kirograph 0.28.1 → 1.1.1

package/README.md

@@ -43,9 +43,9 @@ The result is fewer tool calls, less context used, and faster responses on compl
 | <h4>Security</h4> | |
 | 🔒 **Security (KiroGraph-Sec opt-in  module)** | Goes beyond "this dependency has a CVE" — uses the call graph to determine if vulnerable code is **actually reachable** from your entry points. Maps your **attack surface** (which HTTP routes reach vulnerable deps). Detects **hardcoded secrets** and shows how many entry points expose them. **SAST-lite** finds SQL injection, path traversal, and dangerous eval in your code. **AST-based SAST (opt-in via `enablePatterns`)** runs 10 bundled structural pattern rules via `@ast-grep/napi` — matches actual code structure, not just symbol names. **Supply chain health** checks OpenSSF Scorecard scores and detects dependency confusion attacks. Covers 14 ecosystems, outputs CycloneDX SBOM/VEX and CI-ready SARIF reports. |
 | <h4>Knowledge & Data</h4> | |
-| 🧠 **Persistent Memory (KiroGraph-Mem opt-in module)** | Cross-session observations — decisions, errors, patterns — auto-linked to code symbols. **Conflict detection**: typed relations between observations (`supersedes`, `conflicts_with`, `compatible`) with agent judgment workflow (`kirograph_mem_compare`, `kirograph_mem_judge`). **Stale review**: schedule observations for re-evaluation (`review_after` + `kirograph_mem_review`). **Passive capture**: extract learnings from structured text. **Prompt saving**: session context reconstruction. **Topic key**: stable semantic addressing. Inspired by [Engram](https://github.com/Gentleman-Programming/engram). |
+| 🧠 **Persistent Memory (KiroGraph-Mem opt-in module)** | Cross-session observations — decisions, errors, patterns — auto-linked to code symbols. **Conflict detection**: typed relations between observations (`supersedes`, `conflicts_with`, `compatible`) with agent judgment workflow (`kirograph_mem_compare`, `kirograph_mem_judge`). **Stale review**: schedule observations for re-evaluation (`review_after` + `kirograph_mem_review`). **Passive capture**: extract learnings from structured text. **Prompt saving**: session context reconstruction. **Topic key**: stable semantic addressing. **Strict writes (opt-in via `memoryStrictWrites`)**: rejects an unknown `kind` or blank tags instead of silently corrupting the store. Inspired by [Engram](https://github.com/Gentleman-Programming/engram) and [IWE](https://github.com/iwe-org/iwe)'s schema-validated agent writes. |
 | 👁️ **Watchmen (KiroGraph-Watchmen opt-in module)** ⚠️ *experimental* | Auto-synthesizes accumulated memory observations into workspace briefs and `inclusion: manual` skill files. Fires via the `watchmenReady` signal in `kirograph_mem_store` when threshold is reached. **Local model** (default, `watchmenSynthesisMode: 'local'`): runs `gemma-4-E4B-it-ONNX` on-device via `@huggingface/transformers` — ~3–4 GB one-time download, ~3–5 GB RAM, 8–15 s on Apple Silicon M1+. No API key, no background daemon, no external calls. **Agent mode** also available for Kiro (`watchmenSynthesisMode: 'agent'`, uses active session). ⚠️ **Experimental:** output quality in local mode depends heavily on the model chosen and your hardware. Smaller models or slower machines may produce incomplete briefs and lower-quality skill files. Use `agent` mode for best results. |
-| 📚 **Wiki (KiroGraph-Wiki opt-in module)** | Karpathy-style LLM wiki — a set of markdown pages that compound knowledge across sessions. Three ops: **ingest** (build structured prompt from source text), **apply-diff** (write LLM-generated WIKI_DIFF to SQLite + disk), **lint** (broken links, orphan pages, contradictions). Context enrichment: `kirograph_context` auto-includes relevant wiki pages above score threshold. Two synthesis modes: `agent` (IDE LLM) or `local` (HuggingFace, same infra as Watchmen). Conflict resolution: deterministic by source date when `wikiAutoResolveConflicts: true`. Inspired by [Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f). |
+| 📚 **Wiki (KiroGraph-Wiki opt-in module)** | Karpathy-style LLM wiki — a set of markdown pages that compound knowledge across sessions. Three ops: **ingest** (build structured prompt from source text), **apply-diff** (write LLM-generated WIKI_DIFF to SQLite + disk), **lint** (broken links, orphan pages, contradictions). **Link graph** (`kirograph wiki links <slug>`): outgoing/broken/incoming `[[slug]]` backlinks for a page. **Rename** (`kirograph wiki rename <from> <to>`): moves a page's file and rewrites every `[[slug]]` reference to it across the wiki — a CLI-first port of the navigation/refactor features [IWE](https://github.com/iwe-org/iwe) gets from a full LSP. Context enrichment: `kirograph_context` auto-includes relevant wiki pages above score threshold. Two synthesis modes: `agent` (IDE LLM) or `local` (HuggingFace, same infra as Watchmen). Conflict resolution: deterministic by source date when `wikiAutoResolveConflicts: true`. Inspired by [Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f) and [IWE](https://github.com/iwe-org/iwe). |
 | 📖 **Documentation Indexing (KiroGraph-Doc opt-in  module)** | Section-level retrieval from Markdown, MDX, RST, AsciiDoc, OpenAPI — 92-97% token savings |
 | 📊 **Data Navigation (KiroGraph-Data opt-in  module)** | Query CSV/JSON/Excel/Parquet/**PDF** with filters, aggregations, joins — all server-side in SQLite |
 | <h4>Token Optimization</h4> | |
@@ -176,6 +176,7 @@ KiroGraph is inspired by [CodeGraph](https://github.com/colbymchenry/codegraph)
 - [caveman](https://github.com/JuliusBrussee/caveman) by [Julius Brussee](https://www.linkedin.com/in/julius-brussee/): the caveman mode's agent prose compression concept, multi-level steering injection.
 - [watchmen](https://github.com/firstbatchxyz/watchmen) by [firstbatch](https://github.com/firstbatchxyz): the watchmen module's session-mining concept, workspace brief generation, and `AGENTS.md` mirroring pattern.
 - [LLM Wiki](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f) by [Andrej Karpathy](https://karpathy.ai/): the wiki module's three-op pattern (ingest → apply → lint), WIKI_DIFF block format, two-tool ingest flow, and the principle of knowledge compounding rather than accumulating.
+- [IWE](https://github.com/iwe-org/iwe): a markdown knowledge-graph tool with a full LSP integration and schema-validated agent writes (`expect` guards, per-type document schemas) over MCP. `memoryStrictWrites` (opt-in observation schema validation) and `kirograph wiki links`/`kirograph wiki rename` (link-graph navigation and rename-with-reference-updates, ported to the CLI rather than a full LSP server) both scale down ideas from IWE to fit KiroGraph's existing memory and wiki modules.
 - [jDocMunch-MCP](https://github.com/jgravelle/jdocmunch-mcp) by [J. Gravelle](https://www.linkedin.com/in/j-gravelle-2778223/): the documentation module's section-first retrieval approach, stable section IDs, and byte-offset addressing.
 - [jDataMunch-MCP](https://github.com/jgravelle/jdatamunch-mcp) by [J. Gravelle](https://www.linkedin.com/in/j-gravelle-2778223/): the data module's column profiling, streaming parsers, and server-side aggregation approach.
 - [rtk](https://github.com/rtk-ai/rtk) by [rtk-ai](https://github.com/rtk-ai): the shell compression module's command-family approach and token-optimized output patterns.

package/dist/architecture/index.js

@@ -32,7 +32,10 @@ class ArchitectureAnalyzer {
   async analyze(onProgress) {
     const log = (msg) => onProgress?.(msg);
     log("architecture: parsing manifests");
-    const manifestPackages = await (0, import_manifest.parseAllManifests)(this.projectRoot);
+    const manifestPackages = await (0, import_manifest.parseAllManifests)(this.projectRoot, {
+      include: this.config.include,
+      exclude: this.config.exclude
+    });
     const allFiles = this.db.getAllFiles().map((f) => f.path);
     log("architecture: assigning files to packages");
     const filePackageMap = /* @__PURE__ */ new Map();

package/dist/architecture/index.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/architecture/index.ts"],
-  "sourcesContent": ["/**\n * ArchitectureAnalyzer\n *\n * Orchestrates the full architecture analysis pipeline:\n *   1. Parse manifests \u2192 packages\n *   2. Directory-based fallback for uncovered file trees\n *   3. Detect layers from file paths\n *   4. Roll up package-to-package dependencies from existing import edges\n *   5. Roll up layer-to-layer dependencies\n *   6. Compute coupling metrics (Ca, Ce, instability)\n *\n * Only runs when enableArchitecture=true. Writes to arch_* tables in kirograph.db.\n */\nimport * as path from 'path';\nimport type { GraphDatabase } from '../db/database';\nimport type { KiroGraphConfig } from '../config';\nimport type {\n  ArchPackage, ArchLayer, ArchPackageDep, ArchLayerDep, ArchCoupling, ArchitectureResult,\n} from './types';\nimport { parseAllManifests } from './manifest/index';\nimport { detectAllLayers, buildArchLayers, type FileLayerAssignment } from './layers/index';\n\nexport class ArchitectureAnalyzer {\n  constructor(\n    private readonly db: GraphDatabase,\n    private readonly config: KiroGraphConfig,\n    private readonly projectRoot: string,\n  ) {}\n\n  async analyze(onProgress?: (msg: string) => void): Promise<ArchitectureResult> {\n    const log = (msg: string) => onProgress?.(msg);\n\n    // \u2500\u2500 1. Parse manifests \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    log('architecture: parsing manifests');\n    const manifestPackages = await parseAllManifests(this.projectRoot);\n\n    // \u2500\u2500 2. Get all indexed files \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    const allFiles = this.db.getAllFiles().map(f => f.path); // relative paths\n\n    // \u2500\u2500 3. Assign files to packages (manifest-based) \u2500\u2500\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    log('architecture: assigning files to packages');\n    const filePackageMap = new Map<string, string>(); // filePath \u2192 packageId\n    // Sort packages by path length desc so the most-specific package wins\n    const sortedPkgs = [...manifestPackages].sort((a, b) => b.path.length - a.path.length);\n    for (const file of allFiles) {\n      for (const pkg of sortedPkgs) {\n        const pkgPath = pkg.path === '.' ? '' : pkg.path + '/';\n        if (pkg.path === '.' || file.startsWith(pkgPath)) {\n          filePackageMap.set(file, pkg.id);\n          break;\n        }\n      }\n    }\n\n    // \u2500\u2500 4. Directory-based fallback / subdivision \u2500\u2500\u2500\u2500\u2500\u2500\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    // Three cases:\n    //   A) No manifests at all \u2192 group by top-level directory.\n    //   B) Root manifest (path='.') covers everything \u2192 subdivide its files into\n    //      second-level directory packages so internal structure is visible.\n    //   C) Manifests exist but don't cover the whole tree \u2192 create directory\n    //      packages for uncovered subdirectories (threshold: 3 files).\n    //\n    const SUBDIR_THRESHOLD = 1;\n    const directoryPackages: ArchPackage[] = [];\n\n    const rootManifestIds = new Set(manifestPackages.filter(p => p.path === '.').map(p => p.id));\n    const hasRootManifest = rootManifestIds.size > 0;\n\n    if (manifestPackages.length === 0) {\n      // Case A: no manifests \u2014 group by top-level directory\n      const topDirs = new Set<string>();\n      for (const file of allFiles) {\n        const parts = file.split('/');\n        if (parts.length > 1) topDirs.add(parts[0]);\n      }\n      for (const dir of topDirs) {\n        const pkgId = `pkg:dir:${dir}`;\n        directoryPackages.push({ id: pkgId, name: dir, path: dir, source: 'directory', updatedAt: Date.now() });\n        for (const file of allFiles) {\n          if (file.startsWith(dir + '/')) filePackageMap.set(file, pkgId);\n        }\n      }\n    } else if (hasRootManifest) {\n      // Case B: root manifest(s) cover everything \u2014 subdivide into second-level dirs.\n      // Collect files owned by a root manifest, then re-assign them to more specific\n      // directory packages so internal module boundaries become visible.\n      const rootOwnedFiles = allFiles.filter(f => rootManifestIds.has(filePackageMap.get(f) ?? ''));\n      const subDirCounts = new Map<string, number>();\n      for (const file of rootOwnedFiles) {\n        const parts = file.split('/');\n        if (parts.length > 2) {\n          // Use two-level path (e.g. src/mcp) for granularity inside a src root\n          const dir = parts.slice(0, 2).join('/');\n          subDirCounts.set(dir, (subDirCounts.get(dir) ?? 0) + 1);\n        }\n        // Files directly at one level deep (e.g. src/index.ts) stay with the\n        // root manifest package \u2014 no single-level dir package is created.\n      }\n      for (const [dir, count] of subDirCounts) {\n        if (count >= SUBDIR_THRESHOLD) {\n          const pkgId = `pkg:dir:${dir}`;\n          const name = dir.split('/').pop() ?? dir;\n          const pkg: ArchPackage = { id: pkgId, name, path: dir, source: 'directory', updatedAt: Date.now() };\n          directoryPackages.push(pkg);\n          for (const file of rootOwnedFiles) {\n            if (file.startsWith(dir + '/') || file === dir) {\n              filePackageMap.set(file, pkgId);\n            }\n          }\n        }\n      }\n    } else {\n      // Case C: manifests exist but don't cover root \u2014 create dir packages for uncovered files\n      const uncovered = allFiles.filter(f => !filePackageMap.has(f));\n      const subDirCounts = new Map<string, number>();\n      for (const file of uncovered) {\n        const parts = file.split('/');\n        if (parts.length > 1) {\n          const dir = parts.slice(0, 2).join('/');\n          subDirCounts.set(dir, (subDirCounts.get(dir) ?? 0) + 1);\n        }\n      }\n      for (const [dir, count] of subDirCounts) {\n        if (count >= SUBDIR_THRESHOLD) {\n          const pkgId = `pkg:dir:${dir}`;\n          const name = dir.split('/').pop() ?? dir;\n          const pkg: ArchPackage = { id: pkgId, name, path: dir, source: 'directory', updatedAt: Date.now() };\n          directoryPackages.push(pkg);\n          for (const file of uncovered) {\n            if (file.startsWith(dir + '/') && !filePackageMap.has(file)) {\n              filePackageMap.set(file, pkgId);\n            }\n          }\n        }\n      }\n    }\n\n    const allPackages = [...manifestPackages, ...directoryPackages];\n\n    // \u2500\u2500 5. Detect layers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    log('architecture: detecting layers');\n    const layerAssignments: FileLayerAssignment[] = [];\n    const fileLayerMap = new Map<string, FileLayerAssignment>();\n\n    if (this.config.architectureLayers !== undefined || this.config.enableArchitecture) {\n      const assignments = await detectAllLayers(allFiles, this.projectRoot, this.config.architectureLayers);\n      for (const a of assignments) {\n        layerAssignments.push(a);\n        fileLayerMap.set(a.filePath, a);\n      }\n    }\n\n    const allLayers = buildArchLayers(layerAssignments, this.config.architectureLayers);\n\n    // \u2500\u2500 6. Roll up package dependencies from import edges \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    log('architecture: rolling up package dependencies');\n    const importPairs = this.db.getFileImportPairs();\n    const pkgDepCounts = new Map<string, Map<string, { count: number; files: Array<{ from: string; to: string }> }>>();\n\n    for (const { sourceFile, targetFile } of importPairs) {\n      const sourcePkg = filePackageMap.get(sourceFile);\n      const targetPkg = filePackageMap.get(targetFile);\n      if (!sourcePkg || !targetPkg || sourcePkg === targetPkg) continue;\n\n      if (!pkgDepCounts.has(sourcePkg)) pkgDepCounts.set(sourcePkg, new Map());\n      const inner = pkgDepCounts.get(sourcePkg)!;\n      if (!inner.has(targetPkg)) inner.set(targetPkg, { count: 0, files: [] });\n      const entry = inner.get(targetPkg)!;\n      entry.count++;\n      if (entry.files.length < 5) entry.files.push({ from: sourceFile, to: targetFile });\n    }\n\n    const packageDeps: ArchPackageDep[] = [];\n    for (const [sourcePkg, targets] of pkgDepCounts) {\n      for (const [targetPkg, { count, files }] of targets) {\n        packageDeps.push({ sourcePkg, targetPkg, depCount: count, files });\n      }\n    }\n\n    // \u2500\u2500 7. Roll up layer dependencies \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    const layerDepCounts = new Map<string, Map<string, number>>();\n    for (const dep of packageDeps) {\n      const srcFile = [...filePackageMap.entries()].find(([, pkgId]) => pkgId === dep.sourcePkg)?.[0];\n      const tgtFile = [...filePackageMap.entries()].find(([, pkgId]) => pkgId === dep.targetPkg)?.[0];\n      const srcLayer = srcFile ? fileLayerMap.get(srcFile)?.layerName : undefined;\n      const tgtLayer = tgtFile ? fileLayerMap.get(tgtFile)?.layerName : undefined;\n      if (!srcLayer || !tgtLayer || srcLayer === tgtLayer) continue;\n      const srcLayerId = `layer:${srcLayer}`;\n      const tgtLayerId = `layer:${tgtLayer}`;\n      if (!layerDepCounts.has(srcLayerId)) layerDepCounts.set(srcLayerId, new Map());\n      const inner = layerDepCounts.get(srcLayerId)!;\n      inner.set(tgtLayerId, (inner.get(tgtLayerId) ?? 0) + dep.depCount);\n    }\n\n    const layerDeps: ArchLayerDep[] = [];\n    for (const [srcLayer, targets] of layerDepCounts) {\n      for (const [tgtLayer, count] of targets) {\n        layerDeps.push({ sourceLayer: srcLayer, targetLayer: tgtLayer, depCount: count });\n      }\n    }\n\n    // \u2500\u2500 8. Compute coupling metrics \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    const afferentMap = new Map<string, number>(); // Ca: who depends on me\n    const efferentMap = new Map<string, number>(); // Ce: who I depend on\n    for (const dep of packageDeps) {\n      efferentMap.set(dep.sourcePkg, (efferentMap.get(dep.sourcePkg) ?? 0) + 1);\n      afferentMap.set(dep.targetPkg, (afferentMap.get(dep.targetPkg) ?? 0) + 1);\n    }\n    const coupling: ArchCoupling[] = allPackages.map(pkg => {\n      const ca = afferentMap.get(pkg.id) ?? 0;\n      const ce = efferentMap.get(pkg.id) ?? 0;\n      const instability = ca + ce === 0 ? 0 : ce / (ca + ce);\n      return { packageId: pkg.id, afferent: ca, efferent: ce, instability, updatedAt: Date.now() };\n    });\n\n    // \u2500\u2500 9. Persist to DB \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    log('architecture: persisting to database');\n    this.db.clearArchitecture();\n\n    for (const pkg of allPackages) this.db.upsertArchPackage(pkg);\n    for (const layer of allLayers) this.db.upsertArchLayer(layer);\n\n    for (const [filePath, pkgId] of filePackageMap) this.db.upsertArchFilePackage(filePath, pkgId);\n    for (const a of layerAssignments) {\n      this.db.upsertArchFileLayer(a.filePath, `layer:${a.layerName}`, a.confidence, a.matchedPattern);\n    }\n\n    for (const dep of packageDeps) {\n      this.db.upsertArchPackageDep(dep.sourcePkg, dep.targetPkg, dep.depCount, dep.files);\n    }\n    for (const dep of layerDeps) {\n      this.db.upsertArchLayerDep(dep.sourceLayer, dep.targetLayer, dep.depCount);\n    }\n    for (const c of coupling) this.db.upsertArchCoupling(c);\n\n    // Build return value\n    const filePackages: Record<string, string[]> = {};\n    for (const [filePath, pkgId] of filePackageMap) {\n      if (!filePackages[filePath]) filePackages[filePath] = [];\n      filePackages[filePath].push(pkgId);\n    }\n\n    const fileLayers: Record<string, Array<{ layerId: string; confidence: number; matchedPattern: string }>> = {};\n    for (const a of layerAssignments) {\n      fileLayers[a.filePath] = [{ layerId: `layer:${a.layerName}`, confidence: a.confidence, matchedPattern: a.matchedPattern }];\n    }\n\n    return { packages: allPackages, layers: allLayers, packageDeps, layerDeps, coupling, filePackages, fileLayers };\n  }\n}\n"],
-  "mappings": 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+  "sourcesContent": ["/**\n * ArchitectureAnalyzer\n *\n * Orchestrates the full architecture analysis pipeline:\n *   1. Parse manifests \u2192 packages\n *   2. Directory-based fallback for uncovered file trees\n *   3. Detect layers from file paths\n *   4. Roll up package-to-package dependencies from existing import edges\n *   5. Roll up layer-to-layer dependencies\n *   6. Compute coupling metrics (Ca, Ce, instability)\n *\n * Only runs when enableArchitecture=true. Writes to arch_* tables in kirograph.db.\n */\nimport * as path from 'path';\nimport type { GraphDatabase } from '../db/database';\nimport type { KiroGraphConfig } from '../config';\nimport type {\n  ArchPackage, ArchLayer, ArchPackageDep, ArchLayerDep, ArchCoupling, ArchitectureResult,\n} from './types';\nimport { parseAllManifests } from './manifest/index';\nimport { detectAllLayers, buildArchLayers, type FileLayerAssignment } from './layers/index';\n\nexport class ArchitectureAnalyzer {\n  constructor(\n    private readonly db: GraphDatabase,\n    private readonly config: KiroGraphConfig,\n    private readonly projectRoot: string,\n  ) {}\n\n  async analyze(onProgress?: (msg: string) => void): Promise<ArchitectureResult> {\n    const log = (msg: string) => onProgress?.(msg);\n\n    // \u2500\u2500 1. Parse manifests \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    log('architecture: parsing manifests');\n    const manifestPackages = await parseAllManifests(this.projectRoot, {\n      include: this.config.include,\n      exclude: this.config.exclude,\n    });\n\n    // \u2500\u2500 2. Get all indexed files \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    const allFiles = this.db.getAllFiles().map(f => f.path); // relative paths\n\n    // \u2500\u2500 3. Assign files to packages (manifest-based) \u2500\u2500\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    log('architecture: assigning files to packages');\n    const filePackageMap = new Map<string, string>(); // filePath \u2192 packageId\n    // Sort packages by path length desc so the most-specific package wins\n    const sortedPkgs = [...manifestPackages].sort((a, b) => b.path.length - a.path.length);\n    for (const file of allFiles) {\n      for (const pkg of sortedPkgs) {\n        const pkgPath = pkg.path === '.' ? '' : pkg.path + '/';\n        if (pkg.path === '.' || file.startsWith(pkgPath)) {\n          filePackageMap.set(file, pkg.id);\n          break;\n        }\n      }\n    }\n\n    // \u2500\u2500 4. Directory-based fallback / subdivision \u2500\u2500\u2500\u2500\u2500\u2500\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    // Three cases:\n    //   A) No manifests at all \u2192 group by top-level directory.\n    //   B) Root manifest (path='.') covers everything \u2192 subdivide its files into\n    //      second-level directory packages so internal structure is visible.\n    //   C) Manifests exist but don't cover the whole tree \u2192 create directory\n    //      packages for uncovered subdirectories (threshold: 3 files).\n    //\n    const SUBDIR_THRESHOLD = 1;\n    const directoryPackages: ArchPackage[] = [];\n\n    const rootManifestIds = new Set(manifestPackages.filter(p => p.path === '.').map(p => p.id));\n    const hasRootManifest = rootManifestIds.size > 0;\n\n    if (manifestPackages.length === 0) {\n      // Case A: no manifests \u2014 group by top-level directory\n      const topDirs = new Set<string>();\n      for (const file of allFiles) {\n        const parts = file.split('/');\n        if (parts.length > 1) topDirs.add(parts[0]);\n      }\n      for (const dir of topDirs) {\n        const pkgId = `pkg:dir:${dir}`;\n        directoryPackages.push({ id: pkgId, name: dir, path: dir, source: 'directory', updatedAt: Date.now() });\n        for (const file of allFiles) {\n          if (file.startsWith(dir + '/')) filePackageMap.set(file, pkgId);\n        }\n      }\n    } else if (hasRootManifest) {\n      // Case B: root manifest(s) cover everything \u2014 subdivide into second-level dirs.\n      // Collect files owned by a root manifest, then re-assign them to more specific\n      // directory packages so internal module boundaries become visible.\n      const rootOwnedFiles = allFiles.filter(f => rootManifestIds.has(filePackageMap.get(f) ?? ''));\n      const subDirCounts = new Map<string, number>();\n      for (const file of rootOwnedFiles) {\n        const parts = file.split('/');\n        if (parts.length > 2) {\n          // Use two-level path (e.g. src/mcp) for granularity inside a src root\n          const dir = parts.slice(0, 2).join('/');\n          subDirCounts.set(dir, (subDirCounts.get(dir) ?? 0) + 1);\n        }\n        // Files directly at one level deep (e.g. src/index.ts) stay with the\n        // root manifest package \u2014 no single-level dir package is created.\n      }\n      for (const [dir, count] of subDirCounts) {\n        if (count >= SUBDIR_THRESHOLD) {\n          const pkgId = `pkg:dir:${dir}`;\n          const name = dir.split('/').pop() ?? dir;\n          const pkg: ArchPackage = { id: pkgId, name, path: dir, source: 'directory', updatedAt: Date.now() };\n          directoryPackages.push(pkg);\n          for (const file of rootOwnedFiles) {\n            if (file.startsWith(dir + '/') || file === dir) {\n              filePackageMap.set(file, pkgId);\n            }\n          }\n        }\n      }\n    } else {\n      // Case C: manifests exist but don't cover root \u2014 create dir packages for uncovered files\n      const uncovered = allFiles.filter(f => !filePackageMap.has(f));\n      const subDirCounts = new Map<string, number>();\n      for (const file of uncovered) {\n        const parts = file.split('/');\n        if (parts.length > 1) {\n          const dir = parts.slice(0, 2).join('/');\n          subDirCounts.set(dir, (subDirCounts.get(dir) ?? 0) + 1);\n        }\n      }\n      for (const [dir, count] of subDirCounts) {\n        if (count >= SUBDIR_THRESHOLD) {\n          const pkgId = `pkg:dir:${dir}`;\n          const name = dir.split('/').pop() ?? dir;\n          const pkg: ArchPackage = { id: pkgId, name, path: dir, source: 'directory', updatedAt: Date.now() };\n          directoryPackages.push(pkg);\n          for (const file of uncovered) {\n            if (file.startsWith(dir + '/') && !filePackageMap.has(file)) {\n              filePackageMap.set(file, pkgId);\n            }\n          }\n        }\n      }\n    }\n\n    const allPackages = [...manifestPackages, ...directoryPackages];\n\n    // \u2500\u2500 5. Detect layers \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    log('architecture: detecting layers');\n    const layerAssignments: FileLayerAssignment[] = [];\n    const fileLayerMap = new Map<string, FileLayerAssignment>();\n\n    if (this.config.architectureLayers !== undefined || this.config.enableArchitecture) {\n      const assignments = await detectAllLayers(allFiles, this.projectRoot, this.config.architectureLayers);\n      for (const a of assignments) {\n        layerAssignments.push(a);\n        fileLayerMap.set(a.filePath, a);\n      }\n    }\n\n    const allLayers = buildArchLayers(layerAssignments, this.config.architectureLayers);\n\n    // \u2500\u2500 6. Roll up package dependencies from import edges \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n    log('architecture: rolling up package dependencies');\n    const importPairs = this.db.getFileImportPairs();\n    const pkgDepCounts = new Map<string, Map<string, { count: number; files: Array<{ from: string; to: string }> }>>();\n\n    for (const { sourceFile, targetFile } of importPairs) {\n      const sourcePkg = filePackageMap.get(sourceFile);\n      const targetPkg = filePackageMap.get(targetFile);\n      if (!sourcePkg || !targetPkg || sourcePkg === targetPkg) continue;\n\n      if (!pkgDepCounts.has(sourcePkg)) pkgDepCounts.set(sourcePkg, new Map());\n      const inner = pkgDepCounts.get(sourcePkg)!;\n      if (!inner.has(targetPkg)) inner.set(targetPkg, { count: 0, files: [] });\n      const entry = inner.get(targetPkg)!;\n      entry.count++;\n      if (entry.files.length < 5) entry.files.push({ from: sourceFile, to: targetFile });\n    }\n\n    const packageDeps: ArchPackageDep[] = [];\n    for (const [sourcePkg, targets] of pkgDepCounts) {\n      for (const [targetPkg, { count, files }] of targets) {\n        packageDeps.push({ sourcePkg, targetPkg, depCount: count, files });\n      }\n    }\n\n    // \u2500\u2500 7. Roll up layer dependencies \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    const layerDepCounts = new Map<string, Map<string, number>>();\n    for (const dep of packageDeps) {\n      const srcFile = [...filePackageMap.entries()].find(([, pkgId]) => pkgId === dep.sourcePkg)?.[0];\n      const tgtFile = [...filePackageMap.entries()].find(([, pkgId]) => pkgId === dep.targetPkg)?.[0];\n      const srcLayer = srcFile ? fileLayerMap.get(srcFile)?.layerName : undefined;\n      const tgtLayer = tgtFile ? fileLayerMap.get(tgtFile)?.layerName : undefined;\n      if (!srcLayer || !tgtLayer || srcLayer === tgtLayer) continue;\n      const srcLayerId = `layer:${srcLayer}`;\n      const tgtLayerId = `layer:${tgtLayer}`;\n      if (!layerDepCounts.has(srcLayerId)) layerDepCounts.set(srcLayerId, new Map());\n      const inner = layerDepCounts.get(srcLayerId)!;\n      inner.set(tgtLayerId, (inner.get(tgtLayerId) ?? 0) + dep.depCount);\n    }\n\n    const layerDeps: ArchLayerDep[] = [];\n    for (const [srcLayer, targets] of layerDepCounts) {\n      for (const [tgtLayer, count] of targets) {\n        layerDeps.push({ sourceLayer: srcLayer, targetLayer: tgtLayer, depCount: count });\n      }\n    }\n\n    // \u2500\u2500 8. Compute coupling metrics \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    const afferentMap = new Map<string, number>(); // Ca: who depends on me\n    const efferentMap = new Map<string, number>(); // Ce: who I depend on\n    for (const dep of packageDeps) {\n      efferentMap.set(dep.sourcePkg, (efferentMap.get(dep.sourcePkg) ?? 0) + 1);\n      afferentMap.set(dep.targetPkg, (afferentMap.get(dep.targetPkg) ?? 0) + 1);\n    }\n    const coupling: ArchCoupling[] = allPackages.map(pkg => {\n      const ca = afferentMap.get(pkg.id) ?? 0;\n      const ce = efferentMap.get(pkg.id) ?? 0;\n      const instability = ca + ce === 0 ? 0 : ce / (ca + ce);\n      return { packageId: pkg.id, afferent: ca, efferent: ce, instability, updatedAt: Date.now() };\n    });\n\n    // \u2500\u2500 9. Persist to DB \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\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    log('architecture: persisting to database');\n    this.db.clearArchitecture();\n\n    for (const pkg of allPackages) this.db.upsertArchPackage(pkg);\n    for (const layer of allLayers) this.db.upsertArchLayer(layer);\n\n    for (const [filePath, pkgId] of filePackageMap) this.db.upsertArchFilePackage(filePath, pkgId);\n    for (const a of layerAssignments) {\n      this.db.upsertArchFileLayer(a.filePath, `layer:${a.layerName}`, a.confidence, a.matchedPattern);\n    }\n\n    for (const dep of packageDeps) {\n      this.db.upsertArchPackageDep(dep.sourcePkg, dep.targetPkg, dep.depCount, dep.files);\n    }\n    for (const dep of layerDeps) {\n      this.db.upsertArchLayerDep(dep.sourceLayer, dep.targetLayer, dep.depCount);\n    }\n    for (const c of coupling) this.db.upsertArchCoupling(c);\n\n    // Build return value\n    const filePackages: Record<string, string[]> = {};\n    for (const [filePath, pkgId] of filePackageMap) {\n      if (!filePackages[filePath]) filePackages[filePath] = [];\n      filePackages[filePath].push(pkgId);\n    }\n\n    const fileLayers: Record<string, Array<{ layerId: string; confidence: number; matchedPattern: string }>> = {};\n    for (const a of layerAssignments) {\n      fileLayers[a.filePath] = [{ layerId: `layer:${a.layerName}`, confidence: a.confidence, matchedPattern: a.matchedPattern }];\n    }\n\n    return { packages: allPackages, layers: allLayers, packageDeps, layerDeps, coupling, filePackages, fileLayers };\n  }\n}\n"],
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   "names": []
 }

package/dist/architecture/manifest/index.js

@@ -91,8 +91,19 @@ function registerManifestParser(parser) {
   if (idx >= 0) MANIFEST_PARSERS[idx] = parser;
   else MANIFEST_PARSERS.push(parser);
 }
-async function parseAllManifests(projectRoot) {
-  const manifestPaths = _findManifests(projectRoot);
+async function parseAllManifests(projectRoot, scanOptions) {
+  let manifestPaths = _findManifests(projectRoot);
+  if (scanOptions?.include && scanOptions.include.length > 0) {
+    const picomatch = require("picomatch");
+    const includeMatchers = scanOptions.include.map((p) => picomatch(p));
+    const excludeMatchers = (scanOptions.exclude ?? []).map((p) => picomatch(p));
+    manifestPaths = manifestPaths.filter((absPath) => {
+      const rel = path.relative(projectRoot, absPath).replace(/\\/g, "/");
+      const included = includeMatchers.some((m) => m(rel));
+      if (!included) return false;
+      return !excludeMatchers.some((m) => m(rel));
+    });
+  }
   const all = [];
   const seenIds = /* @__PURE__ */ new Set();
   for (const manifestPath of manifestPaths) {

package/dist/architecture/manifest/index.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../src/architecture/manifest/index.ts"],
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 }

package/dist/architecture/manifest/python.js

@@ -35,11 +35,11 @@ var fs = __toESM(require("fs"));
 var path = __toESM(require("path"));
 const pythonParser = {
   name: "python",
-  manifestFiles: ["pyproject.toml", "setup.py", "setup.cfg"],
+  manifestFiles: ["pyproject.toml", "setup.py", "setup.cfg", "requirements.txt"],
   language: "python",
   canParse(manifestPath) {
     const base = path.basename(manifestPath);
-    return base === "pyproject.toml" || base === "setup.py" || base === "setup.cfg";
+    return base === "pyproject.toml" || base === "setup.py" || base === "setup.cfg" || base === "requirements.txt";
   },
   async parse(manifestPath, projectRoot) {
     let content;

package/dist/architecture/manifest/python.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../src/architecture/manifest/python.ts"],
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 }

package/dist/bin/commands/help.js

@@ -286,6 +286,8 @@ const GROUPS = [
       { name: "wiki page", args: "<slug>", desc: "Print the full content of a wiki page" },
       { name: "wiki list", desc: "List all wiki pages" },
       { name: "wiki lint", desc: "Health check the wiki for broken links, orphans, contradictions" },
+      { name: "wiki links", args: "<slug>", desc: "Show outgoing, broken, and incoming [[slug]] links for a page" },
+      { name: "wiki rename", args: "<from> <to>", desc: "Rename a page slug, moving its file and updating every [[slug]] reference to it" },
       { name: "wiki reindex", desc: "Rebuild SQLite index from .kirograph/wiki/*.md files" },
       { name: "wiki status", desc: "Wiki subsystem stats: page count, source count, oldest/newest page" },
       { name: "wiki synthesize", desc: "Run local-model wiki synthesis over the pending source queue" },
@@ -343,7 +345,7 @@ const GROUPS = [
           "--add <cveId>  Manually register a CVE (requires --package and --version)"
         ]
       },
-      { name: "reachability", args: "<target>", desc: "Check reachability for a CVE or dependency: verdict, call paths, impact" },
+      { name: "reachability", args: "<target>", desc: "Check reachability for a CVE or dependency: verdict, call paths, impact", opts: ["--explain  Plain-English reason for the verdict"] },
       {
         name: "vuln suppress",
         args: "<cveId>",