contextos-agents 1.7.0 → 2.0.0-beta.3

package/.agents/compiler/manifest-compiler.js

@@ -0,0 +1,963 @@
+/**
+ * .agents/compiler/manifest-compiler.js
+ * ContextOS — Manifest Compiler & Registry v2 Generator
+ *
+ * Compiles skill manifests (v1 and v2) into a unified, deterministic,
+ * cryptographically verified registry (registry.v2.json) with:
+ *   - Strict schema validation (fail-closed, additionalProperties: false)
+ *   - Frontmatter parity enforcement between SKILL.md and manifest
+ *   - Dependency closure, cycle detection, self-dependency and conflict validation
+ *   - Resource tree verification & path traversal / symlink escape guards
+ *   - SHA-256 content hashing (entrypointHash, resourceTreeHash, sourceGraphHash)
+ *   - Standardized error contracts & SARIF 2.1.0 reporting
+ *   - Zero install-time runtime dependencies (pure Node.js)
+ */
+
+'use strict';
+
+const fs = require('fs');
+const path = require('path');
+const crypto = require('crypto');
+
+// Standard error codes for manifest diagnostics
+const CODES = {
+  PARSE_ERROR: 'CTX_MANIFEST_PARSE_ERROR',
+  SCHEMA_ERROR: 'CTX_MANIFEST_SCHEMA_ERROR',
+  UNKNOWN_DEPENDENCY: 'CTX_MANIFEST_UNKNOWN_DEPENDENCY',
+  CYCLE_DETECTED: 'CTX_MANIFEST_CYCLE_DETECTED',
+  SELF_DEPENDENCY: 'CTX_MANIFEST_SELF_DEPENDENCY',
+  CONFLICT_VIOLATION: 'CTX_MANIFEST_CONFLICT_VIOLATION',
+  FRONTMATTER_MISMATCH: 'CTX_MANIFEST_FRONTMATTER_MISMATCH',
+  MISSING_ENTRYPOINT: 'CTX_MANIFEST_MISSING_ENTRYPOINT',
+  MISSING_RESOURCE: 'CTX_MANIFEST_MISSING_RESOURCE',
+  INVALID_PATH: 'CTX_MANIFEST_INVALID_PATH',
+  DUPLICATE_ID: 'CTX_MANIFEST_DUPLICATE_ID',
+  DUPLICATE_ALIAS: 'CTX_MANIFEST_DUPLICATE_ALIAS',
+  MISSING_RULE_CHECKER: 'CTX_MANIFEST_MISSING_RULE_CHECKER',
+  INVALID_RULE: 'CTX_MANIFEST_INVALID_RULE',
+};
+
+// Default signals by skill ID (extracted from canonical resolver patterns for v1 backward compatibility)
+const DEFAULT_SIGNALS = {
+  nextjs: {
+    aliases: ['next', 'next.js', 'nextjs'],
+    keywords: [
+      { value: 'next', weight: 40 },
+      { value: 'next.js', weight: 40 },
+      { value: 'app router', weight: 35 },
+      { value: 'server actions', weight: 30 },
+      { value: 'rsc', weight: 30 },
+      { value: 'некст', locale: 'ru', weight: 35 },
+    ],
+    fileGlobs: [
+      { value: 'app/**/*.{tsx,jsx,ts,js}', weight: 30 },
+      { value: '**/next.config.{js,mjs,ts}', weight: 35 },
+    ],
+    packages: [{ ecosystem: 'npm', name: 'next', weight: 35 }],
+  },
+  react: {
+    aliases: ['react', 'reactjs'],
+    keywords: [
+      { value: 'react', weight: 40 },
+      { value: 'useOptimistic', weight: 30 },
+      { value: 'component', weight: 20 },
+      { value: 'hooks', weight: 25 },
+      { value: 'компонент', locale: 'ru', weight: 30 },
+      { value: 'хук', locale: 'ru', weight: 30 },
+    ],
+    fileGlobs: [{ value: '**/*.{tsx,jsx}', weight: 25 }],
+    packages: [{ ecosystem: 'npm', name: 'react', weight: 35 }],
+  },
+  typescript: {
+    aliases: ['ts', 'typescript'],
+    keywords: [
+      { value: 'typescript', weight: 40 },
+      { value: 'type-safe', weight: 30 },
+      { value: 'generics', weight: 25 },
+      { value: 'tsconfig', weight: 30 },
+      { value: 'тайпскрипт', locale: 'ru', weight: 35 },
+      { value: 'типизац', locale: 'ru', weight: 30 },
+    ],
+    fileGlobs: [
+      { value: '**/*.tsx?', weight: 20 },
+      { value: '**/tsconfig.json', weight: 35 },
+    ],
+    packages: [{ ecosystem: 'npm', name: 'typescript', weight: 35 }],
+  },
+  security: {
+    aliases: ['sec', 'auth', 'security'],
+    keywords: [
+      { value: 'security', weight: 40 },
+      { value: 'auth', weight: 35 },
+      { value: 'jwt', weight: 30 },
+      { value: 'csrf', weight: 30 },
+      { value: 'xss', weight: 30 },
+      { value: 'безопасност', locale: 'ru', weight: 35 },
+      { value: 'авториз', locale: 'ru', weight: 30 },
+      { value: 'парол', locale: 'ru', weight: 30 },
+    ],
+    fileGlobs: [
+      { value: '**/*auth*', weight: 25 },
+      { value: '**/*security*', weight: 25 },
+    ],
+    packages: [],
+  },
+  database: {
+    aliases: ['db', 'database', 'sql'],
+    keywords: [
+      { value: 'database', weight: 40 },
+      { value: 'sql', weight: 35 },
+      { value: 'postgres', weight: 35 },
+      { value: 'prisma', weight: 35 },
+      { value: 'drizzle', weight: 35 },
+      { value: 'migration', weight: 30 },
+      { value: 'баз.*данн', locale: 'ru', weight: 35 },
+      { value: 'миграц', locale: 'ru', weight: 30 },
+    ],
+    fileGlobs: [
+      { value: '**/*.prisma', weight: 35 },
+      { value: '**/drizzle.config.*', weight: 35 },
+      { value: '**/migrations/**/*.sql', weight: 30 },
+    ],
+    packages: [
+      { ecosystem: 'npm', name: 'prisma', weight: 30 },
+      { ecosystem: 'npm', name: 'drizzle-orm', weight: 30 },
+    ],
+  },
+  testing: {
+    aliases: ['test', 'tests', 'testing'],
+    keywords: [
+      { value: 'vitest', weight: 40 },
+      { value: 'jest', weight: 40 },
+      { value: 'playwright', weight: 40 },
+      { value: 'tdd', weight: 35 },
+      { value: 'bdd', weight: 30 },
+      { value: 'тестирован', locale: 'ru', weight: 35 },
+      { value: 'юнит', locale: 'ru', weight: 30 },
+    ],
+    fileGlobs: [
+      { value: '**/*.{test,spec}.{ts,js,tsx,jsx}', weight: 35 },
+      { value: '**/vitest.config.*', weight: 35 },
+      { value: '**/playwright.config.*', weight: 35 },
+    ],
+    packages: [],
+  },
+  'ui-ux-pro': {
+    aliases: ['ui', 'ux', 'ui-ux'],
+    keywords: [
+      { value: 'ui', weight: 35 },
+      { value: 'ux', weight: 35 },
+      { value: 'tailwind', weight: 35 },
+      { value: 'styling', weight: 30 },
+      { value: 'дизайн', locale: 'ru', weight: 35 },
+      { value: 'интерфейс', locale: 'ru', weight: 30 },
+    ],
+    fileGlobs: [
+      { value: '**/*.{css,scss,sass}', weight: 25 },
+      { value: '**/tailwind.config.*', weight: 35 },
+    ],
+    packages: [{ ecosystem: 'npm', name: 'tailwindcss', weight: 30 }],
+  },
+  node: {
+    aliases: ['nodejs', 'node'],
+    keywords: [
+      { value: 'node', weight: 35 },
+      { value: 'nodejs', weight: 35 },
+      { value: 'express', weight: 30 },
+      { value: 'fastify', weight: 30 },
+    ],
+    fileGlobs: [{ value: '**/package.json', weight: 15 }],
+    packages: [],
+  },
+  fastapi: {
+    aliases: ['fastapi'],
+    keywords: [
+      { value: 'fastapi', weight: 45 },
+      { value: 'pydantic', weight: 35 },
+      { value: 'uvicorn', weight: 30 },
+    ],
+    fileGlobs: [
+      { value: '**/main.py', weight: 20 },
+      { value: '**/requirements.txt', weight: 15 },
+    ],
+    packages: [{ ecosystem: 'pypi', name: 'fastapi', weight: 40 }],
+  },
+  nestjs: {
+    aliases: ['nestjs', 'nest'],
+    keywords: [
+      { value: 'nestjs', weight: 45 },
+      { value: 'nest.js', weight: 40 },
+      { value: 'injectable', weight: 25 },
+    ],
+    fileGlobs: [{ value: '**/nest-cli.json', weight: 40 }],
+    packages: [{ ecosystem: 'npm', name: '@nestjs/core', weight: 40 }],
+  },
+  docker: {
+    aliases: ['docker'],
+    keywords: [
+      { value: 'docker', weight: 45 },
+      { value: 'dockerfile', weight: 45 },
+      { value: 'compose', weight: 30 },
+      { value: 'докер', locale: 'ru', weight: 40 },
+      { value: 'container', weight: 5 },
+      { value: 'контейнер', locale: 'ru', weight: 5 },
+    ],
+    fileGlobs: [
+      { value: '**/Dockerfile*', weight: 40 },
+      { value: '**/docker-compose*.yml', weight: 40 },
+    ],
+    packages: [],
+  },
+};
+
+/**
+ * Diagnostic error object.
+ */
+class DiagnosticError extends Error {
+  /**
+   * @param {Object} diag - Diagnostic payload
+   */
+  constructor(diag) {
+    super(diag.message);
+    this.name = 'DiagnosticError';
+    this.diag = diag;
+  }
+}
+
+const yaml = require('./vendor/yaml.js');
+
+/**
+ * Robust zero-dep YAML parser for skill manifests.
+ * Handles scalars, inline arrays, block lists, nested maps, and quoted multiline strings.
+ */
+function parseYaml(yamlText) {
+  if (typeof yamlText !== 'string' || !yamlText.trim()) return {};
+  const doc = yaml.parseDocument(yamlText, { merge: true, strict: true, uniqueKeys: true });
+  if (doc.errors && doc.errors.length > 0) {
+    throw new DiagnosticError({
+      message: `YAML Parse Error: ${doc.errors[0].message}`,
+      code: CODES.PARSE_ERROR
+    });
+  }
+  return doc.toJS() || {};
+}
+
+/**
+ * ManifestCompiler class.
+ */
+class ManifestCompiler {
+  constructor(options = {}) {
+    this.rootDir = options.rootDir || process.cwd();
+    this.agentsDir = options.agentsDir || path.join(this.rootDir, '.agents');
+    this.coreSkillsDir = options.coreSkillsDir || path.join(this.agentsDir, 'core', 'skills');
+    this.compiledDir = options.compiledDir || path.join(this.agentsDir, 'compiled');
+    this.diagnostics = [];
+  }
+
+  addDiagnostic(code, message, options = {}) {
+    const diag = {
+      code,
+      severity: options.severity || 'error',
+      component: 'manifest-compiler',
+      file: options.file || '',
+      path: options.path || '',
+      line: options.line,
+      column: options.column,
+      message,
+      remediation: options.remediation || 'Correct the manifest according to the schema specification.',
+    };
+    this.diagnostics.push(diag);
+    return diag;
+  }
+
+  /**
+   * Reads and parses frontmatter from a markdown file.
+   */
+  readFrontmatter(filePath) {
+    if (!fs.existsSync(filePath)) return null;
+    const content = fs.readFileSync(filePath, 'utf8');
+    if (!content.startsWith('---')) return null;
+    const endIdx = content.indexOf('---', 3);
+    if (endIdx === -1) return { malformed: true };
+    const rawYaml = content.slice(3, endIdx).trim();
+    const parsed = parseYaml(rawYaml);
+    return {
+      raw: rawYaml,
+      parsed,
+      contentWithoutFrontmatter: content.slice(endIdx + 3).trim(),
+    };
+  }
+
+  /**
+   * Normalizes a v1 or v2 manifest into canonical SkillManifestV2 format.
+   */
+  normalizeManifest(skillDir, rawYamlText) {
+    const parsed = parseYaml(rawYamlText);
+    const skillId = parsed.id || parsed.name || path.basename(skillDir);
+    const displayName = parsed.displayName || parsed.name || skillId;
+    const isV2 = parsed.schemaVersion === 2;
+
+    const entrypoint = parsed.entrypoint || 'SKILL.md';
+    const version = parsed.version ? String(parsed.version) : '1.0.0';
+    const description = parsed.description || `ContextOS skill for ${displayName}`;
+    const type = parsed.type || 'instruction-only';
+    const category = parsed.category || 'general';
+
+    // Normalizing dependencies
+    const requires = Array.isArray(parsed.dependencies?.requires)
+      ? parsed.dependencies.requires
+      : (Array.isArray(parsed.requires) ? parsed.requires : []);
+    const optional = Array.isArray(parsed.dependencies?.optional)
+      ? parsed.dependencies.optional
+      : (Array.isArray(parsed.optional) ? parsed.optional : []);
+    const conflicts = Array.isArray(parsed.dependencies?.conflicts)
+      ? parsed.dependencies.conflicts
+      : (Array.isArray(parsed.conflicts) ? parsed.conflicts : []);
+
+    // Read SKILL.md frontmatter name if present to ensure alias parity
+    const discoveredAliases = [];
+    const entrypointFile = path.join(skillDir, entrypoint);
+    if (fs.existsSync(entrypointFile)) {
+      const fm = this.readFrontmatter(entrypointFile);
+      if (fm && fm.parsed && fm.parsed.name) {
+        const fmSlug = String(fm.parsed.name).trim().toLowerCase().replace(/\s+/g, '-');
+        discoveredAliases.push(fmSlug);
+      }
+    }
+
+    // Normalizing signals (merge provided signals with default signals for known skills)
+    const defaults = DEFAULT_SIGNALS[skillId] || {};
+    const signals = {
+      aliases: Array.from(new Set([
+        ...(parsed.signals?.aliases || []),
+        ...(defaults.aliases || []),
+        ...discoveredAliases,
+        skillId
+      ])),
+      keywords: parsed.signals?.keywords || defaults.keywords || [],
+      fileGlobs: parsed.signals?.fileGlobs || defaults.fileGlobs || [],
+      packages: parsed.signals?.packages || defaults.packages || [],
+    };
+
+    // Normalizing context
+    const priority = parsed.context?.priority !== undefined
+      ? parsed.context.priority
+      : (parsed.weight !== undefined ? parsed.weight * 10 : 50);
+
+    // Normalizing resources
+    let resources = [];
+    if (Array.isArray(parsed.resources)) {
+      resources = parsed.resources.map(r => {
+        if (typeof r === 'string') return { path: r, mode: 'on-demand' };
+        return { path: r.path, mode: r.mode || 'on-demand' };
+      });
+    }
+
+    const deprecated = Boolean(parsed.deprecated);
+    const canonical = typeof parsed.canonical === 'string' ? parsed.canonical : null;
+    const rules = Array.isArray(parsed.rules) ? parsed.rules : [];
+
+    return {
+      schemaVersion: 2,
+      id: skillId,
+      displayName,
+      version,
+      description,
+      type,
+      category,
+      entrypoint,
+      signals,
+      dependencies: {
+        requires: Array.from(new Set(requires)),
+        optional: Array.from(new Set(optional)),
+        conflicts: Array.from(new Set(conflicts)),
+      },
+      context: {
+        priority,
+        estimatedTokens: 0, // Calculated during compilation
+      },
+      resources,
+      deprecated,
+      canonical,
+      rules,
+      _raw: parsed,
+      _isV2: isV2,
+    };
+  }
+
+  /**
+   * Validates a single manifest against strict security, schema and filesystem rules.
+   */
+  validateSingleManifest(skillDir, manifest, manifestFile) {
+    const relManifestPath = path.relative(this.rootDir, manifestFile);
+
+    // 0. Strict Schema Validation (additionalProperties: false)
+    const allowedKeys = new Set([
+      'schemaVersion', 'id', 'name', 'displayName', 'entrypoint', 'version', 
+      'description', 'type', 'category', 'dependencies', 'requires', 'optional', 
+      'conflicts', 'signals', 'context', 'weight', 'resources', 'deprecated', 
+      'canonical', 'rules'
+    ]);
+    if (manifest._raw) {
+      for (const key of Object.keys(manifest._raw)) {
+        if (!allowedKeys.has(key)) {
+          this.addDiagnostic(
+            CODES.SCHEMA_ERROR,
+            `Strict Schema Validation Failed: Unknown property '${key}' is not allowed in schemaVersion 2.`,
+            { file: relManifestPath, path: `/${key}` }
+          );
+        }
+      }
+    }
+
+    // 1. Check ID format
+    if (!manifest.id || !/^[a-z0-9-]+$/.test(manifest.id)) {
+      this.addDiagnostic(
+        CODES.SCHEMA_ERROR,
+        `Invalid skill id '${manifest.id}'. Must contain only lowercase alphanumeric characters and hyphens.`,
+        { file: relManifestPath, path: '/id' }
+      );
+    }
+
+    // 2. Check entrypoint on disk
+    if (manifest.entrypoint.includes('..') || manifest.entrypoint.startsWith('/') || manifest.entrypoint.startsWith('\\') || manifest.entrypoint.includes('\0')) {
+      this.addDiagnostic(
+        CODES.INVALID_PATH,
+        `Entrypoint path '${manifest.entrypoint}' contains invalid characters or directory traversal.`,
+        { file: relManifestPath, path: '/entrypoint' }
+      );
+    } else {
+      const fullEntrypoint = path.join(skillDir, manifest.entrypoint);
+      if (!fs.existsSync(fullEntrypoint)) {
+        this.addDiagnostic(
+          CODES.MISSING_ENTRYPOINT,
+          `Required entrypoint file '${manifest.entrypoint}' does not exist on disk.`,
+          { file: relManifestPath, path: '/entrypoint', remediation: `Create ${manifest.entrypoint} in ${path.relative(this.rootDir, skillDir)}` }
+        );
+      }
+    }
+
+    // 3. Frontmatter parity check with SKILL.md
+    const skillMdPath = path.join(skillDir, manifest.entrypoint);
+    if (fs.existsSync(skillMdPath)) {
+      const fm = this.readFrontmatter(skillMdPath);
+      if (fm && fm.parsed && fm.parsed.name) {
+        const fmName = String(fm.parsed.name).trim().toLowerCase();
+        const idMatches = manifest.id.toLowerCase() === fmName;
+        const displayNameMatches = manifest.displayName.toLowerCase() === fmName;
+        const aliasMatches = manifest.signals && Array.isArray(manifest.signals.aliases)
+          ? manifest.signals.aliases.some(a => a.toLowerCase() === fmName || a.toLowerCase() === fmName.replace(/\s+/g, '-'))
+          : false;
+
+        if (!idMatches && !displayNameMatches && !aliasMatches) {
+          this.addDiagnostic(
+            CODES.FRONTMATTER_MISMATCH,
+            `Frontmatter name '${fm.parsed.name}' in ${manifest.entrypoint} does not match manifest id '${manifest.id}', displayName '${manifest.displayName}', or registered aliases.`,
+            { file: relManifestPath, path: '/displayName', remediation: `Update ${manifest.entrypoint} frontmatter name to match manifest displayName '${manifest.displayName}' or add '${fm.parsed.name}' to aliases.` }
+          );
+        }
+      }
+    }
+
+    // 4. Resource paths validation
+    const realSkillDir = fs.realpathSync(skillDir);
+    for (let i = 0; i < manifest.resources.length; i++) {
+      const res = manifest.resources[i];
+      const resPath = res.path;
+      if (!resPath || resPath.includes('..') || path.isAbsolute(resPath) || resPath.includes('\0')) {
+        this.addDiagnostic(
+          CODES.INVALID_PATH,
+          `Resource path '${resPath}' is invalid or attempts path traversal.`,
+          { file: relManifestPath, path: `/resources/${i}/path` }
+        );
+        continue;
+      }
+
+      const fullResPath = path.join(skillDir, resPath);
+      if (!fs.existsSync(fullResPath)) {
+        this.addDiagnostic(
+          CODES.MISSING_RESOURCE,
+          `Resource file '${resPath}' listed in manifest does not exist.`,
+          { file: relManifestPath, path: `/resources/${i}/path`, remediation: `Create the file or remove it from resources.` }
+        );
+      } else {
+        // Symlink escape check
+        const realResPath = fs.realpathSync(fullResPath);
+        if (!realResPath.startsWith(realSkillDir)) {
+          this.addDiagnostic(
+            CODES.INVALID_PATH,
+            `Resource file '${resPath}' resolves outside skill directory (symlink escape).`,
+            { file: relManifestPath, path: `/resources/${i}/path` }
+          );
+        }
+      }
+    }
+
+    // 5. Check self-dependency
+    if (manifest.dependencies.requires.includes(manifest.id)) {
+      this.addDiagnostic(
+        CODES.SELF_DEPENDENCY,
+        `Skill '${manifest.id}' cannot require itself.`,
+        { file: relManifestPath, path: '/dependencies/requires' }
+      );
+    }
+
+    // 6. Validate declared rules and checkers
+    if (Array.isArray(manifest.rules)) {
+      const { AUTOMATED_CHECKERS } = require('../rules/rule-catalog.js');
+      for (let i = 0; i < manifest.rules.length; i++) {
+        const rule = manifest.rules[i];
+        if (!rule.id || !/^[A-Z0-9_-]+$/.test(rule.id)) {
+          this.addDiagnostic(
+            CODES.SCHEMA_ERROR,
+            `Rule [${i}] in '${manifest.id}' has invalid ID '${rule.id}'. Must match pattern ^[A-Z0-9_-]+$.`,
+            { file: relManifestPath, path: `/rules/${i}/id` }
+          );
+        }
+        if (!['must', 'should', 'may'].includes(rule.level)) {
+          this.addDiagnostic(
+            CODES.SCHEMA_ERROR,
+            `Rule '${rule.id}' has invalid level '${rule.level}'. Must be 'must', 'should', or 'may'.`,
+            { file: relManifestPath, path: `/rules/${i}/level` }
+          );
+        }
+        if (!['runtime', 'linter', 'prompt-guidance', 'reference', 'example'].includes(rule.enforcement)) {
+          this.addDiagnostic(
+            CODES.SCHEMA_ERROR,
+            `Rule '${rule.id}' has invalid enforcement '${rule.enforcement}'.`,
+            { file: relManifestPath, path: `/rules/${i}/enforcement` }
+          );
+        }
+        if (['runtime', 'linter'].includes(rule.enforcement)) {
+          if (!rule.checker) {
+            this.addDiagnostic(
+              CODES.MISSING_RULE_CHECKER,
+              `Rule '${rule.id}' marked enforcement '${rule.enforcement}' requires an automated checker, but none was provided.`,
+              { file: relManifestPath, path: `/rules/${i}/checker` }
+            );
+          } else if (!AUTOMATED_CHECKERS[rule.checker]) {
+            this.addDiagnostic(
+              CODES.MISSING_RULE_CHECKER,
+              `Rule '${rule.id}' references unknown automated checker '${rule.checker}'.`,
+              { file: relManifestPath, path: `/rules/${i}/checker` }
+            );
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * Validates cross-skill dependency graph (closure, cycles, conflicts).
+   */
+  validateDependencyGraph(manifestsById) {
+    const knownIds = new Set(Object.keys(manifestsById));
+
+    // Well-known external frameworks (not internal skills)
+    const EXTERNAL_NAMES = new Set([
+      'vue', 'angular', 'svelte', 'remix', 'express', 'koa', 'hapi', 'sails',
+      'tailwind', 'prisma', 'drizzle', 'mongoose', 'sequelize', 'typeorm',
+      'next-auth', 'react-query', 'zustand', 'redux', 'mobx', 'jotai', 'valtio',
+      'vitest', 'jest', 'mocha', 'cypress', 'playwright', 'storybook',
+      'graphql', 'trpc', 'apollo', 'relay', 'urql',
+      'sqlite', 'simple-auth', 'kubernetes', 'monitoring', 'cicd', 'cqrs',
+      'redis', 'postgres', 'postgresql', 'jwt', 'auth'
+    ]);
+
+    // 1. Unknown dependencies & direct conflict violations
+    for (const [id, m] of Object.entries(manifestsById)) {
+      for (const req of m.dependencies.requires) {
+        if (!knownIds.has(req)) {
+          this.addDiagnostic(
+            CODES.UNKNOWN_DEPENDENCY,
+            `Skill '${id}' requires unknown skill '${req}'.`,
+            { file: m.source, path: '/dependencies/requires', remediation: `Ensure skill '${req}' is present in .agents/core/skills.` }
+          );
+        }
+
+        // Direct conflict violation
+        if (m.dependencies.conflicts.includes(req)) {
+          this.addDiagnostic(
+            CODES.CONFLICT_VIOLATION,
+            `Skill '${id}' both requires and conflicts with '${req}'.`,
+            { file: m.source, path: '/dependencies/conflicts' }
+          );
+        }
+
+        const reqManifest = manifestsById[req];
+        if (reqManifest && reqManifest.dependencies.conflicts.includes(id)) {
+          this.addDiagnostic(
+            CODES.CONFLICT_VIOLATION,
+            `Skill '${id}' requires '${req}', but '${req}' conflicts with '${id}'.`,
+            { file: m.source, path: '/dependencies/requires' }
+          );
+        }
+      }
+    }
+
+    // 2. Cycle detection via DFS
+    const visited = new Map(); // id -> 'unvisited' | 'visiting' | 'visited'
+    for (const id of knownIds) visited.set(id, 'unvisited');
+
+    const checkCycle = (curr, stack) => {
+      visited.set(curr, 'visiting');
+      stack.push(curr);
+
+      const m = manifestsById[curr];
+      if (m) {
+        for (const dep of m.dependencies.requires) {
+          if (!knownIds.has(dep)) continue;
+          const status = visited.get(dep);
+          if (status === 'visiting') {
+            const cyclePath = [...stack.slice(stack.indexOf(dep)), dep].join(' -> ');
+            this.addDiagnostic(
+              CODES.CYCLE_DETECTED,
+              `Dependency cycle detected: ${cyclePath}`,
+              { file: m.source, path: '/dependencies/requires' }
+            );
+          } else if (status === 'unvisited') {
+            checkCycle(dep, stack);
+          }
+        }
+      }
+
+      stack.pop();
+      visited.set(curr, 'visited');
+    };
+
+    for (const id of knownIds) {
+      if (visited.get(id) === 'unvisited') {
+        checkCycle(id, []);
+      }
+    }
+  }
+
+  /**
+   * Computes sha256 hash for a file.
+   */
+  hashFile(filePath) {
+    if (!fs.existsSync(filePath)) return null;
+    const content = fs.readFileSync(filePath);
+    return 'sha256:' + crypto.createHash('sha256').update(content).digest('hex');
+  }
+
+  /**
+   * Computes sha256 hash for a string.
+   */
+  hashString(str) {
+    return 'sha256:' + crypto.createHash('sha256').update(str, 'utf8').digest('hex');
+  }
+
+  /**
+   * Compiles all skills in coreSkillsDir and plugins.
+   * Generates deterministic CompiledRegistryV2 structure.
+   */
+  compile() {
+    this.diagnostics = [];
+    const manifestsById = {};
+    const skillDirs = [];
+
+    // 1. Discover skill directories
+    if (fs.existsSync(this.coreSkillsDir)) {
+      const entries = fs.readdirSync(this.coreSkillsDir, { withFileTypes: true });
+      for (const entry of entries) {
+        if (entry.isDirectory()) {
+          skillDirs.push(path.join(this.coreSkillsDir, entry.name));
+        }
+      }
+    }
+
+    // Also check plugins
+    const pluginsDir = path.join(this.agentsDir, 'plugins');
+    if (fs.existsSync(pluginsDir)) {
+      const pluginEntries = fs.readdirSync(pluginsDir, { withFileTypes: true });
+      for (const pe of pluginEntries) {
+        if (pe.isDirectory()) {
+          const pSkills = path.join(pluginsDir, pe.name, 'skills');
+          if (fs.existsSync(pSkills)) {
+            const subs = fs.readdirSync(pSkills, { withFileTypes: true });
+            for (const sub of subs) {
+              if (sub.isDirectory()) skillDirs.push(path.join(pSkills, sub.name));
+            }
+          }
+        }
+      }
+    }
+
+    // Sort skill directories for determinism
+    skillDirs.sort();
+
+    // 2. Parse and normalize manifests
+    for (const dir of skillDirs) {
+      const v2File = path.join(dir, 'skill.v2.yaml');
+      const v1File = path.join(dir, 'skill.yaml');
+      const manifestFile = fs.existsSync(v2File) ? v2File : (fs.existsSync(v1File) ? v1File : null);
+
+      if (!manifestFile) {
+        // Synthesize minimal manifest from directory name & SKILL.md
+        const id = path.basename(dir);
+        const norm = this.normalizeManifest(dir, `id: ${id}\nname: ${id}\n`);
+        norm.source = path.relative(this.rootDir, dir).replace(/\\/g, '/');
+        manifestsById[id] = norm;
+        continue;
+      }
+
+      try {
+        const rawYaml = fs.readFileSync(manifestFile, 'utf8');
+        const norm = this.normalizeManifest(dir, rawYaml);
+        norm.source = path.relative(this.rootDir, manifestFile).replace(/\\/g, '/');
+
+        if (manifestsById[norm.id]) {
+          this.addDiagnostic(
+            CODES.DUPLICATE_ID,
+            `Duplicate skill id '${norm.id}' found in ${norm.source}`,
+            { file: norm.source, path: '/id' }
+          );
+        }
+
+        manifestsById[norm.id] = norm;
+        this.validateSingleManifest(dir, norm, manifestFile);
+      } catch (err) {
+        this.addDiagnostic(
+          err.diag ? err.diag.code : CODES.PARSE_ERROR,
+          `Failed to parse manifest at ${path.relative(this.rootDir, manifestFile)}: ${err.message}`,
+          { 
+            file: path.relative(this.rootDir, manifestFile),
+            line: err.diag ? err.diag.line : undefined,
+            column: err.diag ? err.diag.column : undefined
+          }
+        );
+      }
+    }
+
+    // 3. Cross-skill dependency graph validation
+    this.validateDependencyGraph(manifestsById);
+
+    // If any errors exist, stop and return diagnostics
+    const hasErrors = this.diagnostics.some(d => d.severity === 'error');
+    if (hasErrors) {
+      return {
+        success: false,
+        diagnostics: this.diagnostics,
+        registry: null,
+      };
+    }
+
+    // 4. Compute hashes, estimated tokens, aliases and packageMap
+    const compiledSkills = {};
+    const aliases = {};
+    const deprecatedAliases = {};
+    const packageMap = {};
+    const dependencyGraph = {};
+    const rules = {};
+
+    const sortedIds = Object.keys(manifestsById).sort();
+
+    for (const id of sortedIds) {
+      const m = manifestsById[id];
+      const dir = path.join(this.rootDir, path.dirname(m.source));
+      const entrypointFile = path.join(dir, m.entrypoint);
+
+      // Entrypoint hash
+      const entrypointHash = this.hashFile(entrypointFile) || 'sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855';
+
+      // Estimated tokens: entrypoint character length / 3.8
+      let estimatedTokens = 1000;
+      if (fs.existsSync(entrypointFile)) {
+        const chars = fs.readFileSync(entrypointFile, 'utf8').length;
+        estimatedTokens = Math.max(100, Math.ceil(chars / 3.8));
+      }
+
+      // Resource tree hash
+      const resHashes = [];
+      for (const res of m.resources) {
+        const rFile = path.join(dir, res.path);
+        const rHash = this.hashFile(rFile);
+        if (rHash) resHashes.push(`${res.path}:${rHash}`);
+      }
+      resHashes.sort();
+      const resourceTreeHash = this.hashString(resHashes.join('\n'));
+
+      compiledSkills[id] = {
+        id: m.id,
+        displayName: m.displayName,
+        version: m.version,
+        description: m.description,
+        category: m.category,
+        type: m.type,
+        entrypoint: m.entrypoint,
+        entrypointHash,
+        resourceTreeHash,
+        estimatedTokens,
+        source: m.source,
+        signals: {
+          aliases: m.signals.aliases.sort(),
+          keywords: m.signals.keywords,
+          fileGlobs: m.signals.fileGlobs,
+          packages: m.signals.packages,
+        },
+        dependencies: {
+          requires: m.dependencies.requires.sort(),
+          optional: m.dependencies.optional.sort(),
+          conflicts: m.dependencies.conflicts.sort(),
+        },
+        context: {
+          priority: m.context.priority,
+          estimatedTokens,
+        },
+        resources: m.resources,
+        deprecated: m.deprecated || false,
+        canonical: m.canonical || null,
+        rules: m.rules || [],
+      };
+
+      // Register deprecated alias mapping
+      if (m.deprecated && m.canonical) {
+        deprecatedAliases[id] = m.canonical;
+      }
+
+      // Register rules
+      if (Array.isArray(m.rules)) {
+        for (const r of m.rules) {
+          rules[r.id] = {
+            ...r,
+            sourceSkill: id,
+          };
+        }
+      }
+
+      // Register aliases
+      for (const alias of m.signals.aliases) {
+        if (!aliases[alias]) {
+          aliases[alias] = id;
+        }
+      }
+
+      // Register packageMap
+      for (const pkg of m.signals.packages) {
+        packageMap[`${pkg.ecosystem}:${pkg.name}`] = id;
+      }
+
+      // Register dependencyGraph
+      dependencyGraph[id] = m.dependencies.requires.sort();
+    }
+
+    // Overall sourceGraphHash
+    const sourceGraphHash = this.hashString(JSON.stringify({
+      skills: compiledSkills,
+      dependencyGraph,
+    }));
+
+    const registry = {
+      schemaVersion: 2,
+      compilerVersion: '2.0.0',
+      sourceGraphHash,
+      skills: compiledSkills,
+      aliases: sortObjectKeys(aliases),
+      deprecatedAliases: sortObjectKeys(deprecatedAliases),
+      packageMap: sortObjectKeys(packageMap),
+      dependencyGraph: sortObjectKeys(dependencyGraph),
+      rules: sortObjectKeys(rules),
+    };
+
+    return {
+      success: true,
+      diagnostics: this.diagnostics,
+      registry,
+    };
+  }
+
+  /**
+   * Compiles and writes .agents/compiled/registry.v2.json and .agents/compiled/registry.v2.sha256.
+   */
+  compileAndWrite() {
+    const result = this.compile();
+    if (!result.success) {
+      return result;
+    }
+
+    if (!fs.existsSync(this.compiledDir)) {
+      fs.mkdirSync(this.compiledDir, { recursive: true });
+    }
+
+    const registryJsonPath = path.join(this.compiledDir, 'registry.v2.json');
+    const shaPath = path.join(this.compiledDir, 'registry.v2.sha256');
+
+    const jsonString = JSON.stringify(result.registry, null, 2) + '\n';
+    fs.writeFileSync(registryJsonPath, jsonString, 'utf8');
+
+    const shaContent = result.registry.sourceGraphHash + '  registry.v2.json\n';
+    fs.writeFileSync(shaPath, shaContent, 'utf8');
+
+    return {
+      ...result,
+      registryJsonPath,
+      shaPath,
+    };
+  }
+
+  /**
+   * Formats diagnostics as SARIF 2.1.0 output.
+   */
+  formatSarif() {
+    const rules = [];
+    const results = [];
+
+    const ruleIds = new Set(this.diagnostics.map(d => d.code));
+    for (const code of ruleIds) {
+      rules.push({
+        id: code,
+        name: code,
+        shortDescription: { text: `ContextOS Manifest Rule ${code}` },
+      });
+    }
+
+    for (const d of this.diagnostics) {
+      results.push({
+        ruleId: d.code,
+        level: d.severity === 'error' ? 'error' : 'warning',
+        message: { text: d.message },
+        locations: [
+          {
+            physicalLocation: {
+              artifactLocation: { uri: d.file.replace(/\\/g, '/') },
+              ...(d.line ? { region: { startLine: d.line, ...(d.column ? { startColumn: d.column } : {}) } } : {})
+            },
+          },
+        ],
+      });
+    }
+
+    return {
+      $schema: 'https://raw.githubusercontent.com/oasis-tcs/sarif-spec/master/Schemata/sarif-schema-2.1.0.json',
+      version: '2.1.0',
+      runs: [
+        {
+          tool: {
+            driver: {
+              name: 'contextos-manifest-compiler',
+              version: '2.0.0',
+              rules,
+            },
+          },
+          results,
+        },
+      ],
+    };
+  }
+}
+
+function sortObjectKeys(obj) {
+  const sorted = {};
+  for (const k of Object.keys(obj).sort()) {
+    sorted[k] = obj[k];
+  }
+  return sorted;
+}
+
+module.exports = {
+  ManifestCompiler,
+  DiagnosticError,
+  CODES,
+  parseYaml,
+};