fathom-mcp 0.6.3 → 2.0.0

package/src/cli.js

@@ -1,937 +0,0 @@
-#!/usr/bin/env node
-
-/**
- * fathom-mcp CLI
- *
- * Usage:
- *   npx fathom-mcp              — Start MCP server (stdio, for .mcp.json)
- *   npx fathom-mcp init         — Interactive setup wizard
- *   npx fathom-mcp status       — Check server connection + workspace status
- *   npx fathom-mcp update       — Update hook scripts + version file
- *   npx fathom-mcp list         — List workspaces + status (from server)
- */
-
-import fs from "fs";
-import path from "path";
-import readline from "readline";
-import { execFileSync } from "child_process";
-import { fileURLToPath } from "url";
-
-import { findConfigFile, resolveConfig, writeConfig } from "./config.js";
-import { createClient } from "./server-client.js";
-
-const __dirname = path.dirname(fileURLToPath(import.meta.url));
-const SCRIPTS_DIR = path.join(__dirname, "..", "scripts");
-
-// --- Helpers -----------------------------------------------------------------
-
-function ask(rl, question, defaultVal = "") {
-  const suffix = defaultVal ? ` (${defaultVal})` : "";
-  return new Promise((resolve) => {
-    rl.question(`${question}${suffix}: `, (answer) => {
-      resolve(answer.trim() || defaultVal);
-    });
-  });
-}
-
-function askYesNo(rl, question, defaultYes = true) {
-  const hint = defaultYes ? "Y/n" : "y/N";
-  return new Promise((resolve) => {
-    rl.question(`${question} [${hint}]: `, (answer) => {
-      const a = answer.trim().toLowerCase();
-      if (!a) return resolve(defaultYes);
-      resolve(a === "y" || a === "yes");
-    });
-  });
-}
-
-/**
- * Deep merge obj2 into obj1 (mutates obj1). Arrays are replaced, not merged.
- */
-function deepMerge(obj1, obj2) {
-  for (const key of Object.keys(obj2)) {
-    if (
-      obj1[key] &&
-      typeof obj1[key] === "object" &&
-      !Array.isArray(obj1[key]) &&
-      typeof obj2[key] === "object" &&
-      !Array.isArray(obj2[key])
-    ) {
-      deepMerge(obj1[key], obj2[key]);
-    } else {
-      obj1[key] = obj2[key];
-    }
-  }
-  return obj1;
-}
-
-function readJsonFile(filePath) {
-  try {
-    return JSON.parse(fs.readFileSync(filePath, "utf-8"));
-  } catch {
-    return null;
-  }
-}
-
-function writeJsonFile(filePath, data) {
-  fs.mkdirSync(path.dirname(filePath), { recursive: true });
-  fs.writeFileSync(filePath, JSON.stringify(data, null, 2) + "\n");
-}
-
-function appendToGitignore(dir, patterns) {
-  const gitignorePath = path.join(dir, ".gitignore");
-  let existing = "";
-  try {
-    existing = fs.readFileSync(gitignorePath, "utf-8");
-  } catch { /* file doesn't exist */ }
-
-  const missing = patterns.filter((p) => !existing.includes(p));
-  if (missing.length > 0) {
-    const suffix = existing.endsWith("\n") || !existing ? "" : "\n";
-    fs.appendFileSync(gitignorePath, suffix + missing.join("\n") + "\n");
-  }
-}
-
-/**
- * Idempotently register a hook in a settings object.
- * Works for both Claude Code and Gemini CLI (same JSON structure).
- * Returns true if a new hook was added, false if already present.
- */
-/**
- * MCP tool permissions upserted into .claude/settings.local.json during init.
- * Only fathom-vault and memento — the tools init itself provides.
- */
-const INIT_PERMISSIONS = [
-  "mcp__fathom-vault__*",
-  "mcp__memento__*",
-];
-
-/**
- * Upsert permissions into settings.permissions.allow.
- * Returns true if any new entries were added.
- */
-function ensurePermissions(settings, perms = INIT_PERMISSIONS) {
-  if (!settings.permissions) settings.permissions = {};
-  if (!Array.isArray(settings.permissions.allow)) settings.permissions.allow = [];
-  const existing = new Set(settings.permissions.allow);
-  let changed = false;
-  for (const perm of perms) {
-    if (!existing.has(perm)) {
-      settings.permissions.allow.push(perm);
-      changed = true;
-    }
-  }
-  return changed;
-}
-
-function ensureHook(settings, eventName, command, timeout) {
-  const existing = settings.hooks?.[eventName] || [];
-  const alreadyRegistered = existing.some((entry) =>
-    entry.hooks?.some((h) => h.command === command)
-  );
-  if (alreadyRegistered) return false;
-  if (!settings.hooks) settings.hooks = {};
-  settings.hooks[eventName] = [
-    ...existing,
-    { hooks: [{ type: "command", command, timeout }] },
-  ];
-  return true;
-}
-
-function copyScripts(targetDir) {
-  fs.mkdirSync(targetDir, { recursive: true });
-  try {
-    const files = fs.readdirSync(SCRIPTS_DIR);
-    for (const file of files) {
-      const src = path.join(SCRIPTS_DIR, file);
-      const dest = path.join(targetDir, file);
-      fs.copyFileSync(src, dest);
-      fs.chmodSync(dest, 0o755);
-    }
-    return files;
-  } catch {
-    return [];
-  }
-}
-
-// ---------------------------------------------------------------------------
-// CLAUDE.md integration
-// ---------------------------------------------------------------------------
-
-const FATHOM_MD_MARKER_START = "<!-- BEGIN fathom-mcp -->";
-const FATHOM_MD_MARKER_END = "<!-- END fathom-mcp -->";
-
-function appendToClaudeMd(cwd, blob) {
-  const mdPath = path.join(cwd, "CLAUDE.md");
-  let content = "";
-  try { content = fs.readFileSync(mdPath, "utf-8"); } catch { /* new file */ }
-
-  const wrappedBlob = `${FATHOM_MD_MARKER_START}\n${blob}\n${FATHOM_MD_MARKER_END}`;
-
-  const markerRe = new RegExp(
-    `${FATHOM_MD_MARKER_START.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}[\\s\\S]*?${FATHOM_MD_MARKER_END.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}`,
-  );
-
-  if (markerRe.test(content)) {
-    content = content.replace(markerRe, wrappedBlob);
-  } else {
-    content = content.trimEnd() + "\n\n" + wrappedBlob + "\n";
-  }
-
-  fs.writeFileSync(mdPath, content, "utf-8");
-  return mdPath;
-}
-
-/**
- * Check if fathom-server is available on PATH.
- * Returns "installed" or "not-found".
- */
-function detectFathomServer() {
-  try {
-    execFileSync("which", ["fathom-server"], { stdio: "pipe" });
-    return "installed";
-  } catch {
-    return "not-found";
-  }
-}
-
-// --- CLI flag parsing --------------------------------------------------------
-
-function parseFlags(argv) {
-  const flags = {
-    nonInteractive: false,
-    apiKey: null,
-    server: null,
-    workspace: null,
-    agent: null,
-    vaultMode: null,
-  };
-  for (let i = 0; i < argv.length; i++) {
-    if (argv[i] === "-y" || argv[i] === "--yes") {
-      flags.nonInteractive = true;
-    } else if (argv[i] === "--api-key" && argv[i + 1]) {
-      flags.apiKey = argv[i + 1];
-      i++;
-    } else if (argv[i] === "--server" && argv[i + 1]) {
-      flags.server = argv[i + 1];
-      i++;
-    } else if (argv[i] === "--workspace" && argv[i + 1]) {
-      flags.workspace = argv[i + 1];
-      i++;
-    } else if (argv[i] === "--agent" && argv[i + 1]) {
-      flags.agent = argv[i + 1];
-      i++;
-    } else if (argv[i] === "--vault-mode" && argv[i + 1]) {
-      flags.vaultMode = argv[i + 1];
-      i++;
-    }
-  }
-  // Check environment variables as fallback
-  if (!flags.apiKey && process.env.FATHOM_API_KEY) {
-    flags.apiKey = process.env.FATHOM_API_KEY;
-  }
-  return flags;
-}
-
-// --- Agent registry ----------------------------------------------------------
-
-const MCP_SERVER_ENTRY = {
-  command: "npx",
-  args: ["-y", "fathom-mcp"],
-};
-
-/**
- * Per-agent config writers. Each writes the appropriate MCP config file
- * for that agent, merging with existing config if present.
- */
-
-function writeMcpJson(cwd) {
-  const filePath = path.join(cwd, ".mcp.json");
-  const existing = readJsonFile(filePath) || {};
-  deepMerge(existing, { mcpServers: { "fathom-vault": MCP_SERVER_ENTRY } });
-  writeJsonFile(filePath, existing);
-  return ".mcp.json";
-}
-
-function writeGeminiJson(cwd) {
-  const dir = path.join(cwd, ".gemini");
-  fs.mkdirSync(dir, { recursive: true });
-  const filePath = path.join(dir, "settings.json");
-  const existing = readJsonFile(filePath) || {};
-  deepMerge(existing, { mcpServers: { "fathom-vault": MCP_SERVER_ENTRY } });
-  writeJsonFile(filePath, existing);
-  return ".gemini/settings.json";
-}
-
-const AGENTS = {
-  "claude-code": {
-    name: "Claude Code",
-    detect: (cwd) => fs.existsSync(path.join(cwd, ".claude")),
-    configWriter: writeMcpJson,
-    hasHooks: true,
-    nextSteps: 'Add to CLAUDE.md: `ToolSearch query="+fathom" max_results=20`',
-  },
-  "gemini": {
-    name: "Gemini CLI",
-    detect: (cwd) => fs.existsSync(path.join(cwd, ".gemini")),
-    configWriter: writeGeminiJson,
-    hasHooks: true,
-    nextSteps: "Run `gemini` in this directory — fathom tools load automatically.",
-  },
-  "manual": {
-    name: "I'll set up my agent myself",
-    detect: () => false,
-    configWriter: () => "(skipped — manual setup)",
-    hasHooks: false,
-    nextSteps: "Point your agent's MCP config at: npx -y fathom-mcp",
-  },
-};
-
-// Exported for testing
-export { AGENTS, writeMcpJson, writeGeminiJson };
-
-// --- Init wizard -------------------------------------------------------------
-
-async function runInit(flags = {}) {
-  const {
-    nonInteractive = false,
-    apiKey: flagApiKey = null,
-    server: flagServer = null,
-    workspace: flagWorkspace = null,
-    agent: flagAgent = null,
-    vaultMode: flagVaultMode = null,
-  } = flags;
-  const cwd = process.cwd();
-
-  const rl = nonInteractive
-    ? null
-    : readline.createInterface({ input: process.stdin, output: process.stdout });
-
-  console.log(`
-▐▘  ▗ ▌
-▜▘▀▌▜▘▛▌▛▌▛▛▌▄▖▛▛▌▛▘▛▌
-▐ █▌▐▖▌▌▙▌▌▌▌  ▌▌▌▙▖▙▌
-                    ▌
-
-  hifathom.com  ·  fathom@myrakrusemark.com
-`);
-
-  // Non-interactive: require API key
-  if (nonInteractive && !flagApiKey) {
-    console.error("  Error: --api-key required in non-interactive mode.");
-    process.exit(1);
-  }
-
-  // Check for existing config in *this* directory only (don't walk up —
-  // a parent's .fathom.json belongs to a different workspace)
-  const localConfigPath = path.join(cwd, ".fathom.json");
-  if (fs.existsSync(localConfigPath)) {
-    if (nonInteractive) {
-      console.log(`  Overwriting existing config at: ${localConfigPath}`);
-    } else {
-      console.log(`  Found existing config at: ${localConfigPath}`);
-      const proceed = await askYesNo(rl, "  Overwrite?", false);
-      if (!proceed) {
-        console.log("  Aborted.");
-        rl.close();
-        process.exit(0);
-      }
-    }
-  }
-
-  // 1. Workspace name
-  const defaultName = path.basename(cwd);
-  const workspace = nonInteractive
-    ? (flagWorkspace || defaultName)
-    : await ask(rl, "  Workspace name", defaultName);
-
-  // 2. Agent selection — auto-detect and let user choose
-  const agentKeys = Object.keys(AGENTS);
-  const detected = agentKeys.filter((key) => AGENTS[key].detect(cwd));
-
-  let selectedAgents;
-  if (nonInteractive) {
-    if (flagAgent) {
-      // Validate --agent value
-      if (!AGENTS[flagAgent]) {
-        const valid = Object.keys(AGENTS).join(", ");
-        console.error(`  Error: unknown agent "${flagAgent}". Valid agents: ${valid}`);
-        process.exit(1);
-      }
-      selectedAgents = [flagAgent];
-      console.log(`  Agent: ${AGENTS[flagAgent].name} (--agent flag)`);
-    } else {
-      // Auto-detect: use first detected agent, or default to claude-code
-      selectedAgents = detected.length > 0 ? [detected[0]] : ["claude-code"];
-      console.log(`  Agent: ${AGENTS[selectedAgents[0]].name} (auto-detected)`);
-    }
-  } else {
-    console.log("\n  Detected agents:");
-    for (const key of agentKeys) {
-      const agent = AGENTS[key];
-      const isDetected = detected.includes(key);
-      const mark = isDetected ? "✓" : " ";
-      const markers = { "claude-code": ".claude/", "gemini": ".gemini/" };
-      const hint = isDetected ? ` (${markers[key] || key} found)` : "";
-      console.log(`    ${mark} ${agent.name}${hint}`);
-    }
-
-    console.log("\n  Configure for which agents?");
-    agentKeys.forEach((key, i) => {
-      const agent = AGENTS[key];
-      const mark = detected.includes(key) ? " ✓" : "";
-      console.log(`    ${i + 1}. ${agent.name}${mark}`);
-    });
-
-    const defaultSelection = detected.length > 0
-      ? detected.map((key) => agentKeys.indexOf(key) + 1).join(",")
-      : "1";
-    const selectionStr = await ask(rl, "\n  Enter numbers, comma-separated", defaultSelection);
-
-    const selectedIndices = selectionStr
-      .split(",")
-      .map((s) => parseInt(s.trim(), 10))
-      .filter((n) => n >= 1 && n <= agentKeys.length);
-    selectedAgents = [...new Set(selectedIndices.map((i) => agentKeys[i - 1]))];
-
-    if (selectedAgents.length === 0) {
-      console.log("  No agents selected. Defaulting to Claude Code.");
-      selectedAgents.push("claude-code");
-    }
-  }
-
-  // 5. Server URL
-  let serverUrl = nonInteractive
-    ? (flagServer || "http://localhost:4243")
-    : await ask(rl, "\n  Fathom server URL", "http://localhost:4243");
-
-  // 6. API key
-  let apiKey = flagApiKey || (nonInteractive ? "" : await ask(rl, "  API key (from dashboard or server first-run output)", ""));
-
-  // 7. Server probe — check reachability early
-  let regClient = createClient({ server: serverUrl, apiKey, workspace });
-  let serverReachable = serverUrl ? await regClient.healthCheck() : false;
-  const serverOnPath = detectFathomServer();
-
-  // Retry loop for server connectivity (interactive mode)
-  while (!serverReachable && !nonInteractive) {
-    console.log(`\n  ⚠ Fathom server not reachable at ${serverUrl}\n`);
-    if (serverOnPath === "installed") {
-      console.log("  Start it:  fathom-server");
-    } else {
-      console.log("  Install & start it:");
-      console.log("    pip install fathom-server && fathom-server");
-      console.log("    # or: docker run -p 4243:4243 ghcr.io/myra/fathom-server");
-    }
-    console.log("\n  Without the server, only \"local\" and \"none\" vault modes are available.");
-    const retry = await askYesNo(rl, "\n  Try a different server URL or API key?", true);
-    if (!retry) break;
-    serverUrl = await ask(rl, "\n  Fathom server URL", serverUrl);
-    apiKey = await ask(rl, "  API key", apiKey);
-    regClient = createClient({ server: serverUrl, apiKey, workspace });
-    serverReachable = await regClient.healthCheck();
-    if (serverReachable) {
-      console.log("  ✓ Server connected!");
-    }
-  }
-
-  // 8. Vault mode selection
-  let vaultMode;
-  const validVaultModes = ["synced", "local", "none"];
-  if (nonInteractive) {
-    if (!serverReachable && flagServer) {
-      console.error(`\n  Error: Server at ${serverUrl} is not reachable.`);
-      console.error("  Fix the URL or start the server, then re-run init.");
-      process.exit(1);
-    }
-    if (flagVaultMode) {
-      if (!validVaultModes.includes(flagVaultMode)) {
-        console.error(`  Error: unknown vault mode "${flagVaultMode}". Valid modes: ${validVaultModes.join(", ")}`);
-        process.exit(1);
-      }
-      if (flagVaultMode === "synced" && !serverReachable) {
-        console.error(`  Error: vault mode "${flagVaultMode}" requires a reachable server.`);
-        process.exit(1);
-      }
-      vaultMode = flagVaultMode;
-      console.log(`  Vault mode: ${vaultMode} (--vault-mode flag)`);
-    } else {
-      vaultMode = serverReachable ? "synced" : "local";
-      console.log(`  Vault mode: ${vaultMode} (auto-selected)`);
-    }
-  } else {
-    if (serverReachable) {
-      console.log("\n  Vault mode:");
-      console.log("    1. Synced (default) — local vault + server indexing");
-      console.log("    2. Local — vault on disk only, not visible to server");
-      console.log("    3. None — no vault, coordination features only");
-      const modeChoice = await ask(rl, "\n  Select mode", "1");
-      const modeMap = { "1": "synced", "2": "local", "3": "none" };
-      vaultMode = modeMap[modeChoice] || "synced";
-    } else {
-      console.log("\n  Vault mode (server not available — hosted/synced require server):");
-      console.log("    1. Local (default) — vault on disk only");
-      console.log("    2. None — no vault, coordination features only");
-      const modeChoice = await ask(rl, "\n  Select mode", "1");
-      vaultMode = modeChoice === "2" ? "none" : "local";
-    }
-  }
-
-  // Only ask about vault subdirectory if mode needs a local dir
-  const needsLocalVault = vaultMode === "synced" || vaultMode === "local";
-  const vault = needsLocalVault
-    ? (nonInteractive ? "vault" : await ask(rl, "  Vault subdirectory", "vault"))
-    : "vault";
-
-  // 9. Hooks — ask if any hook-supporting agent is selected (Claude Code, Claude SDK, Gemini CLI)
-  const hasClaude = selectedAgents.includes("claude-code");
-  const hasGemini = selectedAgents.includes("gemini");
-  const hasHookAgent = hasClaude || hasGemini;
-  let enableRecallHook = false;
-  let enablePrecompactHook = false;
-  if (hasHookAgent) {
-    if (nonInteractive) {
-      enableRecallHook = true;
-      enablePrecompactHook = true;
-    } else {
-      console.log();
-      enableRecallHook = await askYesNo(rl, "  Enable vault recall on every message?", true);
-      enablePrecompactHook = await askYesNo(rl, "  Enable PreCompact vault snapshot hook?", true);
-    }
-  }
-
-  rl?.close();
-
-  // --- Write files ---
-
-  console.log("\n  Creating files...\n");
-
-  // .fathom.json
-  const configData = {
-    workspace,
-    vaultMode,
-    vault,
-    server: serverUrl,
-    apiKey,
-    agents: selectedAgents,
-    hooks: {
-      "vault-recall": { enabled: enableRecallHook },
-      "precompact-snapshot": { enabled: enablePrecompactHook },
-    },
-  };
-  const configPath = writeConfig(cwd, configData);
-  console.log(`  ✓ ${path.relative(cwd, configPath)}`);
-
-  // ~/.config/fathom-mcp/scripts/ (central, shared across all workspaces)
-  const centralScriptsDir = path.join(process.env.HOME, ".config", "fathom-mcp", "scripts");
-  const copiedScripts = copyScripts(centralScriptsDir);
-  if (copiedScripts.length > 0) {
-    console.log(`  ✓ ~/.config/fathom-mcp/scripts/ (${copiedScripts.length} scripts)`);
-  }
-
-  // vault/ directory — only create for synced/local modes
-  if (needsLocalVault) {
-    const vaultDir = path.join(cwd, vault);
-    if (!fs.existsSync(vaultDir)) {
-      fs.mkdirSync(vaultDir, { recursive: true });
-      console.log(`  ✓ ${vault}/ (created)`);
-    } else {
-      console.log(`  · ${vault}/ (already exists)`);
-    }
-  }
-
-  // fathom-agents.md — boilerplate agent instructions (central)
-  const agentMdSrc = path.join(__dirname, "..", "fathom-agents.md");
-  const agentMdDest = path.join(process.env.HOME, ".config", "fathom-mcp", "fathom-agents.md");
-  try {
-    let template = fs.readFileSync(agentMdSrc, "utf-8");
-    template = template
-      .replace(/\{\{WORKSPACE_NAME\}\}/g, workspace)
-      .replace(/\{\{VAULT_DIR\}\}/g, vault)
-      .replace(/\{\{DESCRIPTION\}\}/g, `${workspace} workspace`);
-    fs.mkdirSync(path.dirname(agentMdDest), { recursive: true });
-    fs.writeFileSync(agentMdDest, template);
-    console.log("  ✓ ~/.config/fathom-mcp/fathom-agents.md");
-  } catch { /* template not found — skip silently */ }
-
-  // Per-agent config files
-  for (const agentKey of selectedAgents) {
-    const agent = AGENTS[agentKey];
-    const result = agent.configWriter(cwd);
-    console.log(`  ✓ ${result}`);
-  }
-
-  // Hook scripts (central location, shared across agents)
-  const sessionStartCmd = "bash ~/.config/fathom-mcp/scripts/fathom-sessionstart.sh";
-  const recallCmd = "bash ~/.config/fathom-mcp/scripts/fathom-recall.sh";
-  const precompactCmd = "bash ~/.config/fathom-mcp/scripts/fathom-precompact.sh";
-
-  // Claude Code hooks
-  const lintCmd = "node ~/.config/fathom-mcp/scripts/vault-frontmatter-lint.js";
-  if (hasClaude) {
-    const settingsPath = path.join(cwd, ".claude", "settings.local.json");
-    const settings = readJsonFile(settingsPath) || {};
-    let changed = ensurePermissions(settings);
-    changed = ensureHook(settings, "SessionStart", sessionStartCmd, 10000) || changed;
-    if (enableRecallHook) changed = ensureHook(settings, "UserPromptSubmit", recallCmd, 10000) || changed;
-    if (enablePrecompactHook) changed = ensureHook(settings, "PreCompact", precompactCmd, 30000) || changed;
-    changed = ensureHook(settings, "PostToolUse", lintCmd, 5000) || changed;
-    if (changed) {
-      writeJsonFile(settingsPath, settings);
-      console.log("  ✓ .claude/settings.local.json (permissions + hooks)");
-    }
-  }
-
-  // Gemini CLI hooks
-  if (hasGemini) {
-    const settingsPath = path.join(cwd, ".gemini", "settings.json");
-    const settings = readJsonFile(settingsPath) || {};
-    let changed = ensureHook(settings, "SessionStart", sessionStartCmd, 10000);
-    if (enableRecallHook) changed = ensureHook(settings, "BeforeAgent", recallCmd, 10000) || changed;
-    if (enablePrecompactHook) changed = ensureHook(settings, "PreCompress", precompactCmd, 30000) || changed;
-    if (changed) {
-      writeJsonFile(settingsPath, settings);
-      console.log("  ✓ .gemini/settings.json (hooks)");
-    }
-  }
-
-  // .gitignore
-  appendToGitignore(cwd, [".fathom.json"]);
-  console.log("  ✓ .gitignore");
-
-  // Register with server — use provision endpoint to get API key + create settings.json entry
-  if (serverReachable) {
-    const provResult = await regClient.provisionWorkspace(workspace, cwd, {
-      vault,
-      agents: selectedAgents,
-      type: vaultMode,
-      execution: "local",
-    });
-    if (provResult.ok) {
-      console.log(`  ✓ Registered workspace "${workspace}" with server`);
-      // Use the server-provisioned API key (overwrites any manually entered one)
-      if (provResult.api_key) {
-        apiKey = provResult.api_key;
-        configData.apiKey = apiKey;
-        writeConfig(cwd, configData);
-        console.log(`  ✓ API key provisioned by server`);
-      }
-    } else if (provResult.error) {
-      console.log(`  · Server registration: ${provResult.error}`);
-      // Fall back to old registration endpoint (server may be older version)
-      const regResult = await regClient.registerWorkspace(workspace, cwd, {
-        vault,
-        agents: selectedAgents,
-        type: vaultMode,
-      });
-      if (regResult.ok) {
-        console.log(`  ✓ Registered workspace "${workspace}" with server (legacy)`);
-      } else if (regResult.error) {
-        console.log(`  · Server registration: ${regResult.error}`);
-      }
-    }
-  }
-
-  // Context-aware next steps
-  console.log(`\n  Done! Fathom MCP is configured for workspace "${workspace}".`);
-  console.log(`  Vault mode: ${vaultMode}`);
-  console.log("\n  Next steps:");
-
-  if (!serverReachable) {
-    if (serverOnPath === "installed") {
-      console.log("    1. Start the server:  fathom-server");
-    } else {
-      console.log("    1. Install & start the server:  pip install fathom-server && fathom-server");
-    }
-  }
-
-  const stepNum = serverReachable ? 1 : 2;
-  switch (vaultMode) {
-    case "synced":
-      console.log(`    ${stepNum}. Local vault indexed by server. Files in ./${vault}/ are the source of truth.`);
-      break;
-    case "local":
-      console.log(`    ${stepNum}. Local vault only. Server can't search or peek into it.`);
-      break;
-    case "none":
-      console.log(`    ${stepNum}. No vault configured. Rooms, messaging, and search still work.`);
-      break;
-  }
-  for (const agentKey of selectedAgents) {
-    const agent = AGENTS[agentKey];
-    console.log(`    · ${agent.name}: ${agent.nextSteps}`);
-  }
-
-  // Show non-interactive equivalent
-  if (!nonInteractive) {
-    const parts = ["npx fathom-mcp init -y"];
-    if (apiKey) parts.push(`--api-key "${apiKey}"`);
-    if (serverUrl && serverUrl !== "http://localhost:4243") parts.push(`--server ${serverUrl}`);
-    parts.push(`--workspace ${workspace}`);
-    parts.push(`--vault-mode ${vaultMode}`);
-    parts.push(`--agent ${selectedAgents[0]}`);
-    console.log(`\n  Non-interactive equivalent:\n    ${parts.join(" ")}\n`);
-  }
-
-  // Append agent instructions to CLAUDE.md
-  let instructionsBlob = "";
-  try {
-    instructionsBlob = fs.readFileSync(agentMdDest, "utf-8");
-  } catch { /* template wasn't created — skip */ }
-
-  if (instructionsBlob) {
-    if (nonInteractive) {
-      const mdPath = appendToClaudeMd(cwd, instructionsBlob);
-      console.log(`\n  ✓ Instructions written to ${path.relative(cwd, mdPath)}\n`);
-    } else {
-      const rl2 = readline.createInterface({ input: process.stdin, output: process.stdout });
-      console.log("\n" + "─".repeat(60));
-      const integrate = await askYesNo(
-        rl2,
-        "\n  Append Fathom instructions to CLAUDE.md?",
-        true,
-      );
-      rl2.close();
-
-      if (integrate) {
-        const mdPath = appendToClaudeMd(cwd, instructionsBlob);
-        console.log(`\n  ✓ Instructions written to ${path.relative(cwd, mdPath)}\n`);
-      } else {
-        printInstructionsFallback(agentMdDest, selectedAgents);
-      }
-    }
-  } else {
-    console.log("\n  No agent instructions template found — skipping integration.\n");
-  }
-}
-
-function printInstructionsFallback(agentMdPath, selectedAgents) {
-  const hasNonClaude = selectedAgents.some((k) => k !== "claude-code");
-  const docTarget = hasNonClaude
-    ? "your CLAUDE.md, AGENTS.md, or equivalent"
-    : "your CLAUDE.md";
-
-  console.log(`
-  Agent instructions saved to: ${path.relative(process.cwd(), agentMdPath)}
-
-  Paste into ${docTarget}, or point your agent at the file
-  and ask it to integrate the instructions.
-`);
-}
-
-// --- Status command ----------------------------------------------------------
-
-async function runStatus() {
-  const config = resolveConfig();
-  const client = createClient(config);
-
-  console.log("\n  Fathom MCP Status\n");
-  console.log(`  Config:    ${config._configPath || "(not found — using defaults)"}`);
-  console.log(`  Workspace: ${config.workspace}`);
-  console.log(`  Vault mode: ${config.vaultMode}`);
-  console.log(`  Vault:     ${config.vault}`);
-  console.log(`  Server:    ${config.server}`);
-  console.log(`  API Key:   ${config.apiKey ? config.apiKey.slice(0, 7) + "..." + config.apiKey.slice(-4) : "(not set)"}`);
-  console.log(`  Agents:    ${config.agents.length > 0 ? config.agents.join(", ") : "(none)"}`);
-
-  // Check vault directory
-  const vaultExists = fs.existsSync(config.vault);
-  console.log(`\n  Vault dir: ${vaultExists ? "✓ exists" : "✗ not found"}`);
-
-  // Check server
-  const isUp = await client.healthCheck();
-  console.log(`  Server:    ${isUp ? "✓ reachable" : "✗ not reachable"}`);
-
-  if (isUp) {
-    const wsResult = await client.listWorkspaces();
-    if (wsResult.profiles) {
-      const names = Object.keys(wsResult.profiles);
-      console.log(`  Workspaces: ${names.join(", ") || "(none)"}`);
-      for (const [name, profile] of Object.entries(wsResult.profiles)) {
-        if (profile.type === "human") {
-          console.log(`    ${name}: human`);
-        } else {
-          const agentLabel = profile.agents?.length > 0
-            ? ` [${profile.agents.join(", ")}]`
-            : "";
-          const runStatus = profile.running ? "running" : "stopped";
-          console.log(`    ${name}: ${runStatus}${agentLabel}`);
-        }
-      }
-    }
-  }
-
-  console.log();
-}
-
-// --- Update command ----------------------------------------------------------
-
-async function runUpdate() {
-  const found = findConfigFile(process.cwd());
-  if (!found) {
-    console.error("  Error: No .fathom.json found. Run `npx fathom-mcp init` first.");
-    process.exit(1);
-  }
-
-  const projectDir = found.dir;
-
-  // Read package version from our own package.json
-  const pkgJsonPath = path.join(__dirname, "..", "package.json");
-  const pkg = readJsonFile(pkgJsonPath);
-  const packageVersion = pkg?.version || "unknown";
-
-  // Copy all scripts to central location
-  const scriptsDir = path.join(process.env.HOME, ".config", "fathom-mcp", "scripts");
-  const copiedScripts = copyScripts(scriptsDir);
-
-  // Ensure SessionStart hook is registered for agents that support hooks
-  // Detect by config agents field or directory presence (older configs may lack agents)
-  const agents = found.config.agents || [];
-  const sessionStartCmd = "bash ~/.config/fathom-mcp/scripts/fathom-sessionstart.sh";
-  const registeredHooks = [];
-
-  // Claude Code
-  const hasClaude = agents.includes("claude-code")
-    || fs.existsSync(path.join(projectDir, ".claude"));
-  if (hasClaude) {
-    const settingsPath = path.join(projectDir, ".claude", "settings.local.json");
-    const settings = readJsonFile(settingsPath) || {};
-    let changed = ensurePermissions(settings);
-    changed = ensureHook(settings, "SessionStart", sessionStartCmd, 10000) || changed;
-    if (changed) {
-      writeJsonFile(settingsPath, settings);
-      registeredHooks.push("Claude Code → .claude/settings.local.json");
-    }
-  }
-
-  // Gemini CLI
-  const hasGemini = agents.includes("gemini")
-    || fs.existsSync(path.join(projectDir, ".gemini"));
-  if (hasGemini) {
-    const settingsPath = path.join(projectDir, ".gemini", "settings.json");
-    const settings = readJsonFile(settingsPath) || {};
-    if (ensureHook(settings, "SessionStart", sessionStartCmd, 10000)) {
-      writeJsonFile(settingsPath, settings);
-      registeredHooks.push("Gemini CLI → .gemini/settings.json");
-    }
-  }
-
-  console.log(`\n  ✓ Fathom hooks updated to v${packageVersion}\n`);
-
-  if (copiedScripts.length > 0) {
-    console.log("  Updated scripts in ~/.config/fathom-mcp/scripts/:");
-    for (const script of copiedScripts) {
-      console.log(`    ${script}`);
-    }
-  }
-
-  if (registeredHooks.length > 0) {
-    console.log("\n  Registered SessionStart hooks:");
-    for (const hook of registeredHooks) {
-      console.log(`    ${hook}`);
-    }
-  }
-
-  console.log("\n  Restart your agent session to pick up changes.\n");
-}
-
-// --- List command (via server API) --------------------------------------------
-
-async function runList() {
-  const config = resolveConfig();
-  const client = createClient(config);
-
-  const isUp = await client.healthCheck();
-  if (!isUp) {
-    console.error(`\n  Error: Server not reachable at ${config.server}`);
-    console.error("  Start the server or check --server URL.\n");
-    process.exit(1);
-  }
-
-  const wsResult = await client.listWorkspaces();
-  if (wsResult.error) {
-    console.error(`\n  Error: ${wsResult.error}\n`);
-    process.exit(1);
-  }
-
-  const profiles = wsResult.profiles || {};
-  const names = Object.keys(profiles);
-
-  if (names.length === 0) {
-    console.log("\n  No workspaces registered on server.\n");
-    return;
-  }
-
-  const cols = { name: 20, type: 10, status: 12 };
-  console.log(
-    "\n  " +
-      "WORKSPACE".padEnd(cols.name) +
-      "TYPE".padEnd(cols.type) +
-      "STATUS".padEnd(cols.status) +
-      "PATH",
-  );
-
-  for (const name of names) {
-    const p = profiles[name];
-    const type = p.type || "local";
-    let status;
-    if (type === "human") {
-      status = "human";
-    } else if (p.process && p.connected) {
-      status = "running";
-    } else if (p.process || p.connected) {
-      status = "partial";
-    } else {
-      status = "stopped";
-    }
-    const dir = (p.path || "").replace(process.env.HOME, "~");
-
-    console.log(
-      "  " +
-        name.padEnd(cols.name) +
-        type.padEnd(cols.type) +
-        status.padEnd(cols.status) +
-        dir,
-    );
-  }
-  console.log();
-}
-
-// --- Main --------------------------------------------------------------------
-
-// Guard: only run CLI when this module is the entry point (not when imported by tests)
-const isMain = process.argv[1] && (
-  process.argv[1].endsWith("/cli.js") || process.argv[1].endsWith("fathom-mcp")
-);
-
-if (isMain) {
-  const command = process.argv[2];
-
-  const asyncHandler = (fn) => fn().catch((e) => {
-    console.error(`Error: ${e.message}`);
-    process.exit(1);
-  });
-
-  if (command === "init") {
-    asyncHandler(() => runInit(parseFlags(process.argv.slice(3))));
-  } else if (command === "status") {
-    asyncHandler(runStatus);
-  } else if (command === "update") {
-    asyncHandler(runUpdate);
-  } else if (command === "list" || command === "ls") {
-    asyncHandler(runList);
-  } else if (!command || command === "serve") {
-    import("./index.js");
-  } else {
-    console.error(`Unknown command: ${command}`);
-    console.error(`Usage: fathom-mcp [command]
-
-  fathom-mcp                                         Start MCP server (stdio)
-  fathom-mcp serve                                   Same as above
-  fathom-mcp init [-y --api-key KEY --vault-mode MODE --agent AGENT]    Interactive/non-interactive setup
-  fathom-mcp status                                  Check connection status
-  fathom-mcp update                                  Update hooks + version
-  fathom-mcp list                                    List workspaces + status (from server)`);
-    process.exit(1);
-  }
-}