;
-
-  const stmt = db.prepare(scanSql);
-  const rows = scanLimit > 0 ? await stmt.all(scanLimit) : await stmt.all();
+  const scoped = Array.isArray(scopeKeys) && scopeKeys.length > 0;
+  const scopeClause = scoped
+    ? `WHERE EXISTS (
+        SELECT 1 FROM document_scopes scoped_ds
+        WHERE scoped_ds.doc_id = m.doc_id
+          AND scoped_ds.scope_key IN (${scopeKeys.map(() => "?").join(",")})
+      )`
+    : "";
+  const scanSql = scanLimit > 0
+    ? `
+      SELECT m.id, m.section_id, m.doc_id, m.content, m.vector, s.breadcrumbs
+      FROM micro_chunks m
+      JOIN sections s ON m.section_id = s.id
+      ${scopeClause}
+      LIMIT ?;
+    `
+    : `
+      SELECT m.id, m.section_id, m.doc_id, m.content, m.vector, s.breadcrumbs
+      FROM micro_chunks m
+      JOIN sections s ON m.section_id = s.id
+      ${scopeClause};
+    `;
+
+  const stmt = db.prepare(scanSql);
+  const scopeParams = scoped ? scopeKeys : [];
+  const rows = scanLimit > 0 ? await stmt.all(...scopeParams, scanLimit) : await stmt.all(...scopeParams);
   const scored = [];
   for (const r of rows) {
     // node:sqlite returns BLOBs as plain Uint8Array (NOT Buffer), the Turso
@@ -244,7 +265,8 @@ export async function batchHybridQuery(queries, options = {}) {
     rerankerEnabled = null,
     instruction = null,
     generateEmbeddings = true,
-    policyExpansion = null,
+    policyExpansion = null,
+    scopeKeys = null,
   } = options;
 
   const db = customDb || await getDatabase();
@@ -277,7 +299,8 @@ export async function batchHybridQuery(queries, options = {}) {
         rerankerEnabled: useReranker,
         instruction,
         generateEmbeddings,
-        policyExpansion: usePolicyExpansion,
+        policyExpansion: usePolicyExpansion,
+        scopeKeys,
         _precomputedVector: queryVectors[i] || null,
       })
     )
@@ -299,7 +322,8 @@ export async function hybridQuery({
   rerankerEnabled = null,
   instruction = null,
   generateEmbeddings = true,
-  policyExpansion = null, // null = use config default
+  policyExpansion = null, // null = use config default
+  scopeKeys = null, // null = all documents; tool surfaces pass global/current-project keys
   _precomputedVector = null, // internal: skip embedText if batch already computed
 }) {
   const db = customDb || await getDatabase();
@@ -327,28 +351,28 @@ export async function hybridQuery({
   let fusedHits = [];
 
   if (algo === "lexical_only" || algo === "bm25_only") {
-    const bm25Hits = await bm25Search(db, query, limit * 4);
+    const bm25Hits = await bm25Search(db, query, limit * 4, scopeKeys);
     fusedHits = bm25Hits.map((hit) => ({
       ...hit,
       score: 1.0 / hit.bm25_rank,
     }));
   } else if (algo === "semantic_only" || algo === "vector_only") {
     const queryVector = await getQueryVector();
-    const vectorHits = await vectorSearch(db, queryVector, limit * 4, 0.10);
+    const vectorHits = await vectorSearch(db, queryVector, limit * 4, 0.10, scopeKeys);
     fusedHits = vectorHits.map((hit) => ({
       ...hit,
       score: hit.cosine_sim,
     }));
   } else if (algo === "rrf") {
-    const bm25Hits = await bm25Search(db, query, 30);
+    const bm25Hits = await bm25Search(db, query, 30, scopeKeys);
     const queryVector = await getQueryVector();
-    const vectorHits = await vectorSearch(db, queryVector, 30, 0.10);
+    const vectorHits = await vectorSearch(db, queryVector, 30, 0.10, scopeKeys);
     fusedHits = rrfFusion(bm25Hits, vectorHits, 60, scoreThreshold);
   } else {
     // Default: RSF
-    const bm25Hits = await bm25Search(db, query, 30);
+    const bm25Hits = await bm25Search(db, query, 30, scopeKeys);
     const queryVector = await getQueryVector();
-    const vectorHits = await vectorSearch(db, queryVector, 30, 0.10);
+    const vectorHits = await vectorSearch(db, queryVector, 30, 0.10, scopeKeys);
     fusedHits = rsfFusion(bm25Hits, vectorHits, alphaWeight, scoreThreshold);
   }
 

package/mcp-server/setup.js

@@ -216,19 +216,23 @@ export async function runSetup() {
             ? "  [OK] Codex: added direct Node.js memory-agent launcher to ~/.codex/config.toml"
             : "  [OK] Codex: migrated memory-agent to a direct Node.js launcher in ~/.codex/config.toml"
         );
-        configuredCount++;
       } else {
         console.log("  [INFO] Codex: direct Node.js memory-agent launcher already configured");
       }
+      configuredCount++;
     } catch (err) {
       console.log("  [FAIL] Codex setup failed:", err.message);
     }
   }
 
   // 5. Global Prompt Instructions (Antigravity, Codex, Claude Code)
-  try {
-    const { enableGlobalPrompt } = await import("./prompt_manager.js");
-    const promptResults = await enableGlobalPrompt();
+  try {
+    const { enableGlobalPrompt } = await import("./prompt_manager.js");
+    const promptTargets = [];
+    if (doAntigravity) promptTargets.push("Antigravity");
+    if (doCodex) promptTargets.push("Codex");
+    if (doClaude) promptTargets.push("Claude Code");
+    const promptResults = await enableGlobalPrompt(promptTargets);
     promptResults.forEach((r) => {
       if (r.status === "enabled") {
         console.log(`  [OK] ${r.name}: enabled global prompt instruction in ${r.filePath}`);
@@ -250,14 +254,16 @@ export async function runSetup() {
     const packageSkillsDir = join(packageDir, "skills");
     if (existsSync(packageSkillsDir)) {
       const opencodeDir = process.env.OPENCODE_CONFIG_DIR || join(home, ".config", "opencode");
-      const targets = [
-        { name: "OpenCode", dir: join(opencodeDir, "skills") },
-        { name: "Antigravity", dir: join(home, ".gemini", "config", "skills") },
-        { name: "Codex", dir: join(home, ".codex", "skills") },
-        { name: "Claude Code", dir: join(home, ".claude", "skills") },
-      ];
-      const cwd = process.cwd();
-      if (existsSync(join(cwd, ".agents"))) {
+      const targets = [];
+      if (doOpenCode) targets.push({ name: "OpenCode", dir: join(opencodeDir, "skills") });
+      if (doAntigravity) targets.push({ name: "Antigravity", dir: join(home, ".gemini", "config", "skills") });
+      if (doCodex) {
+        targets.push({ name: "Codex", dir: join(home, ".codex", "skills") });
+        targets.push({ name: "Codex shared agents", dir: join(home, ".agents", "skills") });
+      }
+      if (doClaude) targets.push({ name: "Claude Code", dir: join(home, ".claude", "skills") });
+      const cwd = process.cwd();
+      if (doAntigravity && existsSync(join(cwd, ".agents"))) {
         targets.push({ name: "Antigravity (local)", dir: join(cwd, ".agents", "skills") });
       }