kirograph 0.28.1 → 1.0.0

package/dist/frameworks/index.js

@@ -188,6 +188,7 @@ function registerFrameworkResolver(resolver) {
 function buildResolutionContext(projectRoot, db) {
   const fileCache = /* @__PURE__ */ new Map();
   const nodeCache = /* @__PURE__ */ new Map();
+  const allIndexedFiles = db.getAllFiles().map((f) => f.path);
   return {
     getNodesInFile(filePath) {
       if (!nodeCache.has(filePath)) {
@@ -202,24 +203,84 @@ function buildResolutionContext(projectRoot, db) {
       return db.getNodesByKind(kind);
     },
     fileExists(filePath) {
-      return fs.existsSync(path.join(projectRoot, filePath));
+      if (fs.existsSync(path.join(projectRoot, filePath))) return true;
+      const basename = path.basename(filePath);
+      if (allIndexedFiles.some((f) => f.endsWith("/" + basename) || f === basename)) return true;
+      try {
+        const entries = fs.readdirSync(projectRoot, { withFileTypes: true });
+        for (const entry of entries) {
+          if (!entry.isDirectory()) continue;
+          if (entry.name === "node_modules" || entry.name === ".git") continue;
+          const candidate = path.join(projectRoot, entry.name, filePath);
+          if (fs.existsSync(candidate)) return true;
+          try {
+            const subEntries = fs.readdirSync(path.join(projectRoot, entry.name), { withFileTypes: true });
+            for (const sub of subEntries) {
+              if (!sub.isDirectory() || sub.name === "node_modules" || sub.name === ".git") continue;
+              if (fs.existsSync(path.join(projectRoot, entry.name, sub.name, filePath))) return true;
+            }
+          } catch {
+          }
+        }
+      } catch {
+      }
+      return false;
     },
     readFile(filePath) {
       if (fileCache.has(filePath)) return fileCache.get(filePath);
+      const rootPath = path.join(projectRoot, filePath);
+      if (fs.existsSync(rootPath)) {
+        try {
+          const content = fs.readFileSync(rootPath, "utf8");
+          fileCache.set(filePath, content);
+          return content;
+        } catch {
+        }
+      }
+      const basename = path.basename(filePath);
+      const match = allIndexedFiles.find((f) => f.endsWith("/" + basename) || f === basename);
+      if (match) {
+        try {
+          const content = fs.readFileSync(path.join(projectRoot, match), "utf8");
+          fileCache.set(filePath, content);
+          return content;
+        } catch {
+        }
+      }
       try {
-        const content = fs.readFileSync(path.join(projectRoot, filePath), "utf8");
-        fileCache.set(filePath, content);
-        return content;
+        const entries = fs.readdirSync(projectRoot, { withFileTypes: true });
+        for (const entry of entries) {
+          if (!entry.isDirectory() || entry.name === "node_modules" || entry.name === ".git") continue;
+          const candidate = path.join(projectRoot, entry.name, filePath);
+          if (fs.existsSync(candidate)) {
+            const content = fs.readFileSync(candidate, "utf8");
+            fileCache.set(filePath, content);
+            return content;
+          }
+          try {
+            const subEntries = fs.readdirSync(path.join(projectRoot, entry.name), { withFileTypes: true });
+            for (const sub of subEntries) {
+              if (!sub.isDirectory() || sub.name === "node_modules" || sub.name === ".git") continue;
+              const deepCandidate = path.join(projectRoot, entry.name, sub.name, filePath);
+              if (fs.existsSync(deepCandidate)) {
+                const content = fs.readFileSync(deepCandidate, "utf8");
+                fileCache.set(filePath, content);
+                return content;
+              }
+            }
+          } catch {
+          }
+        }
       } catch {
-        fileCache.set(filePath, null);
-        return null;
       }
+      fileCache.set(filePath, null);
+      return null;
     },
     getProjectRoot() {
       return projectRoot;
     },
     getAllFiles() {
-      return db.getAllFiles().map((f) => f.path);
+      return allIndexedFiles;
     }
   };
 }

package/dist/frameworks/index.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/frameworks/index.ts"],
-  "sourcesContent": ["/**\n * Framework Resolver Registry\n *\n * Mirrors CodeGraph src/resolution/frameworks/index.ts\n * Manages framework-specific resolvers and detection.\n */\n\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport { logDebug, logWarn } from '../errors';\nimport { updateConfig } from '../config';\nimport type { Node } from '../types';\nimport type { GraphDatabase } from '../db/database';\nimport type { FrameworkResolver, ResolutionContext } from './types';\n\n// Re-export types\nexport type { FrameworkResolver, ResolutionContext, UnresolvedRef, ResolvedRef } from './types';\n\n// Re-export individual resolvers\nexport { reactResolver } from './react';\nexport { svelteResolver } from './svelte';\nexport { expressResolver } from './express';\nexport { djangoResolver, flaskResolver, fastapiResolver } from './python';\nexport { railsResolver } from './ruby';\nexport { springResolver } from './java';\nexport { goResolver } from './go';\nexport { rustResolver } from './rust';\nexport { aspnetResolver } from './csharp';\nexport { swiftUIResolver, uikitResolver, vaporResolver } from './swift';\nexport { laravelResolver, FACADE_MAPPINGS } from './laravel';\nexport { phoenixResolver } from './elixir';\nexport { playResolver } from './scala';\nexport { nuxtResolver, vueResolver } from './vue';\nexport { solidityResolver } from './solidity';\nexport { sstResolver, cdkResolver, serverlessResolver, samResolver } from './iac';\nexport { terraformResolver } from './terraform';\nexport { pulumiResolver } from './pulumi';\nexport { cloudformationResolver } from './cloudformation';\nexport { kubernetesResolver } from './kubernetes';\nexport { dockerComposeResolver } from './docker';\nexport { ansibleResolver } from './ansible';\nexport { angularResolver } from './angular';\nexport { amplifyResolver } from './amplify';\nexport { flutterResolver } from './flutter';\n\n// \u2500\u2500 Registry \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nimport { reactResolver } from './react';\nimport { svelteResolver } from './svelte';\nimport { expressResolver } from './express';\nimport { djangoResolver, flaskResolver, fastapiResolver } from './python';\nimport { railsResolver } from './ruby';\nimport { springResolver } from './java';\nimport { goResolver } from './go';\nimport { rustResolver } from './rust';\nimport { aspnetResolver } from './csharp';\nimport { swiftUIResolver, uikitResolver, vaporResolver } from './swift';\nimport { laravelResolver } from './laravel';\nimport { phoenixResolver } from './elixir';\nimport { playResolver } from './scala';\nimport { nuxtResolver, vueResolver } from './vue';\nimport { solidityResolver } from './solidity';\nimport { sstResolver, cdkResolver, serverlessResolver, samResolver } from './iac';\nimport { terraformResolver } from './terraform';\nimport { pulumiResolver } from './pulumi';\nimport { cloudformationResolver } from './cloudformation';\nimport { kubernetesResolver } from './kubernetes';\nimport { dockerComposeResolver } from './docker';\nimport { ansibleResolver } from './ansible';\nimport { angularResolver } from './angular';\nimport { amplifyResolver } from './amplify';\nimport { flutterResolver } from './flutter';\n\nconst FRAMEWORK_RESOLVERS: FrameworkResolver[] = [\n  // PHP\n  laravelResolver,\n  // JavaScript / TypeScript\n  expressResolver,\n  reactResolver,\n  svelteResolver,\n  angularResolver,\n  // Vue / Nuxt\n  nuxtResolver,\n  vueResolver,\n  // Python\n  djangoResolver,\n  flaskResolver,\n  fastapiResolver,\n  // Ruby\n  railsResolver,\n  // Java\n  springResolver,\n  // Go\n  goResolver,\n  // Rust\n  rustResolver,\n  // C#\n  aspnetResolver,\n  // Swift\n  swiftUIResolver,\n  uikitResolver,\n  vaporResolver,\n  // Elixir\n  phoenixResolver,\n  // Scala\n  playResolver,\n  // Solidity\n  solidityResolver,\n  // Infrastructure as Code\n  sstResolver,\n  cdkResolver,\n  serverlessResolver,\n  samResolver,\n  terraformResolver,\n  pulumiResolver,\n  cloudformationResolver,\n  amplifyResolver,\n  // Containers & Orchestration\n  kubernetesResolver,\n  dockerComposeResolver,\n  // Configuration Management\n  ansibleResolver,\n  // Dart / Flutter\n  flutterResolver,\n];\n\nexport function getAllFrameworkResolvers(): FrameworkResolver[] {\n  return FRAMEWORK_RESOLVERS;\n}\n\nexport function getFrameworkResolver(name: string): FrameworkResolver | undefined {\n  return FRAMEWORK_RESOLVERS.find(r => r.name === name);\n}\n\nexport function registerFrameworkResolver(resolver: FrameworkResolver): void {\n  const index = FRAMEWORK_RESOLVERS.findIndex(r => r.name === resolver.name);\n  if (index !== -1) FRAMEWORK_RESOLVERS.splice(index, 1);\n  FRAMEWORK_RESOLVERS.push(resolver);\n}\n\n// \u2500\u2500 Context builder \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nfunction buildResolutionContext(projectRoot: string, db: GraphDatabase): ResolutionContext {\n  const fileCache = new Map<string, string | null>();\n  const nodeCache = new Map<string, Node[]>();\n\n  return {\n    getNodesInFile(filePath: string): Node[] {\n      if (!nodeCache.has(filePath)) {\n        nodeCache.set(filePath, db.getNodesByFile(filePath));\n      }\n      return nodeCache.get(filePath)!;\n    },\n    getNodesByName(name: string): Node[] {\n      return db.findNodesByExactName(name);\n    },\n    getNodesByKind(kind: Node['kind']): Node[] {\n      return db.getNodesByKind(kind);\n    },\n    fileExists(filePath: string): boolean {\n      return fs.existsSync(path.join(projectRoot, filePath));\n    },\n    readFile(filePath: string): string | null {\n      if (fileCache.has(filePath)) return fileCache.get(filePath)!;\n      try {\n        const content = fs.readFileSync(path.join(projectRoot, filePath), 'utf8');\n        fileCache.set(filePath, content);\n        return content;\n      } catch {\n        fileCache.set(filePath, null);\n        return null;\n      }\n    },\n    getProjectRoot(): string {\n      return projectRoot;\n    },\n    getAllFiles(): string[] {\n      return db.getAllFiles().map(f => f.path);\n    },\n  };\n}\n\n// \u2500\u2500 detectFrameworks \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Detect which frameworks are used in a project.\n * Mirrors CodeGraph detectFrameworks() \u2014 uses ResolutionContext for file access.\n * Records detected framework names in config via updateConfig().\n */\nexport async function detectFrameworks(projectRoot: string, db?: GraphDatabase): Promise<FrameworkResolver[]> {\n  // If no db provided, fall back to package.json-only detection\n  if (!db) {\n    return detectFromPackageJson(projectRoot);\n  }\n\n  const context = buildResolutionContext(projectRoot, db);\n  const detected: FrameworkResolver[] = [];\n\n  for (const resolver of FRAMEWORK_RESOLVERS) {\n    try {\n      if (resolver.detect(context)) {\n        logDebug(`detectFrameworks: detected ${resolver.name}`);\n        detected.push(resolver);\n      }\n    } catch (err) {\n      logWarn(`detectFrameworks: error detecting ${resolver.name}`, { error: String(err) });\n    }\n  }\n\n  if (detected.length > 0) {\n    await updateConfig(projectRoot, { frameworkHints: detected.map(f => f.name) });\n  }\n\n  return detected;\n}\n\n/**\n * Lightweight fallback: detect frameworks from package.json only (no DB needed).\n */\nasync function detectFromPackageJson(projectRoot: string): Promise<FrameworkResolver[]> {\n  const pkgPath = path.join(projectRoot, 'package.json');\n  if (!fs.existsSync(pkgPath)) return [];\n\n  let pkg: Record<string, unknown>;\n  try {\n    pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf8')) as Record<string, unknown>;\n  } catch {\n    return [];\n  }\n\n  const deps: Record<string, string> = {\n    ...((pkg.dependencies as Record<string, string>) ?? {}),\n    ...((pkg.devDependencies as Record<string, string>) ?? {}),\n  };\n\n  const PACKAGE_TO_RESOLVER: Record<string, string> = {\n    react: 'react', next: 'react', 'react-native': 'react',\n    svelte: 'svelte', '@sveltejs/kit': 'svelte',\n    express: 'express', fastify: 'express', koa: 'express',\n  };\n\n  const detectedNames = new Set<string>();\n  const detected: FrameworkResolver[] = [];\n\n  for (const [pkg, resolverName] of Object.entries(PACKAGE_TO_RESOLVER)) {\n    if (Object.prototype.hasOwnProperty.call(deps, pkg) && !detectedNames.has(resolverName)) {\n      const resolver = getFrameworkResolver(resolverName);\n      if (resolver) {\n        detectedNames.add(resolverName);\n        detected.push(resolver);\n      }\n    }\n  }\n\n  if (detected.length > 0) {\n    await updateConfig(projectRoot, { frameworkHints: detected.map(f => f.name) });\n  }\n\n  return detected;\n}\n"],
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+  "sourcesContent": ["/**\n * Framework Resolver Registry\n *\n * Mirrors CodeGraph src/resolution/frameworks/index.ts\n * Manages framework-specific resolvers and detection.\n */\n\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport { logDebug, logWarn } from '../errors';\nimport { updateConfig } from '../config';\nimport type { Node } from '../types';\nimport type { GraphDatabase } from '../db/database';\nimport type { FrameworkResolver, ResolutionContext } from './types';\n\n// Re-export types\nexport type { FrameworkResolver, ResolutionContext, UnresolvedRef, ResolvedRef } from './types';\n\n// Re-export individual resolvers\nexport { reactResolver } from './react';\nexport { svelteResolver } from './svelte';\nexport { expressResolver } from './express';\nexport { djangoResolver, flaskResolver, fastapiResolver } from './python';\nexport { railsResolver } from './ruby';\nexport { springResolver } from './java';\nexport { goResolver } from './go';\nexport { rustResolver } from './rust';\nexport { aspnetResolver } from './csharp';\nexport { swiftUIResolver, uikitResolver, vaporResolver } from './swift';\nexport { laravelResolver, FACADE_MAPPINGS } from './laravel';\nexport { phoenixResolver } from './elixir';\nexport { playResolver } from './scala';\nexport { nuxtResolver, vueResolver } from './vue';\nexport { solidityResolver } from './solidity';\nexport { sstResolver, cdkResolver, serverlessResolver, samResolver } from './iac';\nexport { terraformResolver } from './terraform';\nexport { pulumiResolver } from './pulumi';\nexport { cloudformationResolver } from './cloudformation';\nexport { kubernetesResolver } from './kubernetes';\nexport { dockerComposeResolver } from './docker';\nexport { ansibleResolver } from './ansible';\nexport { angularResolver } from './angular';\nexport { amplifyResolver } from './amplify';\nexport { flutterResolver } from './flutter';\n\n// \u2500\u2500 Registry \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nimport { reactResolver } from './react';\nimport { svelteResolver } from './svelte';\nimport { expressResolver } from './express';\nimport { djangoResolver, flaskResolver, fastapiResolver } from './python';\nimport { railsResolver } from './ruby';\nimport { springResolver } from './java';\nimport { goResolver } from './go';\nimport { rustResolver } from './rust';\nimport { aspnetResolver } from './csharp';\nimport { swiftUIResolver, uikitResolver, vaporResolver } from './swift';\nimport { laravelResolver } from './laravel';\nimport { phoenixResolver } from './elixir';\nimport { playResolver } from './scala';\nimport { nuxtResolver, vueResolver } from './vue';\nimport { solidityResolver } from './solidity';\nimport { sstResolver, cdkResolver, serverlessResolver, samResolver } from './iac';\nimport { terraformResolver } from './terraform';\nimport { pulumiResolver } from './pulumi';\nimport { cloudformationResolver } from './cloudformation';\nimport { kubernetesResolver } from './kubernetes';\nimport { dockerComposeResolver } from './docker';\nimport { ansibleResolver } from './ansible';\nimport { angularResolver } from './angular';\nimport { amplifyResolver } from './amplify';\nimport { flutterResolver } from './flutter';\n\nconst FRAMEWORK_RESOLVERS: FrameworkResolver[] = [\n  // PHP\n  laravelResolver,\n  // JavaScript / TypeScript\n  expressResolver,\n  reactResolver,\n  svelteResolver,\n  angularResolver,\n  // Vue / Nuxt\n  nuxtResolver,\n  vueResolver,\n  // Python\n  djangoResolver,\n  flaskResolver,\n  fastapiResolver,\n  // Ruby\n  railsResolver,\n  // Java\n  springResolver,\n  // Go\n  goResolver,\n  // Rust\n  rustResolver,\n  // C#\n  aspnetResolver,\n  // Swift\n  swiftUIResolver,\n  uikitResolver,\n  vaporResolver,\n  // Elixir\n  phoenixResolver,\n  // Scala\n  playResolver,\n  // Solidity\n  solidityResolver,\n  // Infrastructure as Code\n  sstResolver,\n  cdkResolver,\n  serverlessResolver,\n  samResolver,\n  terraformResolver,\n  pulumiResolver,\n  cloudformationResolver,\n  amplifyResolver,\n  // Containers & Orchestration\n  kubernetesResolver,\n  dockerComposeResolver,\n  // Configuration Management\n  ansibleResolver,\n  // Dart / Flutter\n  flutterResolver,\n];\n\nexport function getAllFrameworkResolvers(): FrameworkResolver[] {\n  return FRAMEWORK_RESOLVERS;\n}\n\nexport function getFrameworkResolver(name: string): FrameworkResolver | undefined {\n  return FRAMEWORK_RESOLVERS.find(r => r.name === name);\n}\n\nexport function registerFrameworkResolver(resolver: FrameworkResolver): void {\n  const index = FRAMEWORK_RESOLVERS.findIndex(r => r.name === resolver.name);\n  if (index !== -1) FRAMEWORK_RESOLVERS.splice(index, 1);\n  FRAMEWORK_RESOLVERS.push(resolver);\n}\n\n// \u2500\u2500 Context builder \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nfunction buildResolutionContext(projectRoot: string, db: GraphDatabase): ResolutionContext {\n  const fileCache = new Map<string, string | null>();\n  const nodeCache = new Map<string, Node[]>();\n  const allIndexedFiles = db.getAllFiles().map(f => f.path);\n\n  return {\n    getNodesInFile(filePath: string): Node[] {\n      if (!nodeCache.has(filePath)) {\n        nodeCache.set(filePath, db.getNodesByFile(filePath));\n      }\n      return nodeCache.get(filePath)!;\n    },\n    getNodesByName(name: string): Node[] {\n      return db.findNodesByExactName(name);\n    },\n    getNodesByKind(kind: Node['kind']): Node[] {\n      return db.getNodesByKind(kind);\n    },\n    fileExists(filePath: string): boolean {\n      // Check root first\n      if (fs.existsSync(path.join(projectRoot, filePath))) return true;\n      // Multi-root workspace: check if any indexed file matches the filename\n      const basename = path.basename(filePath);\n      if (allIndexedFiles.some(f => f.endsWith('/' + basename) || f === basename)) return true;\n      // Note: basename matching is intentionally broad \u2014 config files like angular.json,\n      // docker-compose.yaml are highly specific names unlikely to cause false positives.\n      // Fallback: scan top-level subdirectories for non-indexed config files (e.g., angular.json)\n      try {\n        const entries = fs.readdirSync(projectRoot, { withFileTypes: true });\n        for (const entry of entries) {\n          if (!entry.isDirectory()) continue;\n          if (entry.name === 'node_modules' || entry.name === '.git') continue;\n          const candidate = path.join(projectRoot, entry.name, filePath);\n          if (fs.existsSync(candidate)) return true;\n          // Check one level deeper (module/app/file pattern)\n          try {\n            const subEntries = fs.readdirSync(path.join(projectRoot, entry.name), { withFileTypes: true });\n            for (const sub of subEntries) {\n              if (!sub.isDirectory() || sub.name === 'node_modules' || sub.name === '.git') continue;\n              if (fs.existsSync(path.join(projectRoot, entry.name, sub.name, filePath))) return true;\n            }\n          } catch { /* skip unreadable */ }\n        }\n      } catch { /* fall through */ }\n      return false;\n    },\n    readFile(filePath: string): string | null {\n      if (fileCache.has(filePath)) return fileCache.get(filePath)!;\n      // Try root first\n  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    }\n          } catch { /* skip */ }\n        }\n      } catch { /* fall through */ }\n      fileCache.set(filePath, null);\n      return null;\n    },\n    getProjectRoot(): string {\n      return projectRoot;\n    },\n    getAllFiles(): string[] {\n      return allIndexedFiles;\n    },\n  };\n}\n\n// \u2500\u2500 detectFrameworks \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Detect which frameworks are used in a project.\n * Mirrors CodeGraph detectFrameworks() \u2014 uses ResolutionContext for file access.\n * Records detected framework names in config via updateConfig().\n */\nexport async function detectFrameworks(projectRoot: string, db?: GraphDatabase): 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detectedNames.add(resolverName);\n        detected.push(resolver);\n      }\n    }\n  }\n\n  if (detected.length > 0) {\n    await updateConfig(projectRoot, { frameworkHints: detected.map(f => f.name) });\n  }\n\n  return detected;\n}\n"],
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   "names": ["import_react", "import_svelte", "import_express", "import_python", "import_ruby", "import_java", "import_go", "import_rust", "import_csharp", "import_swift", "import_laravel", "import_elixir", "import_scala", "import_vue", "import_solidity", "import_iac", "import_terraform", "import_pulumi", "import_cloudformation", "import_kubernetes", "import_docker", "import_ansible", "import_angular", "import_amplify", "import_flutter", "pkg"]
 }

package/dist/security/manifest/adapter.js

@@ -54,11 +54,12 @@ const SKIP_DIRS = /* @__PURE__ */ new Set([
   "zig-out"
 ]);
 class SecurityManifestAdapter {
-  constructor(projectRoot) {
+  constructor(projectRoot, scanOptions) {
     this.plugins = /* @__PURE__ */ new Map();
     /** Standalone plugins have no corresponding architecture parser — they own their own discovery. */
     this.standalonePlugins = /* @__PURE__ */ new Map();
     this.projectRoot = projectRoot;
+    this.scanOptions = scanOptions ?? {};
     this.archParsers = (0, import_manifest.getAllManifestParsers)();
   }
   /**
@@ -93,10 +94,24 @@ class SecurityManifestAdapter {
   /**
    * Discover all manifest files in the project tree.
    * Includes files known to architecture parsers AND files from standalone plugins.
+   * Respects config include/exclude patterns when provided.
    * Returns absolute paths.
    */
   discoverManifests() {
-    return this._findManifests(this.projectRoot);
+    const allManifests = this._findManifests(this.projectRoot);
+    if (!this.scanOptions.include || this.scanOptions.include.length === 0) {
+      return allManifests;
+    }
+    const picomatch = require("picomatch");
+    const includeMatchers = this.scanOptions.include.map((p) => picomatch(p));
+    const excludeMatchers = (this.scanOptions.exclude ?? []).map((p) => picomatch(p));
+    return allManifests.filter((absPath) => {
+      const rel = path.relative(this.projectRoot, absPath).replace(/\\/g, "/");
+      const included = includeMatchers.some((m) => m(rel));
+      if (!included) return false;
+      const excluded = excludeMatchers.some((m) => m(rel));
+      return !excluded;
+    });
   }
   /**
    * Run full discovery and extraction:

package/dist/security/manifest/adapter.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../src/security/manifest/adapter.ts"],
-  "sourcesContent": ["/**\n * SecurityManifestAdapter\n *\n * Wraps the existing architecture manifest parsers (11 parsers: npm, cargo, go,\n * gradle, maven, csproj, python, scala, elm, ocaml) to additionally extract\n * version constraints and dependency scopes that the architecture module does\n * not capture.\n *\n * The architecture parsers discover manifest files and extract package names into\n * `ArchPackage.externalDeps`. This adapter reuses that discovery infrastructure\n * and layers version/scope extraction on top via ecosystem-specific plugins.\n */\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport { getAllManifestParsers } from '../../architecture/manifest/index';\nimport type { ManifestParser as ArchManifestParser, ArchPackage } from '../../architecture/types';\nimport type { ParsedDependency, ManifestParseResult } from '../types';\n\n// \u2500\u2500 Plugin Interface \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * A version extraction plugin provides ecosystem-specific logic to extract\n * version constraints and scopes from manifest files. Each plugin corresponds\n * to one or more architecture parsers and enhances their output with security-\n * relevant metadata.\n */\nexport interface VersionExtractionPlugin {\n  /** Ecosystem identifier matching the architecture parser name (e.g. 'npm', 'maven', 'go') */\n  ecosystem: string;\n  /** Manifest filenames this plugin handles (should match the architecture parser's manifestFiles) */\n  manifestFiles: string[];\n  /** Returns true if this plugin can handle the given manifest file path */\n  canExtract(manifestPath: string): boolean;\n  /**\n   * Extract version constraints and scopes from a manifest file.\n   * This is called AFTER the architecture parser has already discovered the manifest.\n   * The plugin receives the manifest path and project root, and returns detailed\n   * dependency information including versions and scopes.\n   */\n  extract(manifestPath: string, projectRoot: string): Promise<ParsedDependency[]>;\n}\n\n// \u2500\u2500 Directories to skip (mirrors architecture module's SKIP_DIRS) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nconst SKIP_DIRS = new Set([\n  'node_modules', '.git', 'dist', 'build', 'target', '.gradle', '__pycache__',\n  '.kirograph', 'vendor', '.cache', 'coverage', '.nyc_output', '_build', '_opam',\n  'elm-stuff', 'zig-cache', 'zig-out',\n]);\n\n// \u2500\u2500 SecurityManifestAdapter \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport class SecurityManifestAdapter {\n  private readonly archParsers: ArchManifestParser[];\n  private readonly plugins: Map<string, VersionExtractionPlugin> = new Map();\n  /** Standalone plugins have no corresponding architecture parser \u2014 they own their own discovery. */\n  private readonly standalonePlugins: Map<string, VersionExtractionPlugin> = new Map();\n  private readonly projectRoot: string;\n\n  constructor(projectRoot: string) {\n    this.projectRoot = projectRoot;\n    this.archParsers = getAllManifestParsers();\n  }\n\n  /**\n   * Register a version extraction plugin for an ecosystem that has a\n   * corresponding architecture parser. The plugin's `ecosystem` field\n   * must equal the architecture parser's `name` for the lookup to work.\n   */\n  registerPlugin(plugin: VersionExtractionPlugin): void {\n    this.plugins.set(plugin.ecosystem, plugin);\n  }\n\n  /**\n   * Register a standalone version extraction plugin for an ecosystem that\n   * has NO corresponding architecture parser. The plugin's `manifestFiles`\n   * list drives discovery \u2014 the adapter will scan for those filenames and\n   * invoke the plugin directly when found.\n   */\n  registerStandalonePlugin(plugin: VersionExtractionPlugin): void {\n    this.standalonePlugins.set(plugin.ecosystem, plugin);\n  }\n\n  /**\n   * Get all registered version extraction plugins (wrapped + standalone).\n   */\n  getPlugins(): VersionExtractionPlugin[] {\n    return [...this.plugins.values(), ...this.standalonePlugins.values()];\n  }\n\n  /**\n   * Get the architecture parsers being wrapped.\n   */\n  getArchParsers(): ArchManifestParser[] {\n    return this.archParsers;\n  }\n\n  /**\n   * Discover all manifest files in the project tree.\n   * Includes files known to architecture parsers AND files from standalone plugins.\n   * Returns absolute paths.\n   */\n  discoverManifests(): string[] {\n    return this._findManifests(this.projectRoot);\n  }\n\n  /**\n   * Run full discovery and extraction:\n   * 1. Discover manifest files (reusing architecture's SKIP_DIRS logic)\n   * 2. For each manifest, find the matching architecture parser\n   * 3. If a version extraction plugin is registered for that ecosystem,\n   *    use it to extract detailed version/scope information\n   * 4. Otherwise, fall back to basic extraction from the architecture parser's\n   *    ArchPackage.externalDeps (names only, no version info)\n   */\n  async extractAll(): Promise<ManifestParseResult> {\n    const manifestPaths = this.discoverManifests();\n    const allDeps: ParsedDependency[] = [];\n    const warnings: Array<{ file: string; line?: number; message: string }> = [];\n    const errors: Array<{ file: string; message: string }> = [];\n    let manifestsParsed = 0;\n\n    for (const manifestPath of manifestPaths) {\n      const archParser = this.archParsers.find(p => p.canParse(manifestPath));\n      if (!archParser) continue;\n\n      const relManifest = path.relative(this.projectRoot, manifestPath).replace(/\\\\/g, '/');\n      const plugin = this.plugins.get(archParser.name);\n\n      if (plugin && plugin.canExtract(manifestPath)) {\n        // Use the version extraction plugin for detailed parsing\n        try {\n          const deps = await plugin.extract(manifestPath, this.projectRoot);\n          allDeps.push(...deps);\n          manifestsParsed++;\n        } catch (err) {\n          const message = err instanceof Error ? err.message : String(err);\n          errors.push({ file: relManifest, message });\n        }\n      } else {\n        // Fallback: use architecture parser output (names only, no versions)\n        try {\n          const packages = await archParser.parse(manifestPath, this.projectRoot);\n          const deps = this._fallbackExtract(packages, archParser.name, relManifest);\n          allDeps.push(...deps);\n          manifestsParsed++;\n\n          if (!plugin) {\n            warnings.push({\n              file: relManifest,\n              message: `No version extraction plugin registered for ecosystem '${archParser.name}'; dependency names extracted without version constraints`,\n            });\n          }\n        } catch (err) {\n          const message = err instanceof Error ? err.message : String(err);\n          errors.push({ file: relManifest, message });\n        }\n      }\n    }\n\n    return {\n      dependenciesCreated: allDeps.length,\n      manifestsParsed,\n      warnings,\n      errors,\n    };\n  }\n\n  /**\n   * Extract dependencies for a single manifest file.\n   * Tries standalone plugins first (when there is no arch parser), then\n   * wrapped plugins, then falls back to arch parser output.\n   */\n  async extractFromManifest(manifestPath: string): Promise<ParsedDependency[]> {\n    const archParser = this.archParsers.find(p => p.canParse(manifestPath));\n\n    if (!archParser) {\n      // No arch parser \u2014 try standalone plugins\n      const standalonePlugin = [...this.standalonePlugins.values()]\n        .find(p => p.canExtract(manifestPath));\n      if (standalonePlugin) {\n        return standalonePlugin.extract(manifestPath, this.projectRoot);\n      }\n      return [];\n    }\n\n    const plugin = this.plugins.get(archParser.name);\n\n    if (plugin && plugin.canExtract(manifestPath)) {\n      return plugin.extract(manifestPath, this.projectRoot);\n    }\n\n    // Fallback: architecture parser output (names only)\n    const packages = await archParser.parse(manifestPath, this.projectRoot);\n    const relManifest = path.relative(this.projectRoot, manifestPath).replace(/\\\\/g, '/');\n    return this._fallbackExtract(packages, archParser.name, relManifest);\n  }\n\n  /**\n   * Get the ecosystem name for a given manifest file path.\n   * Returns undefined if no parser handles this file.\n   */\n  getEcosystem(manifestPath: string): string | undefined {\n    const parser = this.archParsers.find(p => p.canParse(manifestPath));\n    return parser?.name;\n  }\n\n  // \u2500\u2500 Private helpers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n  /**\n   * Fallback extraction: converts ArchPackage.externalDeps (names only) into\n   * ParsedDependency records with empty version constraints and default scope.\n   */\n  private _fallbackExtract(\n    packages: ArchPackage[],\n    ecosystem: string,\n    sourceManifest: string,\n  ): ParsedDependency[] {\n    const deps: ParsedDependency[] = [];\n    for (const pkg of packages) {\n      if (!pkg.externalDeps) continue;\n      for (const depName of pkg.externalDeps) {\n        deps.push({\n          name: depName,\n          declaredConstraint: '*',\n          scope: 'production',\n          ecosystem,\n          sourceManifest,\n        });\n      }\n    }\n    return deps;\n  }\n\n  /**\n   * Walk the project directory tree looking for manifest files.\n   * Mirrors the architecture module's _findManifests() logic, respecting SKIP_DIRS.\n   * Includes manifest filenames from standalone plugins in addition to arch parsers.\n   */\n  private _findManifests(dir: string, results: string[] = []): string[] {\n    const manifestFilenames = new Set([\n      ...this.archParsers.flatMap(p => p.manifestFiles),\n      ...Array.from(this.standalonePlugins.values()).flatMap(p => p.manifestFiles),\n    ]);\n\n    return this._walkDir(dir, manifestFilenames, results);\n  }\n\n  private _walkDir(dir: string, manifestFilenames: Set<string>, results: string[]): string[] {\n    let entries: fs.Dirent[];\n    try {\n      entries = fs.readdirSync(dir, { withFileTypes: true });\n    } catch {\n      return results;\n    }\n\n    for (const entry of entries) {\n      if (entry.isDirectory()) {\n        if (!SKIP_DIRS.has(entry.name)) {\n          this._walkDir(path.join(dir, entry.name), manifestFilenames, results);\n        }\n      } else if (entry.isFile()) {\n        if (manifestFilenames.has(entry.name) || entry.name.endsWith('.csproj')) {\n          results.push(path.join(dir, entry.name));\n        }\n      }\n    }\n\n    return results;\n  }\n}\n"],
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+  "sourcesContent": ["/**\n * SecurityManifestAdapter\n *\n * Wraps the existing architecture manifest parsers (11 parsers: npm, cargo, go,\n * gradle, maven, csproj, python, scala, elm, ocaml) to additionally extract\n * version constraints and dependency scopes that the architecture module does\n * not capture.\n *\n * The architecture parsers discover manifest files and extract package names into\n * `ArchPackage.externalDeps`. This adapter reuses that discovery infrastructure\n * and layers version/scope extraction on top via ecosystem-specific plugins.\n */\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport { getAllManifestParsers } from '../../architecture/manifest/index';\nimport type { ManifestParser as ArchManifestParser, ArchPackage } from '../../architecture/types';\nimport type { ParsedDependency, ManifestParseResult } from '../types';\n\n// \u2500\u2500 Include/Exclude filter support \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport interface ManifestScanOptions {\n  /** Glob patterns for paths to include (relative to projectRoot). Empty = all. */\n  include?: string[];\n  /** Glob patterns for paths to exclude (relative to projectRoot). */\n  exclude?: string[];\n}\n\n// \u2500\u2500 Plugin Interface \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * A version extraction plugin provides ecosystem-specific logic to extract\n * version constraints and scopes from manifest files. Each plugin corresponds\n * to one or more architecture parsers and enhances their output with security-\n * relevant metadata.\n */\nexport interface VersionExtractionPlugin {\n  /** Ecosystem identifier matching the architecture parser name (e.g. 'npm', 'maven', 'go') */\n  ecosystem: string;\n  /** Manifest filenames this plugin handles (should match the architecture parser's manifestFiles) */\n  manifestFiles: string[];\n  /** Returns true if this plugin can handle the given manifest file path */\n  canExtract(manifestPath: string): boolean;\n  /**\n   * Extract version constraints and scopes from a manifest file.\n   * This is called AFTER the architecture parser has already discovered the manifest.\n   * The plugin receives the manifest path and project root, and returns detailed\n   * dependency information including versions and scopes.\n   */\n  extract(manifestPath: string, projectRoot: string): Promise<ParsedDependency[]>;\n}\n\n// \u2500\u2500 Directories to skip (mirrors architecture module's SKIP_DIRS) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nconst SKIP_DIRS = new Set([\n  'node_modules', '.git', 'dist', 'build', 'target', '.gradle', '__pycache__',\n  '.kirograph', 'vendor', '.cache', 'coverage', '.nyc_output', '_build', '_opam',\n  'elm-stuff', 'zig-cache', 'zig-out',\n]);\n\n// \u2500\u2500 SecurityManifestAdapter \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nexport class SecurityManifestAdapter {\n  private readonly archParsers: ArchManifestParser[];\n  private readonly plugins: Map<string, VersionExtractionPlugin> = new Map();\n  /** Standalone plugins have no corresponding architecture parser \u2014 they own their own discovery. */\n  private readonly standalonePlugins: Map<string, VersionExtractionPlugin> = new Map();\n  private readonly projectRoot: string;\n  private readonly scanOptions: ManifestScanOptions;\n\n  constructor(projectRoot: string, scanOptions?: ManifestScanOptions) {\n    this.projectRoot = projectRoot;\n    this.scanOptions = scanOptions ?? {};\n    this.archParsers = getAllManifestParsers();\n  }\n\n  /**\n   * Register a version extraction plugin for an ecosystem that has a\n   * corresponding architecture parser. The plugin's `ecosystem` field\n   * must equal the architecture parser's `name` for the lookup to work.\n   */\n  registerPlugin(plugin: VersionExtractionPlugin): void {\n    this.plugins.set(plugin.ecosystem, plugin);\n  }\n\n  /**\n   * Register a standalone version extraction plugin for an ecosystem that\n   * has NO corresponding architecture parser. The plugin's `manifestFiles`\n   * list drives discovery \u2014 the adapter will scan for those filenames and\n   * invoke the plugin directly when found.\n   */\n  registerStandalonePlugin(plugin: VersionExtractionPlugin): void {\n    this.standalonePlugins.set(plugin.ecosystem, plugin);\n  }\n\n  /**\n   * Get all registered version extraction plugins (wrapped + standalone).\n   */\n  getPlugins(): VersionExtractionPlugin[] {\n    return [...this.plugins.values(), ...this.standalonePlugins.values()];\n  }\n\n  /**\n   * Get the architecture parsers being wrapped.\n   */\n  getArchParsers(): ArchManifestParser[] {\n    return this.archParsers;\n  }\n\n  /**\n   * Discover all manifest files in the project tree.\n   * Includes files known to architecture parsers AND files from standalone plugins.\n   * Respects config include/exclude patterns when provided.\n   * Returns absolute paths.\n   */\n  discoverManifests(): string[] {\n    const allManifests = this._findManifests(this.projectRoot);\n\n    // If no include patterns, return all discovered manifests\n    if (!this.scanOptions.include || this.scanOptions.include.length === 0) {\n      return allManifests;\n    }\n\n    // Filter manifests to only those within included paths\n    const picomatch = require('picomatch');\n    const includeMatchers = this.scanOptions.include.map((p: string) => picomatch(p));\n    const excludeMatchers = (this.scanOptions.exclude ?? []).map((p: string) => picomatch(p));\n\n    return allManifests.filter(absPath => {\n      const rel = path.relative(this.projectRoot, absPath).replace(/\\\\/g, '/');\n      const included = includeMatchers.some((m: (s: string) => boolean) => m(rel));\n      if (!included) return false;\n      const excluded = excludeMatchers.some((m: (s: string) => boolean) => m(rel));\n      return !excluded;\n    });\n  }\n\n  /**\n   * Run full discovery and extraction:\n   * 1. Discover manifest files (reusing architecture's SKIP_DIRS logic)\n   * 2. For each manifest, find the matching architecture parser\n   * 3. If a version extraction plugin is registered for that ecosystem,\n   *    use it to extract detailed version/scope information\n   * 4. Otherwise, fall back to basic extraction from the architecture parser's\n   *    ArchPackage.externalDeps (names only, no version info)\n   */\n  async extractAll(): Promise<ManifestParseResult> {\n    const manifestPaths = this.discoverManifests();\n    const allDeps: ParsedDependency[] = [];\n    const warnings: Array<{ file: string; line?: number; message: string }> = [];\n    const errors: Array<{ file: string; message: string }> = [];\n    let manifestsParsed = 0;\n\n    for (const manifestPath of manifestPaths) {\n      const archParser = this.archParsers.find(p => p.canParse(manifestPath));\n      if (!archParser) continue;\n\n      const relManifest = path.relative(this.projectRoot, manifestPath).replace(/\\\\/g, '/');\n      const plugin = this.plugins.get(archParser.name);\n\n      if (plugin && plugin.canExtract(manifestPath)) {\n        // Use the version extraction plugin for detailed parsing\n        try {\n          const deps = await plugin.extract(manifestPath, this.projectRoot);\n          allDeps.push(...deps);\n          manifestsParsed++;\n        } catch (err) {\n          const message = err instanceof Error ? err.message : String(err);\n          errors.push({ file: relManifest, message });\n        }\n      } else {\n        // Fallback: use architecture parser output (names only, no versions)\n        try {\n          const packages = await archParser.parse(manifestPath, this.projectRoot);\n          const deps = this._fallbackExtract(packages, archParser.name, relManifest);\n          allDeps.push(...deps);\n          manifestsParsed++;\n\n          if (!plugin) {\n            warnings.push({\n              file: relManifest,\n              message: `No version extraction plugin registered for ecosystem '${archParser.name}'; dependency names extracted without version constraints`,\n            });\n          }\n        } catch (err) {\n          const message = err instanceof Error ? err.message : String(err);\n          errors.push({ file: relManifest, message });\n        }\n      }\n    }\n\n    return {\n      dependenciesCreated: allDeps.length,\n      manifestsParsed,\n      warnings,\n      errors,\n    };\n  }\n\n  /**\n   * Extract dependencies for a single manifest file.\n   * Tries standalone plugins first (when there is no arch parser), then\n   * wrapped plugins, then falls back to arch parser output.\n   */\n  async extractFromManifest(manifestPath: string): Promise<ParsedDependency[]> {\n    const archParser = this.archParsers.find(p => p.canParse(manifestPath));\n\n    if (!archParser) {\n      // No arch parser \u2014 try standalone plugins\n      const standalonePlugin = [...this.standalonePlugins.values()]\n        .find(p => p.canExtract(manifestPath));\n      if (standalonePlugin) {\n        return standalonePlugin.extract(manifestPath, this.projectRoot);\n      }\n      return [];\n    }\n\n    const plugin = this.plugins.get(archParser.name);\n\n    if (plugin && plugin.canExtract(manifestPath)) {\n      return plugin.extract(manifestPath, this.projectRoot);\n    }\n\n    // Fallback: architecture parser output (names only)\n    const packages = await archParser.parse(manifestPath, this.projectRoot);\n    const relManifest = path.relative(this.projectRoot, manifestPath).replace(/\\\\/g, '/');\n    return this._fallbackExtract(packages, archParser.name, relManifest);\n  }\n\n  /**\n   * Get the ecosystem name for a given manifest file path.\n   * Returns undefined if no parser handles this file.\n   */\n  getEcosystem(manifestPath: string): string | undefined {\n    const parser = this.archParsers.find(p => p.canParse(manifestPath));\n    return parser?.name;\n  }\n\n  // \u2500\u2500 Private helpers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n  /**\n   * Fallback extraction: converts ArchPackage.externalDeps (names only) into\n   * ParsedDependency records with empty version constraints and default scope.\n   */\n  private _fallbackExtract(\n    packages: ArchPackage[],\n    ecosystem: string,\n    sourceManifest: string,\n  ): ParsedDependency[] {\n    const deps: ParsedDependency[] = [];\n    for (const pkg of packages) {\n      if (!pkg.externalDeps) continue;\n      for (const depName of pkg.externalDeps) {\n        deps.push({\n          name: depName,\n          declaredConstraint: '*',\n          scope: 'production',\n          ecosystem,\n          sourceManifest,\n        });\n      }\n    }\n    return deps;\n  }\n\n  /**\n   * Walk the project directory tree looking for manifest files.\n   * Mirrors the architecture module's _findManifests() logic, respecting SKIP_DIRS.\n   * Includes manifest filenames from standalone plugins in addition to arch parsers.\n   */\n  private _findManifests(dir: string, results: string[] = []): string[] {\n    const manifestFilenames = new Set([\n      ...this.archParsers.flatMap(p => p.manifestFiles),\n      ...Array.from(this.standalonePlugins.values()).flatMap(p => p.manifestFiles),\n    ]);\n\n    return this._walkDir(dir, manifestFilenames, results);\n  }\n\n  private _walkDir(dir: string, manifestFilenames: Set<string>, results: string[]): string[] {\n    let entries: fs.Dirent[];\n    try {\n      entries = fs.readdirSync(dir, { withFileTypes: true });\n    } catch {\n      return results;\n    }\n\n    for (const entry of entries) {\n      if (entry.isDirectory()) {\n        if (!SKIP_DIRS.has(entry.name)) {\n          this._walkDir(path.join(dir, entry.name), manifestFilenames, results);\n        }\n      } else if (entry.isFile()) {\n        if (manifestFilenames.has(entry.name) || entry.name.endsWith('.csproj')) {\n          results.push(path.join(dir, entry.name));\n        }\n      }\n    }\n\n    return results;\n  }\n}\n"],
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 }

package/dist/security/manifest/parser.js

@@ -237,10 +237,10 @@ function deduplicateDependencies(deps) {
   return [...map.values()];
 }
 class ManifestParser {
-  constructor(db, projectRoot) {
+  constructor(db, projectRoot, scanOptions) {
     this.db = db;
     this.projectRoot = projectRoot;
-    this.adapter = new import_adapter.SecurityManifestAdapter(projectRoot);
+    this.adapter = new import_adapter.SecurityManifestAdapter(projectRoot, scanOptions);
     this.adapter.registerPlugin(createNpmPlugin());
     this.adapter.registerPlugin(createMavenPlugin());
     this.adapter.registerPlugin(createGoPlugin());

package/dist/security/manifest/parser.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../src/security/manifest/parser.ts"],
-  "sourcesContent": ["/**\n * ManifestParser Orchestrator\n *\n * Orchestrates manifest discovery, version extraction, deduplication, and\n * database persistence. Uses the SecurityManifestAdapter for discovery and\n * extraction, registers all 12 version extraction plugins:\n *   Wrapped (arch parser exists): npm, maven, go, pip, cargo, nuget, gradle\n *   Standalone (no arch parser):  rubygems, composer, swift, pubspec, hex\n *\n * Node ID format: `dep:<ecosystem>:<name>` (e.g. `dep:npm:express`)\n */\nimport { SecurityManifestAdapter, type VersionExtractionPlugin } from './adapter';\nimport { parseNpmManifest } from './plugins/npm';\nimport { parseMavenManifest } from './plugins/maven';\nimport { parseGoManifest } from './plugins/go';\nimport { parsePipManifest } from './plugins/pip';\nimport { parseCargoManifest } from './plugins/cargo';\nimport { parseNugetManifest } from './plugins/nuget';\nimport { parseGradleManifest } from './plugins/gradle';\nimport { parseRubygemsManifest } from './plugins/rubygems';\nimport { parseComposerManifest } from './plugins/composer';\nimport { parseSwiftManifest } from './plugins/swift';\nimport { parsePubspecManifest } from './plugins/pubspec';\nimport { parseHexManifest } from './plugins/hex';\nimport { parsePyprojectManifest } from './plugins/pyproject';\nimport type { GraphDatabase } from '../../db/database';\nimport type { ParsedDependency, ManifestParseResult } from '../types';\nimport type { Node, Edge } from '../../types';\nimport { logWarn, logError } from '../../errors';\n\n// \u2500\u2500 Plugin Definitions \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Create the npm version extraction plugin wrapping parseNpmManifest.\n */\nfunction createNpmPlugin(): VersionExtractionPlugin {\n  return {\n    ecosystem: 'npm',\n    manifestFiles: ['package.json'],\n    canExtract(manifestPath: string): boolean {\n      return manifestPath.endsWith('package.json');\n    },\n    extract: parseNpmManifest,\n  };\n}\n\n/**\n * Create the Maven version extraction plugin wrapping parseMavenManifest.\n */\nfunction createMavenPlugin(): VersionExtractionPlugin {\n  return {\n    ecosystem: 'maven',\n    manifestFiles: ['pom.xml'],\n    canExtract(manifestPath: string): boolean {\n      return manifestPath.endsWith('pom.xml');\n    },\n    extract: parseMavenManifest,\n  };\n}\n\n/**\n * Create the Go version extraction plugin wrapping parseGoManifest.\n */\nfunction createGoPlugin(): VersionExtractionPlugin {\n  return {\n    ecosystem: 'go',\n    manifestFiles: ['go.mod'],\n    canExtract(manifestPath: string): boolean {\n      return manifestPath.endsWith('go.mod');\n    },\n    extract: parseGoManifest,\n  };\n}\n\n/**\n * Create the pip version extraction plugin wrapping parsePipManifest.\n */\nfunction createPipPlugin(): VersionExtractionPlugin {\n  return {\n    ecosystem: 'python',\n    manifestFiles: ['requirements.txt'],\n    canExtract(manifestPath: string): boolean {\n      return manifestPath.endsWith('requirements.txt');\n    },\n    extract: parsePipManifest,\n  };\n}\n\n/**\n * Create the Cargo version extraction plugin wrapping parseCargoManifest.\n */\nfunction createCargoPlugin(): VersionExtractionPlugin {\n  return {\n    ecosystem: 'cargo',\n    manifestFiles: ['Cargo.toml'],\n    canExtract(manifestPath: string): boolean {\n      return manifestPath.endsWith('Cargo.toml');\n    },\n    extract: parseCargoManifest,\n  };\n}\n\n/**\n * Create the NuGet version extraction plugin wrapping parseNugetManifest.\n * ecosystem = 'csproj' to match the architecture parser name for lookup;\n * ParsedDependency.ecosystem is set to 'nuget' inside the plugin function.\n */\nfunction createNugetPlugin(): VersionExtractionPlugin {\n  return {\n    ecosystem: 'csproj',\n    manifestFiles: ['.csproj'],\n    canExtract(manifestPath: string): boolean {\n      return manifestPath.endsWith('.csproj');\n    },\n    extract: parseNugetManifest,\n  };\n}\n\n/**\n * Create the Gradle version extraction plugin wrapping parseGradleManifest.\n */\nfunction createGradlePlugin(): VersionExtractionPlugin {\n  return {\n    ecosystem: 'gradle',\n    manifestFiles: ['build.gradle', 'build.gradle.kts'],\n    canExtract(manifestPath: string): boolean {\n      const base = manifestPath.split('/').pop() ?? 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dep.declaredConstraint;\n}\n\n// \u2500\u2500 Deduplication \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * A deduplicated dependency entry combining data from multiple manifests.\n */\ninterface DeduplicatedDependency {\n  name: string;\n  ecosystem: string;\n  /** The highest declared constraint across all manifests */\n  declaredConstraint: string;\n  /** The highest resolved version across all manifests (if any) */\n  resolvedVersion?: string;\n  /** Scope from the manifest with the highest version */\n  scope: ParsedDependency['scope'];\n  /** All source manifests that declared this dependency */\n  sourceManifests: string[];\n  /** License from manifest, if available */\n  license?: string;\n}\n\n/**\n * Deduplicate dependencies by (name, ecosystem) pair, keeping the entry\n * with the highest version and collecting all source manifests.\n */\nexport function deduplicateDependencies(deps: ParsedDependency[]): DeduplicatedDependency[] {\n  const map = new Map<string, DeduplicatedDependency>();\n\n  for (const dep of deps) {\n    const key = `${dep.ecosystem}:${dep.name}`;\n    const existing = map.get(key);\n\n    if (!existing) {\n      map.set(key, {\n        name: dep.name,\n        ecosystem: dep.ecosystem,\n        declaredConstraint: dep.declaredConstraint,\n        resolvedVersion: dep.resolvedVersion,\n        scope: dep.scope,\n        sourceManifests: [dep.sourceManifest],\n        license: dep.license,\n      });\n    } else {\n      // Add source manifest if not already present\n      if (!existing.sourceManifests.includes(dep.sourceManifest)) {\n        existing.sourceManifests.push(dep.sourceManifest);\n      }\n\n      // Keep the highest version\n      const existingVersion = existing.resolvedVersion ?? existing.declaredConstraint;\n      const newVersion = getEffectiveVersion(dep);\n\n      if (compareVersions(newVersion, existingVersion) > 0) {\n        existing.declaredConstraint = dep.declaredConstraint;\n        existing.resolvedVersion = dep.resolvedVersion;\n        existing.scope = dep.scope;\n        // Update license if the winning version entry has one\n        if (dep.license !== undefined) {\n          existing.license = dep.license;\n        }\n      } else if (existing.license === undefined && dep.license !== undefined) {\n        // Even if version didn't win, adopt the license if we don't have one\n        existing.license = dep.license;\n      }\n    }\n  }\n\n  return [...map.values()];\n}\n\n// \u2500\u2500 ManifestParser Class \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * ManifestParser orchestrates manifest discovery, parsing, deduplication,\n * and database persistence for the security module.\n */\nexport class ManifestParser {\n  private readonly adapter: SecurityManifestAdapter;\n  private readonly db: GraphDatabase;\n  private readonly projectRoot: string;\n\n  constructor(db: GraphDatabase, projectRoot: string) {\n    this.db = db;\n    this.projectRoot = projectRoot;\n    this.adapter = new SecurityManifestAdapter(projectRoot);\n\n    // Wrapped plugins (arch parser exists \u2014 ecosystem must match archParser.name)\n    this.adapter.registerPlugin(createNpmPlugin());\n    this.adapter.registerPlugin(createMavenPlugin());\n    this.adapter.registerPlugin(createGoPlugin());\n    this.adapter.registerPlugin(createPipPlugin());\n    this.adapter.registerPlugin(createCargoPlugin());\n    this.adapter.registerPlugin(createNugetPlugin());\n    this.adapter.registerPlugin(createGradlePlugin());\n\n    // Standalone plugins (no arch parser \u2014 own manifest discovery via manifestFiles)\n    this.adapter.registerStandalonePlugin(createPyprojectPlugin());\n    this.adapter.registerStandalonePlugin(createRubygemsPlugin());\n    this.adapter.registerStandalonePlugin(createComposerPlugin());\n    this.adapter.registerStandalonePlugin(createSwiftPlugin());\n    this.adapter.registerStandalonePlugin(createPubspecPlugin());\n    this.adapter.registerStandalonePlugin(createHexPlugin());\n  }\n\n  /**\n   * Get the underlying adapter (useful for testing).\n   */\n  getAdapter(): SecurityManifestAdapter {\n    return this.adapter;\n  }\n\n  /**\n   * Run full manifest discovery, parsing, deduplication, and database persistence.\n   *\n   * Steps:\n   * 1. Discover manifest files via the adapter (reuses architecture parsers)\n   * 2. Extract dependencies with version/scope data via registered plugins\n   * 3. Deduplicate: same (name, ecosystem) \u2192 single entry with highest version\n   * 4. Create Dependency_Nodes in the database (nodes + sec_dependencies tables)\n   * 5. Create `declared_in` edges linking dependencies to their source manifests\n   */\n  async parseAll(): Promise<ManifestParseResult> {\n    const warnings: Array<{ file: string; line?: number; message: string }> = [];\n    const errors: Array<{ file: string; message: string }> = [];\n\n    // Step 1 & 2: Discover and extract all dependencies\n    const allDeps: ParsedDependency[] = [];\n    const manifestPaths = this.adapter.discoverManifests();\n    let manifestsParsed = 0;\n\n    for (const manifestPath of manifestPaths) {\n      try {\n        const deps = await this.adapter.extractFromManifest(manifestPath);\n        if (deps.length > 0) {\n          allDeps.push(...deps);\n          manifestsParsed++;\n        } else {\n          // Manifest was parsed but had no dependencies \u2014 still counts\n          manifestsParsed++;\n        }\n      } catch (err) {\n        const message = err instanceof Error ? err.message : String(err);\n        const relPath = manifestPath.replace(this.projectRoot + '/', '').replace(/\\\\/g, '/');\n        errors.push({ file: relPath, message });\n        logError(`[sec:parser] Failed to parse manifest ${relPath}: ${message}`);\n      }\n    }\n\n    if (allDeps.length === 0) {\n      return {\n        dependenciesCreated: 0,\n        manifestsParsed,\n        warnings,\n        errors,\n      };\n    }\n\n    // Step 3: Deduplicate by (name, ecosystem)\n    const deduplicated = deduplicateDependencies(allDeps);\n\n    // Step 4 & 5: Persist to database\n    let dependenciesCreated = 0;\n    const rawDb = this.db.getRawDb();\n\n    for (const dep of deduplicated) {\n      try {\n        const nodeId = `dep:${dep.ecosystem}:${dep.name}`;\n\n        // Create the node in the nodes table via upsertNode\n        const node: Node = {\n          id: nodeId,\n          kind: 'dependency',\n          name: dep.name,\n          qualifiedName: `${dep.ecosystem}/${dep.name}`,\n          filePath: dep.sourceManifests[0] ?? '',\n          language: 'unknown',\n          startLine: 0,\n          endLine: 0,\n          startColumn: 0,\n          endColumn: 0,\n          signature: dep.resolvedVersion ?? dep.declaredConstraint,\n          isExported: false,\n          isAsync: false,\n          isStatic: false,\n          isAbstract: false,\n          updatedAt: Date.now(),\n        };\n\n        this.db.upsertNode(node);\n\n        // Insert/update the sec_dependencies row\n        rawDb.run(\n          `INSERT OR REPLACE INTO sec_dependencies\n            (node_id, ecosystem, package_name, declared_constraint, resolved_version, scope, source_manifests, license)\n           VALUES (?, ?, ?, ?, ?, ?, ?, ?)`,\n          [\n            nodeId,\n            dep.ecosystem,\n            dep.name,\n            dep.declaredConstraint,\n            dep.resolvedVersion ?? null,\n            dep.scope,\n            JSON.stringify(dep.sourceManifests),\n            dep.license ?? null,\n          ],\n        );\n\n        // Create `declared_in` edges from the dependency to each source manifest\n        for (const manifest of dep.sourceManifests) {\n          const edge: Edge = {\n            source: nodeId,\n            target: manifest,\n            kind: 'declared_in',\n          };\n          this.db.insertEdge(edge);\n        }\n\n        dependenciesCreated++;\n      } catch (err) {\n        const message = err instanceof Error ? err.message : String(err);\n        warnings.push({\n          file: dep.sourceManifests[0] ?? 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dep.declaredConstraint;\n}\n\n// \u2500\u2500 Deduplication \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * A deduplicated dependency entry combining data from multiple manifests.\n */\ninterface DeduplicatedDependency {\n  name: string;\n  ecosystem: string;\n  /** The highest declared constraint across all manifests */\n  declaredConstraint: string;\n  /** The highest resolved version across all manifests (if any) */\n  resolvedVersion?: string;\n  /** Scope from the manifest with the highest version */\n  scope: ParsedDependency['scope'];\n  /** All source manifests that declared this dependency */\n  sourceManifests: string[];\n  /** License from manifest, if available */\n  license?: string;\n}\n\n/**\n * Deduplicate dependencies by (name, ecosystem) pair, keeping the entry\n * with the highest version and collecting all source manifests.\n */\nexport function deduplicateDependencies(deps: ParsedDependency[]): DeduplicatedDependency[] {\n  const map = new Map<string, DeduplicatedDependency>();\n\n  for (const dep of deps) {\n    const key = `${dep.ecosystem}:${dep.name}`;\n    const existing = map.get(key);\n\n    if (!existing) {\n      map.set(key, {\n        name: dep.name,\n        ecosystem: dep.ecosystem,\n        declaredConstraint: dep.declaredConstraint,\n        resolvedVersion: dep.resolvedVersion,\n        scope: dep.scope,\n        sourceManifests: [dep.sourceManifest],\n        license: dep.license,\n      });\n    } else {\n      // Add source manifest if not already present\n      if (!existing.sourceManifests.includes(dep.sourceManifest)) {\n        existing.sourceManifests.push(dep.sourceManifest);\n      }\n\n      // Keep the highest version\n      const existingVersion = existing.resolvedVersion ?? 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Discover manifest files via the adapter (reuses architecture parsers)\n   * 2. Extract dependencies with version/scope data via registered plugins\n   * 3. Deduplicate: same (name, ecosystem) \u2192 single entry with highest version\n   * 4. Create Dependency_Nodes in the database (nodes + sec_dependencies tables)\n   * 5. 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'unknown',\n          message: `Failed to persist dependency ${dep.ecosystem}/${dep.name}: ${message}`,\n        });\n        logWarn(`[sec:parser] Failed to persist dependency ${dep.ecosystem}/${dep.name}: ${message}`);\n      }\n    }\n\n    return {\n      dependenciesCreated,\n      manifestsParsed,\n      warnings,\n      errors,\n    };\n  }\n}\n"],
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 }

package/dist/security/pipeline.js

@@ -51,7 +51,10 @@ class SecurityPipeline {
       duration: 0
     };
     onProgress?.("manifest-parsing", 0, 4);
-    const parser = new import_parser.ManifestParser(this.db, this.projectRoot);
+    const parser = new import_parser.ManifestParser(this.db, this.projectRoot, {
+      include: this.config.include,
+      exclude: this.config.exclude
+    });
     const parseResult = await parser.parseAll();
     result.manifestsDiscovered = parseResult.manifestsParsed;
     result.dependenciesCreated = parseResult.dependenciesCreated;

package/dist/security/pipeline.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/security/pipeline.ts"],
-  "sourcesContent": ["/**\n * SecurityPipeline \u2014 Orchestrates the security analysis phases.\n *\n * Phases (in order):\n *   1. Manifest parsing \u2014 discover and parse dependency manifests\n *   2. Dependency integration \u2014 link dependencies to code symbols\n *   3. Vulnerability enrichment \u2014 query databases for CVEs (if securityAutoEnrich)\n *   4. Reachability analysis \u2014 determine if vulnerable code is reachable\n *\n * Reports progress via callback and returns a SecurityResult with counts and duration.\n *\n * Requirements: 9.3, 9.5\n */\n\nimport type { GraphDatabase } from '../db/database';\nimport type { KiroGraphConfig } from '../config';\nimport type { SecurityResult } from './types';\nimport { ManifestParser } from './manifest/parser';\nimport { DependencyGraphIntegrator } from './integrator';\nimport { VulnerabilityDatabaseClient } from './vuln/client';\nimport { OsvAdapter } from './vuln/osv-adapter';\nimport { ReachabilityAnalyzer } from './reachability';\nimport { logWarn } from '../errors';\n\n/**\n * SecurityPipeline orchestrates the full security analysis workflow.\n */\nexport class SecurityPipeline {\n  private readonly db: GraphDatabase;\n  private readonly config: KiroGraphConfig;\n  private readonly projectRoot: string;\n\n  constructor(db: GraphDatabase, config: KiroGraphConfig, projectRoot: string) {\n    this.db = db;\n    this.config = config;\n    this.projectRoot = projectRoot;\n  }\n\n  /**\n   * Run the full security analysis pipeline.\n   *\n   * @param onProgress - 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start;\n    return result;\n  }\n\n  /**\n   * Create vulnerability database adapters based on config.\n   */\n  private createVulnAdapters(): import('./vuln/types').VulnDatabaseAdapter[] {\n    const adapters: import('./vuln/types').VulnDatabaseAdapter[] = [];\n\n    for (const dbName of this.config.securityDatabases) {\n      switch (dbName.toUpperCase()) {\n        case 'OSV':\n          adapters.push(new OsvAdapter());\n          break;\n        default:\n          logWarn(`[sec:pipeline] Unknown vulnerability database \"${dbName}\", skipping`);\n          break;\n      }\n    }\n\n    // Fallback to OSV if no valid adapters configured\n    if (adapters.length === 0) {\n      adapters.push(new OsvAdapter());\n    }\n\n    return adapters;\n  }\n}\n"],
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+  "sourcesContent": ["/**\n * SecurityPipeline \u2014 Orchestrates the security analysis phases.\n *\n * Phases (in order):\n *   1. Manifest parsing \u2014 discover and parse dependency manifests\n *   2. Dependency integration \u2014 link dependencies to code symbols\n *   3. Vulnerability enrichment \u2014 query databases for CVEs (if securityAutoEnrich)\n *   4. Reachability analysis \u2014 determine if vulnerable code is reachable\n *\n * Reports progress via callback and returns a SecurityResult with counts and duration.\n *\n * Requirements: 9.3, 9.5\n */\n\nimport type { GraphDatabase } from '../db/database';\nimport type { KiroGraphConfig } from '../config';\nimport type { SecurityResult } from './types';\nimport { ManifestParser } from './manifest/parser';\nimport { DependencyGraphIntegrator } from './integrator';\nimport { VulnerabilityDatabaseClient } from './vuln/client';\nimport { OsvAdapter } from './vuln/osv-adapter';\nimport { ReachabilityAnalyzer } from './reachability';\nimport { logWarn } from '../errors';\n\n/**\n * SecurityPipeline orchestrates the full security analysis workflow.\n */\nexport class SecurityPipeline {\n  private readonly db: GraphDatabase;\n  private readonly config: KiroGraphConfig;\n  private readonly projectRoot: string;\n\n  constructor(db: GraphDatabase, config: KiroGraphConfig, projectRoot: string) {\n    this.db = db;\n    this.config = config;\n    this.projectRoot = projectRoot;\n  }\n\n  /**\n   * Run the full security analysis pipeline.\n   *\n   * @param onProgress - Optional callback reporting (phase, current, total)\n   * @returns SecurityResult with counts and duration\n   */\n  async run(\n    onProgress?: (phase: string, current: number, total: number) => void,\n  ): Promise<SecurityResult> {\n    const start = Date.now();\n\n    const result: SecurityResult = {\n      manifestsDiscovered: 0,\n      dependenciesCreated: 0,\n      vulnerabilitiesFound: 0,\n      affectedCount: 0,\n      notAffectedCount: 0,\n      underInvestigationCount: 0,\n      duration: 0,\n    };\n\n    // \u2500\u2500 Phase 1: Manifest Parsing \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    onProgress?.('manifest-parsing', 0, 4);\n\n    const parser = new ManifestParser(this.db, this.projectRoot, {\n      include: this.config.include,\n      exclude: this.config.exclude,\n    });\n    const parseResult = await parser.parseAll();\n\n    result.manifestsDiscovered = parseResult.manifestsParsed;\n    result.dependenciesCreated = parseResult.dependenciesCreated;\n\n    onProgress?.('manifest-parsing', 1, 4);\n\n    // \u2500\u2500 Phase 2: Dependency Integration \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    onProgress?.('dependency-integration', 1, 4);\n\n    const integrator = new DependencyGraphIntegrator(this.db, this.projectRoot);\n    await integrator.integrate();\n    await integrator.resolveTransitives(10);\n    await integrator.cleanup();\n\n    onProgress?.('dependency-integration', 2, 4);\n\n    // \u2500\u2500 Phase 3: Vulnerability Enrichment (conditional) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    if (this.config.securityAutoEnrich) {\n      onProgress?.('vulnerability-enrichment', 2, 4);\n\n      const adapters = this.createVulnAdapters();\n      const vulnClient = new VulnerabilityDatabaseClient(adapters, this.db);\n      const enrichResult = await vulnClient.enrichAll();\n\n      result.vulnerabilitiesFound = enrichResult.vulnerabilitiesFound;\n\n      onProgress?.('vulnerability-enrichment', 3, 4);\n    } else {\n      onProgress?.('vulnerability-enrichment', 3, 4);\n    }\n\n    // \u2500\u2500 Phase 4: Reachability Analysis \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    onProgress?.('reachability-analysis', 3, 4);\n\n    const reachability = new ReachabilityAnalyzer(this.db, this.config);\n    const reachResults = await reachability.analyzeAll();\n\n    // Count verdicts\n    for (const [, reachResult] of reachResults) {\n      switch (reachResult.verdict) {\n        case 'affected':\n          result.affectedCount++;\n          break;\n        case 'not_affected':\n          result.notAffectedCount++;\n          break;\n        case 'under_investigation':\n          result.underInvestigationCount++;\n          break;\n      }\n    }\n\n    // Generate impact summaries for affected vulnerabilities\n    for (const [vulnNodeId, reachResult] of reachResults) {\n      if (reachResult.verdict === 'affected') {\n        await reachability.getImpactSummary(vulnNodeId);\n      }\n    }\n\n    onProgress?.('reachability-analysis', 4, 4);\n\n    result.duration = Date.now() - 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