graph-indexer 1.1.0 → 1.2.0

package/mcp-server.mjs

@@ -1,142 +1,120 @@
 #!/usr/bin/env node
 /**
  * @file mcp-server.mjs
- * @description MCP Server — graph-indexer hybrid search with infinite scalability,
- *              cross-file symbol resolution, and query-driven token pruning.
+ * @description MCP server bootstrap. Resolves configuration, selects the storage
+ *              backend (in-memory by default, SQLite when configured), registers
+ *              the tool surface (mcp-tools.mjs) and connects over stdio. All
+ *              retrieval logic lives in the store + search-core; all tool logic in
+ *              mcp-tools — this file is wiring only.
  * @author MaquinaTech <https://github.com/MaquinaTech>
  * @copyright (c) 2026 MaquinaTech. All rights reserved.
  * @license MIT
  */
-import { McpServer, ResourceTemplate } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
-import { z } from "zod";
-import fs from "fs";
-import path, { resolve } from "path";
-import { fileURLToPath } from "url";
-import { spawn } from "child_process";
-import { MemoryGraphIndex } from "./core-engine.mjs";
-import { getLocalEmbedding, getParserForFile, extractFileSkeleton } from './parser-utils.mjs';
-
-const PROJECT_ROOT = process.env.MCP_PROJECT_ROOT || process.cwd();
-const INDEX_PATH = resolve(PROJECT_ROOT, "code-index.json");
-const PID_FILE = resolve(PROJECT_ROOT, ".idx-daemon.pid");
-
-// Single source of truth for the version: graph-indexer's own package.json
-// (next to this file), never the consumer project's package.json.
+import { McpServer, ResourceTemplate } from '@modelcontextprotocol/sdk/server/mcp.js';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import fs from 'fs';
+import path, { resolve } from 'path';
+import { fileURLToPath } from 'url';
+import { spawn } from 'child_process';
+import { resolveConfig } from './config.mjs';
+import { createStore } from './storage.mjs';
+import { registerTools } from './mcp-tools.mjs';
+
+const config = resolveConfig();
+const PROJECT_ROOT = config.projectRoot;
+const PID_FILE = resolve(PROJECT_ROOT, '.idx-daemon.pid');
 const PACKAGE_DIR = path.dirname(fileURLToPath(import.meta.url));
+
 function readPackageVersion() {
     try {
-        return JSON.parse(fs.readFileSync(path.join(PACKAGE_DIR, "package.json"), "utf-8")).version || "0.0.0";
-    } catch { return "0.0.0"; }
+        return JSON.parse(fs.readFileSync(path.join(PACKAGE_DIR, 'package.json'), 'utf-8')).version || '0.0.0';
+    } catch { return '0.0.0'; }
 }
 
-// ─── Daemon Orchestration ─────────────────────────────────────────────────────
-
+// ─── Watch-daemon orchestration (both backends) ─────────────────────────────────
+// The incremental watcher keeps the configured backend fresh: it rewrites the
+// JSON snapshot for the in-memory engine (picked up below via an fs watch), and
+// applies per-file WAL transactions for SQLite (picked up by the store via
+// PRAGMA data_version). Either way, a long-running MCP server stays consistent
+// with the working tree without restarts or full re-indexes.
 function ensureDaemonRunning() {
     if (fs.existsSync(PID_FILE)) {
         const pid = parseInt(fs.readFileSync(PID_FILE, 'utf-8'), 10);
-        try {
-            process.kill(pid, 0);
-            process.stderr.write(`✅ Daemon already active (PID: ${pid}).\n`);
-            return;
-        } catch {
-            fs.unlinkSync(PID_FILE);
-        }
+        try { process.kill(pid, 0); process.stderr.write(`✅ Daemon already active (PID: ${pid}).\n`); return; }
+        catch { fs.unlinkSync(PID_FILE); }
     }
-    const __dirname = path.dirname(fileURLToPath(import.meta.url));
-    const daemonPath = path.join(__dirname, "watch-daemon.mjs");
-    const logPath = path.join(PROJECT_ROOT, ".idx-daemon.log");
+    const daemonPath = path.join(PACKAGE_DIR, 'watch-daemon.mjs');
+    const logPath = path.join(PROJECT_ROOT, '.idx-daemon.log');
     process.stderr.write(`🚀 Starting Watcher Daemon...\n   Log: ${logPath}\n`);
     let logFd;
     try { logFd = fs.openSync(logPath, 'a'); } catch { logFd = null; }
     const child = spawn(process.execPath, [daemonPath], {
         detached: true,
         stdio: logFd !== null ? ['ignore', logFd, logFd] : 'ignore',
-        env: { ...process.env, MCP_PROJECT_ROOT: PROJECT_ROOT }
+        env: { ...process.env, MCP_PROJECT_ROOT: PROJECT_ROOT },
     });
     child.unref();
     if (logFd !== null) fs.closeSync(logFd);
     fs.writeFileSync(PID_FILE, child.pid.toString());
 }
 
-// ─── Frontier 3: Query-Driven Body Pruning ───────────────────────────────────
-
-/**
- * Extracts just the function signature (first N lines up to opening brace).
- */
-function extractSignatureLine(codeSnippet) {
-    if (!codeSnippet) return '';
-    const lines = codeSnippet.split('\n');
-    const sigLines = [];
-    for (let i = 0; i < Math.min(lines.length, 10); i++) {
-        sigLines.push(lines[i]);
-        const l = lines[i];
-        // Stop at opening brace or arrow that ends the signature
-        if (i > 0 && (l.trimEnd().endsWith('{') || l.includes('=>') || l.trimEnd().endsWith(':'))) break;
-    }
-    return sigLines.join('\n');
-}
-
-/**
- * Prune a function body: keep signature + lines containing any query token + return/throw lines.
- * Falls back to first maxLines lines when no match found.
- */
-function pruneBodyByQuery(codeSnippet, queryTokens, maxLines = 40) {
-    if (!codeSnippet) return '';
-    const lines = codeSnippet.split('\n');
-    if (lines.length <= maxLines) return codeSnippet;
-
-    const querySet = new Set(queryTokens.filter(t => t.length >= 3).map(t => t.toLowerCase()));
-    if (querySet.size === 0) return lines.slice(0, maxLines).join('\n') + '\n// …';
-
-    // Always include: opening lines (signature + brace), closing lines, return/throw
-    const SIG_LINES = Math.min(5, lines.length);
-    const TAIL_LINES = Math.min(3, lines.length);
-    const sigBlock = lines.slice(0, SIG_LINES);
-    const tailBlock = lines.slice(Math.max(lines.length - TAIL_LINES, SIG_LINES));
+// ─── Boot ──────────────────────────────────────────────────────────────────────
 
-    const bodyLines = lines.slice(SIG_LINES, lines.length - TAIL_LINES);
-    const relevant = bodyLines.filter(line => {
-        const ll = line.toLowerCase();
-        if (/^\s*(return|throw|raise|yield)\b/.test(ll)) return true;
-        return [...querySet].some(token => ll.includes(token));
-    });
-
-    if (relevant.length === 0) return lines.slice(0, maxLines).join('\n') + '\n// …';
-    return [...sigBlock, ...relevant, ...tailBlock].join('\n');
+if (config.storage === 'sqlite') {
+    process.stderr.write('🗄  Storage backend: SQLite (disk-backed, live daemon updates).\n');
 }
-
-// ─── Server Initialization ────────────────────────────────────────────────────
-
 ensureDaemonRunning();
-const version = readPackageVersion();
-const server = new McpServer({ name: "graph-indexer", version });
 
-// Use lazy (disk-backed) vector loading for large corpora — cacheEmbeddings:false
-const db = new MemoryGraphIndex(INDEX_PATH, { cacheEmbeddings: false });
-try { db.load(); } catch { process.stderr.write("⏳ Waiting for initial indexing…\n"); }
+const version = readPackageVersion();
+const server = new McpServer({ name: 'graph-indexer', version });
+
+const db = await createStore(config, { cacheEmbeddings: false });
+try { db.load(); } catch (err) { process.stderr.write(`⏳ Waiting for initial indexing… (${err.message})\n`); }
+
+// In-memory backend: the daemon is a separate process that rewrites
+// code-index.json — without reloading, this server would answer from a stale
+// snapshot until restart. (The SQLite store refreshes itself per query via
+// PRAGMA data_version, so no watcher is needed there.)
+if (config.storage !== 'sqlite' && typeof db.reload === 'function') {
+    let reloadTimer = null;
+    const scheduleReload = () => {
+        if (reloadTimer) clearTimeout(reloadTimer);
+        reloadTimer = setTimeout(() => {
+            reloadTimer = null;
+            try {
+                db.reload();
+                process.stderr.write('🔄 Index reloaded from disk (daemon update).\n');
+            } catch (err) {
+                process.stderr.write(`⚠️ Index reload failed: ${err.message}\n`);
+            }
+        }, 1000);
+    };
+    try {
+        fs.watch(path.dirname(config.indexPath), (event, name) => {
+            if (name === path.basename(config.indexPath)) scheduleReload();
+        });
+    } catch { /* fs.watch unavailable — index stays load-time static */ }
+}
 
-// Graceful shutdown
 process.on('SIGTERM', () => { db.close(); process.exit(0); });
 process.on('SIGINT', () => { db.close(); process.exit(0); });
 
-// ─── Graph Resource ───────────────────────────────────────────────────────────
-
+// ─── Graph dependency resource ─────────────────────────────────────────────────
 server.resource(
-    "graph-dependencies",
-    new ResourceTemplate("graph://dependencies/{file_path}", {
+    'graph-dependencies',
+    new ResourceTemplate('graph://dependencies/{file_path}', {
         list: async () => ({
             resources: Object.keys(db.graph.dependencies).map(fp => ({
                 uri: `graph://dependencies/${encodeURIComponent(fp)}`,
-                name: fp, mimeType: "text/markdown",
+                name: fp, mimeType: 'text/markdown',
                 description: `Dependency topology for ${fp}`,
             }))
         })
     }),
     async (uri, { file_path }) => {
         const p = decodeURIComponent(String(file_path));
-        const deps = db.graph.dependencies[p] || [];
-        const usedBy = db.graph.importedBy[p] || [];
+        const deps = db.getDependencies(p);
+        const usedBy = db.getImportedBy(p);
         const md = [
             `# Dependency Topology: \`${p}\``, '',
             `## Imports (${deps.length})`,
@@ -144,485 +122,21 @@ server.resource(
             `## Imported By (${usedBy.length})`,
             usedBy.length ? usedBy.map(d => `- \`${d}\``).join('\n') : '_No files import this_',
         ].join('\n');
-        return { contents: [{ uri: uri.href, mimeType: "text/markdown", text: md }] };
-    }
-);
-
-// ─── search_code ──────────────────────────────────────────────────────────────
-
-server.tool(
-    "search_code",
-    "CRITICAL: ALWAYS USE THIS TOOL FIRST to find code. High-precision AST hybrid search returning exact chunks and cross-file topology.",
-    {
-        query: z.string().describe("Natural language description of the logic to find."),
-        exact_tokens: z.string().optional().describe("Exact symbol name for guaranteed rank-1 placement."),
-        include_topology: z.boolean().default(true),
-        min_score: z.number().min(0).max(1).default(0.3),
-        top_k: z.number().int().min(1).max(20).default(5),
-        token_budget: z.number().int().min(100).optional().describe(
-            "Token budget for code bodies (1 token ≈ 4 chars). Omit to use smart default."
-        ),
-        detail: z.enum(['signatures', 'smart', 'full']).default('smart').describe(
-            "'signatures': compact cards only (~20 tok each, no bodies) — fastest. " +
-            "'smart' (default): signatures + query-relevant body snippets. " +
-            "'full': signatures + complete bodies."
-        ),
-    },
-    async ({ query, exact_tokens, include_topology, min_score, top_k, token_budget, detail }) => {
-        try {
-            const fullQuery = exact_tokens ? `${query} ${exact_tokens}` : query;
-            let queryVector = null;
-            try { queryVector = await getLocalEmbedding(fullQuery); } catch { /* lexical fallback */ }
-
-            const matches = db.searchHybrid(fullQuery, queryVector, top_k, min_score, exact_tokens || null);
-            if (matches.length === 0) return { content: [{ type: "text", text: "No results found." }] };
-
-            const depSignature = (depPath) => {
-                const syms = [];
-                for (const c of db.chunks.values()) {
-                    if (c.file_path === depPath && c.name && c.node_type !== 'expression_statement') {
-                        syms.push(c.name);
-                        if (syms.length >= 4) break;
-                    }
-                }
-                return syms.length ? `${depPath} [${syms.join(', ')}]` : depPath;
-            };
-
-            const lines = [`🔍 QUERY: "${fullQuery}" — ${matches.length} result(s)\n`];
-
-            // Phase 1: Signature cards (always emitted)
-            for (let i = 0; i < matches.length; i++) {
-                const { score, chunk } = matches[i];
-                lines.push(`${'─'.repeat(50)}`);
-                lines.push(`#${i + 1} · **${chunk.name}** [${chunk.node_type}]`);
-                lines.push(`📄 ${chunk.file_path}:${chunk.start_line}–${chunk.end_line} · ID: \`${chunk.id}\` · RRF: ${score.toFixed(4)}`);
-
-                // Frontier 3: show return type and key params in card
-                const sig = [];
-                if (chunk.params?.length) sig.push(`(${chunk.params.slice(0, 4).join(', ')})`);
-                if (chunk.return_type) sig.push(`→ ${chunk.return_type}`);
-                if (chunk.type_refs?.length) sig.push(`types: ${chunk.type_refs.slice(0, 4).join(', ')}`);
-                if (sig.length) lines.push(`🔤 ${sig.join('  ')}`);
-
-                if (chunk.docstring) lines.push(`💬 ${chunk.docstring.slice(0, 140).replace(/\n/g, ' ')}`);
-
-                if (include_topology) {
-                    const deps = (db.graph.dependencies[chunk.file_path] || []).slice(0, 3);
-                    const usedBy = (db.graph.importedBy[chunk.file_path] || []).slice(0, 3);
-                    if (deps.length) lines.push(`⬇️  Deps:    ${deps.map(depSignature).join(' | ')}`);
-                    if (usedBy.length) lines.push(`⬆️  Used by: ${usedBy.join(', ')}`);
-                    if (chunk.calls?.length) lines.push(`🔗 Calls:   ${chunk.calls.slice(0, 6).join(', ')}`);
-                }
-                lines.push(`↩️  Expand: get_chunk("${chunk.id}")`);
-            }
-
-            // Phase 2: Code bodies — controlled by `detail`
-            if (detail !== 'signatures') {
-                const CHARS_PER_TOKEN = 4;
-                const defaultBudget = detail === 'full' ? 6000 : 2000;
-                let remainingChars = token_budget != null ? token_budget * CHARS_PER_TOKEN : defaultBudget;
-
-                lines.push(`\n${'═'.repeat(50)}`);
-                lines.push(`CODE BODIES (detail: ${detail}, budget: ~${Math.round(remainingChars / CHARS_PER_TOKEN)} tok)\n`);
-
-                const queryTokens = fullQuery.toLowerCase().split(/[\s\W_]+/).filter(t => t.length >= 3);
-
-                for (const { chunk } of matches) {
-                    if (remainingChars <= 0) break;
-                    const raw = chunk.code_snippet || '';
-                    if (!raw) continue;
-
-                    let snippet;
-                    if (detail === 'full') {
-                        snippet = raw.slice(0, remainingChars);
-                    } else {
-                        // 'smart': query-driven pruning for long functions
-                        snippet = pruneBodyByQuery(raw, queryTokens).slice(0, remainingChars);
-                    }
-
-                    lines.push(`### ${chunk.name} — ${chunk.file_path}`);
-                    lines.push('```\n' + snippet + '\n```\n');
-                    remainingChars -= snippet.length;
-                }
-            }
-
-            return { content: [{ type: "text", text: lines.join("\n") }] };
-        } catch (err) {
-            return { content: [{ type: "text", text: `Error: ${err.message}` }], isError: true };
-        }
-    }
-);
-
-// ─── get_chunk ────────────────────────────────────────────────────────────────
-
-server.tool(
-    "get_chunk",
-    "CRITICAL: Use this INSTEAD of reading full files. Returns the complete body of a function/class by its chunk_id from search_code results.",
-    {
-        chunk_id: z.string().describe("The chunk ID shown in search_code results."),
-        view: z.enum(['full', 'signature']).default('full').describe(
-            "'full': complete source body. 'signature': just the function signature line (~5 tokens)."
-        ),
-    },
-    async ({ chunk_id, view }) => {
-        try {
-            const chunk = db.chunks.get(chunk_id);
-            if (!chunk) return { content: [{ type: "text", text: `Chunk '${chunk_id}' not found. Run search_code to get valid IDs.` }] };
-
-            const parts = [
-                `# ${chunk.name}`,
-                `**File:** \`${chunk.file_path}\` · **Lines:** ${chunk.start_line}–${chunk.end_line} · **Type:** ${chunk.node_type}`,
-            ];
-            if (chunk.params?.length) parts.push(`**Params:** ${chunk.params.join(', ')}`);
-            if (chunk.return_type) parts.push(`**Returns:** ${chunk.return_type}`);
-            if (chunk.type_refs?.length) parts.push(`**Type refs:** ${chunk.type_refs.join(', ')}`);
-            if (chunk.docstring) parts.push(`**Doc:** ${chunk.docstring}`);
-
-            const deps = db.graph.dependencies[chunk.file_path] || [];
-            const usedBy = db.graph.importedBy[chunk.file_path] || [];
-            if (deps.length) parts.push(`⬇️ Imports: ${deps.join(', ')}`);
-            if (usedBy.length) parts.push(`⬆️ Used by: ${usedBy.join(', ')}`);
-            if (chunk.calls?.length) parts.push(`🔗 Calls: ${chunk.calls.join(', ')}`);
-
-            if (view === 'signature') {
-                parts.push('', '```', extractSignatureLine(chunk.code_snippet), '```');
-            } else {
-                parts.push('', '```', chunk.code_snippet, '```');
-            }
-            return { content: [{ type: "text", text: parts.join('\n') }] };
-        } catch (err) {
-            return { content: [{ type: "text", text: `Error: ${err.message}` }], isError: true };
-        }
-    }
-);
-
-// ─── resolve_symbol (Frontier 2) ─────────────────────────────────────────────
-
-server.tool(
-    "resolve_symbol",
-    "Frontier 2: Instantly finds the definition of any symbol (function, class, type, variable) by exact name — O(1) lookup, no search needed. Returns the defining chunk and cross-file topology.",
-    {
-        symbol: z.string().describe("Exact symbol name (e.g. 'validateToken', 'User', 'PaymentService')."),
-    },
-    async ({ symbol }) => {
-        try {
-            const key = symbol.toLowerCase().trim();
-            const chunkIds = db.symbolTable.get(key);
-
-            if (!chunkIds || chunkIds.size === 0) {
-                return { content: [{ type: "text", text: `Symbol '${symbol}' not in index. Try search_code(query="${symbol}") for fuzzy search.` }] };
-            }
-
-            const lines = [`# Symbol: \`${symbol}\` — ${chunkIds.size} definition(s)\n`];
-            for (const chunkId of chunkIds) {
-                const chunk = db.chunks.get(chunkId);
-                if (!chunk) continue;
-                lines.push(`${'─'.repeat(50)}`);
-                lines.push(`**${chunk.name}** [${chunk.node_type}]`);
-                lines.push(`📄 ${chunk.file_path}:${chunk.start_line}–${chunk.end_line} · ID: \`${chunk.id}\``);
-                if (chunk.params?.length) lines.push(`🔤 Params: ${chunk.params.join(', ')}`);
-                if (chunk.return_type) lines.push(`🔤 Returns: ${chunk.return_type}`);
-                if (chunk.type_refs?.length) lines.push(`🔗 Type refs: ${chunk.type_refs.join(', ')}`);
-                if (chunk.docstring) lines.push(`💬 ${chunk.docstring.slice(0, 160).replace(/\n/g, ' ')}`);
-                const deps = (db.graph.dependencies[chunk.file_path] || []).slice(0, 4);
-                const usedBy = (db.graph.importedBy[chunk.file_path] || []).slice(0, 4);
-                if (deps.length) lines.push(`⬇️  Imports: ${deps.join(', ')}`);
-                if (usedBy.length) lines.push(`⬆️  Used by: ${usedBy.join(', ')}`);
-                if (chunk.calls?.length) lines.push(`🔗 Calls: ${chunk.calls.slice(0, 8).join(', ')}`);
-                lines.push(`\n\`\`\`\n${extractSignatureLine(chunk.code_snippet)}\n\`\`\``);
-                lines.push(`↩️  Full body: get_chunk("${chunk.id}")`);
-            }
-            return { content: [{ type: "text", text: lines.join('\n') }] };
-        } catch (err) {
-            return { content: [{ type: "text", text: `Error: ${err.message}` }], isError: true };
-        }
-    }
-);
-
-// ─── get_chunk_summary (Frontier 3) ──────────────────────────────────────────
-
-server.tool(
-    "get_chunk_summary",
-    "Returns the function/class signature + docstring + called functions — no full body. ~50 tokens vs ~300 for full body. Use when you only need to understand the interface, not the implementation.",
-    {
-        chunk_id: z.string().describe("The chunk ID from search_code results."),
-    },
-    async ({ chunk_id }) => {
-        try {
-            const chunk = db.chunks.get(chunk_id);
-            if (!chunk) return { content: [{ type: "text", text: `Chunk '${chunk_id}' not found.` }] };
-
-            const lines = [
-                `# ${chunk.name} · ${chunk.file_path}:${chunk.start_line}–${chunk.end_line}`,
-                `**Type:** ${chunk.node_type}`,
-            ];
-            if (chunk.params?.length) lines.push(`**Params:** ${chunk.params.join(', ')}`);
-            if (chunk.return_type) lines.push(`**Returns:** ${chunk.return_type}`);
-            if (chunk.type_refs?.length) lines.push(`**Type refs:** ${chunk.type_refs.join(', ')}`);
-            if (chunk.docstring) lines.push(`\n**Doc:** ${chunk.docstring.slice(0, 300)}`);
-            if (chunk.calls?.length) lines.push(`**Calls:** ${chunk.calls.join(', ')}`);
-            lines.push('', '```', extractSignatureLine(chunk.code_snippet), '```');
-            lines.push(`\n↩️  Full body: get_chunk("${chunk.id}")`);
-
-            return { content: [{ type: "text", text: lines.join('\n') }] };
-        } catch (err) {
-            return { content: [{ type: "text", text: `Error: ${err.message}` }], isError: true };
-        }
-    }
-);
-
-// ─── get_file_skeleton ────────────────────────────────────────────────────────
-
-server.tool(
-    "get_file_skeleton",
-    "Returns all top-level exports and definitions in a file with line numbers — no code bodies (~50 tokens vs 5000).",
-    { file_path: z.string().describe("Relative path (e.g. 'src/app.ts').") },
-    async ({ file_path }) => {
-        try {
-            const absolutePath = resolve(PROJECT_ROOT, file_path);
-            const safeRoot = path.normalize(PROJECT_ROOT);
-            if (!path.normalize(absolutePath).startsWith(safeRoot + path.sep) &&
-                path.normalize(absolutePath) !== safeRoot) {
-                throw new Error("Access denied: path is outside the project root.");
-            }
-            if (!fs.existsSync(absolutePath)) throw new Error("File not found.");
-            const content = fs.readFileSync(absolutePath, 'utf-8');
-            const ext = path.extname(absolutePath);
-            const parser = getParserForFile(ext);
-            if (!parser) return { content: [{ type: "text", text: "Language not supported." }] };
-            const tree = parser.parse((offset) => offset < content.length ? content.slice(offset, offset + 4096) : null);
-            const skeleton = extractFileSkeleton(tree.rootNode, content);
-            return { content: [{ type: "text", text: `# Skeleton: ${file_path}\n\n${skeleton || "_No semantic signatures found_"}` }] };
-        } catch (err) {
-            return { content: [{ type: "text", text: `Error: ${err.message}` }], isError: true };
-        }
-    }
-);
-
-// ─── get_call_graph ───────────────────────────────────────────────────────────
-
-server.tool(
-    "get_call_graph",
-    "Finds all chunks that call a specific function. CRITICAL for safe refactoring.",
-    { target_function: z.string().describe("Exact function name (e.g. 'validateToken').") },
-    async ({ target_function }) => {
-        try {
-            const callers = [];
-            for (const chunk of db.chunks.values()) {
-                if (chunk.calls?.includes(target_function)) {
-                    callers.push(`- [${chunk.node_type}] \`${chunk.name}\` in \`${chunk.file_path}\` (lines ${chunk.start_line}–${chunk.end_line})`);
-                }
-            }
-            if (callers.length === 0) {
-                return { content: [{ type: "text", text: `✅ Safe to modify: no callers of '${target_function}' found.` }] };
-            }
-            return {
-                content: [{
-                    type: "text", text: [
-                        `# ⚠️ Call Graph: \`${target_function}\``,
-                        `${callers.length} caller(s) depend on this — review before changing signature:`,
-                        ...callers
-                    ].join('\n')
-                }]
-            };
-        } catch (err) {
-            return { content: [{ type: "text", text: `Error: ${err.message}` }], isError: true };
-        }
-    }
-);
-
-// ─── get_repo_map ─────────────────────────────────────────────────────────────
-
-/**
- * Compute simplified PageRank over the file dependency graph.
- * Files imported by many others receive higher rank (= more important).
- */
-function computePageRank(graph, iters = 30, damping = 0.85) {
-    const files = Object.keys(graph.dependencies || {});
-    const N = files.length;
-    if (N === 0) return new Map();
-
-    const idx = new Map(files.map((f, i) => [f, i]));
-    const ranks = new Float64Array(N).fill(1.0 / N);
-    const outDeg = files.map(f => Math.max((graph.dependencies[f] || []).length, 1));
-
-    for (let iter = 0; iter < iters; iter++) {
-        const next = new Float64Array(N).fill((1 - damping) / N);
-        for (let i = 0; i < N; i++) {
-            const contrib = damping * ranks[i] / outDeg[i];
-            for (const dep of (graph.dependencies[files[i]] || [])) {
-                const j = idx.get(dep);
-                if (j !== undefined) next[j] += contrib;
-            }
-        }
-        ranks.set(next);
-    }
-    return new Map(files.map((f, i) => [f, ranks[i]]));
-}
-
-server.tool(
-    "get_repo_map",
-    "Returns a compact symbol map of the entire codebase grouped by file, ordered by importance (most-imported files first via PageRank). Use this FIRST to orient yourself in an unfamiliar codebase — ~1-2k tokens vs reading every file. Combine with path_filter to focus on a subsystem.",
-    {
-        path_filter: z.string().optional().describe(
-            "Only include files whose path contains this string (e.g. 'auth', 'api/v2', 'src/core')."
-        ),
-        max_files: z.number().int().min(1).max(300).default(80).describe(
-            "Max files to include in the map."
-        ),
-        sort_by: z.enum(['importance', 'path']).default('importance').describe(
-            "'importance' (default): most-imported files first (PageRank). 'path': alphabetical."
-        ),
-    },
-    async ({ path_filter, max_files, sort_by }) => {
-        try {
-            // Group chunks by file
-            const fileChunks = new Map();
-            for (const chunk of db.chunks.values()) {
-                if (path_filter && !chunk.file_path.toLowerCase().includes(path_filter.toLowerCase())) continue;
-                if (chunk.name === 'anonymous' || chunk.name === 'default_export') continue;
-                if (!fileChunks.has(chunk.file_path)) fileChunks.set(chunk.file_path, []);
-                fileChunks.get(chunk.file_path).push(chunk);
-            }
-
-            if (fileChunks.size === 0) {
-                return {
-                    content: [{
-                        type: 'text', text: path_filter
-                            ? `No files found matching '${path_filter}'. Try a broader filter.`
-                            : 'Index is empty. Run `npm run mcp:index` first.'
-                    }]
-                };
-            }
-
-            // Sort files
-            let sortedFiles = Array.from(fileChunks.keys());
-            if (sort_by === 'importance') {
-                const pr = computePageRank(db.graph);
-                sortedFiles.sort((a, b) => (pr.get(b) ?? 0) - (pr.get(a) ?? 0));
-            } else {
-                sortedFiles.sort();
-            }
-            sortedFiles = sortedFiles.slice(0, max_files);
-
-            // Render compact map
-            const totalFiles = fileChunks.size;
-            const totalSymbols = Array.from(fileChunks.values()).reduce((s, a) => s + a.length, 0);
-            const lines = [
-                `# Repo Map — ${totalSymbols} symbols across ${totalFiles} files`,
-                path_filter ? `(filtered to '${path_filter}')` : '',
-                sortedFiles.length < totalFiles
-                    ? `(showing top ${sortedFiles.length} by ${sort_by}; use path_filter to narrow)\n`
-                    : '',
-            ].filter(Boolean);
-
-            for (const filePath of sortedFiles) {
-                const chunks = fileChunks.get(filePath);
-                lines.push(`\n${filePath}`);
-                // Deduplicate by name (prefer class/function over expression_statement)
-                const seen = new Set();
-                const deduped = [];
-                for (const c of chunks) {
-                    const key = c.name.toLowerCase();
-                    if (seen.has(key)) continue;
-                    seen.add(key);
-                    deduped.push(c);
-                }
-                for (const c of deduped.slice(0, 8)) {
-                    const kind = c.node_type.includes('class') ? 'class'
-                        : c.node_type.includes('interface') ? 'interface'
-                            : c.node_type.includes('enum') ? 'enum'
-                                : c.node_type.includes('struct') ? 'struct'
-                                    : c.node_type.includes('trait') ? 'trait'
-                                        : 'fn';
-                    const params = c.params?.length
-                        ? `(${c.params.slice(0, 3).join(', ')}${c.params.length > 3 ? ', …' : ''})`
-                        : '';
-                    const ret = c.return_type ? ` → ${c.return_type.slice(0, 40)}` : '';
-                    lines.push(`  ${kind} ${c.name}${params}${ret}`);
-                }
-                if (deduped.length > 8) lines.push(`  … (${deduped.length - 8} more)`);
-            }
-            if (totalFiles > max_files) {
-                lines.push(`\n… ${totalFiles - max_files} more files not shown. Use path_filter or increase max_files.`);
-            }
-
-            return { content: [{ type: 'text', text: lines.join('\n') }] };
-        } catch (err) {
-            return { content: [{ type: 'text', text: `Error: ${err.message}` }], isError: true };
-        }
-    }
-);
-
-// ─── list_index_stats ─────────────────────────────────────────────────────────
-
-server.tool(
-    "list_index_stats",
-    "Returns index health: chunk count, embedding status, daemon status, search mode, and index freshness.",
-    {},
-    async () => {
-        try {
-            const chunkCount = db.chunks.size;
-            const fileSet = new Set([...db.chunks.values()].map(c => c.file_path));
-            const hasVectors = db.vectors.size > 0 || db._vecOffsets.size > 0;
-            const embeddingsEnabled = process.env.INDEXER_EMBEDDINGS !== 'off';
-
-            let indexAge = 'unknown';
-            try {
-                const ageMs = Date.now() - fs.statSync(INDEX_PATH).mtimeMs;
-                const ageSec = Math.floor(ageMs / 1000);
-                indexAge = ageSec < 60 ? `${ageSec}s ago` : ageSec < 3600 ? `${Math.floor(ageSec / 60)}m ago` : `${Math.floor(ageSec / 3600)}h ago`;
-            } catch { }
-
-            let daemonStatus = 'unknown';
-            try {
-                if (fs.existsSync(PID_FILE)) {
-                    const pid = parseInt(fs.readFileSync(PID_FILE, 'utf-8'), 10);
-                    process.kill(pid, 0);
-                    daemonStatus = `running (PID: ${pid})`;
-                } else { daemonStatus = 'not running'; }
-            } catch { daemonStatus = 'not running (stale PID)'; }
-
-            const extCounts = new Map();
-            for (const chunk of db.chunks.values()) {
-                const ext = chunk.file_path.split('.').pop() || 'unknown';
-                extCounts.set(ext, (extCounts.get(ext) || 0) + 1);
-            }
-
-            const lazyModeActive = db._lazyMode;
-            const vectorSource = lazyModeActive
-                ? (db._vecFd >= 0 ? 'disk-backed fd' : 'buffer-lazy')
-                : 'eager (in-memory matrix)';
-            const searchMode = !embeddingsEnabled
-                ? '🔤 Lexical only (INDEXER_EMBEDDINGS=off)'
-                : hasVectors
-                    ? `🧠 Hybrid (semantic + lexical RRF) — vectors: ${vectorSource}`
-                    : '🔤 Lexical only (Ollama unavailable or not yet indexed)';
-
-            const lines = [
-                `# 📊 graph-indexer Index Stats`, '',
-                `| Metric | Value |`, `| :--- | :--- |`,
-                `| **Chunks** | ${chunkCount} |`,
-                `| **Files indexed** | ${fileSet.size} |`,
-                `| **Symbols in table** | ${db.symbolTable.size} |`,
-                `| **Vector entries** | ${lazyModeActive ? db._vecOffsets.size : db.vectors.size} |`,
-                `| **Search mode** | ${searchMode} |`,
-                `| **Lazy vec mode** | ${lazyModeActive ? '✅ Yes (enterprise scale)' : '❌ No (small corpus)'} |`,
-                `| **Daemon** | ${daemonStatus} |`,
-                `| **Index age** | ${indexAge} |`,
-                '', `## Extension Breakdown`,
-                ...Array.from(extCounts.entries()).sort((a, b) => b[1] - a[1]).map(([e, n]) => `- .${e}: ${n} chunks`),
-            ];
-            if (chunkCount === 0) lines.push('', `⚠️ Index empty. Run \`npm run mcp:index\`.`);
-            return { content: [{ type: "text", text: lines.join('\n') }] };
-        } catch (err) {
-            return { content: [{ type: "text", text: `Error: ${err.message}` }], isError: true };
-        }
+        return { contents: [{ uri: uri.href, mimeType: 'text/markdown', text: md }] };
     }
 );
 
-// ─── Connect ──────────────────────────────────────────────────────────────────
+// ─── Tools ───────────────────────────────────────────────────────────────────
+registerTools(server, db, {
+    projectRoot: PROJECT_ROOT,
+    artifactPath: config.storage === 'sqlite' ? config.sqlitePath : config.indexPath,
+    pidFile: PID_FILE,
+    embeddingsEnabled: config.embeddingsEnabled,
+    ollamaHost: config.ollamaHost,
+    embedModel: config.embedModel,
+    rerank: config.rerank,
+});
 
 const transport = new StdioServerTransport();
 await server.connect(transport);
-process.stderr.write(`✅ graph-indexer MCP server running (v${version}).\n`);
+process.stderr.write(`✅ graph-indexer MCP server running (v${version}, ${config.storage} backend).\n`);