@lotargo/memory_plugin 1.4.621 → 1.5.0

package/mcp-server/index.js

@@ -1,679 +1,42 @@
-#!/usr/bin/env node
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
-import * as z from "zod/v4";
-import { ensureDir, readMemory, readMemoryRaw, writeMemory, today, MEMORY_DIR, GLOBAL_KEY, scopeKey, projectKey, projectName, canonicalPath, listProjectStores, storeFilePath } from "./memory.js";
-import {
-  parseFactEntry,
-  factText,
-  factMeta,
-  withMeta,
-  nextFactId,
-  isKeepFact,
-  displayFact,
-  formatFactEntry,
-  matchesQuery,
-  matchesTags,
-  inDateRange,
-} from "./fact_format.js";
-import { readFile } from "node:fs/promises";
-import { join } from "node:path";
-
-// Resolve a fact reference (1-based number, metadata id, or text) to an index.
-function resolveFactIndex(entries, ref) {
-  const trimmed = String(ref || "").trim();
-  if (!trimmed) return -1;
-  const num = parseInt(trimmed, 10);
-  if (/^\d+$/.test(trimmed) && num >= 1 && num <= entries.length) return num - 1;
-  const idIdx = entries.findIndex((e) => factMeta(e).id === trimmed);
-  if (idIdx !== -1) return idIdx;
-  const textIdx = entries.findIndex((e) => factText(e).toLowerCase().includes(trimmed.toLowerCase()));
-  return textIdx;
-}
-
-const cliArgs = process.argv.slice(2);
-
-if (cliArgs.includes("setup") || cliArgs.includes("install") || cliArgs.includes("--setup") || cliArgs.includes("-s")) {
-  const { runSetup } = await import("./setup.js");
-  await runSetup();
-  process.exit(0);
-}
-
-if (cliArgs.includes("cli") || cliArgs.includes("config") || cliArgs.includes("--cli") || cliArgs.includes("-c") || cliArgs.includes("login") || cliArgs.includes("logout") || cliArgs.includes("auth-status") || cliArgs.includes("auth_status") || cliArgs.includes("auth")) {
-  const { runCli } = await import("./cli.js");
-  await runCli();
-  process.exit(0);
-}
-
-await ensureDir();
-
-const server = new McpServer({
-  name: "memory-agent",
-  version: "1.0.0",
-});
-
-// Optional string/number that tolerates null (some tool-call layers fill omitted
-// optional args with null). Linking fields must NEVER be mandatory.
-const optStr = () => z.string().optional().nullable();
-const optNum = () => z.number().optional().nullable();
-const defStr = (fallback) =>
-  z
-    .string()
-    .nullish()
-    .transform((v) => (v === null || v === undefined || v === "" ? fallback : v));
-const defBool = (fallback) => z.boolean().nullish().transform((v) => (v === null || v === undefined ? fallback : v));
-const defNum = (fallback) => z.number().nullish().transform((v) => (v === null || v === undefined ? fallback : v));
-
-// --- Legacy Key-Value Memory Tools ---
-
-// --- Legacy Key-Value Memory Tools & Agent Graph Linking ---
-
-server.registerTool(
-  "remember",
-  {
-    description:
-      "Save an important, durable fact to memory. Only use for high-signal information " +
-      "(name, goals, constraints, tech preferences, project conventions). " +
-      "docId/startLine/endLine/relationType are OPTIONAL and only used to link the fact to a " +
-      "Knowledge Base document or line range; omit them when no linking is needed. " +
-      "ttl is OPTIONAL (e.g. '90d', '2w', '24h') — expired facts are shown with [EXPIRED] but not auto-deleted. " +
-      "keep=true protects the fact from forget deletion unless force=true. " +
-      "tags is OPTIONAL comma-separated text for filtering. " +
-      "supersedes is OPTIONAL: a number (from recall), id, or text of a fact this one replaces; " +
-      "the target is then marked [SUPERSEDED]. " +
-      "Translate the fact into English and keep it concise. " +
-      "scope: 'project' (default) or 'global'",
-    inputSchema: z.object({
-      fact: z.string().describe("The fact to remember, written in English"),
-      scope: defStr("project").describe("'project' (default) or 'global'"),
-      docId: optStr().describe("Optional document ID, title, or path to link this fact to"),
-      startLine: optNum().describe("Optional starting line number in target document"),
-      endLine: optNum().describe("Optional ending line number in target document"),
-      relationType: defStr("LINKS_TO").describe("Relation type (e.g. 'RULES_FOR', 'IMPLEMENTS', 'REFERENCES')"),
-      ttl: optStr().describe("Optional time-to-live, e.g. '90d', '2w', '24h', '12m'"),
-      keep: defBool(false).describe("Protect the fact from forget deletion unless force=true"),
-      tags: optStr().describe("Optional comma-separated tags, e.g. 'pref,arch'"),
-      supersedes: optStr().describe("Optional number, id, or text of the fact this one replaces"),
-    }),
-  },
-  async ({ fact, scope, docId, startLine, endLine, relationType, ttl, keep, tags, supersedes }) => {
-    const key = scopeKey(scope, null, null);
-    const entries = await readMemory(key);
-    const factNormalized = fact.toLowerCase().trim();
-    let duplicate = false;
-    if (entries.some((e) => factText(e).toLowerCase().trim() === factNormalized)) {
-      duplicate = true;
-    }
-
-    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 targetMeta = factMeta(entries[targetIdx]);
-          const targetId = targetMeta.id || 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 {
-          supersededInfo = " (note: supersedes target not found)";
-        }
-      }
-      if (!meta.id) meta.id = nextFactId(entries);
-      entries.push(formatFactEntry({ date, time, text: fact, meta }));
-      await writeMemory(key, entries);
-    }
-
-    let linkInfo = "";
-    if (docId) {
-      const { linkFactToDocument } = await import("./graph/knowledge_linker.js");
-      try {
-        const linkRes = linkFactToDocument({
-          factKey: key,
-          factText: fact,
-          docId,
-          startLine,
-          endLine,
-          relationType,
-        });
-        const linesStr = startLine ? `:L${startLine}${endLine ? `-${endLine}` : ""}` : "";
-        linkInfo = ` [Linked to Doc: "${linkRes.docTitle}"${linesStr}]`;
-      } catch (err) {
-        linkInfo = ` (Note: Fact saved, but document link failed: ${err.message})`;
-      }
-    }
-
-    return { content: [{ type: "text", text: `Memory updated${supersededInfo}${linkInfo}` }] };
-  }
-);
-
-server.registerTool(
-  "recall",
-  {
-    description:
-      "Show saved facts with any Agent-linked Knowledge Base documents/lines. " +
-      "scope: 'project', 'global', 'all' (default), or 'list_projects'. " +
-      "Use project: '<directory path>' with scope 'project'/'all' to read facts of a specific project from any working directory. " +
-      "query filters by keyword (all space-separated terms must match). " +
-      "tags filters by comma-separated tags. since/until filter by date (YYYY-MM-DD, inclusive). " +
-      "Expired facts are shown with [EXPIRED], protected ones with [KEEP]. The response includes the store file paths.",
-    inputSchema: z.object({
-      scope: defStr("all").describe("'project', 'global', 'all', or 'list_projects'"),
-      project: optStr().describe("Directory path of the project to read facts from (e.g. 'F:/projects/plugins/memory')"),
-      query: optStr().describe("Optional keyword filter; all space-separated terms must match"),
-      tags: optStr().describe("Optional comma-separated tag filter (any match)"),
-      since: optStr().describe("Optional start date filter, YYYY-MM-DD (inclusive)"),
-      until: optStr().describe("Optional end date filter, YYYY-MM-DD (inclusive)"),
-    }),
-  },
-  async ({ scope, project, query, tags, since, until }) => {
-    const { getLinksForFact } = await import("./graph/knowledge_linker.js");
-    const results = [];
-
-    const formatFactWithLinks = async (factLine, key) => {
-      let line = displayFact(factLine);
-      try {
-        const links = await getLinksForFact(key, factText(factLine));
-        if (links && links.length > 0) {
-          const docStr = links
-            .map((l) => {
-              const range = l.start_line ? `:L${l.start_line}${l.end_line ? `-${l.end_line}` : ""}` : "";
-              return `${l.doc_title || l.doc_path}${range}`;
-            })
-            .join(", ");
-          line += ` 🔗 [Linked Docs: ${docStr}]`;
-        }
-      } catch (e) {}
-      return line;
-    };
-
-    const collect = async (entries, key) => {
-      const matched = entries.filter(
-        (e) => matchesQuery(e, query) && matchesTags(e, tags) && inDateRange(e, since, until)
-      );
-      if (!matched.length) return;
-      if (results.length) results.push("");
-      results.push(`--- ${key === GLOBAL_KEY ? "Global" : `Project: ${key === target ? label : key}`} ---`);
-      for (let i = 0; i < matched.length; i++) {
-        results.push(`${i + 1}. ${await formatFactWithLinks(matched[i], key)}`);
-      }
-      results.push(`Store file: ${storeFilePath(key)}`);
-    };
-
-    if (scope === "list_projects") {
-      const stores = await listProjectStores();
-      if (!stores.length) {
-        return { content: [{ type: "text", text: "No project memory stores found." }] };
-      }
-      const lines = stores.map(
-        (s, i) => `${i + 1}. ${s.basename} — ${s.count} fact(s) [${s.file}]${s.path ? ` (bound to ${s.path})` : " (unbound legacy store)"}`
-      );
-      return {
-        content: [
-          {
-            type: "text",
-            text: `Project Memory Stores:\n${lines.join("\n")}\n\nUse recall(scope: "project", project: "<path>") to read a specific store.\n\nMemory dir: ${MEMORY_DIR}`,
-          },
-        ],
-      };
-    }
-
-    const target = project ? canonicalPath(project) : projectKey(null, null);
-    const label = project ? target : projectName();
-    if (scope !== "project") {
-      const global = await readMemory(GLOBAL_KEY);
-      await collect(global, GLOBAL_KEY);
-    }
-    if (scope !== "global") {
-      const local = await readMemory(target);
-      await collect(local, target);
-    }
-    const filtered = Boolean(query || tags || since || until);
-    const text = results.length
-      ? `${results.join("\n")}\n\nMemory dir: ${MEMORY_DIR}`
-      : filtered
-        ? "No facts match the search."
-        : "Memory is empty.";
-    return { content: [{ type: "text", text }] };
-  }
-);
-
-server.registerTool(
-  "forget",
-  {
-    description:
-      "Delete a fact by number (from recall), by range (e.g. '3-30', inclusive), or by text search. " +
-      "Protected facts (remember with keep=true) are skipped unless force=true.",
-    inputSchema: z.object({
-      query: z.string().describe("Number, range like '3-30', or text to search for"),
-      scope: defStr("project").describe("'project' (default) or 'global'"),
-      force: defBool(false).describe("Also delete protected (keep) facts"),
-    }),
-  },
-  async ({ query, scope, force }) => {
-    const key = scopeKey(scope, null, null);
-    const entries = await readMemory(key);
-    const rangeMatch = /^\s*(\d+)\s*-\s*(\d+)\s*$/.exec(query);
-    const num = parseInt(query, 10);
-    let indices = [];
-    if (rangeMatch) {
-      const from = parseInt(rangeMatch[1], 10);
-      const to = parseInt(rangeMatch[2], 10);
-      if (from > 0 && to >= from && to <= entries.length) {
-        for (let i = from - 1; i < to; i++) indices.push(i);
-      }
-    }
-    if (!indices.length && !isNaN(num) && num > 0 && num <= entries.length) {
-      indices.push(num - 1);
-    }
-    if (!indices.length) {
-      const q = query.toLowerCase();
-      indices = entries.reduce((acc, e, i) => (e.toLowerCase().includes(q) ? acc.concat(i) : acc), []);
-    }
-    if (!indices.length) {
-      return { content: [{ type: "text", text: "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);
-    }
-    let text = removable.length ? "Memory updated" : "Nothing removed.";
-    if (protectedCount) text += ` (${protectedCount} protected fact(s) skipped; use force=true to override)`;
-    return { content: [{ type: "text", text }] };
-  }
-);
-
-server.registerTool(
-  "update_fact",
-  {
-    description:
-      "Update the text of an existing fact by number (from recall), id, or text match, " +
-      "preserving its original date and metadata. Linked Knowledge Base documents are re-pointed to the new text.",
-    inputSchema: z.object({
-      id: z.string().describe("Number (from recall), metadata id, or text of the fact to update"),
-      newText: z.string().describe("New fact text"),
-      scope: defStr("project").describe("'project' (default) or 'global'"),
-    }),
-  },
-  async ({ id, newText, scope }) => {
-    const key = scopeKey(scope, null, null);
-    const entries = await readMemory(key);
-    const idx = resolveFactIndex(entries, id);
-    if (idx === -1) throw new Error(`Fact not found: ${id}`);
-    const p = parseFactEntry(entries[idx]);
-    const oldText = p ? p.text : entries[idx];
-    const newLine = formatFactEntry({ date: p.date, time: p.time, text: newText, meta: p.meta });
-    entries[idx] = newLine;
-    await writeMemory(key, entries);
-
-    let linksUpdated = 0;
-    try {
-      const { getDatabase } = await import("./db/database.js");
-      const db = await getDatabase();
-      const res = await db
-        .prepare(
-          "UPDATE knowledge_links SET fact_text = ? WHERE fact_key = ? AND fact_text = ?"
-        )
-        .run(newText, key, oldText);
-      linksUpdated = res.changes;
-    } catch (e) {}
-
-    return {
-      content: [
-        { type: "text", text: `Fact updated${linksUpdated ? `, ${linksUpdated} doc link(s) updated` : ""}` },
-      ],
-    };
-  }
-);
-
-server.registerTool(
-  "memory_info",
-  {
-    description:
-      "Show memory storage paths (store file locations, MEMORY_DIR, SQLite DB), fact counts, " +
-      "Knowledge Base stats, and the installed package version.",
-    inputSchema: z.object({}),
-  },
-  async () => {
-    const dbPath = join(MEMORY_DIR, "storage", "memory.sqlite");
-    const globalFile = storeFilePath(GLOBAL_KEY);
-    const projectFile = storeFilePath(projectKey(null, null));
-
-    let version = "unknown";
-    try {
-      version = JSON.parse(await readFile(new URL("../package.json", import.meta.url), "utf-8")).version;
-    } catch (e) {}
-
-    let rag = {};
-    try {
-      const { getDatabase } = await import("./db/database.js");
-      const db = await getDatabase();
-      const docCountRow = await db.prepare("SELECT COUNT(*) AS c FROM documents").get();
-      rag.documents = docCountRow ? docCountRow.c : 0;
-      const secCountRow = await db.prepare("SELECT COUNT(*) AS c FROM sections").get();
-      rag.sections = secCountRow ? secCountRow.c : 0;
-      const chunkCountRow = await db.prepare("SELECT COUNT(*) AS c FROM micro_chunks").get();
-      rag.chunks = chunkCountRow ? chunkCountRow.c : 0;
-      const edgeCountRow = await db.prepare("SELECT COUNT(*) AS c FROM graph_edges").get();
-      rag.edges = edgeCountRow ? edgeCountRow.c : 0;
-      const linkCountRow = await db.prepare("SELECT COUNT(*) AS c FROM knowledge_links").get();
-      rag.links = linkCountRow ? linkCountRow.c : 0;
-    } catch (e) {
-      rag.error = e.message;
-    }
-
-    const stores = await listProjectStores();
-    const lines = [
-      `Version: ${version}`,
-      `MEMORY_DIR: ${MEMORY_DIR}`,
-      `SQLite DB: ${dbPath}`,
-      `Global store: ${globalFile}`,
-      `Project store: ${projectFile}`,
-      `Project stores: ${stores.length}`,
-      `Facts (global): ${(await readMemoryRaw(GLOBAL_KEY)).length}`,
-      `Facts (project): ${(await readMemoryRaw(projectKey(null, null))).length}`,
-    ];
-    if (rag.error) lines.push(`RAG: unavailable (${rag.error})`);
-    else lines.push(
-      `RAG: ${rag.documents} doc(s), ${rag.sections} section(s), ${rag.chunks} chunk(s), ${rag.edges} edge(s), ${rag.links} memory link(s)`
-    );
-    return { content: [{ type: "text", text: lines.join("\n") }] };
-  }
-);
-
-server.registerTool(
-  "link_knowledge",
-  {
-    description:
-      "Explicitly link a Notebook memory fact to a Knowledge Base document, section, or line range. " +
-      "Creates Agent-driven Graph Edges connecting memory to RAG documents.",
-    inputSchema: z.object({
-      action: z.enum(["link", "list_links", "get_doc_links"]).nullish().transform((v) => v || "link").describe("Action type"),
-      factText: optStr().describe("Memory fact text or keyword"),
-      docId: optStr().describe("Document ID, title, or file path"),
-      scope: defStr("project").describe("'project' (default) or 'global'"),
-      startLine: optNum().describe("Starting line number in target document"),
-      endLine: optNum().describe("Ending line number in target document"),
-      relationType: defStr("LINKS_TO").describe("Relation type (e.g. 'RULES_FOR', 'IMPLEMENTS', 'EXPLAINS')"),
-    }),
-  },
-  async ({ action, factText, docId, scope, startLine, endLine, relationType }) => {
-    const { linkFactToDocument, getLinksForDoc, listAllLinks } = await import("./graph/knowledge_linker.js");
-    const key = scopeKey(scope, null, null);
-
-    if (action === "link") {
-      if (!factText || !docId) {
-        throw new Error("factText and docId are required parameters for link action");
-      }
-      const res = linkFactToDocument({
-        factKey: key,
-        factText,
-        docId,
-        startLine,
-        endLine,
-        relationType,
-      });
-      return {
-        content: [{ type: "text", text: JSON.stringify(res, null, 2) }],
-      };
-    }
-
-    if (action === "get_doc_links") {
-      if (!docId) throw new Error("docId parameter is required for get_doc_links action");
-      const links = getLinksForDoc(docId);
-      return {
-        content: [{ type: "text", text: JSON.stringify(links, null, 2) }],
-      };
-    }
-
-    if (action === "list_links") {
-      const links = listAllLinks(key);
-      return {
-        content: [{ type: "text", text: JSON.stringify(links, null, 2) }],
-      };
-    }
-
-    throw new Error(`Unknown action: ${action}`);
-  }
-);
-
-// --- Hybrid RAG Knowledge Engine Tools ---
-
-server.registerTool(
-  "ingest_document",
-  {
-    description:
-      "Ingest a document into the RAG knowledge base. " +
-      "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). " +
-      "Processes document through 3-tier hierarchy chunking (Big/Medium/Small), " +
-      "computes dense vectors, and extracts GraphRAG code symbols.",
-    inputSchema: z.object({
-      content: z.string().describe("Raw text content, file path, or web URL. For type='file' this can be the file path (reads from disk) or the file content directly"),
-      type: z.enum(["text", "file", "url"]).nullish().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({
-      content,
-      type,
-      title: title || null,
-      path: path || null,
-      generateEmbeddings,
-    });
-    return {
-      content: [
-        {
-          type: "text",
-          text: JSON.stringify(
-            {
-              status: "success",
-              docId: result.docId,
-              title: result.title,
-              sectionsCount: result.sectionsCount,
-              microChunksCount: result.microChunksCount,
-              deduplicated: result.deduplicated,
-            },
-            null,
-            2
-          ),
-        },
-      ],
-    };
-  }
-);
-
-server.registerTool(
-  "query_knowledge_base",
-  {
-    description:
-      "Perform 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"),
-      limit: defNum(5).describe("Maximum number of sections to return"),
-      instruction: optStr().describe(
-        "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 }) => {
-    const { hybridQuery } = await import("./retrieval/retriever.js");
-    const { getConfig } = await import("./config/config_manager.js");
-    const activeConfig = getConfig();
-
-    const results = await hybridQuery({
-      query,
-      limit,
-      generateEmbeddings,
-      instruction: instruction || null,
-    });
-
-    if (!results || results.length === 0) {
-      return {
-        content: [
-          {
-            type: "text",
-            text: `[Active Model: ${activeConfig.embeddingModel}]\nNo matching knowledge found for query.`,
-          },
-        ],
-      };
-    }
-
-    const headerNote = `[Active Model: ${activeConfig.embeddingModel} | Fusion: ${activeConfig.fusionAlgorithm.toUpperCase()}]\n\n`;
-
-    const formatted = results
-      .map((r, i) => {
-        let header = `### [${i + 1}] ${r.doc_title || "Untitled"}`;
-        if (r.heading) header += ` > ${r.heading}`;
-        if (r.breadcrumbs) header += ` (${r.breadcrumbs})`;
-        let body = `Score: ${(r.score || 0).toFixed(4)}\n`;
-        if (r.defined_symbols && r.defined_symbols.length > 0) {
-          body += `Defined Symbols: ${r.defined_symbols.join(", ")}\n`;
-        }
-        body += `\n${r.snippet || r.full_section_content || ""}`;
-        return `${header}\n${body}`;
-      })
-      .join("\n\n---\n\n");
-
-    return { content: [{ type: "text", text: headerNote + formatted }] };
-  }
-);
-
-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.",
-    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;
-      return {
-        content: [
-          {
-            type: "text",
-            text: JSON.stringify(
-              {
-                documents: docCount,
-                sections: secCount,
-                micro_chunks: chunkCount,
-                graph_edges: edgeCount,
-              },
-              null,
-              2
-            ),
-          },
-        ],
-      };
-    }
-
-    if (action === "list") {
-      const docs = await db
-        .prepare("SELECT id, title, path, blob_hash, created_at FROM documents ORDER BY created_at DESC")
-        .all();
-      return {
-        content: [{ type: "text", text: JSON.stringify(docs, null, 2) }],
-      };
-    }
-
-    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);
-      if (!doc) {
-        throw new Error(`Document not found in knowledge base for docId: ${docId}`);
-      }
-      const { readBlob } = await import("./storage/blob_store.js");
-      const rawContent = await readBlob(doc.blob_hash);
-      return {
-        content: [
-          {
-            type: "text",
-            text: JSON.stringify(
-              {
-                id: doc.id,
-                title: doc.title,
-                path: doc.path,
-                created_at: doc.created_at,
-                content: rawContent,
-              },
-              null,
-              2
-            ),
-          },
-        ],
-      };
-    }
-
-    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);
-      return {
-        content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
-      };
-    }
-
-    if (action === "export_snapshot") {
-      const { exportSnapshot } = await import("./admin/snapshot.js");
-      const result = await exportSnapshot({ customDb: db, outputPath: snapshotPath || null });
-      return {
-        content: [
-          {
-            type: "text",
-            text: snapshotPath
-              ? `Snapshot exported successfully to ${snapshotPath}`
-              : JSON.stringify(result, null, 2),
-          },
-        ],
-      };
-    }
-
-    if (action === "import_snapshot") {
-      if (!snapshotPath) throw new Error("snapshotPath parameter is required for import_snapshot action");
-      const { importSnapshot } = await import("./admin/snapshot.js");
-      const result = await importSnapshot({ customDb: db, snapshotPathOrData: snapshotPath });
-      return {
-        content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
-      };
-    }
-
-    throw new Error(`Unknown action: ${action}`);
-  }
-);
-
-const transport = new StdioServerTransport();
-await server.connect(transport);
-console.error(`memory-agent MCP server running, data dir: ${MEMORY_DIR}`);
+#!/usr/bin/env node
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { ensureDir, MEMORY_DIR } from "./memory.js";
+import { registerAllTools } from "./tools/index.js";
+
+const cliArgs = process.argv.slice(2);
+
+if (cliArgs.includes("setup") || cliArgs.includes("install") || cliArgs.includes("--setup") || cliArgs.includes("-s")) {
+  const { runSetup } = await import("./setup.js");
+  await runSetup();
+  process.exit(0);
+}
+
+if (
+  cliArgs.includes("cli") ||
+  cliArgs.includes("config") ||
+  cliArgs.includes("--cli") ||
+  cliArgs.includes("-c") ||
+  cliArgs.includes("login") ||
+  cliArgs.includes("logout") ||
+  cliArgs.includes("auth-status") ||
+  cliArgs.includes("auth_status") ||
+  cliArgs.includes("auth")
+) {
+  const { runCli } = await import("./cli.js");
+  await runCli();
+  process.exit(0);
+}
+
+await ensureDir();
+
+const server = new McpServer({
+  name: "memory-agent",
+  version: "1.5.0",
+});
+
+registerAllTools(server);
+
+const transport = new StdioServerTransport();
+await server.connect(transport);
+console.error(`memory-agent MCP server running, data dir: ${MEMORY_DIR}`);