contextos-agents 2.0.0-beta.3 → 2.1.0

package/LICENSE

@@ -1,21 +1,201 @@
-MIT License
-
-Copyright (c) 2026 contextos-agents contributors
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or exemplary damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2026 ContextOS Contributors
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

package/NOTICE

@@ -0,0 +1,4 @@
+ContextOS (contextos-agents)
+Copyright 2026 ContextOS Contributors
+
+This product includes software developed at ContextOS (https://github.com/kok-o/contextos-agents).

package/README.md

@@ -1,13 +1,36 @@
-# <img src="./Frame%202.png" height="40" align="absmiddle" /> contextos-agents
-
-[![npm version](https://img.shields.io/npm/v/contextos-agents.svg)](https://www.npmjs.com/package/contextos-agents)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Node.js](https://img.shields.io/badge/node-%3E%3D18.0.0-brightgreen.svg)](https://nodejs.org/)
-[![CI](https://github.com/kok-o/contextos-agents/actions/workflows/validate-skills.yml/badge.svg)](https://github.com/kok-o/contextos-agents/actions/workflows/validate-skills.yml)
-
-**One source of truth for every coding agent.**
-
-ContextOS is a deterministic context and policy compiler for AI coding agents. It transforms your team's version-controlled engineering rules into a minimal, verifiable context payload for Cursor, Claude Code, GitHub Copilot, Aider, and Zed—and detects configuration drift in CI.
+<p align="center">
+  <a href="https://github.com/kok-o/contextos-agents">
+    <img src="./Frame%202.png" alt="ContextOS Logo" width="88" height="88" />
+  </a>
+</p>
+
+<h1 align="center">contextos-agents</h1>
+
+<p align="center">
+  <strong>One version-controlled source of engineering rules for supported coding agents.</strong>
+</p>
+
+<p align="center">
+  <a href="https://www.npmjs.com/package/contextos-agents"><img src="https://img.shields.io/npm/v/contextos-agents?color=18181b&logo=npm" alt="npm version" /></a>
+  <a href="https://www.npmjs.com/package/contextos-agents"><img src="https://img.shields.io/npm/dt/contextos-agents?color=18181b&logo=npm&label=downloads" alt="npm downloads" /></a>
+  <a href="https://nodejs.org/"><img src="https://img.shields.io/badge/node-%3E%3D22.0.0-18181b?logo=node.js" alt="Node.js" /></a>
+  <a href="./LICENSE"><img src="https://img.shields.io/badge/license-Apache_2.0-18181b" alt="License" /></a>
+  <a href="https://github.com/kok-o/contextos-agents/actions/workflows/validate-skills.yml"><img src="https://img.shields.io/github/actions/workflow/status/kok-o/contextos-agents/validate-skills.yml?label=ci&color=18181b&logo=github" alt="CI" /></a>
+</p>
+
+<p align="center">
+  <a href="#installation">Installation</a> •
+  <a href="./GUIDE.md">Guide</a> •
+  <a href="./docs/product/onboarding.md">Onboarding</a> •
+  <a href="./docs/ADAPTER_COMPATIBILITY.md">Adapters</a> •
+  <a href="#supported-agents--compilation">Supported Agents</a> •
+  <a href="./CONTRIBUTING.md">Contributing</a> •
+  <a href="https://www.npmjs.com/package/contextos-agents">npm</a>
+</p>
+
+---
+
+ContextOS is a deterministic context and policy compiler for AI coding agents. It transforms your team's version-controlled engineering rules into focused, verifiable context for Gemini, Claude Code, Cursor, GitHub Copilot, Aider, and Zed - and detects configuration drift in CI.
 
 ## Installation
 
@@ -34,22 +57,24 @@ npx contextos-agents --skip-compile     # Skip auto-compilation step
 
 ## Why ContextOS?
 
-Most AI coding assistants suffer from two extremes: they either operate in a vacuum with zero knowledge of your architectural standards, or they are choked with massive monolithic system prompts that cause context overflow and lazy code stubs (`// TODO`).
+Modern development teams face fragmented AI tooling: engineers use Cursor, Claude Code, GitHub Copilot, Gemini, Zed, and Aider. Each tool requires its own proprietary rules format, leading to configuration drift, contradictory standards, and unvetted AI slop (`// TODO`, leaked secrets).
 
-**ContextOS is not another coding agent.** It governs the context and policies used by the agents your team already has.
+Artificially truncating skills to save tokens degrades model reasoning and induces hallucinations. Instead, ContextOS ensures that agents receive complete, high-fidelity engineering context from a single version-controlled source.
+
+**ContextOS is not another coding agent.** It is the deterministic context compiler and policy engine for the agents your team already uses.
 
 ### The Three Pillars
 
-1. **Portable:** Define your engineering rules once. ContextOS exports optimized configurations for all major AI editors (Cursor, Claude Code, Copilot, Aider, Zed).
-2. **Minimal:** The dynamic resolver selects only the relevant skills and rules needed for a specific task, eliminating prompt bloat and token waste.
-3. **Verifiable:** Lockfiles, provenance, drift detection, and CI gates make generated agent configuration reproducible and auditable.
+1. **Portable (Multi-Agent):** Define your engineering skills once in standard Markdown. ContextOS compiles native configurations for all supported agents (Gemini, Claude Code, Cursor, Copilot, Aider, and Zed).
+2. **High-Fidelity & Focused:** The resolver maps domain skills to relevant tasks without lossy truncation, delivering rich, complete context to the model.
+3. **Verifiable in CI:** Lockfile v2 provenance, dual-hash verification, and CI quality gates detect configuration drift and enforce quality guardrails before merge.
 
 ## How it works
 
 1. Define version-controlled engineering policies once.
-2. Resolve only the policies relevant to the current task.
+2. Resolve the complete, relevant skill policies for the current task.
 3. Compile native configuration for each coding agent.
-4. Detect configuration drift in CI.
+4. Detect configuration drift and policy violations in CI.
 
 ```bash
 contextos resolve "review authentication changes" \
@@ -62,10 +87,10 @@ Selected:
   engineering-workflow  required dependency
 
 Excluded:
-  context-manager       context budget
+  context-manager       domain relevance filter
 
 Risk: high
-Estimated context: 2,840 tokens
+Context status: complete and verified
 
 ## Dynamic Skill Resolution & Unified CLI (`contextos` / `ctx.js`)
 
@@ -108,9 +133,35 @@ contextos doctor
 contextos export all       # Compile for all agents
 ```
 
-### CI Quality Gate Action (`contextos-gate`)
+### Staged Index Security Scanner (`contextos scan`)
 
-Guard your repository against skill drift, secret leaks, and rule regressions using the official GitHub Composite Action:
+Scan staged changes directly from the Git index for secret leaks, blocked credential files, unfinished lazy stubs, and write-scope containment:
+
+```bash
+contextos scan --staged --enforce
+contextos scan --staged --placeholders --scope .agents/task-scope.json --json
+```
+
+### Safe Git Pre-Commit Hooks (`contextos hook`)
+
+Install or remove isolated pre-commit hooks that run fast security checks without clobbering existing developer hooks:
+
+```bash
+contextos hook install
+contextos hook uninstall
+```
+
+### CI Quality Gate (`contextos gate`)
+
+Run the complete 8-point production quality gate locally:
+
+```bash
+contextos gate
+```
+
+### CI Quality Gate Action (contextos-gate)
+
+Guard your repository against skill drift, missing outputs, and rule regressions using the official GitHub Composite Action:
 
 ```yaml
 # .github/workflows/pr-gate.yml
@@ -121,29 +172,31 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: kok-o/contextos-agents/.github/actions/contextos-gate@main
+      - uses: kok-o/contextos-agents/.github/actions/contextos-gate@v2.0.0
+        with:
+          version: '2.0.0'       # Pinned version of contextos-agents runner
+          adapters: 'all'        # Adapters to verify (or specific: 'cursor', 'claude')
+          working-directory: '.' # Project root directory
 ```
 
-## ContextOS MCP Bridge (Beta)
+The action executes the verified ContextOS quality gate in-process from the pinned package version, verifying generated AI adapter configs against source skills without executing untrusted scripts from pull requests, and without requiring a Node.js project or running `npm test`.
 
-ContextOS provides a read-only **Model Context Protocol (MCP)** server to allow compatible agents (like Claude Desktop) to dynamically read project rules, resolve context, and check project status.
+## Optional MCP integration (Beta)
 
-> [!WARNING]
-> **Separation of Concerns:** The MCP Bridge and experimental runtime orchestration tools are distributed separately in the `@contextos/mcp` package (Beta). The `--with-mcp` flag in the Core CLI is deprecated.
+The MCP server is a separate beta package. It is not part of the stable `contextos-agents` core.
 
-Install the optional MCP Bridge:
+Install it separately if you want to try the beta integration:
 
-`ash
+```bash
 npm install --save-dev @contextos/mcp
 npx contextos-mcp --dir .
-`
+```
 
-The MCP Bridge is read-only by default. Experimental execution tools require
-the explicit --enable-runtime flag and should only be used in trusted repositories.
+The MCP server is read-only by default. Runtime execution remains experimental and is outside the stable core scope.
 
-## Security — Third-Party Skills
+## Security - Third-Party Skills
 
-ContextOS skills are **executable context** — they become part of the system prompt that controls your AI agent's behavior. A malicious skill could instruct the AI agent to exfiltrate environment variables, modify files, or ignore your project's security policies.
+ContextOS skills are **executable context** - they become part of the system prompt that controls your AI agent's behavior. A malicious skill could instruct the AI agent to exfiltrate environment variables, modify files, or ignore your project's security policies.
 
 > [!CAUTION]
 > **Install skills only from repositories you trust as you would trust executable code.** Skills installed via `ctx.js skill add` from npm or GitHub are not sandboxed.
@@ -154,4 +207,4 @@ We are open to pull requests! See [CONTRIBUTING.md](./CONTRIBUTING.md) for a ste
 
 ## License
 
-Distributed under the MIT License. You can freely use, modify, and distribute this code.
+Distributed under the Apache License, Version 2.0. See [LICENSE](./LICENSE) and [NOTICE](./NOTICE) for details.

package/bin/commands/hook.js

@@ -0,0 +1,129 @@
+/**
+ * bin/commands/hook.js
+ * ContextOS Git Hook Installer & Lifecycle Manager
+ *
+ * Safely installs and uninstalls the pre-commit governance hook.
+ * Preserves pre-existing user hooks, supports core.hooksPath and worktrees,
+ * and operates idempotently.
+ */
+
+'use strict';
+
+const fs = require('fs');
+const path = require('path');
+const { findHooksDir } = require('../lib/git-snapshot.js');
+
+const HOOK_MARKER_START = '# BEGIN CONTEXTOS HOOK';
+const HOOK_MARKER_END = '# END CONTEXTOS HOOK';
+
+const HOOK_PAYLOAD = `${HOOK_MARKER_START}
+npx contextos-agents scan --staged --enforce || exit 1
+${HOOK_MARKER_END}`;
+
+function installHook(cwd = process.cwd()) {
+  const hooksDir = findHooksDir(cwd);
+
+  if (!hooksDir) {
+    console.error('[ERROR] Not a Git repository or Git hooks directory not found.');
+    process.exit(1);
+  }
+
+  if (!fs.existsSync(hooksDir)) {
+    fs.mkdirSync(hooksDir, { recursive: true });
+  }
+
+  const hookFile = path.join(hooksDir, 'pre-commit');
+
+  if (fs.existsSync(hookFile)) {
+    const existing = fs.readFileSync(hookFile, 'utf8');
+
+    if (existing.includes(HOOK_MARKER_START)) {
+      // Replace existing block cleanly
+      const regex = new RegExp(`${HOOK_MARKER_START}[\\s\\S]*?${HOOK_MARKER_END}`);
+      const updated = existing.replace(regex, HOOK_PAYLOAD);
+      fs.writeFileSync(hookFile, updated, 'utf8');
+      console.log(`✓ ContextOS pre-commit hook updated in ${hookFile}`);
+    } else {
+      // Append while preserving user's existing hook script
+      const separator = existing.endsWith('\n') ? '\n' : '\n\n';
+      const updated = existing + separator + HOOK_PAYLOAD + '\n';
+      fs.writeFileSync(hookFile, updated, 'utf8');
+      console.log(`✓ ContextOS pre-commit hook appended to existing hook in ${hookFile}`);
+    }
+  } else {
+    // Fresh hook installation with shebang
+    const fresh = `#!/bin/sh\n\n${HOOK_PAYLOAD}\n`;
+    fs.writeFileSync(hookFile, fresh, 'utf8');
+    console.log(`✓ ContextOS pre-commit hook installed in ${hookFile}`);
+  }
+
+  try {
+    fs.chmodSync(hookFile, 0o755);
+  } catch {
+    // Best effort on platforms that do not support POSIX file modes
+  }
+}
+
+function uninstallHook(cwd = process.cwd()) {
+  const hooksDir = findHooksDir(cwd);
+
+  if (!hooksDir) {
+    console.error('[ERROR] Not a Git repository or Git hooks directory not found.');
+    process.exit(1);
+  }
+
+  const hookFile = path.join(hooksDir, 'pre-commit');
+
+  if (!fs.existsSync(hookFile)) {
+    console.log('✓ No pre-commit hook found to uninstall.');
+    return;
+  }
+
+  const existing = fs.readFileSync(hookFile, 'utf8');
+
+  if (!existing.includes(HOOK_MARKER_START)) {
+    console.log('✓ No ContextOS hook block detected in pre-commit hook.');
+    return;
+  }
+
+  // Remove exclusively the ContextOS demarcated block
+  const regex = new RegExp(`\\n?${HOOK_MARKER_START}[\\s\\S]*?${HOOK_MARKER_END}\\n?`, 'g');
+  const remaining = existing.replace(regex, '').trim();
+
+  // If file contains only shebang or is empty, remove it completely
+  if (!remaining || remaining === '#!/bin/sh' || remaining === '#!/bin/bash') {
+    fs.unlinkSync(hookFile);
+    console.log(`✓ ContextOS pre-commit hook uninstalled and empty ${hookFile} removed.`);
+  } else {
+    // Preserve remaining user scripts
+    fs.writeFileSync(hookFile, remaining + '\n', 'utf8');
+    console.log(`✓ ContextOS block removed from ${hookFile}; user commands preserved.`);
+  }
+}
+
+function hookCommand(args, flags) {
+  const subCommand = args[1] ? args[1].toLowerCase().trim() : null;
+
+  if (subCommand === 'install') {
+    installHook(process.cwd());
+    process.exit(0);
+  } else if (subCommand === 'uninstall') {
+    uninstallHook(process.cwd());
+    process.exit(0);
+  } else {
+    console.log('\nUsage: contextos hook <install|uninstall>\n');
+    console.log('Commands:');
+    console.log('  install    Safely install pre-commit quality gate hook');
+    console.log('  uninstall  Remove ContextOS block while preserving custom hooks\n');
+    process.exit(1);
+  }
+}
+
+module.exports = {
+  installHook,
+  uninstallHook,
+  hookCommand,
+  HOOK_MARKER_START,
+  HOOK_MARKER_END,
+  HOOK_PAYLOAD,
+};

package/bin/commands/scan.js

@@ -0,0 +1,70 @@
+/**
+ * bin/commands/scan.js
+ * ContextOS CLI Command Handler: scan
+ *
+ * Runs security, placeholder, and write-scope checks against Git staged files.
+ */
+
+'use strict';
+
+const { runScan } = require('../lib/scan.js');
+
+function scanCommand(args, flags) {
+  const isJson = flags.json || args.includes('--json');
+  const enforce = flags.enforce || args.includes('--enforce');
+  const checkPlaceholders = flags.placeholders || args.includes('--placeholders');
+  const checkSecrets = !args.includes('--no-secrets');
+
+  const scopeIdx = args.indexOf('--scope');
+  const scopeFile = scopeIdx !== -1 && args[scopeIdx + 1] ? args[scopeIdx + 1] : null;
+
+  const result = runScan({
+    cwd: process.cwd(),
+    staged: true,
+    secrets: checkSecrets,
+    placeholders: checkPlaceholders,
+    scope: scopeFile,
+    enforce,
+  });
+
+  if (isJson) {
+    console.log(JSON.stringify(result, null, 2));
+    process.exit(result.code);
+  }
+
+  console.log('\n══════════════════════════════════════════════════════');
+  console.log('  ContextOS Staged Index Scanner');
+  console.log('══════════════════════════════════════════════════════\n');
+
+  if (result.code === 2) {
+    console.error(`  [ERROR] ${result.error || 'Scan incomplete'}\n`);
+    process.exit(2);
+  }
+
+  console.log(`  Staged Files Scanned : ${result.stats.stagedFilesCount}`);
+  console.log(`  Enforcement Mode     : ${enforce ? 'STRICT (fails on findings)' : 'ADVISORY (warnings only)'}`);
+  console.log(`  Violations Found     : ${result.stats.violationsCount}\n`);
+
+  if (result.findings.length > 0) {
+    console.log('  Findings:');
+    for (const f of result.findings) {
+      const loc = f.line ? `${f.file}:${f.line}` : f.file;
+      const tag = f.severity === 'error' ? 'ERROR' : 'WARN';
+      console.log(`    • [${f.ruleId}] [${tag}] ${loc}`);
+      console.log(`      ${f.details}`);
+    }
+    console.log('');
+  }
+
+  console.log('──────────────────────────────────────────────────────');
+  if (result.ok) {
+    console.log('  RESULT: PASSED (No blocking violations in staged index)');
+  } else {
+    console.log('  RESULT: FAILED (Commit blocked due to staged violations)');
+  }
+  console.log('──────────────────────────────────────────────────────\n');
+
+  process.exit(result.code);
+}
+
+module.exports = scanCommand;

package/bin/commands/update.js

@@ -32,6 +32,7 @@ const {
 } = require('../lib/safe-writer.js');
 
 const pkg = require('../../package.json');
+const profiles = require('../../.agents/profiles.js');
 
 /**
  * Collect all distributable files from the source .agents directory.
@@ -112,13 +113,9 @@ function planUpdate(projectDir, sourceAgentsDir, options = {}) {
   // Determine active profile exclusions if available
   let excludedSkills = [];
   try {
-    const profilesPath = path.join(projectDir, '.agents', 'profiles.js');
-    if (fs.existsSync(profilesPath)) {
-      const profilesModule = require(profilesPath);
-      const active = profilesModule.getActiveProfile(projectDir);
-      if (active && Array.isArray(active.exclude_skills)) {
-        excludedSkills = active.exclude_skills;
-      }
+    const active = profiles.getActiveProfile(projectDir);
+    if (active && Array.isArray(active.exclude_skills)) {
+      excludedSkills = active.exclude_skills;
     }
   } catch {}
 
@@ -299,7 +296,9 @@ function runUpdate(projectDir = process.cwd(), options = {}) {
 
   // Re-compile if ctx.js exists and not skipped
   if (!options.skipCompile) {
-    const ctxPath = path.join(projectDir, '.agents', 'ctx.js');
+    // Run the compiler shipped with this package. The project's .agents/ctx.js
+    // is user-controlled and must never be executed implicitly during update.
+    const ctxPath = path.join(sourceAgentsDir, 'ctx.js');
     if (fs.existsSync(ctxPath)) {
       try {
         const { execFileSync } = require('child_process');