context-mcp-server 1.0.8 → 1.1.1

package/src/cli.js

@@ -107,45 +107,28 @@ function printSection(title, meta = '') {
 function printUsage() {
   printBanner();
 
-  // Terminal commands (ctx / context ...)
-  printSection('Terminal commands', 'run from your shell  (ctx … or context …)');
+  printSection('Commands');
   const cmd = (c, desc) => console.log(`  ${accent(c.padEnd(40))} ${faint(desc)}`);
   cmd('ctx',                           'open interactive mode');
   cmd('ctx list [project]',            'list entries + discussions + graphs');
   cmd('ctx search <query>',            'keyword → semantic fallback search');
   cmd('ctx add',                       'add entry interactively');
+  cmd('ctx save --title "…" --content "…" --project <p> --type <t>', 'non-interactive save (scripts/hooks)');
   cmd('ctx delete <id-prefix>',        'delete one entry');
   cmd('ctx delete project <name|id>',  'delete all entries for a project');
   cmd('ctx summary [project]',         'summarize recent entries');
   cmd('ctx projects',                  'show all projects + graphs');
   cmd('ctx discuss [project]',         'show discussions');
-  cmd('ctx benchmark',                 'token savings report (memory + graph)');
   console.log('');
-  cmd('ctx install --initial',         'install / update Node.js + Python (codegraph) deps');
-  cmd('ctx install --<platform>',      'write MCP config + skill/rules for an AI platform');
-  cmd('ctx install --all',             'install for all platforms at once');
+  cmd('ctx install --initial',         'install / update Node.js + Python (codegraph) deps only');
+  cmd('ctx install --<platform>',      'write MCP config + skill/rules file only (no uv/npm)');
+  cmd('ctx install --all',             'write config + skill files for all platforms');
   cmd('ctx online [--port N]',         'start HTTP server for Claude.ai / ChatGPT');
   cmd('ctx online --close',            'stop the running HTTP server');
   cmd('ctx settings',                  'view and edit config (port, host, client id/secret)');
   cmd('ctx update',                    'check for and apply latest version');
   cmd('ctx help',                      'show this screen');
   console.log('');
-
-  // Interactive mode commands (no prefix needed)
-  printSection('Interactive mode', 'type these inside the UI — no "ctx" prefix needed');
-  const icmd = (c, desc) => console.log(`  ${accent(c.padEnd(40))} ${faint(desc)}`);
-  icmd('list [project]',               'list entries');
-  icmd('search <query>',               'search context');
-  icmd('add',                          'add entry');
-  icmd('projects',                     'show all projects');
-  icmd('discuss [project]',            'show discussions');
-  icmd('summary [project]',            'summarize recent entries');
-  icmd('benchmark',                    'token savings report');
-  icmd('install --<platform>',         'install for a platform');
-  icmd('settings',                     'edit config');
-  icmd('clear',                        'clear screen');
-  icmd('exit / quit / q',              'exit interactive mode');
-  console.log('');
 }
 function clearScreen() {
   // \x1b[2J = clear screen, \x1b[3J = clear scrollback, \x1b[H = cursor home
@@ -155,7 +138,8 @@ function clearScreen() {
 // ── List (grouped by project) ─────────────────────────────────────────────────
 
 function cmdList(args) {
-  const filterProject  = args[0];
+  const projectFlagIdx = args.indexOf('--project');
+  const filterProject  = projectFlagIdx !== -1 ? args[projectFlagIdx + 1] : args[0];
   const entries        = getContext({ project: filterProject, limit: 100 });
   const allDiscussions = listDiscussions({ project: filterProject });
   const allGraphs      = listGraphs();
@@ -163,7 +147,6 @@ function cmdList(args) {
 
   printSection('Context', filterProject ? `project: ${filterProject}` : 'all projects');
 
-  // Build per-project map, split entries into their three trees
   const projects = {};
   const ensureProj = p => {
     if (!projects[p]) projects[p] = { context: [], summary: [], plans: [] };
@@ -213,13 +196,12 @@ function cmdList(args) {
         const id   = item.id.slice(0, 8);
         const tags = safeTags(item.tags);
         const pipe = secIsLast ? ' ' : '│';
-        console.log(`  ${color(C.darkgray, pipe)}  ${color(C.darkgray, br)} ${pill(item.type || 'note')}  ${bold(item.title || '(no title)')}  ${faint('id:' + id)}  ${faint(date)}`);
+        console.log(`  ${color(C.darkgray, pipe)}  ${color(C.darkgray, br)} ${bold(item.title || '(no title)')}  ${faint('id:' + id)}  ${faint(date)}`);
         if (tags.length) console.log(`  ${color(C.darkgray, pipe)}     ${faint(tags.map(t => '#' + t).join(' '))}`);
       });
       if (!secIsLast) console.log(`  ${color(C.darkgray, '│')}`);
     };
 
-    // ── Graph (build stats only) ──────────────────────────────────────────────
     if (graphBuild) {
       secIdx++;
       const isLast  = secIdx === sections.length;
@@ -228,13 +210,11 @@ function cmdList(args) {
       if (!isLast) console.log(`  ${color(C.darkgray, '│')}`);
     }
 
-    // ── Context ───────────────────────────────────────────────────────────────
     if (pData.context.length) {
       secIdx++;
       renderEntries(pData.context, 'context', secIdx === sections.length);
     }
 
-    // ── Summary (compaction digests only — no type labels) ───────────────────
     if (pData.summary.length) {
       secIdx++;
       const isLast = secIdx === sections.length;
@@ -248,7 +228,6 @@ function cmdList(args) {
       if (!isLast) console.log(`  ${color(C.darkgray, '│')}`);
     }
 
-    // ── Plans ─────────────────────────────────────────────────────────────────
     if (pData.plans.length) {
       secIdx++;
       const isLast = secIdx === sections.length;
@@ -285,7 +264,7 @@ function cmdSearch(args) {
     const id     = entry.id.slice(0, 8);
     const type   = entry.type || 'note';
     const isLast = index === results.length - 1;
-    console.log(`  ${color(C.darkgray, isLast ? '└─' : '├─')} ${bold(entry.title || '(no title)')}${score}  ${pill(type)}  ${faint('id:' + id)}  ${faint(date)}`);
+    console.log(`  ${color(C.darkgray, isLast ? '└─' : '├─')} ${bold(entry.title || '(no title)')}${score}  ${faint('id:' + id)}  ${faint(date)}`);
   });
   console.log('');
   console.log(line());
@@ -313,7 +292,6 @@ function cmdProjects() {
     console.log(`\n  ${color(C.dblue, '◆')} ${bold(lblue(project.name))}${idTag}  ${bar}  ${faint(project.count + ' entries')}`);
     console.log(`  ${color(C.darkgray, '│')}`);
 
-    // Graph status
     if (graph) {
       const builtAt = (graph.builtAt || '').slice(0, 10);
       console.log(`  ${color(C.darkgray, '├─')} ${accent('⬡')} ${muted('graph')}  ${faint(`${graph.nodes}n · ${graph.edges}e · ${graph.communities} clusters · ${builtAt}`)}`);
@@ -321,18 +299,15 @@ function cmdProjects() {
       console.log(`  ${color(C.darkgray, '├─')} ${faint('⬡ no graph')}`);
     }
 
-    // Recent context
     if (entries.length) {
       console.log(`  ${color(C.darkgray, '├─')} ${muted('recent')}`);
       entries.forEach((e, i) => {
         const br   = i === entries.length - 1 && !activeD.length ? '└─' : '├─';
-        const type = e.type || 'note';
         const date = (e.createdAt || '').slice(0, 10);
-        console.log(`  ${color(C.darkgray, '│')}  ${color(C.darkgray, br)} ${pill(type)}  ${bold(e.title || '(no title)')}  ${faint(date)}`);
+        console.log(`  ${color(C.darkgray, '│')}  ${color(C.darkgray, br)} ${bold(e.title || '(no title)')}  ${faint(date)}`);
       });
     }
 
-    // Active discussions
     if (activeD.length) {
       console.log(`  ${color(C.darkgray, '├─')} ${muted('discussions')}`);
       activeD.forEach((d, i) => {
@@ -354,7 +329,8 @@ function cmdProjects() {
 // ── Discussions ───────────────────────────────────────────────────────────────
 
 function cmdDiscussions(args) {
-  const filterProject = args[0];
+  const projectFlagIdx = args.indexOf('--project');
+  const filterProject  = projectFlagIdx !== -1 ? args[projectFlagIdx + 1] : args[0];
   const discussions   = listDiscussions({ project: filterProject });
   printSection('Discussions', filterProject || 'all projects');
 
@@ -392,7 +368,8 @@ function cmdDiscussions(args) {
 // ── Summary ───────────────────────────────────────────────────────────────────
 
 function cmdSummary(args) {
-  const project = args[0];
+  const projectFlagIdx = args.indexOf('--project');
+  const project        = projectFlagIdx !== -1 ? args[projectFlagIdx + 1] : args[0];
   const entries = getContext({ project, limit: 50 });
   printSection('Summary', project || 'global');
   if (!entries.length) { console.log(`  ${faint('no entries to summarize')}`); return; }
@@ -408,143 +385,6 @@ function cmdSummary(args) {
   console.log('');
 }
 
-// ── Benchmark ────────────────────────────────────────────────────────────────
-
-
-function _walkBytes(dirPath) {
-  const walkScript =
-    `const fs=require('fs'),path=require('path');` +
-    `function walk(d,t=0){try{for(const f of fs.readdirSync(d)){` +
-    `const p=path.join(d,f);try{const s=fs.statSync(p);` +
-    `if(s.isDirectory()&&!['node_modules','.git','codegraph-cache','.venv','venv','__pycache__','dist','build','.next'].includes(f))t+=walk(p);` +
-    `else if(s.isFile()&&/\\.(js|jsx|ts|tsx|py|json|md|yaml|yml|toml|sh|bash|env|txt|css|html|sql|go|rs|java|rb|php|c|cpp|h)$/.test(f)&&!/^(package-lock|uv\.lock|yarn\.lock|Pipfile\.lock|poetry\.lock)$/.test(path.basename(f,path.extname(f))+path.extname(f)))t+=s.size;}catch{}}}catch{}return t;}` +
-    `console.log(walk(${JSON.stringify(dirPath)}));`;
-  const res = spawnSync('node', ['-e', walkScript], { encoding: 'utf8', timeout: 8000 });
-  return res.stdout ? parseInt(res.stdout.trim()) : null;
-}
-
-function _sampleQueryTokens(graphPath) {
-  const questions = ['what does the server do', 'how is the graph built', 'what calls save'];
-  const sizes = [];
-  for (const q of questions) {
-    const req = JSON.stringify({ tool: 'codegraph_query', args: { path: graphPath, question: q, token_budget: 2000 } });
-    const res = spawnSync('uv', ['run', 'python', '-m', 'codegraph'],
-      { input: req, encoding: 'utf8', cwd: process.cwd(), timeout: 12000 });
-    if (res.stdout) { try { const r = JSON.parse(res.stdout); if (!r.error) sizes.push(res.stdout.length); } catch {} }
-  }
-  return { avgTok: sizes.length ? Math.round(sizes.reduce((a, b) => a + b, 0) / sizes.length / 4) : 472, measured: sizes.length > 0 };
-}
-
-function cmdBenchmark() {
-  const graphs   = listGraphs();
-  const projects = listProjects();
-  printSection('Benchmark', 'real token savings');
-
-  const RESUME_LIMIT = 15;
-  const COMPACT_AT   = 20;
-
-  // ── Measure entry sizes from actual stored data ──────────────────────────────
-  const allEntries   = getContext({ limit: 500, compact: false });
-  const totalEntries = allEntries.length;
-  let avgFullTok = 155, avgCompactTok = 50;
-  if (allEntries.length) {
-    const fullSizes    = allEntries.map(e => JSON.stringify(e).length);
-    const compactSizes = allEntries.map(e =>
-      ([e.title || '', (e.content || '').slice(0, 200), (e.tags || []).join(' ')].join(' ')).length);
-    avgFullTok    = Math.round(fullSizes.reduce((a, b) => a + b, 0) / fullSizes.length / 4);
-    avgCompactTok = Math.round(compactSizes.reduce((a, b) => a + b, 0) / compactSizes.length / 4);
-  }
-
-  // ── Run graph queries once, reuse in both sections ────────────────────────────
-  let avgQueryTok = 472, queryMeasured = false;
-  if (graphs.length) {
-    const r = _sampleQueryTokens(graphs[0].path);
-    avgQueryTok   = r.avgTok;
-    queryMeasured = r.measured;
-  }
-
-  // ── Corpus size (run once) ────────────────────────────────────────────────────
-  let corpusToks = null;
-  if (graphs.length) {
-    const bytes = _walkBytes(graphs[0].path);
-    if (bytes) corpusToks = Math.round(bytes / 4);
-  }
-
-  // ── Memory ───────────────────────────────────────────────────────────────────
-  // Without context-mcp: AI reads all entries at full size every conversation
-  // With context-mcp:    AI loads min(15, N) entries as compact previews via resume
-  console.log(`\n  ${bold(lblue('Memory'))}  ${faint('measured from actual stored entries')}`);
-  if (totalEntries) {
-    const resumeCount   = Math.min(RESUME_LIMIT, totalEntries);
-    const withoutMemTok = totalEntries * avgFullTok;         // load all entries full
-    const withMemTok    = resumeCount  * avgCompactTok;      // resume: compact previews only
-    const memSaved      = withoutMemTok - withMemTok;
-    const memReduction  = (withoutMemTok / withMemTok).toFixed(1);
-    const memPct        = ((1 - withMemTok / withoutMemTok) * 100).toFixed(1);
-
-    console.log(`    ${faint('avg entry size (full):   ')} ${muted(avgFullTok)} tok  ${faint('(measured)')}`);
-    console.log(`    ${faint('avg entry size (compact):')} ${muted(avgCompactTok)} tok  ${faint('(measured)')}`);
-    console.log(`    ${faint('stored:                  ')} ${muted(totalEntries)} entries  ${faint('across')} ${muted(projects.length)} project(s)`);
-    console.log(`    ${faint('without — load all full: ')} ${warn('~' + withoutMemTok.toLocaleString('en-US'))} tokens`);
-    console.log(`    ${faint('with    — resume compact:')} ${ok('~' + withMemTok.toLocaleString('en-US'))} tokens  ${faint(`(${resumeCount} of ${totalEntries} entries)`)}`);
-    console.log(`    ${faint('saved per chat:          ')} ${ok('~' + memSaved.toLocaleString('en-US'))} tokens  ${highlight(memReduction + '×')}  ${ok(memPct + '%')} reduction`);
-    console.log(`    ${faint('auto-compact at:         ')} ${faint(COMPACT_AT + ' entries → oldest summarized to 1')}`);
-    console.log('');
-    for (const p of projects) {
-      const pToks  = p.count * avgFullTok;
-      const barLen = Math.min(Math.ceil(p.count / 2), 24);
-      const bar    = color(C.dblue, '█'.repeat(barLen)) + color(C.darkgray, '░'.repeat(24 - barLen));
-      console.log(`    ${color(C.darkgray, '·')} ${muted(p.name.padEnd(22))} ${bar}  ${faint(p.count + ' entries · ~' + pToks.toLocaleString('en-US') + ' tok full')}`);
-    }
-  } else {
-    console.log(`    ${faint('no entries yet')}`);
-  }
-
-  // ── CodeGraph ─────────────────────────────────────────────────────────────────
-  // Without context-mcp: AI reads all source files to answer structural questions
-  // With context-mcp:    AI calls codegraph_query → focused NODE/EDGE subgraph
-  console.log(`\n  ${bold(lblue('CodeGraph'))}  ${faint('measured from live graph queries')}`);
-  if (!graphs.length) {
-    console.log(`    ${faint('no graphs — run codegraph_build first')}`);
-  } else {
-    for (const g of graphs) {
-      const pathShort  = g.path.replace(/\\/g, '/').split('/').slice(-2).join('/');
-      const builtAt    = (g.builtAt || '').slice(0, 10);
-      const graphReduce = corpusToks ? (corpusToks / avgQueryTok).toFixed(0) + '×' : null;
-      const graphPct    = corpusToks ? ((1 - avgQueryTok / corpusToks) * 100).toFixed(2) : null;
-
-      console.log(`\n    ${accent('⬡')} ${bold(pathShort)}  ${faint(builtAt)}`);
-      console.log(`      ${faint('nodes:')} ${muted(g.nodes)}  ${faint('edges:')} ${muted(g.edges)}  ${faint('clusters:')} ${muted(g.communities)}`);
-      if (corpusToks) console.log(`      ${faint('without — read all files:')} ${warn('~' + corpusToks.toLocaleString('en-US'))} tokens  ${faint('(all source + config + doc files)')}`);
-      console.log(`      ${faint('with    — graph query:   ')} ${ok('~' + avgQueryTok.toLocaleString('en-US'))} tokens  ${faint(queryMeasured ? '(avg of 3 live queries)' : '(calibrated fallback)')}`);
-      if (graphReduce) console.log(`      ${faint('saved per query:         ')} ${highlight(graphReduce)}  ${ok(graphPct + '%')} fewer tokens`);
-    }
-  }
-
-  // ── Combined ──────────────────────────────────────────────────────────────────
-  // Without: read all files (no graph) + load all entries full (no memory system)
-  // With:    compact resume (memory) + one graph query (codegraph)
-  if (graphs.length) {
-    const resumeCount   = Math.min(RESUME_LIMIT, totalEntries);
-    const withMemTok    = resumeCount * avgCompactTok;
-    const withMcp       = withMemTok + avgQueryTok;
-    const withoutMemTok = totalEntries * avgFullTok;
-    const withoutMcp    = withoutMemTok + (corpusToks || graphs[0].nodes * 80);
-    const totalRed      = withoutMcp > 0 ? (withoutMcp / withMcp).toFixed(0) : '—';
-    const totalPct      = withoutMcp > 0 ? ((1 - withMcp / withoutMcp) * 100).toFixed(2) : '—';
-
-    console.log(`\n  ${bold(lblue('Combined'))}  ${faint('per conversation')}`);
-    console.log(`    ${faint('without context-mcp:  ')} ${warn('~' + withoutMcp.toLocaleString('en-US'))} tokens  ${faint('(all entries full + all files read directly)')}`);
-    console.log(`    ${faint('with context-mcp:     ')} ${ok('~' + withMcp.toLocaleString('en-US'))} tokens  ${faint('(compact resume + 1 graph query)')}`);
-    console.log(`    ${faint('total reduction:      ')} ${highlight(totalRed + '×')}  ${ok(totalPct + '%')} fewer tokens`);
-  }
-
-  console.log('');
-  console.log(line());
-  console.log(faint('  token estimate: chars ÷ 4  ·  corpus = all source/config/doc files (excl. lock files, .venv, node_modules)'));
-}
-
-
 // ── Install ───────────────────────────────────────────────────────────────────
 
 const TPLS = join(__dirname, 'templates');
@@ -574,6 +414,7 @@ const _GLOBAL_GITIGNORE_ENTRIES = [
   '.gemini/',
   '.codex/',
   '.windsurf/',
+  '.agents/',
   // Build outputs and session artifacts
   'codegraph-cache/',
   '.mcp.json',
@@ -588,6 +429,7 @@ function _graphForProject(graphs, projectName) {
 
 const _PROJECT_GITIGNORE_ENTRIES = [
   '.claude/', '.cursor/', '.vscode/', '.gemini/', '.codex/',
+  '.agents/',
   'codegraph-cache/', '.mcp.json', 'CLAUDE.md', 'GEMINI.md', 'AGENTS.md',
 ];
 
@@ -630,7 +472,7 @@ function _updateGlobalGitignore() {
 }
 
 function _writeCommands(baseDir) {
-  const cmdsDir = join(TPLS, 'commands');
+  const cmdsDir = join(TPLS, 'claude', 'commands');
   const destDir = join(baseDir, '.claude', 'commands');
   for (const [name, label] of [
     ['context-resume.md', '/context-resume'],
@@ -646,20 +488,136 @@ function _writeCommands(baseDir) {
 
 const MCP_SERVER_CMD = { command: 'npx', args: ['-y', 'context-mcp-server@latest'] };
 
+function _tomlString(value) {
+  return JSON.stringify(value);
+}
+
+function _copyHooks(platform, dotDir, dir, hookFiles) {
+  const hooksSrc = join(TPLS, platform, 'hooks');
+  const hooksDest = join(dir, dotDir, 'hooks');
+  for (const file of hookFiles) {
+    const src = join(hooksSrc, file);
+    if (existsSync(src)) {
+      _writeFile(join(hooksDest, file), readFileSync(src, 'utf8'), `${dotDir}/hooks/${file}`);
+    }
+  }
+}
+
+function _copyCodexHooks(dir) {
+  _copyHooks('codex', '.codex', dir, [
+    'context-mcp-pre-tool-use.js',
+    'context-mcp-post-tool-use.js',
+  ]);
+}
+
+// Read JSON from path (returns {} on missing/invalid), run mutateFn, write back.
+function _mergeJsonFile(filePath, label, mutateFn) {
+  let obj = {};
+  try { obj = JSON.parse(readFileSync(filePath, 'utf8')); } catch {}
+  mutateFn(obj);
+  _writeFile(filePath, JSON.stringify(obj, null, 2), label);
+  return obj;
+}
+
+// Merge `entries` ({ EventName: [hookGroup] }) into an existing settings.json
+// hooks object, replacing any previously installed context-mcp groups.
+function _mergeHooksIntoSettings(settingsPath, entries, label) {
+  let settings = {};
+  try { settings = JSON.parse(readFileSync(settingsPath, 'utf8')); } catch {}
+  settings.hooks = settings.hooks || {};
+  for (const [event, groups] of Object.entries(entries)) {
+    const existing = Array.isArray(settings.hooks[event]) ? settings.hooks[event] : [];
+    settings.hooks[event] = existing
+      .filter(g => !(g.hooks || []).some(h => String(h.command || '').includes('context-mcp-')))
+      .concat(groups);
+  }
+  _writeFile(settingsPath, JSON.stringify(settings, null, 2), label);
+  return settings;
+}
+
+function _codexConfigToml(dir, includeHooks = false) {
+  const lines = [
+    '[mcp_servers.context-mcp]',
+    'command = "npx"',
+    'args    = ["-y", "context-mcp-server@latest"]',
+    'default_tools_approval_mode = "prompt"',
+    '',
+    '[mcp_servers.context-mcp.tools.context]',
+    'approval_mode = "approve"',
+    '',
+    '[mcp_servers.context-mcp.tools.search]',
+    'approval_mode = "approve"',
+    '',
+    '[mcp_servers.context-mcp.tools.codegraph_query]',
+    'approval_mode = "approve"',
+  ];
+
+  if (includeHooks) {
+    const preHook = join(dir, '.codex', 'hooks', 'context-mcp-pre-tool-use.js');
+    const postHook = join(dir, '.codex', 'hooks', 'context-mcp-post-tool-use.js');
+    lines.push(
+      '',
+      '[[hooks.PreToolUse]]',
+      'matcher = "^Bash$"',
+      '',
+      '[[hooks.PreToolUse.hooks]]',
+      'type = "command"',
+      `command = ${_tomlString(`node ${_tomlString(preHook)}`)}`,
+      `command_windows = ${_tomlString(`node ${_tomlString(preHook)}`)}`,
+      'timeout = 30',
+      'statusMessage = "Checking shell command"',
+      '',
+      '[[hooks.PostToolUse]]',
+      'matcher = "^Bash$"',
+      '',
+      '[[hooks.PostToolUse.hooks]]',
+      'type = "command"',
+      `command = ${_tomlString(`node ${_tomlString(postHook)}`)}`,
+      `command_windows = ${_tomlString(`node ${_tomlString(postHook)}`)}`,
+      'timeout = 30',
+      'statusMessage = "Saving failed shell context"',
+    );
+  }
+
+  return `${lines.join('\n')}\n`;
+}
+
 const PLATFORMS = {
   claude: {
     label: 'Claude Code',
     restartNote: 'Type /context-resume in Claude Code to start using context-mcp.',
     install(dir, scope) {
-      // Install as a skill (global, works across all projects) instead of a flat CLAUDE.md
-      const skillSrc = join(TPLS, 'skills', 'SKILL.md');
+      // Skill — user-global, works across all projects
+      const skillSrc = join(TPLS, 'claude', 'skills', 'SKILL.md');
       const skillDest = join(homedir(), '.claude', 'skills', 'context-mcp', 'SKILL.md');
       if (existsSync(skillSrc)) {
         _writeFile(skillDest, readFileSync(skillSrc, 'utf8'), '~/.claude/skills/context-mcp/');
       }
-      // Slash commands are always user-global (not project-scoped)
+      // Slash commands — user-global
       _writeCommands(homedir());
-      // Register via claude CLI so the server is trusted immediately (no manual trust prompt)
+      // Hooks — write into the appropriate settings.json scope
+      // Project hooks live in .claude/hooks/ and are committed; user hooks in ~/.claude/hooks/
+      const hooksBase = scope === 'project' ? dir : homedir();
+      _copyHooks('claude', '.claude', hooksBase, [
+        'context-mcp-pre-tool-use.js',
+        'context-mcp-post-tool-use.js',
+      ]);
+      const preHook = join(hooksBase, '.claude', 'hooks', 'context-mcp-pre-tool-use.js');
+      const postHook = join(hooksBase, '.claude', 'hooks', 'context-mcp-post-tool-use.js');
+      const settingsPath = scope === 'project'
+        ? join(dir, '.claude', 'settings.json')
+        : join(homedir(), '.claude', 'settings.json');
+      _mergeHooksIntoSettings(settingsPath, {
+        PreToolUse: [{
+          matcher: 'Bash',
+          hooks: [{ type: 'command', command: preHook, timeout: 30, statusMessage: 'Checking shell command' }],
+        }],
+        PostToolUse: [{
+          matcher: 'Bash',
+          hooks: [{ type: 'command', command: postHook, timeout: 30, statusMessage: 'Saving failed shell context' }],
+        }],
+      }, scope === 'project' ? '.claude/settings.json' : '~/.claude/settings.json');
+      // Register MCP server via claude CLI
       const scopeFlag = scope === 'global' ? 'user' : 'project';
       const reg = spawnSync(
         'claude', ['mcp', 'add', '--scope', scopeFlag, 'context-mcp', '--', 'npx', '-y', 'context-mcp-server@latest'],
@@ -676,17 +634,34 @@ const PLATFORMS = {
     label: 'Cursor',
     restartNote: 'Restart Cursor to load the new MCP server.',
     install(dir, scope) {
+      // MCP config
       const mcpJson = JSON.stringify({ mcpServers: { 'context-mcp': MCP_SERVER_CMD } }, null, 2);
       _writeFile(join(dir, '.cursor', 'mcp.json'), mcpJson, '.cursor/mcp.json');
       if (scope === 'project') {
-        const mdc = _tpl('cursor-rules.mdc');
+        // Rules
+        const mdc = _tpl('cursor/cursor-rules.mdc');
         if (mdc) _writeFile(join(dir, '.cursor', 'rules', 'context-mcp.mdc'), mdc, '.cursor/rules/context-mcp.mdc');
+        // Slash commands
+        const cmdsSrc = join(TPLS, 'cursor', 'commands');
+        for (const file of ['context-resume.md', 'graph-build.md', 'save-context.md']) {
+          const src = join(cmdsSrc, file);
+          if (existsSync(src)) _writeFile(join(dir, '.cursor', 'commands', file), readFileSync(src, 'utf8'), `.cursor/commands/${file}`);
+        }
+        // Hook script
+        _copyHooks('cursor', '.cursor', dir, ['context-mcp-post-tool-use.js']);
+        const hookPath = join(dir, '.cursor', 'hooks', 'context-mcp-post-tool-use.js');
+        // Merge into .cursor/hooks.json (must keep "version": 1)
+        _mergeJsonFile(join(dir, '.cursor', 'hooks.json'), '.cursor/hooks.json', obj => {
+          obj.version = 1;
+          obj.hooks = obj.hooks || {};
+          const strip = arr => (arr || []).filter(h => !String(h.command || '').includes('context-mcp-'));
+          obj.hooks.postToolUse = strip(obj.hooks.postToolUse).concat([
+            { command: `node "${hookPath}"`, timeout: 30 },
+          ]);
+        });
       }
-      // Try to enable via cursor CLI (enable/disable only — no add command)
-      const reg = spawnSync(
-        'cursor', ['agent', 'mcp', 'enable', 'context-mcp'],
-        { encoding: 'utf8', shell: true },
-      );
+      // Try to enable via cursor CLI
+      const reg = spawnSync('cursor', ['agent', 'mcp', 'enable', 'context-mcp'], { encoding: 'utf8', shell: true });
       if (reg.status === 0) {
         console.log(`  ${ok('✓')} ${'enabled via cursor agent mcp'.padEnd(28)}`);
       }
@@ -695,21 +670,79 @@ const PLATFORMS = {
   vscode: {
     label: 'VS Code Copilot',
     restartNote: 'Reload VS Code window (Ctrl+Shift+P → "Reload Window").',
-    install(dir) {
+    install(dir, scope) {
+      // MCP config
       const mcpJson = JSON.stringify({
         servers: { 'context-mcp': { type: 'stdio', ...MCP_SERVER_CMD } },
       }, null, 2);
       _writeFile(join(dir, '.vscode', 'mcp.json'), mcpJson, '.vscode/mcp.json');
+      if (scope === 'project') {
+        // Prompt files (.github/prompts/)
+        const cmdsSrc = join(TPLS, 'vscode', 'commands');
+        for (const file of ['context-resume.prompt.md', 'graph-build.prompt.md', 'save-context.prompt.md']) {
+          const src = join(cmdsSrc, file);
+          if (existsSync(src)) _writeFile(join(dir, '.github', 'prompts', file), readFileSync(src, 'utf8'), `.github/prompts/${file}`);
+        }
+        // Hook script
+        _copyHooks('vscode', '.vscode', dir, ['context-mcp-post-tool-use.js']);
+        const hookPath = join(dir, '.vscode', 'hooks', 'context-mcp-post-tool-use.js');
+        // Merge hooks into .vscode/settings.json under github.copilot.chat.agent.hooks
+        _mergeJsonFile(join(dir, '.vscode', 'settings.json'), '.vscode/settings.json', obj => {
+          const hooks = obj['github.copilot.chat.agent.hooks'] || {};
+          const strip = arr => (arr || []).filter(h => !String(h.command || '').includes('context-mcp-'));
+          hooks.PostToolUse = strip(hooks.PostToolUse).concat([
+            { type: 'command', command: `node "${hookPath}"`, timeout: 30, windows: `node "${hookPath}"` },
+          ]);
+          obj['github.copilot.chat.agent.hooks'] = hooks;
+        });
+      }
     },
   },
   gemini: {
     label: 'Gemini CLI',
     restartNote: 'Restart your Gemini CLI session.',
     install(dir, scope) {
-      const cfg = JSON.stringify({ mcpServers: { 'context-mcp': MCP_SERVER_CMD } }, null, 2);
-      _writeFile(join(dir, '.gemini', 'settings.json'), cfg, '.gemini/settings.json');
+      // MCP server config — merged into existing settings.json
+      const settingsPath = scope === 'project'
+        ? join(dir, '.gemini', 'settings.json')
+        : join(homedir(), '.gemini', 'settings.json');
+      let settings = {};
+      try { settings = JSON.parse(readFileSync(settingsPath, 'utf8')); } catch {}
+      settings.mcpServers = settings.mcpServers || {};
+      settings.mcpServers['context-mcp'] = MCP_SERVER_CMD;
+      // Hooks — write BeforeTool/AfterTool into settings.json
+      const hooksBase = scope === 'project' ? dir : homedir();
+      _copyHooks('gemini', '.gemini', hooksBase, [
+        'context-mcp-before-tool.js',
+        'context-mcp-after-tool.js',
+      ]);
+      const beforeHook = join(hooksBase, '.gemini', 'hooks', 'context-mcp-before-tool.js');
+      const afterHook = join(hooksBase, '.gemini', 'hooks', 'context-mcp-after-tool.js');
+      settings.hooks = settings.hooks || {};
+      const stripOld = (arr) => (arr || []).filter(
+        g => !(g.hooks || []).some(h => String(h.command || '').includes('context-mcp-')),
+      );
+      settings.hooks.BeforeTool = stripOld(settings.hooks.BeforeTool).concat([{
+        matcher: 'run_shell_command',
+        hooks: [{ type: 'command', command: `node ${beforeHook}`, timeout: 30 }],
+      }]);
+      settings.hooks.AfterTool = stripOld(settings.hooks.AfterTool).concat([{
+        matcher: 'run_shell_command',
+        hooks: [{ type: 'command', command: `node ${afterHook}`, timeout: 30 }],
+      }]);
+      _writeFile(settingsPath,
+        JSON.stringify(settings, null, 2),
+        scope === 'project' ? '.gemini/settings.json' : '~/.gemini/settings.json',
+      );
+      // Slash commands (.toml) — project-scoped only
       if (scope === 'project') {
-        const md = _tpl('GEMINI.md');
+        const cmdsSrc = join(TPLS, 'gemini', 'commands');
+        const cmdsDest = join(dir, '.gemini', 'commands');
+        for (const file of ['context-resume.toml', 'graph-build.toml', 'save-context.toml']) {
+          const src = join(cmdsSrc, file);
+          if (existsSync(src)) _writeFile(join(cmdsDest, file), readFileSync(src, 'utf8'), `.gemini/commands/${file}`);
+        }
+        const md = _tpl('gemini/GEMINI.md');
         if (md) _writeFile(join(dir, 'GEMINI.md'), md, 'GEMINI.md');
       }
     },
@@ -718,12 +751,21 @@ const PLATFORMS = {
     label: 'Codex CLI',
     restartNote: 'Restart your Codex CLI session.',
     install(dir, scope) {
-      const toml = `[[mcp_servers]]\nname    = "context-mcp"\ncommand = "npx"\nargs    = ["-y", "context-mcp-server@latest"]\n`;
-      _writeFile(join(dir, '.codex', 'config.toml'), toml, '.codex/config.toml');
+      const includeHooks = scope === 'project';
+      if (includeHooks) _copyCodexHooks(dir);
+      _writeFile(join(dir, '.codex', 'config.toml'), _codexConfigToml(dir, includeHooks), '.codex/config.toml');
       if (scope === 'project') {
-        const md = _tpl('AGENTS.md');
+        const md = _tpl('codex/AGENTS.md');
         if (md) _writeFile(join(dir, 'AGENTS.md'), md, 'AGENTS.md');
       }
+      // Prompts (slash commands) — always user-global; Codex only loads ~/.codex/prompts/
+      const promptsSrc = join(TPLS, 'codex', 'prompts');
+      for (const file of ['context-resume.md', 'graph-build.md', 'save-context.md']) {
+        const src = join(promptsSrc, file);
+        if (existsSync(src)) {
+          _writeFile(join(homedir(), '.codex', 'prompts', file), readFileSync(src, 'utf8'), `~/.codex/prompts/${file}`);
+        }
+      }
       // Register via codex CLI so server is active immediately
       const reg = spawnSync(
         'codex', ['mcp', 'add', 'context-mcp', '--', 'npx', '-y', 'context-mcp-server@latest'],
@@ -739,15 +781,63 @@ const PLATFORMS = {
   windsurf: {
     label: 'Windsurf',
     restartNote: 'Restart Windsurf to load the updated MCP config.',
-    install(dir) {
-      const rules = _tpl('windsurf-rules.md');
+    install(dir, scope) {
+      // Rules file
+      const rules = _tpl('windsurf/windsurf-rules.md');
       if (rules) _writeFile(join(dir, '.windsurf', 'rules', 'context-mcp.md'), rules, '.windsurf/rules/context-mcp.md');
-      const globalCfgPath = join(homedir(), '.codeium', 'windsurf', 'mcp_config.json');
-      let existing = {};
-      try { existing = JSON.parse(readFileSync(globalCfgPath, 'utf8')); } catch {}
-      existing.mcpServers = existing.mcpServers || {};
-      existing.mcpServers['context-mcp'] = { command: 'npx', args: ['-y', 'context-mcp-server@latest'] };
-      _writeFile(globalCfgPath, JSON.stringify(existing, null, 2), '~/.codeium/windsurf/mcp_config.json');
+      // Global MCP config (~/.codeium/windsurf/mcp_config.json)
+      _mergeJsonFile(join(homedir(), '.codeium', 'windsurf', 'mcp_config.json'), '~/.codeium/windsurf/mcp_config.json', obj => {
+        obj.mcpServers = obj.mcpServers || {};
+        obj.mcpServers['context-mcp'] = { command: 'npx', args: ['-y', 'context-mcp-server@latest'] };
+      });
+      if (scope === 'project') {
+        // Workflows (slash commands)
+        const wfSrc = join(TPLS, 'windsurf', 'workflows');
+        for (const file of ['context-resume.md', 'graph-build.md', 'save-context.md']) {
+          const src = join(wfSrc, file);
+          if (existsSync(src)) _writeFile(join(dir, '.windsurf', 'workflows', file), readFileSync(src, 'utf8'), `.windsurf/workflows/${file}`);
+        }
+        // Hook script + .windsurf/hooks.json
+        _copyHooks('windsurf', '.windsurf', dir, ['context-mcp-post-run-command.js']);
+        const hookPath = join(dir, '.windsurf', 'hooks', 'context-mcp-post-run-command.js');
+        _mergeJsonFile(join(dir, '.windsurf', 'hooks.json'), '.windsurf/hooks.json', obj => {
+          obj.hooks = obj.hooks || {};
+          const strip = arr => (arr || []).filter(h => !String(h.command || '').includes('context-mcp-'));
+          obj.hooks.post_run_command = strip(obj.hooks.post_run_command).concat([{
+            command: `node "${hookPath}"`,
+            powershell: `node "${hookPath}"`,
+            show_output: false,
+          }]);
+        });
+      }
+    },
+  },
+  antigravity: {
+    label: 'Antigravity IDE',
+    restartNote: 'Restart your Antigravity session to pick up hooks and rules.',
+    install(dir, scope) {
+      // Antigravity uses stdio-incompatible MCP transport — integrate via ctx CLI + GEMINI.md instead.
+      if (scope === 'project') {
+        // Post-tool hook — saves failed tool calls to context-mcp via ctx CLI
+        _copyHooks('antigravity', '.agents', dir, ['context-mcp-post-tool-use.js']);
+        const hookPath = join(dir, '.agents', 'hooks', 'context-mcp-post-tool-use.js');
+        _mergeJsonFile(join(dir, '.agents', 'hooks.json'), '.agents/hooks.json', obj => {
+          const strip = arr => (arr || []).filter(h => !String(h.command || '').includes('context-mcp-'));
+          obj.hooks = strip(obj.hooks).concat([{
+            event: 'PostToolUse',
+            command: `node "${hookPath}"`,
+          }]);
+        });
+        // Workflows (slash commands) — .agents/workflows/
+        const wfSrc = join(TPLS, 'antigravity', 'workflows');
+        for (const file of ['context-resume.md', 'graph-build.md', 'save-context.md']) {
+          const src = join(wfSrc, file);
+          if (existsSync(src)) _writeFile(join(dir, '.agents', 'workflows', file), readFileSync(src, 'utf8'), `.agents/workflows/${file}`);
+        }
+        // Rules file — Antigravity reads GEMINI.md at project root
+        const md = _tpl('antigravity/GEMINI.md');
+        if (md) _writeFile(join(dir, 'GEMINI.md'), md, 'GEMINI.md');
+      }
     },
   },
 };
@@ -796,13 +886,22 @@ async function cmdInstall(args) {
         console.log(`  ${ok('✓')} Python environment ready — codegraph enabled`);
       }
     }
+    // Bootstrap store structure — creates ~/.context-mcp/, projects/, contextconfig.json
+    console.log(`  ${bold(lblue('Store'))}`);
+    try {
+      getConfig(); // triggers DATA_DIR creation + contextconfig.json generation
+      console.log(`  ${ok('✓')} store ready          ${faint(getStorePath())}`);
+      console.log(`  ${ok('✓')} config ready         ${faint(getConfigPath())}`);
+    } catch (e) {
+      console.log(`  ${bad('✗')} store init failed: ${faint(e.message)}`);
+    }
     console.log('');
     return;
   }
 
   if (!keys.length) {
     printSection('Install');
-    console.log(`  ${muted('Usage:')}  ctx install ${faint('[--initial] [--claude] [--cursor] [--vscode] [--gemini] [--codex] [--windsurf] [--all]')}`);
+    console.log(`  ${muted('Usage:')}  ctx install ${faint('[--initial] [--claude] [--cursor] [--vscode] [--gemini] [--codex] [--windsurf] [--antigravity] [--all]')}`);
     console.log('');
     console.log(`  ${accent('--initial      ')}  ${faint('Install / update Node.js + Python (codegraph) deps')}`);
     console.log('');
@@ -871,27 +970,6 @@ async function cmdInstall(args) {
   // ── Global gitignore — add context-mcp runtime files if global gitignore exists ──
   _updateGlobalGitignore();
   console.log('');
-
-  // ── Python / uv setup (codegraph) ─────────────────────────────────────────
-  console.log(`  ${bold(lblue('Python Codegraph'))}`);
-  const uvCheck = spawnSync('uv', ['--version'], { encoding: 'utf8' });
-  if (uvCheck.error || uvCheck.status !== 0) {
-    console.log(`  ${bad('✗')} uv not found — install it from ${accent('https://docs.astral.sh/uv/')} to enable codegraph`);
-    console.log('');
-    return;
-  }
-  console.log(`  ${ok('✓')} uv found: ${faint(uvCheck.stdout.trim())}`);
-
-  // Package root is one level up from src/
-  const __dirname_cli = dirname(fileURLToPath(import.meta.url));
-  const pkgRoot = join(__dirname_cli, '..');
-  const sync = spawnSync('uv', ['--directory', pkgRoot, 'sync', '--no-dev'], { encoding: 'utf8' });
-  if (sync.status !== 0) {
-    console.log(`  ${bad('✗')} uv sync failed:\n${faint((sync.stderr || sync.stdout || '').trim())}`);
-  } else {
-    console.log(`  ${ok('✓')} Python environment ready — codegraph enabled`);
-  }
-  console.log('');
 }
 
 // ── Online ────────────────────────────────────────────────────────────────────
@@ -1077,7 +1155,7 @@ async function cmdAdd(existingRl) {
   const content = await ask('Content:');
   const project = await ask('Project (blank = global):');
   const tagsRaw = await ask('Tags (comma-separated):');
-  const type    = await ask('Type (note/decision/code/bug/architecture/config/error):');
+  const type    = await ask('Type (note/compaction):');
 
   if (!existingRl) rl.close();
   if (!content.trim()) { console.log(`  ${bad('✗')} content required`); return; }
@@ -1094,6 +1172,30 @@ async function cmdAdd(existingRl) {
   console.log(`  ${ok('✓')} ${bold(entry.title || '(no title)')}  ${faint('id:' + entry.id.slice(0, 8))}`);
 }
 
+// ── Save (non-interactive, flag-based — used by hooks and scripts) ───────────
+
+function cmdSave(args) {
+  // Usage: ctx save --title "..." --content "..." --project <p> --type <t> --tags <t1,t2>
+  const flags = {};
+  for (let i = 0; i < args.length; i++) {
+    if (args[i].startsWith('--')) {
+      flags[args[i].slice(2)] = args[i + 1] || '';
+      i++;
+    }
+  }
+  const content = flags.content || flags.c;
+  if (!content) { console.log(`  ${bad('✗')} --content required`); process.exit(1); }
+  const entry = saveContext({
+    title:   (flags.title || flags.t || '').trim(),
+    content: content.trim(),
+    project: (flags.project || flags.p || '').trim() || 'global',
+    tags:    (flags.tags || '').split(',').map(s => s.trim()).filter(Boolean),
+    type:    (flags.type || 'note').trim(),
+    source:  'cli',
+  });
+  console.log(`  ${ok('✓')} saved "${entry.title || entry.id.slice(0, 8)}" → ${entry.project}`);
+}
+
 // ── Delete ────────────────────────────────────────────────────────────────────
 
 function cmdDelete(args) {
@@ -1193,8 +1295,6 @@ async function interactive() {
           clearScreen(); printCompactHeader('discussions'); cmdDiscussions(rest); break;
         case 'summary':
           clearScreen(); printCompactHeader('summary'); cmdSummary(rest); break;
-        case 'benchmark': case 'bench':
-          clearScreen(); printCompactHeader('benchmark'); cmdBenchmark(); break;
         case 'install':
           clearScreen(); printCompactHeader('install'); await cmdInstall(rest); break;
         case 'online':
@@ -1203,6 +1303,8 @@ async function interactive() {
           clearScreen(); printCompactHeader('settings'); await cmdSettings(rl); break;
         case 'add':
           clearScreen(); printCompactHeader('add'); await cmdAdd(rl); break;
+        case 'save':
+          cmdSave(rest); break;
         case 'delete': case 'del': case 'rm':
           clearScreen(); printCompactHeader('delete'); cmdDelete(rest); break;
         case 'help': case '?':
@@ -1257,8 +1359,6 @@ async function checkForUpdate() {
       cmdDiscussions(rest); break;
     case 'summary':
       cmdSummary(rest); break;
-    case 'benchmark': case 'bench':
-      cmdBenchmark(); break;
     case 'install':
       await cmdInstall(rest);
       process.exit(0);
@@ -1284,6 +1384,8 @@ async function checkForUpdate() {
       await cmdSettings(); break;
     case 'add':
       await cmdAdd(); break;
+    case 'save':
+      cmdSave(rest); break;
     case 'delete': case 'del': case 'rm':
       cmdDelete(rest); break;
     case 'help': case '--help': case '-h':