sigmap 6.1.0 → 6.3.0

package/AGENTS.md

@@ -9,28 +9,53 @@ When writing generated signature content, never overwrite human-written notes ab
 Use this marker block for all appendable context files:
 
 ```
+## Tools
+
+<!-- sigmap-tools -->
+
+```json
+[
+  {
+    "name": "sigmap_ask",
+    "description": "Rank source files by relevance to a natural-language query. Run before exploring the codebase.",
+    "command": "sigmap ask \"$QUERY\""
+  },
+  {
+    "name": "sigmap_validate",
+    "description": "Validate SigMap config and measure context coverage. Run after changing config or source dirs.",
+    "command": "sigmap validate"
+  },
+  {
+    "name": "sigmap_judge",
+    "description": "Score an LLM response for groundedness against source context. Use to verify answer quality.",
+    "command": "sigmap judge --response \"$RESPONSE\" --context \"$CONTEXT\""
+  },
+  {
+    "name": "sigmap_query",
+    "description": "Rank all files by relevance using TF-IDF and write a focused mini-context.",
+    "command": "sigmap --query \"$QUERY\" --context"
+  },
+  {
+    "name": "sigmap_weights",
+    "description": "Show learned file-ranking multipliers accumulated from past sessions.",
+    "command": "sigmap weights"
+  }
+]
+```
+
 ## Auto-generated signatures
 <!-- Updated by gen-context.js -->
 # Code signatures
 
-## SigMap commands
-
-| When | Command |
-|------|---------|
-| Before answering a question | `sigmap ask "<your question>"` |
-| After code changes | `sigmap validate` |
-| To query by topic | `sigmap --query "<topic>"` |
-
-Always run `sigmap ask` or `sigmap --query` before searching for files relevant to a task.
-## changes (last 5 commits — 31 minutes ago)
+## changes (last 5 commits — 0 seconds ago)
 ```
 src/learning/weights.js                       +exportWeights  +importWeights  ~resetWeights
-packages/adapters/codex.js                    ~format
+packages/adapters/codex.js                    ~write  ~format
+packages/adapters/claude.js                   ~format  ~write
 packages/adapters/gemini.js                   ~format
 packages/adapters/copilot.js                  ~format
-packages/adapters/openai.js                   ~format
-packages/adapters/claude.js                   ~format
 packages/adapters/cursor.js                   ~format
+packages/adapters/openai.js                   ~format
 packages/adapters/windsurf.js                 ~format
 ```
 
@@ -99,33 +124,25 @@ function outputPath(cwd) → string
 function write(context, cwd, opts = {})
 ```
 
-### packages/adapters/gemini.js
+### packages/adapters/claude.js
 ```
 module.exports = { name, format, outputPath, write }
 function format(context, opts = {}) → string
+function _confidenceMeta(opts)
 function outputPath(cwd) → string
 function write(context, cwd, opts = {})
-function _confidenceMeta(opts)
 ```
 
-### packages/adapters/copilot.js
+### packages/adapters/gemini.js
 ```
 module.exports = { name, format, outputPath, write }
 function format(context, opts = {}) → string
-function _confidenceMeta(opts)
 function outputPath(cwd) → string
 function write(context, cwd, opts = {})
-```
-
-### packages/adapters/openai.js
-```
-module.exports = { name, format, outputPath }
-function format(context, opts = {}) → string
-function outputPath(cwd) → string
 function _confidenceMeta(opts)
 ```
 
-### packages/adapters/claude.js
+### packages/adapters/copilot.js
 ```
 module.exports = { name, format, outputPath, write }
 function format(context, opts = {}) → string
@@ -142,6 +159,14 @@ function _confidenceMeta(opts)
 function outputPath(cwd) → string
 ```
 
+### packages/adapters/openai.js
+```
+module.exports = { name, format, outputPath }
+function format(context, opts = {}) → string
+function outputPath(cwd) → string
+function _confidenceMeta(opts)
+```
+
 ### packages/adapters/windsurf.js
 ```
 module.exports = { name, format, outputPath }

package/CHANGELOG.md

@@ -10,6 +10,22 @@ Format: [Semantic Versioning](https://semver.org/)
 
 ---
 
+## [6.3.0] — 2026-04-22
+
+### Added
+
+- **Native tool registration (Level 3)** — `codex.write()` injects a `## Tools` JSON block into AGENTS.md with 5 named sigmap shell tools (`sigmap_ask`, `sigmap_validate`, `sigmap_judge`, `sigmap_query`, `sigmap_weights`); Codex CLI and OpenCode surface these in their tool picker. `claude.write()` injects a `## Bash allowlist` section into CLAUDE.md with `permissions.allow` patterns for all sigmap commands; adding these to `.claude/settings.json` bypasses the Claude Code confirmation prompt. Both sections are idempotent and preserve human content.
+
+---
+
+## [6.2.0] — 2026-04-22
+
+### Added
+
+- **`--setup` MCP auto-wire for 4 new targets** — `sigmap --setup` now registers the MCP server in `.vscode/mcp.json` (GitHub Copilot in VS Code 1.99+), `opencode.json` and `~/.config/opencode/config.json` (OpenCode), `~/.gemini/settings.json` (Gemini CLI), and `~/.codex/config.yaml` (Codex CLI — YAML format). All 5 new targets are idempotent and only written if the file already exists. Total `--setup` targets: 5 → 10.
+
+---
+
 ## [6.1.0] — 2026-04-22
 
 ### Added

package/gen-context.js

@@ -5387,7 +5387,7 @@ __factories["./src/mcp/server"] = function(module, exports) {
   
   const SERVER_INFO = {
     name: 'sigmap',
-  version: '6.1.0',
+  version: '6.3.0',
     description: 'SigMap MCP server — code signatures on demand',
   };
   
@@ -6789,6 +6789,36 @@ __factories["./packages/adapters/claude"] = function(module, exports) {
   const fs = require('fs');
   const name = 'claude';
   const CLAUDE_MARKER = '\n\n## Auto-generated signatures\n<!-- Updated by gen-context.js -->\n';
+  const CLAUDE_ALLOWLIST_MARKER = '<!-- sigmap-bash-allowlist -->';
+  const CLAUDE_ALLOWLIST_BLOCK = [
+    '## Bash allowlist',
+    '',
+    CLAUDE_ALLOWLIST_MARKER,
+    '',
+    'The following sigmap commands are pre-approved — Claude Code will not prompt for confirmation:',
+    '',
+    '```json',
+    JSON.stringify({
+      permissions: {
+        allow: [
+          'Bash(sigmap ask*)',
+          'Bash(sigmap validate*)',
+          'Bash(sigmap judge*)',
+          'Bash(sigmap weights*)',
+          'Bash(sigmap history*)',
+          'Bash(sigmap --query*)',
+          'Bash(sigmap --diff*)',
+          'Bash(sigmap --health*)',
+          'Bash(sigmap --coverage*)',
+          'Bash(node gen-context.js*)',
+        ],
+      },
+    }, null, 2),
+    '```',
+    '',
+    'Add the `permissions.allow` array above to `.claude/settings.json` to activate.',
+    '',
+  ].join('\n');
   function format(context, opts = {}) {
     if (!context || typeof context !== 'string') return '';
     const version = (opts && opts.version) || 'unknown';
@@ -6812,9 +6842,17 @@ __factories["./packages/adapters/claude"] = function(module, exports) {
     if (fs.existsSync(filePath)) existing = fs.readFileSync(filePath, 'utf8');
     const formatted = format(context, opts);
     const markerIdx = existing.indexOf('## Auto-generated signatures');
-    const newContent = markerIdx !== -1
+    let newContent = markerIdx !== -1
       ? existing.slice(0, markerIdx) + CLAUDE_MARKER.trimStart() + formatted
       : existing + CLAUDE_MARKER + formatted;
+    if (!newContent.includes(CLAUDE_ALLOWLIST_MARKER)) {
+      const sigPos = newContent.indexOf('## Auto-generated signatures');
+      if (sigPos !== -1) {
+        newContent = newContent.slice(0, sigPos) + CLAUDE_ALLOWLIST_BLOCK + '\n' + newContent.slice(sigPos);
+      } else {
+        newContent = CLAUDE_ALLOWLIST_BLOCK + '\n' + newContent;
+      }
+    }
     fs.writeFileSync(filePath, newContent, 'utf8');
   }
   module.exports = { name, format, outputPath, write };
@@ -6941,6 +6979,23 @@ __factories["./packages/adapters/codex"] = function(module, exports) {
   const fs = require('fs');
   const name = 'codex';
   const CODEX_MARKER = '\n\n## Auto-generated signatures\n<!-- Updated by gen-context.js -->\n';
+  const CODEX_TOOLS_MARKER = '<!-- sigmap-tools -->';
+  const CODEX_TOOLS_BLOCK = [
+    '## Tools',
+    '',
+    CODEX_TOOLS_MARKER,
+    '',
+    '```json',
+    JSON.stringify([
+      { name: 'sigmap_ask', description: 'Rank source files by relevance to a natural-language query. Run before exploring the codebase.', command: 'sigmap ask "$QUERY"' },
+      { name: 'sigmap_validate', description: 'Validate SigMap config and measure context coverage. Run after changing config or source dirs.', command: 'sigmap validate' },
+      { name: 'sigmap_judge', description: 'Score an LLM response for groundedness against source context. Use to verify answer quality.', command: 'sigmap judge --response "$RESPONSE" --context "$CONTEXT"' },
+      { name: 'sigmap_query', description: 'Rank all files by relevance using TF-IDF and write a focused mini-context.', command: 'sigmap --query "$QUERY" --context' },
+      { name: 'sigmap_weights', description: 'Show learned file-ranking multipliers accumulated from past sessions.', command: 'sigmap weights' },
+    ], null, 2),
+    '```',
+    '',
+  ].join('\n');
   function format(context, opts = {}) {
     if (!context || typeof context !== 'string' || !context.trim()) return '';
     const toolBlock = [
@@ -6965,9 +7020,17 @@ __factories["./packages/adapters/codex"] = function(module, exports) {
     const formatted = format(context, opts);
     const markerIdx = existing.indexOf('## Auto-generated signatures');
     const isLegacyGenerated = existing.includes('<!-- Generated by SigMap gen-context.js') || existing.includes('## Code Signatures') || existing.includes('# Code signatures');
-    const newContent = markerIdx !== -1
+    let newContent = markerIdx !== -1
       ? existing.slice(0, markerIdx) + CODEX_MARKER.trimStart() + formatted
       : (isLegacyGenerated ? CODEX_MARKER.trimStart() + formatted : existing + CODEX_MARKER + formatted);
+    if (!newContent.includes(CODEX_TOOLS_MARKER)) {
+      const sigPos = newContent.indexOf('## Auto-generated signatures');
+      if (sigPos !== -1) {
+        newContent = newContent.slice(0, sigPos) + CODEX_TOOLS_BLOCK + '\n' + newContent.slice(sigPos);
+      } else {
+        newContent = CODEX_TOOLS_BLOCK + '\n' + newContent;
+      }
+    }
     fs.writeFileSync(filePath, newContent, 'utf8');
   }
   module.exports = { name, format, outputPath, write };
@@ -7159,7 +7222,7 @@ const path = require('path');
 const os = require('os');
 const { execSync } = require('child_process');
 
-const VERSION = '6.1.0';
+const VERSION = '6.3.0';
 const MARKER = '\n\n## Auto-generated signatures\n<!-- Updated by gen-context.js -->\n';
 
 function requireSourceOrBundled(key) {
@@ -8862,34 +8925,67 @@ Output: .github/copilot-instructions.md (default)
 // ---------------------------------------------------------------------------
 // MCP auto-registration
 // ---------------------------------------------------------------------------
+function _displayPath(p, cwd) {
+  return p.startsWith(os.homedir()) ? '~' + p.slice(os.homedir().length) : path.relative(cwd, p);
+}
+
+function _registerMcpJson(filePath, serverEntry, cwd) {
+  if (!fs.existsSync(filePath)) return;
+  try {
+    const raw = fs.readFileSync(filePath, 'utf8');
+    const settings = JSON.parse(raw);
+    if (!settings.mcpServers) settings.mcpServers = {};
+    if (settings.mcpServers['sigmap']) return;
+    settings.mcpServers['sigmap'] = serverEntry;
+    fs.writeFileSync(filePath, JSON.stringify(settings, null, 2) + '\n');
+    console.warn(`[sigmap] registered MCP server in ${_displayPath(filePath, cwd)}`);
+  } catch (err) {
+    console.warn(`[sigmap] could not update ${_displayPath(filePath, cwd)}: ${err.message}`);
+  }
+}
+
+function _registerCodexYaml(filePath, scriptPath) {
+  if (!fs.existsSync(filePath)) return;
+  try {
+    const raw = fs.readFileSync(filePath, 'utf8');
+    if (raw.includes('sigmap')) return; // already registered
+    const yamlBlock = [
+      '',
+      'mcpServers:',
+      '  sigmap:',
+      `    command: node`,
+      `    args:`,
+      `      - ${path.resolve(scriptPath)}`,
+      `      - --mcp`,
+    ].join('\n');
+    fs.writeFileSync(filePath, raw.trimEnd() + yamlBlock + '\n');
+    console.warn('[sigmap] registered MCP server in ~/.codex/config.yaml');
+  } catch (err) {
+    console.warn(`[sigmap] could not update ~/.codex/config.yaml: ${err.message}`);
+  }
+}
+
 function registerMcp(cwd, scriptPath) {
   const serverEntry = {
     command: 'node',
     args: [path.resolve(scriptPath), '--mcp'],
   };
 
-  // mcpServers shape: Claude (.claude/settings.json), Cursor (.cursor/mcp.json),
-  // Windsurf project (.windsurf/mcp.json) and global (~/.codeium/windsurf/mcp_config.json)
-  const targets = [
+  // JSON mcpServers targets: Claude, Cursor, Windsurf project, Windsurf global,
+  // VS Code (GitHub Copilot 1.99+), OpenCode project, OpenCode global, Gemini CLI
+  const jsonTargets = [
     path.join(cwd, '.claude', 'settings.json'),
     path.join(cwd, '.cursor', 'mcp.json'),
     path.join(cwd, '.windsurf', 'mcp.json'),
     path.join(os.homedir(), '.codeium', 'windsurf', 'mcp_config.json'),
+    path.join(cwd, '.vscode', 'mcp.json'),
+    path.join(cwd, 'opencode.json'),
+    path.join(os.homedir(), '.config', 'opencode', 'config.json'),
+    path.join(os.homedir(), '.gemini', 'settings.json'),
   ];
 
-  for (const settingsPath of targets) {
-    if (!fs.existsSync(settingsPath)) continue;
-    try {
-      const raw = fs.readFileSync(settingsPath, 'utf8');
-      const settings = JSON.parse(raw);
-      if (!settings.mcpServers) settings.mcpServers = {};
-      if (settings.mcpServers['sigmap']) continue; // already registered
-      settings.mcpServers['sigmap'] = serverEntry;
-      fs.writeFileSync(settingsPath, JSON.stringify(settings, null, 2) + '\n');
-      console.warn(`[sigmap] registered MCP server in ${settingsPath.startsWith(os.homedir()) ? '~' + settingsPath.slice(os.homedir().length) : path.relative(cwd, settingsPath)}`);
-    } catch (err) {
-      console.warn(`[sigmap] could not update ${path.relative(cwd, settingsPath)}: ${err.message}`);
-    }
+  for (const target of jsonTargets) {
+    _registerMcpJson(target, serverEntry, cwd);
   }
 
   // Zed uses context_servers (different shape from mcpServers)
@@ -8911,12 +9007,24 @@ function registerMcp(cwd, scriptPath) {
     }
   }
 
-  // Print manual snippets for all 4 tools
+  // Codex CLI uses YAML (~/.codex/config.yaml)
+  _registerCodexYaml(path.join(os.homedir(), '.codex', 'config.yaml'), scriptPath);
+
+  // Print manual snippets for all targets
   console.warn('[sigmap] MCP / context server config snippets:');
-  console.warn('  Claude / Cursor / Windsurf (.claude/settings.json | .cursor/mcp.json | .windsurf/mcp.json):');
+  console.warn('  Claude / Cursor / Windsurf / VS Code / OpenCode / Gemini CLI:');
   console.warn(JSON.stringify({ mcpServers: { sigmap: serverEntry } }, null, 2));
   console.warn('  Zed (~/.config/zed/settings.json):');
   console.warn(JSON.stringify({ context_servers: { sigmap: { command: { path: 'node', args: [path.resolve(scriptPath), '--mcp'] } } } }, null, 2));
+  console.warn('  Codex CLI (~/.codex/config.yaml):');
+  console.warn([
+    'mcpServers:',
+    '  sigmap:',
+    `    command: node`,
+    `    args:`,
+    `      - ${path.resolve(scriptPath)}`,
+    `      - --mcp`,
+  ].join('\n'));
 }
 
 // ---------------------------------------------------------------------------

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "sigmap",
-  "version": "6.1.0",
+  "version": "6.3.0",
   "description": "Zero-dependency AI context engine — 97% token reduction. No npm install. Runs on Node 18+.",
   "main": "gen-context.js",
   "exports": {

package/packages/adapters/claude.js

@@ -16,6 +16,37 @@ const fs = require('fs');
 const name = 'claude';
 
 const MARKER = '\n\n## Auto-generated signatures\n<!-- Updated by gen-context.js -->\n';
+const ALLOWLIST_MARKER = '<!-- sigmap-bash-allowlist -->';
+
+const ALLOWLIST_BLOCK = [
+  '## Bash allowlist',
+  '',
+  ALLOWLIST_MARKER,
+  '',
+  'The following sigmap commands are pre-approved — Claude Code will not prompt for confirmation:',
+  '',
+  '```json',
+  JSON.stringify({
+    permissions: {
+      allow: [
+        'Bash(sigmap ask*)',
+        'Bash(sigmap validate*)',
+        'Bash(sigmap judge*)',
+        'Bash(sigmap weights*)',
+        'Bash(sigmap history*)',
+        'Bash(sigmap --query*)',
+        'Bash(sigmap --diff*)',
+        'Bash(sigmap --health*)',
+        'Bash(sigmap --coverage*)',
+        'Bash(node gen-context.js*)',
+      ],
+    },
+  }, null, 2),
+  '```',
+  '',
+  'Add the `permissions.allow` array above to `.claude/settings.json` to activate.',
+  '',
+].join('\n');
 
 /**
  * Format context suited for CLAUDE.md.
@@ -82,6 +113,17 @@ function write(context, cwd, opts = {}) {
   } else {
     newContent = existing + MARKER + formatted;
   }
+
+  // Inject ## Bash allowlist above the sig marker if not already present
+  if (!newContent.includes(ALLOWLIST_MARKER)) {
+    const sigMarkerPos = newContent.indexOf('## Auto-generated signatures');
+    if (sigMarkerPos !== -1) {
+      newContent = newContent.slice(0, sigMarkerPos) + ALLOWLIST_BLOCK + '\n' + newContent.slice(sigMarkerPos);
+    } else {
+      newContent = ALLOWLIST_BLOCK + '\n' + newContent;
+    }
+  }
+
   fs.writeFileSync(filePath, newContent, 'utf8');
 }
 

package/packages/adapters/codex.js

@@ -17,6 +17,44 @@ const fs = require('fs');
 
 const name = 'codex';
 const MARKER = '\n\n## Auto-generated signatures\n<!-- Updated by gen-context.js -->\n';
+const TOOLS_MARKER = '<!-- sigmap-tools -->';
+
+const TOOLS_BLOCK = [
+  '## Tools',
+  '',
+  TOOLS_MARKER,
+  '',
+  '```json',
+  JSON.stringify([
+    {
+      name: 'sigmap_ask',
+      description: 'Rank source files by relevance to a natural-language query. Run before exploring the codebase.',
+      command: 'sigmap ask "$QUERY"',
+    },
+    {
+      name: 'sigmap_validate',
+      description: 'Validate SigMap config and measure context coverage. Run after changing config or source dirs.',
+      command: 'sigmap validate',
+    },
+    {
+      name: 'sigmap_judge',
+      description: 'Score an LLM response for groundedness against source context. Use to verify answer quality.',
+      command: 'sigmap judge --response "$RESPONSE" --context "$CONTEXT"',
+    },
+    {
+      name: 'sigmap_query',
+      description: 'Rank all files by relevance using TF-IDF and write a focused mini-context.',
+      command: 'sigmap --query "$QUERY" --context',
+    },
+    {
+      name: 'sigmap_weights',
+      description: 'Show learned file-ranking multipliers accumulated from past sessions.',
+      command: 'sigmap weights',
+    },
+  ], null, 2),
+  '```',
+  '',
+].join('\n');
 
 /**
  * Format context for AGENTS.md — clean markdown, no LLM preamble.
@@ -80,6 +118,16 @@ function write(context, cwd, opts = {}) {
       : existing + MARKER + formatted;
   }
 
+  // Inject ## Tools block above the sig marker if not already present
+  if (!newContent.includes(TOOLS_MARKER)) {
+    const sigMarkerPos = newContent.indexOf('## Auto-generated signatures');
+    if (sigMarkerPos !== -1) {
+      newContent = newContent.slice(0, sigMarkerPos) + TOOLS_BLOCK + '\n' + newContent.slice(sigMarkerPos);
+    } else {
+      newContent = TOOLS_BLOCK + '\n' + newContent;
+    }
+  }
+
   fs.writeFileSync(filePath, newContent, 'utf8');
 }
 

package/packages/cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "sigmap-cli",
-  "version": "6.1.0",
+  "version": "6.3.0",
   "description": "SigMap CLI wrapper — thin adapter for programmatic CLI invocation",
   "main": "index.js",
   "keywords": [

package/packages/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "sigmap-core",
-  "version": "6.1.0",
+  "version": "6.3.0",
   "description": "SigMap core library — zero-dependency code signature extraction, retrieval, and security scanning",
   "main": "index.js",
   "keywords": [

package/src/mcp/server.js

@@ -18,7 +18,7 @@ const { readContext, searchSignatures, getMap, createCheckpoint, getRouting, exp
 
 const SERVER_INFO = {
   name: 'sigmap',
-  version: '6.1.0',
+  version: '6.3.0',
   description: 'SigMap MCP server — code signatures on demand',
 };