repogenome 0.1.0

package/dist/cli.js

@@ -0,0 +1,1998 @@
+#!/usr/bin/env node
+
+// src/cli.ts
+import { Command as Command5 } from "commander";
+import { createRequire as createRequire2 } from "module";
+
+// src/banner.ts
+import chalk from "chalk";
+import { createRequire } from "module";
+var _MUGM = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var require2 = createRequire(import.meta.url);
+var { version } = require2("../package.json");
+function printBanner() {
+  const g = chalk.green;
+  const w = chalk.white.bold;
+  const d = chalk.gray;
+  console.log();
+  console.log(w(" \u2588\u2588\u2588\u2588\u2588\u2588\u2557 \u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557\u2588\u2588\u2588\u2588\u2588\u2588\u2557  \u2588\u2588\u2588\u2588\u2588\u2588\u2557  \u2588\u2588\u2588\u2588\u2588\u2588\u2557 \u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557\u2588\u2588\u2588\u2557   \u2588\u2588\u2557 \u2588\u2588\u2588\u2588\u2588\u2588\u2557 \u2588\u2588\u2588\u2557   \u2588\u2588\u2588\u2557\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557"));
+  console.log(w(" \u2588\u2588\u2554\u2550\u2550\u2588\u2588\u2557\u2588\u2588\u2554\u2550\u2550\u2550\u2550\u255D\u2588\u2588\u2554\u2550\u2550\u2588\u2588\u2557\u2588\u2588\u2554\u2550\u2550\u2550\u2588\u2588\u2557\u2588\u2588\u2554\u2550\u2550\u2550\u2550\u255D \u2588\u2588\u2554\u2550\u2550\u2550\u2550\u255D\u2588\u2588\u2588\u2588\u2557  \u2588\u2588\u2551\u2588\u2588\u2554\u2550\u2550\u2550\u2588\u2588\u2557\u2588\u2588\u2588\u2588\u2557 \u2588\u2588\u2588\u2588\u2551\u2588\u2588\u2554\u2550\u2550\u2550\u2550\u255D"));
+  console.log(g(" \u2588\u2588\u2588\u2588\u2588\u2588\u2554\u255D\u2588\u2588\u2588\u2588\u2588\u2557  \u2588\u2588\u2588\u2588\u2588\u2588\u2554\u255D\u2588\u2588\u2551   \u2588\u2588\u2551\u2588\u2588\u2551  \u2588\u2588\u2588\u2557\u2588\u2588\u2588\u2588\u2588\u2557  \u2588\u2588\u2554\u2588\u2588\u2557 \u2588\u2588\u2551\u2588\u2588\u2551   \u2588\u2588\u2551\u2588\u2588\u2554\u2588\u2588\u2588\u2588\u2554\u2588\u2588\u2551\u2588\u2588\u2588\u2588\u2588\u2557  "));
+  console.log(w(" \u2588\u2588\u2554\u2550\u2550\u2588\u2588\u2557\u2588\u2588\u2554\u2550\u2550\u255D  \u2588\u2588\u2554\u2550\u2550\u2550\u255D \u2588\u2588\u2551   \u2588\u2588\u2551\u2588\u2588\u2551   \u2588\u2588\u2551\u2588\u2588\u2554\u2550\u2550\u255D  \u2588\u2588\u2551\u255A\u2588\u2588\u2557\u2588\u2588\u2551\u2588\u2588\u2551   \u2588\u2588\u2551\u2588\u2588\u2551\u255A\u2588\u2588\u2554\u255D\u2588\u2588\u2551\u2588\u2588\u2554\u2550\u2550\u255D  "));
+  console.log(w(" \u2588\u2588\u2551  \u2588\u2588\u2551\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557\u2588\u2588\u2551     \u255A\u2588\u2588\u2588\u2588\u2588\u2588\u2554\u255D\u255A\u2588\u2588\u2588\u2588\u2588\u2588\u2554\u255D\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557\u2588\u2588\u2551 \u255A\u2588\u2588\u2588\u2588\u2551\u255A\u2588\u2588\u2588\u2588\u2588\u2588\u2554\u255D\u2588\u2588\u2551 \u255A\u2550\u255D \u2588\u2588\u2551\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557"));
+  console.log(d(" \u255A\u2550\u255D  \u255A\u2550\u255D\u255A\u2550\u2550\u2550\u2550\u2550\u2550\u255D\u255A\u2550\u255D      \u255A\u2550\u2550\u2550\u2550\u2550\u255D  \u255A\u2550\u2550\u2550\u2550\u2550\u255D \u255A\u2550\u2550\u2550\u2550\u2550\u2550\u255D\u255A\u2550\u255D  \u255A\u2550\u2550\u2550\u255D \u255A\u2550\u2550\u2550\u2550\u2550\u255D \u255A\u2550\u255D     \u255A\u2550\u255D\u255A\u2550\u2550\u2550\u2550\u2550\u2550\u255D"));
+  console.log();
+  console.log(d(" \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500"));
+  console.log(d("   git for software architecture  \xB7  snapshot \xB7 drift \xB7 blame \xB7 compare"));
+  console.log();
+  console.log(g("   \u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8"));
+  console.log(d("    \u2572   \u2571   \u2572   \u2571   \u2572   \u2571   \u2572   \u2571   \u2572   \u2571   \u2572   \u2571   \u2572   \u2571   \u2572   \u2571   \u2572   \u2571   \u2572   \u2571   \u2572  "));
+  console.log(w("   \u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9\u2500\u254C\u2500\u25C8\u2500\u254C\u2500\u25C9"));
+  console.log();
+  console.log(d(`   v${version}  \xB7  MIT  \xB7  npx repogenome init`));
+  console.log();
+}
+
+// src/commands/init.ts
+import { Command } from "commander";
+import { mkdir, writeFile, access } from "fs/promises";
+import { join as join5, resolve } from "path";
+import { createInterface } from "readline";
+import chalk3 from "chalk";
+import ora from "ora";
+
+// src/scanner/walker.ts
+import { readdir } from "fs/promises";
+import { join, relative } from "path";
+var _MUGM2 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var SKIP_DIRS = /* @__PURE__ */ new Set([
+  "node_modules",
+  ".git",
+  "dist",
+  "build",
+  "coverage",
+  ".next",
+  ".nuxt",
+  ".cache",
+  "__pycache__",
+  ".tox",
+  "vendor",
+  "target",
+  ".gradle",
+  "bin",
+  "obj"
+]);
+function isHidden(name) {
+  return name.startsWith(".") && name !== ".";
+}
+async function walkFiles(rootPath) {
+  const results = [];
+  async function walk(dir) {
+    let entries;
+    try {
+      entries = await readdir(dir, { withFileTypes: true });
+    } catch {
+      return;
+    }
+    for (const entry of entries) {
+      if (SKIP_DIRS.has(entry.name) || isHidden(entry.name)) continue;
+      const fullPath = join(dir, entry.name);
+      if (entry.isDirectory()) {
+        await walk(fullPath);
+      } else if (entry.isFile()) {
+        results.push(relative(rootPath, fullPath).replace(/\\/g, "/"));
+      }
+    }
+  }
+  await walk(rootPath);
+  return results;
+}
+
+// src/scanner/classifier.ts
+import { basename, extname, dirname } from "path";
+var _MUGM3 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var EXT_LANG_MAP = {
+  ".ts": "typescript",
+  ".tsx": "typescript",
+  ".js": "javascript",
+  ".jsx": "javascript",
+  ".mjs": "javascript",
+  ".cjs": "javascript",
+  ".py": "python",
+  ".go": "go",
+  ".java": "java",
+  ".kt": "kotlin",
+  ".kts": "kotlin"
+};
+function classifyFile(relativePath) {
+  const ext = extname(relativePath).toLowerCase();
+  const language = EXT_LANG_MAP[ext];
+  if (!language) return null;
+  return {
+    path: relativePath,
+    name: basename(relativePath, ext),
+    extension: ext,
+    directory: dirname(relativePath).replace(/\\/g, "/"),
+    language
+  };
+}
+function classifyFiles(paths) {
+  return paths.flatMap((p) => {
+    const info = classifyFile(p);
+    return info ? [info] : [];
+  });
+}
+
+// src/scanner/naming.ts
+var _MUGM4 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var KNOWN_PREFIXES = ["get", "set", "create", "update", "delete", "fetch", "handle", "build", "make", "find", "load", "save", "send", "parse", "format"];
+var KNOWN_SUFFIXES = [".service", ".repository", ".controller", ".handler", ".middleware", ".factory", ".manager", ".helper", ".util", ".model", ".entity", ".dto", ".spec", ".test", ".config", ".module", ".resolver", ".guard", ".pipe", ".decorator"];
+function detectCasing(name) {
+  if (/^[a-z][a-zA-Z0-9]*$/.test(name) && /[A-Z]/.test(name)) return "camelCase";
+  if (/^[A-Z][a-zA-Z0-9]*$/.test(name)) return "PascalCase";
+  if (/^[a-z][a-z0-9_]*$/.test(name) && name.includes("_")) return "snake_case";
+  if (/^[a-z][a-z0-9-]*$/.test(name) && name.includes("-")) return "kebab-case";
+  return null;
+}
+function increment(map, key) {
+  map[key] = (map[key] ?? 0) + 1;
+}
+function extractNamingSignals(files) {
+  const prefixes = {};
+  const suffixes = {};
+  const casing = {};
+  for (const file of files) {
+    const name = file.name.toLowerCase();
+    for (const prefix of KNOWN_PREFIXES) {
+      if (name.startsWith(prefix)) {
+        increment(prefixes, prefix);
+        break;
+      }
+    }
+    const fullName = file.name + file.extension;
+    for (const suffix of KNOWN_SUFFIXES) {
+      if (fullName.toLowerCase().includes(suffix)) {
+        increment(suffixes, suffix);
+        break;
+      }
+    }
+    const casingStyle = detectCasing(file.name);
+    if (casingStyle) increment(casing, casingStyle);
+  }
+  return { prefixes, suffixes, casing };
+}
+
+// src/scanner/imports.ts
+import { readFile } from "fs/promises";
+import { join as join2 } from "path";
+var _MUGM5 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var PATTERNS = {
+  typescript: [
+    /import\s+(?:[\w*{},\s]+)\s+from\s+['"]([^'"]+)['"]/g,
+    /require\s*\(\s*['"]([^'"]+)['"]\s*\)/g
+  ],
+  javascript: [
+    /import\s+(?:[\w*{},\s]+)\s+from\s+['"]([^'"]+)['"]/g,
+    /require\s*\(\s*['"]([^'"]+)['"]\s*\)/g
+  ],
+  python: [
+    /^import\s+([\w.]+)/gm,
+    /^from\s+([\w.]+)\s+import/gm
+  ],
+  go: [
+    /import\s+"([^"]+)"/g,
+    /^\s+"([^"]+)"/gm
+  ],
+  java: [
+    /^import\s+([\w.]+);/gm
+  ],
+  kotlin: [
+    /^import\s+([\w.]+)/gm
+  ]
+};
+async function extractImports(rootPath, files) {
+  const result = {};
+  await Promise.all(
+    files.map(async (file) => {
+      const patterns = PATTERNS[file.language];
+      if (!patterns) return;
+      let content;
+      try {
+        content = await readFile(join2(rootPath, file.path), "utf-8");
+      } catch {
+        return;
+      }
+      const imports = /* @__PURE__ */ new Set();
+      for (const pattern of patterns) {
+        pattern.lastIndex = 0;
+        let match;
+        while ((match = pattern.exec(content)) !== null) {
+          if (match[1]) imports.add(match[1]);
+        }
+      }
+      if (imports.size > 0) {
+        result[file.path] = [...imports];
+      }
+    })
+  );
+  return result;
+}
+
+// src/scanner/structure.ts
+var _MUGM6 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function analyzeDirectoryStructure(files) {
+  const dirMap = /* @__PURE__ */ new Map();
+  for (const file of files) {
+    const dir = file.directory || ".";
+    if (!dirMap.has(dir)) dirMap.set(dir, { files: [] });
+    dirMap.get(dir).files.push(file);
+  }
+  for (const dir of [...dirMap.keys()]) {
+    const parts = dir.split("/");
+    for (let i = 1; i < parts.length; i++) {
+      const parent = parts.slice(0, i).join("/");
+      if (!dirMap.has(parent)) dirMap.set(parent, { files: [] });
+    }
+  }
+  const infos = [];
+  for (const [path, { files: dirFiles }] of dirMap) {
+    const depth = path === "." ? 0 : path.split("/").length;
+    const languages = [...new Set(dirFiles.map((f) => f.language))];
+    const isMixed = languages.length > 1 || dirFiles.length > 0 && hasMultiplePurposes(dirFiles);
+    infos.push({
+      path,
+      depth,
+      fileCount: dirFiles.length,
+      languages,
+      isMixed
+    });
+  }
+  return infos.sort((a, b) => a.depth - b.depth || a.path.localeCompare(b.path));
+}
+function hasMultiplePurposes(files) {
+  const ROLE_MARKERS = [".service", ".controller", ".repository", ".model", ".handler", ".middleware"];
+  const roles = /* @__PURE__ */ new Set();
+  for (const file of files) {
+    const fullName = (file.name + file.extension).toLowerCase();
+    for (const marker of ROLE_MARKERS) {
+      if (fullName.includes(marker)) {
+        roles.add(marker);
+        break;
+      }
+    }
+  }
+  return roles.size > 1;
+}
+
+// src/scanner/identifiers.ts
+import { readFile as readFile2 } from "fs/promises";
+import { join as join3 } from "path";
+var _MUGM7 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var PATTERNS2 = {
+  typescript: [
+    /class\s+(\w+)/g,
+    /function\s+(\w+)/g,
+    /(?:const|let|var)\s+(\w+)\s*=/g,
+    /interface\s+(\w+)/g,
+    /type\s+(\w+)\s*=/g,
+    /enum\s+(\w+)/g
+  ],
+  javascript: [
+    /class\s+(\w+)/g,
+    /function\s+(\w+)/g,
+    /(?:const|let|var)\s+(\w+)\s*=/g
+  ],
+  python: [
+    /^class\s+(\w+)/gm,
+    /^def\s+(\w+)/gm,
+    /^(\w+)\s*=/gm
+  ],
+  go: [
+    /^func\s+(\w+)/gm,
+    /^type\s+(\w+)/gm,
+    /^var\s+(\w+)/gm
+  ],
+  java: [
+    /class\s+(\w+)/g,
+    /interface\s+(\w+)/g,
+    /(?:public|private|protected)\s+\w+\s+(\w+)\s*\(/g
+  ],
+  kotlin: [
+    /class\s+(\w+)/g,
+    /fun\s+(\w+)/g,
+    /(?:val|var)\s+(\w+)/g
+  ]
+};
+var GENERIC_WORDS = /* @__PURE__ */ new Set([
+  "index",
+  "main",
+  "app",
+  "i",
+  "j",
+  "k",
+  "x",
+  "y",
+  "z",
+  "err",
+  "error",
+  "result",
+  "res",
+  "req",
+  "ctx",
+  "next",
+  "true",
+  "false",
+  "null",
+  "undefined"
+]);
+async function extractIdentifiers(rootPath, files) {
+  const result = {};
+  await Promise.all(
+    files.map(async (file) => {
+      const patterns = PATTERNS2[file.language];
+      if (!patterns) return;
+      let content;
+      try {
+        content = await readFile2(join3(rootPath, file.path), "utf-8");
+      } catch {
+        return;
+      }
+      const identifiers = /* @__PURE__ */ new Set();
+      for (const pattern of patterns) {
+        pattern.lastIndex = 0;
+        let match;
+        while ((match = pattern.exec(content)) !== null) {
+          const name = match[1];
+          if (name && name.length > 1 && !GENERIC_WORDS.has(name.toLowerCase())) {
+            identifiers.add(name);
+          }
+        }
+      }
+      if (identifiers.size > 0) {
+        result[file.path] = [...identifiers];
+      }
+    })
+  );
+  return result;
+}
+
+// src/scanner/index.ts
+var _MUGM8 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+async function scan(rootPath) {
+  const allPaths = await walkFiles(rootPath);
+  const files = classifyFiles(allPaths);
+  const [imports, identifiers] = await Promise.all([
+    extractImports(rootPath, files),
+    extractIdentifiers(rootPath, files)
+  ]);
+  const naming = extractNamingSignals(files);
+  const directories = analyzeDirectoryStructure(files);
+  return { files, directories, naming, imports, identifiers };
+}
+
+// src/analyzer/index.ts
+import { readFile as readFile3 } from "fs/promises";
+import { join as join4 } from "path";
+
+// src/analyzer/architecture.ts
+var _MUGM9 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var LAYER_KEYWORDS = /* @__PURE__ */ new Set(["controller", "controllers", "service", "services", "repository", "repositories", "model", "models", "middleware", "route", "routes", "handler", "handlers", "resolver", "resolvers"]);
+var MODULAR_INDICATORS = /* @__PURE__ */ new Set(["auth", "billing", "payments", "notifications", "users", "orders", "products", "admin", "core", "shared", "accounts", "inventory", "catalog", "reporting"]);
+function basename2(p) {
+  return p.split("/").pop().toLowerCase();
+}
+function parentOf(p) {
+  const parts = p.split("/");
+  return parts.length > 1 ? parts.slice(0, -1).join("/") : "";
+}
+function detectArchitecture(directories) {
+  const maxDepth = Math.max(0, ...directories.map((d) => d.depth));
+  const byParent = /* @__PURE__ */ new Map();
+  for (const dir of directories) {
+    const parent = parentOf(dir.path);
+    if (!byParent.has(parent)) byParent.set(parent, []);
+    byParent.get(parent).push(basename2(dir.path));
+  }
+  for (const [parent, children] of byParent) {
+    const domainChildren = children.filter((c) => MODULAR_INDICATORS.has(c));
+    if (domainChildren.length >= 2) {
+      const domainWithLayers = domainChildren.filter((dc) => {
+        const subChildren = byParent.get(parent ? `${parent}/${dc}` : dc) ?? [];
+        return subChildren.some((sc) => LAYER_KEYWORDS.has(sc));
+      });
+      if (domainWithLayers.length >= 1) {
+        const confidence = Math.min(0.99, 0.4 + domainChildren.length * 0.1);
+        return { style: "modular", layers: domainChildren, depth: maxDepth, confidence };
+      }
+    }
+  }
+  for (const [, children] of byParent) {
+    const layerChildren = children.filter((c) => LAYER_KEYWORDS.has(c));
+    if (layerChildren.length >= 2) {
+      const confidence = Math.min(0.99, 0.5 + layerChildren.length * 0.1);
+      return { style: "layered", layers: layerChildren, depth: maxDepth, confidence };
+    }
+  }
+  return { style: "flat", layers: [], depth: maxDepth, confidence: 0.5 };
+}
+
+// src/analyzer/patterns.ts
+var _MUGM10 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var PATTERN_RULES = {
+  repository: {
+    fileNameMatches: [/\.repository\./i, /Repository\./],
+    identifierMatches: [/Repository$/]
+  },
+  service: {
+    fileNameMatches: [/\.service\./i, /Service\./],
+    identifierMatches: [/Service$/]
+  },
+  controller: {
+    fileNameMatches: [/\.controller\./i, /Controller\./],
+    identifierMatches: [/Controller$/]
+  },
+  factory: {
+    fileNameMatches: [/\.factory\./i, /Factory\./],
+    identifierMatches: [/Factory$/, /^create[A-Z]/]
+  },
+  middleware: {
+    fileNameMatches: [/\.middleware\./i, /Middleware\./],
+    identifierMatches: [/Middleware$/],
+    dirMatches: [/middleware/i]
+  },
+  handler: {
+    fileNameMatches: [/\.handler\./i, /Handler\./],
+    identifierMatches: [/Handler$/]
+  },
+  manager: {
+    fileNameMatches: [/\.manager\./i, /Manager\./],
+    identifierMatches: [/Manager$/]
+  }
+};
+function detectPatterns(files, identifiers) {
+  const results = {};
+  for (const [patternName, rule] of Object.entries(PATTERN_RULES)) {
+    const matchedFiles = /* @__PURE__ */ new Set();
+    for (const file of files) {
+      const fullName = file.name + file.extension;
+      const nameMatch = rule.fileNameMatches.some((r) => r.test(fullName));
+      const dirMatch = rule.dirMatches?.some((r) => r.test(file.directory)) ?? false;
+      if (nameMatch || dirMatch) {
+        matchedFiles.add(file.path);
+        continue;
+      }
+      const fileIdentifiers = identifiers[file.path] ?? [];
+      const identifierMatch = fileIdentifiers.some((id) => rule.identifierMatches.some((r) => r.test(id)));
+      if (identifierMatch) matchedFiles.add(file.path);
+    }
+    const count = matchedFiles.size;
+    const detected = count > 0;
+    const confidence = detected ? Math.min(0.99, 0.4 + count / Math.max(files.length, 1) * 3) : 0;
+    results[patternName] = { detected, confidence: parseFloat(confidence.toFixed(2)), count, files: [...matchedFiles] };
+  }
+  return results;
+}
+
+// src/analyzer/naming.ts
+var _MUGM11 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function topKeys(map, n = 5) {
+  return Object.entries(map).sort((a, b) => b[1] - a[1]).slice(0, n).map(([k]) => k);
+}
+function dominantKey(map) {
+  let best = "";
+  let max = 0;
+  for (const [k, v] of Object.entries(map)) {
+    if (v > max) {
+      max = v;
+      best = k;
+    }
+  }
+  return best;
+}
+function analyzeNaming(signals) {
+  return {
+    prefixes: topKeys(signals.prefixes),
+    suffixes: topKeys(signals.suffixes),
+    casing: dominantKey(signals.casing) || "camelCase"
+  };
+}
+
+// src/analyzer/concepts.ts
+var _MUGM12 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var GENERIC_WORDS2 = /* @__PURE__ */ new Set([
+  "index",
+  "main",
+  "app",
+  "utils",
+  "util",
+  "helpers",
+  "helper",
+  "common",
+  "base",
+  "abstract",
+  "shared",
+  "types",
+  "type",
+  "interface",
+  "config",
+  "constant",
+  "constants",
+  "enum",
+  "enums",
+  "default",
+  "test",
+  "spec",
+  "mock",
+  "stub",
+  "fixture",
+  "error",
+  "errors",
+  "exception",
+  "logger",
+  "log",
+  "debug",
+  "console",
+  "init",
+  "setup",
+  "boot",
+  "start",
+  "run",
+  "get",
+  "set",
+  "create",
+  "update",
+  "delete",
+  "fetch",
+  "handle",
+  "build",
+  "make",
+  "find",
+  "load",
+  "save",
+  "send",
+  "parse",
+  "format",
+  "validate",
+  "dto",
+  "vo",
+  "entity",
+  "module",
+  "component",
+  "service",
+  "controller",
+  "repository",
+  "middleware",
+  "handler",
+  "factory",
+  "manager",
+  "provider",
+  "resolver",
+  "guard",
+  "pipe",
+  "decorator",
+  "mixin",
+  "plugin"
+]);
+function splitIntoWords(identifier) {
+  return identifier.replace(/([a-z])([A-Z])/g, "$1 $2").replace(/([A-Z]+)([A-Z][a-z])/g, "$1 $2").replace(/[_\-./]/g, " ").split(" ").map((w) => w.toLowerCase()).filter((w) => w.length > 2);
+}
+function extractConcepts(identifiers, directories, topN = 20) {
+  const freq = {};
+  for (const dir of directories) {
+    const parts = dir.split("/");
+    for (const part of parts) {
+      const words = splitIntoWords(part);
+      for (const word of words) {
+        if (!GENERIC_WORDS2.has(word) && word.length > 2) {
+          freq[word] = (freq[word] ?? 0) + 3;
+        }
+      }
+    }
+  }
+  for (const ids of Object.values(identifiers)) {
+    for (const id of ids) {
+      const words = splitIntoWords(id);
+      for (const word of words) {
+        if (!GENERIC_WORDS2.has(word) && word.length > 2) {
+          freq[word] = (freq[word] ?? 0) + 1;
+        }
+      }
+    }
+  }
+  return Object.entries(freq).sort((a, b) => b[1] - a[1]).slice(0, topN).map(([word]) => word);
+}
+
+// src/analyzer/dependencies.ts
+var _MUGM13 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var DB_CLIENTS = ["prisma", "mongoose", "sequelize", "typeorm", "knex", "pg", "mysql", "sqlite", "mongodb", "redis", "drizzle", "@prisma/client", "pg-promise"];
+var LAYER_ORDER = {
+  controller: 0,
+  controllers: 0,
+  route: 0,
+  routes: 0,
+  resolver: 0,
+  resolvers: 0,
+  service: 1,
+  services: 1,
+  repository: 2,
+  repositories: 2,
+  model: 3,
+  models: 3,
+  entity: 3,
+  entities: 3
+};
+function getLayer(filePath) {
+  const parts = filePath.toLowerCase().split("/");
+  for (const part of parts) {
+    if (part in LAYER_ORDER) return LAYER_ORDER[part];
+  }
+  return -1;
+}
+function dirOf(filePath) {
+  const parts = filePath.split("/");
+  return parts.length > 1 ? parts[0] : ".";
+}
+function analyzeDependencies(files, imports) {
+  let directDbAccess = 0;
+  let crossLayerViolations = 0;
+  for (const file of files) {
+    const fileImports = imports[file.path] ?? [];
+    const fileLayer = getLayer(file.path);
+    for (const imp of fileImports) {
+      const impLower = imp.toLowerCase();
+      const isDbClient = DB_CLIENTS.some((db) => impLower.includes(db));
+      if (isDbClient && fileLayer !== 2 && fileLayer !== 3) {
+        directDbAccess++;
+      }
+      if (fileLayer === 0) {
+        const impLayer = getLayer(imp);
+        if (impLayer === 2) crossLayerViolations++;
+      }
+    }
+  }
+  const adjMap = {};
+  for (const file of files) {
+    const fileDir = dirOf(file.path);
+    adjMap[fileDir] = adjMap[fileDir] ?? [];
+    for (const imp of imports[file.path] ?? []) {
+      if (imp.startsWith(".")) {
+        const parts = imp.replace(/^\.\//, "").split("/");
+        if (parts.length > 1) {
+          const targetDir = parts[0];
+          if (targetDir !== fileDir && !adjMap[fileDir].includes(targetDir)) {
+            adjMap[fileDir].push(targetDir);
+          }
+        }
+      }
+    }
+  }
+  const circularImports = countCycles(adjMap);
+  return { directDbAccess, crossLayerViolations, circularImports };
+}
+function countCycles(graph) {
+  const visited = /* @__PURE__ */ new Set();
+  const inStack = /* @__PURE__ */ new Set();
+  let cycles = 0;
+  function dfs(node) {
+    visited.add(node);
+    inStack.add(node);
+    for (const neighbor of graph[node] ?? []) {
+      if (!visited.has(neighbor)) {
+        dfs(neighbor);
+      } else if (inStack.has(neighbor)) {
+        cycles++;
+      }
+    }
+    inStack.delete(node);
+  }
+  for (const node of Object.keys(graph)) {
+    if (!visited.has(node)) dfs(node);
+  }
+  return cycles;
+}
+
+// src/analyzer/index.ts
+var _MUGM14 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+async function computeSizes(rootPath, signals) {
+  const lineCounts = await Promise.all(
+    signals.files.map(async (f) => {
+      try {
+        const content = await readFile3(join4(rootPath, f.path), "utf-8");
+        return { path: f.path, lines: content.split("\n").length };
+      } catch {
+        return { path: f.path, lines: 0 };
+      }
+    })
+  );
+  const totalLines = lineCounts.reduce((sum, f) => sum + f.lines, 0);
+  const avgFileLines = signals.files.length > 0 ? Math.round(totalLines / signals.files.length) : 0;
+  const largestFiles = [...lineCounts].sort((a, b) => b.lines - a.lines).slice(0, 5).map((f) => f.path);
+  return { totalFiles: signals.files.length, avgFileLines, largestFiles };
+}
+async function analyze(signals, rootPath = ".") {
+  const architecture = detectArchitecture(signals.directories);
+  const patterns = detectPatterns(signals.files, signals.identifiers);
+  const naming = analyzeNaming(signals.naming);
+  const concepts = extractConcepts(
+    signals.identifiers,
+    signals.directories.map((d) => d.path)
+  );
+  const dependencies = analyzeDependencies(signals.files, signals.imports);
+  const sizes = await computeSizes(rootPath, signals);
+  return {
+    version: 1,
+    timestamp: (/* @__PURE__ */ new Date()).toISOString(),
+    architecture,
+    patterns,
+    naming,
+    concepts,
+    dependencies,
+    sizes
+  };
+}
+
+// src/output/initReport.ts
+import chalk2 from "chalk";
+var _MUGM15 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var SEP = chalk2.gray("\u2500".repeat(51));
+function label(text) {
+  return chalk2.gray(text.padEnd(18));
+}
+function val(text) {
+  return chalk2.white(text);
+}
+function printInitReport(genome) {
+  const { architecture, patterns, naming, concepts, dependencies, sizes } = genome;
+  console.log();
+  console.log(chalk2.green.bold("RepoGenome Init"));
+  console.log(SEP);
+  console.log();
+  console.log(chalk2.gray(`Scanning ${sizes.totalFiles} files across ${genome.architecture.layers.length || 1} ${architecture.style === "modular" ? "modules" : "layers"}...`));
+  console.log();
+  console.log(chalk2.green.bold("Genome Captured"));
+  console.log();
+  const layerStr = architecture.layers.length > 0 ? `${architecture.layers.join(" \u2192 ")} (${architecture.layers.length} layers)` : `depth ${architecture.depth}`;
+  console.log(`${label("Architecture:")}${val(`${capitalise(architecture.style)} \u2014 ${layerStr}`)}`);
+  const detectedPatterns = Object.entries(patterns).filter(([, p]) => p.detected).map(([name, p]) => `${capitalise(name)} (${p.count})`).join(", ");
+  console.log(`${label("Patterns:")}${val(detectedPatterns || "none detected")}`);
+  const namingParts = [naming.casing];
+  if (naming.prefixes.length) namingParts.push(naming.prefixes.map((p) => `${p}*`).join(" \xB7 "));
+  if (naming.suffixes.length) namingParts.push(naming.suffixes.join(" \xB7 "));
+  console.log(`${label("Naming:")}${val(namingParts.join("  \xB7  "))}`);
+  console.log(`${label("Concepts:")}${val(concepts.slice(0, 8).join(" \xB7 ") || "none")}`);
+  console.log(`${label("Direct DB Access:")}${val(String(dependencies.directDbAccess) + " files")}`);
+  console.log(`${label("Cross-layer:")}${val(dependencies.crossLayerViolations + " violations")}`);
+  console.log(`${label("Circular Imports:")}${val(String(dependencies.circularImports))}`);
+  console.log(`${label("Avg file size:")}${val(sizes.avgFileLines + " lines")}`);
+  console.log();
+  console.log(SEP);
+  console.log(chalk2.green("  Baseline saved to ") + chalk2.white(".repogenome/genome.json"));
+  console.log(chalk2.gray("  Commit this file to track drift over time."));
+  console.log();
+  console.log(chalk2.gray("  Tip: add .repogenome/history/ to .gitignore"));
+  console.log();
+}
+function capitalise(s) {
+  return s.charAt(0).toUpperCase() + s.slice(1);
+}
+
+// src/output/json.ts
+var _MUGM16 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function buildJsonEnvelope(command, data) {
+  return {
+    version: 1,
+    command,
+    timestamp: (/* @__PURE__ */ new Date()).toISOString(),
+    data
+  };
+}
+function printJson(command, data) {
+  console.log(JSON.stringify(buildJsonEnvelope(command, data), null, 2));
+}
+
+// src/commands/init.ts
+var _MUGM17 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+async function fileExists(p) {
+  try {
+    await access(p);
+    return true;
+  } catch {
+    return false;
+  }
+}
+async function prompt(question) {
+  const rl = createInterface({ input: process.stdin, output: process.stdout });
+  return new Promise((resolve5) => rl.question(question, (ans) => {
+    rl.close();
+    resolve5(ans.trim());
+  }));
+}
+function initCommand() {
+  return new Command("init").description("Scan the repository and create a baseline genome").option("--path <dir>", "Scan a subdirectory instead of root", ".").option("--lang <language>", "Hint the primary language (auto-detected by default)").option("--format <fmt>", "Output format: terminal | json", "terminal").option("--silent", "No output, just write the file").action(async (options) => {
+    const rootPath = resolve(options.path);
+    const outputDir = join5(rootPath, ".repogenome");
+    const outputFile = join5(outputDir, "genome.json");
+    const silent = options.silent ?? false;
+    const isJson = options.format === "json";
+    try {
+      if (await fileExists(outputFile)) {
+        if (silent) {
+        } else {
+          const answer = await prompt(chalk3.yellow("  Baseline already exists. Overwrite? (y/n) "));
+          if (answer.toLowerCase() !== "y") {
+            console.log(chalk3.gray("  Aborted."));
+            process.exit(0);
+          }
+        }
+      }
+      const spinner = silent || isJson ? null : ora({ text: chalk3.gray("Scanning files\u2026"), color: "green" }).start();
+      const signals = await scan(rootPath);
+      if (signals.files.length === 0) {
+        spinner?.fail(chalk3.red("No supported files found. Nothing to scan."));
+        process.exit(3);
+      }
+      if (spinner) spinner.text = chalk3.gray("Building genome\u2026");
+      const genome = await analyze(signals, rootPath);
+      spinner?.stop();
+      await mkdir(outputDir, { recursive: true });
+      await writeFile(outputFile, JSON.stringify(genome, null, 2), "utf-8");
+      if (!silent) {
+        if (isJson) {
+          printJson("init", genome);
+        } else {
+          printInitReport(genome);
+        }
+      }
+    } catch (err) {
+      const message = err instanceof Error ? err.message : String(err);
+      console.error(chalk3.red(`  Error: ${message}`));
+      process.exit(3);
+    }
+  });
+}
+
+// src/commands/audit.ts
+import { Command as Command2 } from "commander";
+import { readFile as readFile5, writeFile as writeFile3, mkdir as mkdir2, access as access2 } from "fs/promises";
+import { join as join6, resolve as resolve2 } from "path";
+import chalk5 from "chalk";
+import ora2 from "ora";
+
+// src/diff/architecture.ts
+var _MUGM18 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function diffArchitecture(a, b) {
+  const details = [];
+  let score = 0;
+  if (a.architecture.style !== b.architecture.style) {
+    score += 0.6;
+    details.push(`architecture style changed: ${a.architecture.style} \u2192 ${b.architecture.style}`);
+  }
+  const aLayers = new Set(a.architecture.layers);
+  const bLayers = new Set(b.architecture.layers);
+  const added = b.architecture.layers.filter((l) => !aLayers.has(l));
+  const removed = a.architecture.layers.filter((l) => !bLayers.has(l));
+  if (added.length) {
+    score += Math.min(0.2, added.length * 0.07);
+    details.push(`layers added: ${added.join(", ")}`);
+  }
+  if (removed.length) {
+    score += Math.min(0.2, removed.length * 0.07);
+    details.push(`layers removed: ${removed.join(", ")}`);
+  }
+  const depthDelta = Math.abs(b.architecture.depth - a.architecture.depth);
+  if (depthDelta > 0) {
+    score += Math.min(0.1, depthDelta * 0.03);
+    details.push(`nesting depth changed: ${a.architecture.depth} \u2192 ${b.architecture.depth}`);
+  }
+  return { score: Math.min(1, parseFloat(score.toFixed(3))), details };
+}
+
+// src/diff/patterns.ts
+var _MUGM19 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function diffPatterns(a, b) {
+  const details = [];
+  const added = [];
+  const removed = [];
+  const changed = [];
+  let score = 0;
+  const allKeys = /* @__PURE__ */ new Set([...Object.keys(a.patterns), ...Object.keys(b.patterns)]);
+  for (const key of allKeys) {
+    const pa = a.patterns[key];
+    const pb = b.patterns[key];
+    if (!pa?.detected && pb?.detected) {
+      added.push(key);
+      score += 0.15;
+      details.push(`+ ${key} pattern introduced (confidence: ${pb.confidence}, ${pb.count} files)`);
+    } else if (pa?.detected && !pb?.detected) {
+      removed.push(key);
+      score += 0.2;
+      details.push(`- ${key} pattern removed`);
+    } else if (pa?.detected && pb?.detected) {
+      const drop = pa.confidence - pb.confidence;
+      if (drop > 0.2) {
+        changed.push(key);
+        score += drop * 0.3;
+        details.push(`~ ${key} pattern weakening  ${(pa.confidence * 100).toFixed(0)}% \u2192 ${(pb.confidence * 100).toFixed(0)}% presence`);
+      }
+    }
+  }
+  return {
+    dimension: { score: Math.min(1, parseFloat(score.toFixed(3))), details },
+    added,
+    removed,
+    changed
+  };
+}
+
+// src/diff/naming.ts
+var _MUGM20 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function diffNaming(a, b) {
+  const details = [];
+  const changed = [];
+  let score = 0;
+  if (a.naming.casing !== b.naming.casing) {
+    score += 0.5;
+    details.push(`casing changed: ${a.naming.casing} \u2192 ${b.naming.casing}`);
+    changed.push(`casing: ${a.naming.casing} \u2192 ${b.naming.casing}`);
+  }
+  const aPreSet = new Set(a.naming.prefixes);
+  const bPreSet = new Set(b.naming.prefixes);
+  const newPrefixes = b.naming.prefixes.filter((p) => !aPreSet.has(p));
+  const gonePrefixes = a.naming.prefixes.filter((p) => !bPreSet.has(p));
+  if (newPrefixes.length) {
+    score += Math.min(0.2, newPrefixes.length * 0.05);
+    details.push(`new prefixes: ${newPrefixes.join(", ")}`);
+    changed.push(`new prefixes: ${newPrefixes.join(", ")}`);
+  }
+  if (gonePrefixes.length) {
+    score += Math.min(0.15, gonePrefixes.length * 0.05);
+    details.push(`removed prefixes: ${gonePrefixes.join(", ")}`);
+    changed.push(`removed prefixes: ${gonePrefixes.join(", ")}`);
+  }
+  const aSufSet = new Set(a.naming.suffixes);
+  const bSufSet = new Set(b.naming.suffixes);
+  const newSuffixes = b.naming.suffixes.filter((s) => !aSufSet.has(s));
+  const goneSuffixes = a.naming.suffixes.filter((s) => !bSufSet.has(s));
+  if (newSuffixes.length) {
+    score += Math.min(0.2, newSuffixes.length * 0.05);
+    details.push(`new suffixes: ${newSuffixes.join(", ")}`);
+    changed.push(`new suffixes: ${newSuffixes.join(", ")}`);
+  }
+  if (goneSuffixes.length) {
+    score += Math.min(0.15, goneSuffixes.length * 0.05);
+    details.push(`removed suffixes: ${goneSuffixes.join(", ")}`);
+    changed.push(`removed suffixes: ${goneSuffixes.join(", ")}`);
+  }
+  return { dimension: { score: Math.min(1, parseFloat(score.toFixed(3))), details }, changed };
+}
+
+// src/diff/concepts.ts
+var _MUGM21 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function diffConcepts(a, b) {
+  const aSet = new Set(a.concepts);
+  const bSet = new Set(b.concepts);
+  const added = b.concepts.filter((c) => !aSet.has(c));
+  const removed = a.concepts.filter((c) => !bSet.has(c));
+  const details = [];
+  if (added.length) details.push(`+ concepts: ${added.slice(0, 5).join(", ")}`);
+  if (removed.length) details.push(`- concepts: ${removed.slice(0, 5).join(", ")}`);
+  const total = Math.max(a.concepts.length, b.concepts.length, 1);
+  const score = Math.min(1, (added.length + removed.length) / total);
+  return { dimension: { score: parseFloat(score.toFixed(3)), details }, added, removed };
+}
+
+// src/diff/dependencies.ts
+var _MUGM22 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function scoreDelta(before, after, label2, details, changed) {
+  const delta = after - before;
+  if (delta === 0) return 0;
+  const direction = delta > 0 ? "increasing" : "decreasing";
+  details.push(`${label2} ${direction}: ${before} \u2192 ${after}`);
+  changed.push(`${label2}: ${before} \u2192 ${after}`);
+  return delta > 0 ? Math.min(1, delta * 0.15) : 0;
+}
+function diffDependencies(a, b) {
+  const depDetails = [];
+  const violDetails = [];
+  const changed = [];
+  let depScore = 0;
+  let violScore = 0;
+  depScore += scoreDelta(a.dependencies.directDbAccess, b.dependencies.directDbAccess, "direct DB access", depDetails, changed);
+  depScore += scoreDelta(a.dependencies.circularImports, b.dependencies.circularImports, "circular imports", depDetails, changed);
+  violScore += scoreDelta(a.dependencies.crossLayerViolations, b.dependencies.crossLayerViolations, "cross-layer violations", violDetails, changed);
+  return {
+    depDimension: { score: Math.min(1, parseFloat(depScore.toFixed(3))), details: depDetails },
+    violationDimension: { score: Math.min(1, parseFloat(violScore.toFixed(3))), details: violDetails },
+    changed
+  };
+}
+
+// src/diff/scorer.ts
+var _MUGM23 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var WEIGHTS = {
+  architecture: 0.2,
+  patterns: 0.25,
+  naming: 0.15,
+  concepts: 0.15,
+  dependencies: 0.15,
+  violations: 0.1
+};
+function scoreDrift(dimensions) {
+  const weighted = dimensions.architecture.score * WEIGHTS.architecture + dimensions.patterns.score * WEIGHTS.patterns + dimensions.naming.score * WEIGHTS.naming + dimensions.concepts.score * WEIGHTS.concepts + dimensions.dependencies.score * WEIGHTS.dependencies + dimensions.layerViolations.score * WEIGHTS.violations;
+  return parseFloat((weighted * 100).toFixed(1));
+}
+
+// src/diff/risk.ts
+var _MUGM24 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function classifyRisk(drift) {
+  if (drift < 10) return "Low";
+  if (drift <= 30) return "Medium";
+  return "High";
+}
+
+// src/diff/index.ts
+var _MUGM25 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function diff(a, b) {
+  const architecture = diffArchitecture(a, b);
+  const patternResult = diffPatterns(a, b);
+  const namingResult = diffNaming(a, b);
+  const conceptResult = diffConcepts(a, b);
+  const depResult = diffDependencies(a, b);
+  const dimensions = {
+    architecture,
+    patterns: patternResult.dimension,
+    naming: namingResult.dimension,
+    concepts: conceptResult.dimension,
+    dependencies: depResult.depDimension,
+    layerViolations: depResult.violationDimension
+  };
+  const overallDrift = scoreDrift(dimensions);
+  const riskLevel = classifyRisk(overallDrift);
+  return {
+    overallDrift,
+    dimensions,
+    added: { patterns: patternResult.added, concepts: conceptResult.added },
+    removed: { patterns: patternResult.removed, concepts: conceptResult.removed },
+    changed: {
+      patterns: patternResult.changed,
+      naming: namingResult.changed,
+      dependencies: depResult.changed
+    },
+    riskLevel
+  };
+}
+
+// src/output/auditReport.ts
+import chalk4 from "chalk";
+var _MUGM26 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var SEP2 = chalk4.gray("\u2500".repeat(51));
+function stabilityBar(pct) {
+  const filled = Math.round(pct / 5);
+  const empty = 20 - filled;
+  return chalk4.green("\u2588".repeat(filled)) + chalk4.gray("\u2591".repeat(empty));
+}
+function riskColor(level) {
+  if (level === "High") return chalk4.red(level);
+  if (level === "Medium") return chalk4.yellow(level);
+  return chalk4.green(level);
+}
+function printAuditReport(baseline, current, result) {
+  const stability = parseFloat((100 - result.overallDrift).toFixed(1));
+  console.log();
+  console.log(chalk4.green.bold("RepoGenome Audit"));
+  console.log(SEP2);
+  console.log(chalk4.gray(`Baseline:  commit ${baseline.commit ?? "unknown"} (${baseline.timestamp.slice(0, 10)})`));
+  console.log(chalk4.gray(`Current:   commit ${current.commit ?? "unknown"} (${current.timestamp.slice(0, 10)})`));
+  console.log();
+  const arrow = result.overallDrift > 0 ? chalk4.red(" \u25BC") : chalk4.green(" \u25B2");
+  console.log(`${chalk4.white.bold("Genome Stability:")} ${chalk4.white.bold(stability + "%")}${arrow} from 100%`);
+  console.log(`  ${stabilityBar(stability)}`);
+  console.log();
+  const hasChanges = result.added.patterns.length || result.removed.patterns.length || result.changed.patterns.length || result.added.concepts.length || result.removed.concepts.length || result.changed.naming.length || result.changed.dependencies.length || result.dimensions.architecture.details.length;
+  if (hasChanges) {
+    console.log(chalk4.white.bold("Changes Detected:"));
+    console.log();
+    for (const d of result.dimensions.architecture.details) {
+      console.log(`  ${chalk4.yellow("~")} ${d}`);
+    }
+    for (const p of result.added.patterns) {
+      const pat = current.patterns[p];
+      console.log(`  ${chalk4.green("+")} ${p} pattern introduced       (confidence: ${pat?.confidence ?? "?"}, ${pat?.count ?? 0} files)`);
+    }
+    for (const p of result.removed.patterns) {
+      console.log(`  ${chalk4.red("-")} ${p} pattern removed`);
+    }
+    for (const p of result.changed.patterns) {
+      const a = baseline.patterns[p];
+      const b = current.patterns[p];
+      console.log(`  ${chalk4.yellow("~")} ${p} pattern weakening     ${((a?.confidence ?? 0) * 100).toFixed(0)}% \u2192 ${((b?.confidence ?? 0) * 100).toFixed(0)}% presence`);
+    }
+    for (const d of result.dimensions.dependencies.details) {
+      const sym = d.includes("increasing") ? chalk4.red("+") : chalk4.green("-");
+      console.log(`  ${sym} ${d}`);
+    }
+    for (const d of result.dimensions.layerViolations.details) {
+      console.log(`  ${chalk4.red("+")} ${d}`);
+    }
+    if (result.added.concepts.length) {
+      console.log(`  ${chalk4.yellow("~")} concept vocabulary expanding: ${result.added.concepts.slice(0, 4).join(", ")}`);
+    }
+    console.log();
+  } else {
+    console.log(chalk4.green("  No architectural changes detected."));
+    console.log();
+  }
+  console.log(`${chalk4.gray("Layer Violations:")}     ${baseline.dependencies.crossLayerViolations} \u2192 ${current.dependencies.crossLayerViolations}`);
+  console.log(`${chalk4.gray("Circular Imports:")}     ${baseline.dependencies.circularImports} \u2192 ${current.dependencies.circularImports}`);
+  console.log(`${chalk4.gray("Direct DB Access:")}     ${baseline.dependencies.directDbAccess} \u2192 ${current.dependencies.directDbAccess} files`);
+  console.log();
+  console.log(`${chalk4.white("Risk Level:")} ${riskColor(result.riskLevel)}`);
+  console.log();
+  if (result.overallDrift > 0) {
+    console.log(chalk4.gray(`  Tip: Run ${chalk4.white("repogenome blame")} to see which directories are driving this drift.`));
+  }
+  console.log();
+}
+
+// src/output/html.ts
+import { writeFile as writeFile2 } from "fs/promises";
+var _MUGM27 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function riskClass(level) {
+  if (level === "High") return "high";
+  if (level === "Medium") return "medium";
+  return "low";
+}
+function stabilityBar2(stability) {
+  const pct = Math.max(0, Math.min(100, stability));
+  const color = pct >= 90 ? "#4ade80" : pct >= 70 ? "#facc15" : "#f87171";
+  return `<div class="bar-wrap"><div class="bar" style="width:${pct}%;background:${color}"></div></div>`;
+}
+function patternRows(a, b, added, removed, changed) {
+  const rows = [];
+  for (const p of added) {
+    const pat = b.patterns[p];
+    rows.push(`<tr>
+      <td>${p}</td>
+      <td><span class="badge added">added</span></td>
+      <td>${(pat?.confidence ?? 0 * 100).toFixed(0)}%</td>
+      <td>${pat?.count ?? 0}</td>
+    </tr>`);
+  }
+  for (const p of removed) {
+    const pat = a.patterns[p];
+    rows.push(`<tr>
+      <td>${p}</td>
+      <td><span class="badge removed">removed</span></td>
+      <td>${(pat?.confidence ?? 0 * 100).toFixed(0)}%</td>
+      <td>${pat?.count ?? 0}</td>
+    </tr>`);
+  }
+  for (const p of changed) {
+    const pa = a.patterns[p];
+    const pb = b.patterns[p];
+    rows.push(`<tr>
+      <td>${p}</td>
+      <td><span class="badge changed">weakened</span></td>
+      <td>${((pa?.confidence ?? 0) * 100).toFixed(0)}% \u2192 ${((pb?.confidence ?? 0) * 100).toFixed(0)}%</td>
+      <td>${pb?.count ?? 0}</td>
+    </tr>`);
+  }
+  if (rows.length === 0) {
+    rows.push('<tr><td colspan="4" class="meta">No pattern changes detected</td></tr>');
+  }
+  return rows.join("\n");
+}
+var CSS = `
+  *{box-sizing:border-box;margin:0;padding:0}
+  body{font-family:system-ui,-apple-system,sans-serif;background:#0f1117;color:#d4d4d8;max-width:920px;margin:2rem auto;padding:0 1.5rem;line-height:1.6}
+  h1{color:#4ade80;font-size:1.4rem;font-weight:700;margin-bottom:.25rem}
+  h2{font-size:1rem;font-weight:600;color:#a1a1aa;text-transform:uppercase;letter-spacing:.08em;margin:2rem 0 .75rem}
+  .meta{color:#52525b;font-size:.82rem}
+  .drift{font-size:3rem;font-weight:800;margin:.5rem 0}
+  .low{color:#4ade80}.medium{color:#facc15}.high{color:#f87171}
+  .bar-wrap{background:#1e1e2e;border-radius:4px;height:10px;overflow:hidden;margin:.5rem 0 1rem}
+  .bar{height:100%;border-radius:4px;transition:width .3s}
+  table{width:100%;border-collapse:collapse;font-size:.9rem;margin-bottom:1.5rem}
+  th{text-align:left;padding:.5rem .75rem;border-bottom:2px solid #27272a;color:#71717a;font-size:.78rem;font-weight:600;text-transform:uppercase;letter-spacing:.06em}
+  td{padding:.5rem .75rem;border-bottom:1px solid #1c1c24}
+  tr:hover td{background:#17171f}
+  .badge{display:inline-block;padding:.15rem .5rem;border-radius:4px;font-size:.78rem;font-weight:600}
+  .added{background:#14532d;color:#4ade80}.removed{background:#450a0a;color:#f87171}.changed{background:#422006;color:#fdba74}
+  .risk-tag{display:inline-block;padding:.3rem .9rem;border-radius:6px;font-size:1.1rem;font-weight:700}
+  .risk-low{background:#14532d;color:#4ade80}.risk-medium{background:#422006;color:#facc15}.risk-high{background:#450a0a;color:#f87171}
+  .concept-list{display:flex;flex-wrap:wrap;gap:.4rem;margin:.5rem 0 1.5rem}
+  .concept{background:#18181b;border:1px solid #3f3f46;padding:.2rem .6rem;border-radius:4px;font-size:.85rem}
+  .concept.add{border-color:#16a34a;color:#4ade80}.concept.rem{border-color:#dc2626;color:#f87171}
+  hr{border:none;border-top:1px solid #27272a;margin:1.5rem 0}
+  footer{margin-top:3rem;color:#3f3f46;font-size:.78rem;text-align:center}
+`;
+function buildHtml(title, body) {
+  return `<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <meta name="viewport" content="width=device-width,initial-scale=1">
+  <meta name="author" content="Muhammad Usman" data-gh="MuhammadUsmanGM" data-sig="MUGM-b4e2">
+  <title>${escHtml(title)}</title>
+  <style>${CSS}</style>
+</head>
+<body>
+${body}
+<footer>Generated by <strong>RepoGenome</strong> &mdash; ${escHtml((/* @__PURE__ */ new Date()).toISOString())}</footer>
+<!-- MuhammadUsmanGM &#x200B;&#x200C;&#x200B; MUGM-b4e2 -->
+</body>
+</html>`;
+}
+function escHtml(s) {
+  return s.replace(/&/g, "&amp;").replace(/</g, "&lt;").replace(/>/g, "&gt;").replace(/"/g, "&quot;");
+}
+function generateAuditHtml(baseline, current, result) {
+  const stability = parseFloat((100 - result.overallDrift).toFixed(1));
+  const rc = riskClass(result.riskLevel);
+  const addedConcepts = result.added.concepts.slice(0, 12).map((c) => `<span class="concept add">+${escHtml(c)}</span>`).join("");
+  const removedConcepts = result.removed.concepts.slice(0, 12).map((c) => `<span class="concept rem">-${escHtml(c)}</span>`).join("");
+  const archDetails = result.dimensions.architecture.details.map((d) => `<tr><td>${escHtml(d)}</td></tr>`).join("");
+  const depDetails = [
+    ...result.dimensions.dependencies.details,
+    ...result.dimensions.layerViolations.details
+  ].map((d) => `<tr><td>${escHtml(d)}</td></tr>`).join("");
+  const body = `
+<h1>RepoGenome Audit Report</h1>
+<p class="meta">Baseline: ${escHtml(baseline.timestamp.slice(0, 10))} &nbsp;|&nbsp; Current: ${escHtml(current.timestamp.slice(0, 10))}</p>
+<hr>
+
+<h2>Genome Stability</h2>
+<div class="drift ${rc}">${stability}%</div>
+${stabilityBar2(stability)}
+<p class="meta">Overall drift: <strong>${result.overallDrift}%</strong></p>
+
+<h2>Patterns</h2>
+<table>
+  <thead><tr><th>Pattern</th><th>Status</th><th>Confidence</th><th>Files</th></tr></thead>
+  <tbody>${patternRows(baseline, current, result.added.patterns, result.removed.patterns, result.changed.patterns)}</tbody>
+</table>
+
+${addedConcepts || removedConcepts ? `
+<h2>Concepts</h2>
+<div class="concept-list">${addedConcepts}${removedConcepts}</div>
+` : ""}
+
+${archDetails || depDetails ? `
+<h2>Architecture &amp; Dependencies</h2>
+<table><tbody>${archDetails}${depDetails}</tbody></table>
+` : ""}
+
+<h2>Risk Level</h2>
+<p><span class="risk-tag risk-${rc}">${escHtml(result.riskLevel)}</span></p>
+
+<hr>
+<h2>Metrics</h2>
+<table>
+  <thead><tr><th>Metric</th><th>Baseline</th><th>Current</th></tr></thead>
+  <tbody>
+    <tr><td>Total Files</td><td>${baseline.sizes.totalFiles}</td><td>${current.sizes.totalFiles}</td></tr>
+    <tr><td>Avg File Lines</td><td>${baseline.sizes.avgFileLines}</td><td>${current.sizes.avgFileLines}</td></tr>
+    <tr><td>Cross-Layer Violations</td><td>${baseline.dependencies.crossLayerViolations}</td><td>${current.dependencies.crossLayerViolations}</td></tr>
+    <tr><td>Circular Imports</td><td>${baseline.dependencies.circularImports}</td><td>${current.dependencies.circularImports}</td></tr>
+    <tr><td>Direct DB Access</td><td>${baseline.dependencies.directDbAccess}</td><td>${current.dependencies.directDbAccess}</td></tr>
+  </tbody>
+</table>`;
+  return buildHtml("RepoGenome Audit Report", body);
+}
+function generateCompareHtml(a, b, result, ref1, ref2) {
+  const rc = riskClass(result.riskLevel);
+  const addedConcepts = result.added.concepts.slice(0, 12).map((c) => `<span class="concept add">+${escHtml(c)}</span>`).join("");
+  const removedConcepts = result.removed.concepts.slice(0, 12).map((c) => `<span class="concept rem">-${escHtml(c)}</span>`).join("");
+  const archDetails = result.dimensions.architecture.details.map((d) => `<tr><td>${escHtml(d)}</td></tr>`).join("");
+  const depDetails = [
+    ...result.dimensions.dependencies.details,
+    ...result.dimensions.layerViolations.details
+  ].map((d) => `<tr><td>${escHtml(d)}</td></tr>`).join("");
+  const body = `
+<h1>RepoGenome Compare Report</h1>
+<p class="meta">${escHtml(ref1)} &nbsp;\u2192&nbsp; ${escHtml(ref2)}</p>
+<hr>
+
+<h2>Genome Drift</h2>
+<div class="drift ${rc}">${result.overallDrift}%</div>
+${stabilityBar2(100 - result.overallDrift)}
+<p class="meta">Architecture style: <strong>${escHtml(a.architecture.style)}</strong> \u2192 <strong>${escHtml(b.architecture.style)}</strong></p>
+
+<h2>Patterns</h2>
+<table>
+  <thead><tr><th>Pattern</th><th>Status</th><th>Confidence</th><th>Files</th></tr></thead>
+  <tbody>${patternRows(a, b, result.added.patterns, result.removed.patterns, result.changed.patterns)}</tbody>
+</table>
+
+${addedConcepts || removedConcepts ? `
+<h2>Concepts</h2>
+<div class="concept-list">${addedConcepts}${removedConcepts}</div>
+` : ""}
+
+${archDetails || depDetails ? `
+<h2>Architecture &amp; Dependencies</h2>
+<table><tbody>${archDetails}${depDetails}</tbody></table>
+` : ""}
+
+<h2>Risk Level</h2>
+<p><span class="risk-tag risk-${rc}">${escHtml(result.riskLevel)}</span></p>`;
+  return buildHtml(`RepoGenome Compare: ${ref1} \u2192 ${ref2}`, body);
+}
+async function writeHtmlReport(html, outputPath) {
+  await writeFile2(outputPath, html, "utf-8");
+}
+
+// src/commands/audit.ts
+var _MUGM28 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+async function fileExists2(p) {
+  try {
+    await access2(p);
+    return true;
+  } catch {
+    return false;
+  }
+}
+function parseGenomeFile(raw) {
+  try {
+    return JSON.parse(raw);
+  } catch {
+    console.error(chalk5.red("  Error: genome.json is corrupted or invalid JSON. Run `repogenome init` to regenerate it."));
+    process.exit(3);
+  }
+}
+function auditCommand() {
+  return new Command2("audit").description("Compare the current repository state against the baseline genome").option("--threshold <n>", "Exit with code 1 if drift exceeds n%").option("--format <fmt>", "Output format: terminal | json | html", "terminal").option("--output <file>", "Output file path (for --format html)", "repogenome-report.html").option("--save", "Save snapshot to history (default: true)", true).option("--no-save", "Skip writing snapshot to history").option("--baseline <file>", "Use a specific genome file instead of default").action(async (options) => {
+    const rootPath = resolve2(".");
+    const repoDir = join6(rootPath, ".repogenome");
+    const baselineFile = options.baseline ? resolve2(options.baseline) : join6(repoDir, "genome.json");
+    if (!await fileExists2(baselineFile)) {
+      console.error(chalk5.red("  Error: No baseline found. Run `repogenome init` first."));
+      process.exit(2);
+    }
+    const isJson = options.format === "json";
+    const isHtml = options.format === "html";
+    const spinner = isJson || isHtml ? null : ora2({ text: chalk5.gray("Scanning files\u2026"), color: "green" }).start();
+    if (options.threshold !== void 0 && isNaN(parseFloat(options.threshold))) {
+      console.error(chalk5.red(`  Error: --threshold must be a number, got "${options.threshold}"`));
+      process.exit(3);
+    }
+    try {
+      const baselineRaw = await readFile5(baselineFile, "utf-8");
+      const baseline = parseGenomeFile(baselineRaw);
+      if (spinner) spinner.text = chalk5.gray("Analyzing current state\u2026");
+      const signals = await scan(rootPath);
+      if (signals.files.length === 0) {
+        spinner?.fail(chalk5.red("No supported files found."));
+        process.exit(3);
+      }
+      const current = await analyze(signals, rootPath);
+      spinner?.stop();
+      const result = diff(baseline, current);
+      if (isJson) {
+        printJson("audit", { baseline, current, diff: result });
+      } else if (isHtml) {
+        const html = generateAuditHtml(baseline, current, result);
+        const outPath = resolve2(options.output ?? "repogenome-report.html");
+        await writeHtmlReport(html, outPath);
+        console.log(chalk5.green(`  HTML report written to ${outPath}`));
+      } else {
+        printAuditReport(baseline, current, result);
+      }
+      if (options.save !== false) {
+        await mkdir2(join6(repoDir, "history"), { recursive: true });
+        const ts = (/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-");
+        await writeFile3(
+          join6(repoDir, "history", `${ts}.json`),
+          JSON.stringify(current, null, 2),
+          "utf-8"
+        );
+      }
+      if (options.threshold !== void 0) {
+        const threshold = parseFloat(options.threshold);
+        if (result.overallDrift > threshold) {
+          if (!isJson) console.error(chalk5.red(`  Drift ${result.overallDrift}% exceeds threshold ${threshold}%`));
+          process.exit(1);
+        }
+      }
+    } catch (err) {
+      spinner?.stop();
+      const message = err instanceof Error ? err.message : String(err);
+      console.error(chalk5.red(`  Error: ${message}`));
+      process.exit(3);
+    }
+  });
+}
+
+// src/commands/compare.ts
+import { Command as Command3 } from "commander";
+import { readdir as readdir2, readFile as readFile6 } from "fs/promises";
+import { join as join8, resolve as resolve3 } from "path";
+import chalk7 from "chalk";
+import ora3 from "ora";
+
+// src/output/compareReport.ts
+import chalk6 from "chalk";
+var _MUGM29 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var SEP3 = chalk6.gray("\u2500".repeat(51));
+function printCompareReport(a, b, result, ref1, ref2) {
+  console.log();
+  console.log(chalk6.green.bold("RepoGenome Compare"));
+  console.log(SEP3);
+  console.log(`${chalk6.white(ref1)}  ${chalk6.gray("\u2192")}  ${chalk6.white(ref2)}`);
+  console.log();
+  const driftStr = result.overallDrift > 0 ? chalk6.red(`+${result.overallDrift}%`) : chalk6.green(`${result.overallDrift}%`);
+  console.log(`${chalk6.white("Genome Drift:")} ${driftStr}`);
+  console.log();
+  const hasPatternChanges = result.added.patterns.length || result.removed.patterns.length || result.changed.patterns.length;
+  if (hasPatternChanges) {
+    console.log(chalk6.white.bold("Patterns:"));
+    for (const p of result.removed.patterns) {
+      console.log(`  ${chalk6.red("-")} ${p} pattern removed from ${ref2}`);
+    }
+    for (const p of result.added.patterns) {
+      const pat = b.patterns[p];
+      console.log(`  ${chalk6.green("+")} ${p} pattern introduced (${pat?.count ?? 0} files)`);
+    }
+    for (const p of result.changed.patterns) {
+      const pa = a.patterns[p];
+      const pb = b.patterns[p];
+      console.log(`  ${chalk6.yellow("~")} ${p} pattern weakening  ${((pa?.confidence ?? 0) * 100).toFixed(0)}% \u2192 ${((pb?.confidence ?? 0) * 100).toFixed(0)}%`);
+    }
+    console.log();
+  }
+  if (result.added.concepts.length || result.removed.concepts.length) {
+    console.log(chalk6.white.bold("Concepts:"));
+    if (result.added.concepts.length) console.log(`  ${chalk6.green("+")} ${result.added.concepts.slice(0, 6).join(" \xB7 ")}`);
+    if (result.removed.concepts.length) console.log(`  ${chalk6.red("-")} ${result.removed.concepts.slice(0, 6).join(" \xB7 ")}`);
+    console.log();
+  }
+  const archDetails = result.dimensions.architecture.details;
+  const depDetails = [
+    ...result.dimensions.dependencies.details,
+    ...result.dimensions.layerViolations.details
+  ];
+  if (archDetails.length || depDetails.length) {
+    console.log(chalk6.white.bold("Layer Changes:"));
+    for (const d of archDetails) console.log(`  ${chalk6.yellow("~")} ${d}`);
+    for (const d of depDetails) console.log(`  ${chalk6.red("!")} ${d}`);
+    console.log();
+  }
+  const riskColor2 = result.riskLevel === "High" ? chalk6.red : result.riskLevel === "Medium" ? chalk6.yellow : chalk6.green;
+  console.log(`${chalk6.white("Risk Level:")} ${riskColor2(result.riskLevel)}`);
+  console.log();
+  if (result.overallDrift > 0) {
+    const newVocab = [...result.added.patterns, ...result.added.concepts.slice(0, 3)];
+    if (newVocab.length) {
+      console.log(chalk6.gray(`  Recommendation: ${ref2} introduces new architectural vocabulary`));
+      console.log(chalk6.gray(`  (${newVocab.join(", ")}) that diverges from ${ref1}. Consider aligning before merge.`));
+    } else {
+      console.log(chalk6.gray(`  Recommendation: ${ref2} shows ${result.overallDrift}% drift from ${ref1}.`));
+    }
+    console.log();
+  }
+}
+
+// src/git/index.ts
+import { execSync } from "child_process";
+import { mkdtempSync } from "fs";
+import { tmpdir } from "os";
+import { join as join7 } from "path";
+var _MUGM30 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function git(cmd, cwd = ".") {
+  try {
+    return execSync(`git ${cmd}`, { cwd, stdio: ["pipe", "pipe", "pipe"] }).toString().trim();
+  } catch (err) {
+    const msg = err instanceof Error ? err.message : String(err);
+    if (msg.includes("not a git repository")) throw new Error("Not a git repository.");
+    if (msg.includes("not found") || msg.includes("command not found")) throw new Error("git is not installed or not in PATH.");
+    throw new Error(`git error: ${msg.split("\n")[0]}`);
+  }
+}
+function isGitRepo(cwd = ".") {
+  try {
+    git("rev-parse --git-dir", cwd);
+    return true;
+  } catch {
+    return false;
+  }
+}
+function resolveRef(ref, cwd = ".") {
+  try {
+    return git(`rev-parse --verify ${ref}`, cwd);
+  } catch {
+    throw new Error(`Git ref not found: "${ref}"`);
+  }
+}
+function checkoutToTemp(ref, cwd = ".") {
+  const resolved = resolveRef(ref, cwd);
+  const tempDir = mkdtempSync(join7(tmpdir(), "repogenome-"));
+  git(`worktree add --detach "${tempDir}" ${resolved}`, cwd);
+  return tempDir;
+}
+function cleanupTemp(worktreePath, cwd = ".") {
+  try {
+    git(`worktree remove --force "${worktreePath}"`, cwd);
+  } catch {
+  }
+}
+
+// src/commands/compare.ts
+var _MUGM31 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+async function loadHistoryGenome(historyDir, ref) {
+  let entries;
+  try {
+    entries = await readdir2(historyDir);
+  } catch {
+    throw new Error(`No history found at ${historyDir}. Run repogenome audit first to build history.`);
+  }
+  const jsonFiles = entries.filter((e) => e.endsWith(".json")).sort();
+  if (!jsonFiles.length) throw new Error("No history snapshots found. Run repogenome audit to build history.");
+  let target;
+  if (ref === "latest" || ref === "HEAD") {
+    target = jsonFiles[jsonFiles.length - 1];
+  } else if (ref === "oldest" || ref === "BASE") {
+    target = jsonFiles[0];
+  } else {
+    const match = jsonFiles.find((f) => f.includes(ref));
+    if (!match) throw new Error(`No history snapshot matching "${ref}". Available: ${jsonFiles.join(", ")}`);
+    target = match;
+  }
+  const raw = await readFile6(join8(historyDir, target), "utf-8");
+  try {
+    return JSON.parse(raw);
+  } catch {
+    throw new Error(`History snapshot "${target}" is corrupted or invalid JSON.`);
+  }
+}
+async function scanRef(ref, cwd) {
+  const tempPath = checkoutToTemp(ref, cwd);
+  try {
+    const signals = await scan(tempPath);
+    return await analyze(signals, tempPath);
+  } finally {
+    cleanupTemp(tempPath, cwd);
+  }
+}
+function compareCommand() {
+  return new Command3("compare").description("Compare the genomes of two git references").argument("<ref1>", "First git reference (branch, commit, tag)").argument("<ref2>", "Second git reference (branch, commit, tag)").option("--format <fmt>", "Output format: terminal | json | html", "terminal").option("--output <file>", "Output file path (for --format html)", "repogenome-report.html").option("--no-checkout", "Use pre-saved history snapshots instead of live checkout").action(async (ref1, ref2, options) => {
+    const rootPath = resolve3(".");
+    const historyDir = join8(rootPath, ".repogenome", "history");
+    const isJson = options.format === "json";
+    const isHtml = options.format === "html";
+    const noCheckout = options.checkout === false;
+    const spinner = isJson || isHtml ? null : ora3({ text: chalk7.gray(`Comparing ${ref1} \u2192 ${ref2}\u2026`), color: "green" }).start();
+    try {
+      let genomeA;
+      let genomeB;
+      if (noCheckout) {
+        spinner && (spinner.text = chalk7.gray("Loading history snapshots\u2026"));
+        [genomeA, genomeB] = await Promise.all([
+          loadHistoryGenome(historyDir, ref1),
+          loadHistoryGenome(historyDir, ref2)
+        ]);
+      } else {
+        if (!isGitRepo(rootPath)) {
+          spinner?.fail(chalk7.red("Not a git repository."));
+          process.exit(3);
+        }
+        try {
+          resolveRef(ref1, rootPath);
+          resolveRef(ref2, rootPath);
+        } catch (err) {
+          spinner?.fail(chalk7.red(err instanceof Error ? err.message : String(err)));
+          process.exit(3);
+        }
+        spinner && (spinner.text = chalk7.gray(`Checking out ${ref1}\u2026`));
+        genomeA = await scanRef(ref1, rootPath);
+        spinner && (spinner.text = chalk7.gray(`Checking out ${ref2}\u2026`));
+        genomeB = await scanRef(ref2, rootPath);
+      }
+      spinner?.stop();
+      const result = diff(genomeA, genomeB);
+      if (isJson) {
+        printJson("compare", { ref1, ref2, diff: result });
+      } else if (isHtml) {
+        const html = generateCompareHtml(genomeA, genomeB, result, ref1, ref2);
+        const outPath = resolve3(options.output ?? "repogenome-report.html");
+        await writeHtmlReport(html, outPath);
+        console.log(chalk7.green(`  HTML report written to ${outPath}`));
+      } else {
+        printCompareReport(genomeA, genomeB, result, ref1, ref2);
+      }
+    } catch (err) {
+      spinner?.stop();
+      console.error(chalk7.red(`  Error: ${err instanceof Error ? err.message : String(err)}`));
+      process.exit(3);
+    }
+  });
+}
+
+// src/commands/blame.ts
+import { Command as Command4 } from "commander";
+import { readFile as readFile7, access as access3 } from "fs/promises";
+import { join as join10, resolve as resolve4 } from "path";
+import chalk9 from "chalk";
+import ora4 from "ora";
+
+// src/blame/directoryScanner.ts
+import { readdir as readdir3 } from "fs/promises";
+import { statSync } from "fs";
+import { join as join9 } from "path";
+var _MUGM32 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var SKIP = /* @__PURE__ */ new Set(["node_modules", ".git", "dist", "build", "coverage", ".repogenome", ".cache"]);
+async function scanDirectories(rootPath) {
+  let entries;
+  try {
+    entries = await readdir3(rootPath);
+  } catch {
+    return [];
+  }
+  const dirs = entries.filter((e) => {
+    if (e.startsWith(".") || SKIP.has(e)) return false;
+    try {
+      return statSync(join9(rootPath, e)).isDirectory();
+    } catch {
+      return false;
+    }
+  });
+  const results = [];
+  for (const name of dirs) {
+    const dirPath = join9(rootPath, name);
+    try {
+      const signals = await scan(dirPath);
+      if (signals.files.length === 0) continue;
+      const genome = await analyze(signals, dirPath);
+      results.push({ name, path: dirPath, genome });
+    } catch {
+    }
+  }
+  return results;
+}
+
+// src/blame/fileBlame.ts
+var _MUGM33 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var IMPACT_ORDER = { high: 0, medium: 1, low: 2 };
+function buildFileBlame(baseline, current, result) {
+  const raw = [];
+  for (const p of result.added.patterns) {
+    for (const f of current.patterns[p]?.files ?? []) {
+      raw.push({ file: f, reason: `introduced ${p} pattern`, impact: "high" });
+    }
+  }
+  for (const p of result.removed.patterns) {
+    const baseFiles = baseline.patterns[p]?.files ?? [];
+    const currFiles = new Set(current.patterns[p]?.files ?? []);
+    for (const f of baseFiles) {
+      if (!currFiles.has(f)) {
+        raw.push({ file: f, reason: `removed from ${p} pattern`, impact: "high" });
+      }
+    }
+  }
+  for (const p of result.changed.patterns) {
+    const baseFiles = new Set(baseline.patterns[p]?.files ?? []);
+    const currFiles = new Set(current.patterns[p]?.files ?? []);
+    for (const f of baseFiles) {
+      if (!currFiles.has(f)) {
+        raw.push({ file: f, reason: `weakened ${p} pattern`, impact: "medium" });
+      }
+    }
+    for (const f of currFiles) {
+      if (!baseFiles.has(f)) {
+        raw.push({ file: f, reason: `strengthened ${p} pattern`, impact: "low" });
+      }
+    }
+  }
+  const seen = /* @__PURE__ */ new Map();
+  for (const e of raw) {
+    const existing = seen.get(e.file);
+    if (!existing || IMPACT_ORDER[e.impact] < IMPACT_ORDER[existing.impact]) {
+      seen.set(e.file, e);
+    }
+  }
+  return [...seen.values()].sort((a, b) => IMPACT_ORDER[a.impact] - IMPACT_ORDER[b.impact]);
+}
+
+// src/blame/conceptGrouper.ts
+var _MUGM34 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var GENERIC = /* @__PURE__ */ new Set(["src", "lib", "app", "api", "web", "cli", "the", "and", "for", "new"]);
+function extractWords(dirName) {
+  return dirName.toLowerCase().split(/[-_/]/).filter((w) => w.length > 2 && !GENERIC.has(w));
+}
+function groupByConcept(dirs) {
+  const conceptMap = /* @__PURE__ */ new Map();
+  for (const dir of dirs) {
+    for (const word of extractWords(dir.name)) {
+      if (!conceptMap.has(word)) conceptMap.set(word, []);
+      conceptMap.get(word).push(dir.name);
+    }
+  }
+  const groups = [];
+  const grouped = /* @__PURE__ */ new Set();
+  for (const [concept, dirNames] of conceptMap) {
+    if (dirNames.length < 2) continue;
+    const totalContribution = dirs.filter((d) => dirNames.includes(d.name)).reduce((sum, d) => sum + d.contribution, 0);
+    groups.push({
+      concept,
+      directories: dirNames,
+      totalContribution: parseFloat(totalContribution.toFixed(1))
+    });
+    for (const n of dirNames) grouped.add(n);
+  }
+  for (const dir of dirs) {
+    if (!grouped.has(dir.name)) {
+      groups.push({
+        concept: dir.name,
+        directories: [dir.name],
+        totalContribution: dir.contribution
+      });
+    }
+  }
+  return groups.sort((a, b) => b.totalContribution - a.totalContribution);
+}
+
+// src/blame/index.ts
+var _MUGM35 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+function topLevelDir(filePath) {
+  return filePath.replace(/\\/g, "/").split("/")[0];
+}
+function attributeDrift(baseline, current, result, dirScans) {
+  const scores = /* @__PURE__ */ new Map();
+  for (const d of dirScans) {
+    scores.set(d.name, { points: 0, addedPatterns: [], removedPatterns: [], addedConcepts: [], removedConcepts: [], violations: 0 });
+  }
+  const addTo = (dir, delta) => {
+    const s = scores.get(dir);
+    if (s) s.points += delta;
+  };
+  for (const p of result.added.patterns) {
+    for (const f of current.patterns[p]?.files ?? []) {
+      const dir = topLevelDir(f);
+      const s = scores.get(dir);
+      if (s) {
+        addTo(dir, 1);
+        if (!s.addedPatterns.includes(p)) s.addedPatterns.push(p);
+      }
+    }
+  }
+  for (const p of result.removed.patterns) {
+    for (const f of baseline.patterns[p]?.files ?? []) {
+      const dir = topLevelDir(f);
+      const s = scores.get(dir);
+      if (s) {
+        addTo(dir, 1);
+        if (!s.removedPatterns.includes(p)) s.removedPatterns.push(p);
+      }
+    }
+  }
+  for (const p of result.changed.patterns) {
+    const baseSet = new Set(baseline.patterns[p]?.files ?? []);
+    const currSet = new Set(current.patterns[p]?.files ?? []);
+    for (const f of baseSet) {
+      if (!currSet.has(f)) {
+        const dir = topLevelDir(f);
+        const s = scores.get(dir);
+        if (s) {
+          addTo(dir, 0.5);
+          if (!s.removedPatterns.includes(p)) s.removedPatterns.push(p);
+        }
+      }
+    }
+  }
+  for (const concept of result.added.concepts) {
+    for (const d of dirScans) {
+      if (d.genome.concepts.includes(concept)) {
+        const s = scores.get(d.name);
+        addTo(d.name, 0.4);
+        if (!s.addedConcepts.includes(concept)) s.addedConcepts.push(concept);
+      }
+    }
+  }
+  for (const concept of result.removed.concepts) {
+    for (const d of dirScans) {
+      if (d.name.toLowerCase().includes(concept.toLowerCase())) {
+        const s = scores.get(d.name);
+        addTo(d.name, 0.4);
+        if (!s.removedConcepts.includes(concept)) s.removedConcepts.push(concept);
+      }
+    }
+  }
+  const violationDelta = current.dependencies.crossLayerViolations - baseline.dependencies.crossLayerViolations;
+  if (violationDelta > 0) {
+    const active = dirScans.filter((d) => Object.values(d.genome.patterns).some((p) => p.detected));
+    const share = violationDelta / Math.max(active.length, 1);
+    for (const d of active) {
+      const s = scores.get(d.name);
+      addTo(d.name, share * 0.3);
+      s.violations += Math.ceil(share);
+    }
+  }
+  const totalPoints = [...scores.values()].reduce((sum, s) => sum + s.points, 0);
+  return dirScans.map((d) => {
+    const s = scores.get(d.name) ?? { points: 0, addedPatterns: [], removedPatterns: [], addedConcepts: [], removedConcepts: [], violations: 0 };
+    const contribution = totalPoints > 0 ? parseFloat((s.points / totalPoints * 100).toFixed(1)) : 0;
+    return {
+      name: d.name,
+      contribution,
+      drift: parseFloat((contribution / 100 * result.overallDrift).toFixed(1)),
+      addedPatterns: s.addedPatterns,
+      removedPatterns: s.removedPatterns,
+      addedConcepts: s.addedConcepts,
+      removedConcepts: s.removedConcepts,
+      violations: s.violations
+    };
+  }).sort((a, b) => b.contribution - a.contribution);
+}
+function runBlame(baseline, current, result, dirScans, topN = 10) {
+  const dirs = attributeDrift(baseline, current, result, dirScans).slice(0, topN);
+  const conceptGroups = groupByConcept(dirs);
+  const files = buildFileBlame(baseline, current, result);
+  return {
+    dirs,
+    conceptGroups,
+    files,
+    topDir: dirs[0]?.name ?? "",
+    totalAttributed: parseFloat(dirs.reduce((sum, d) => sum + d.contribution, 0).toFixed(1))
+  };
+}
+
+// src/output/blameReport.ts
+import chalk8 from "chalk";
+var _MUGM36 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var SEP4 = chalk8.gray("\u2500".repeat(51));
+function driftBar(contribution) {
+  const filled = Math.round(contribution / 5);
+  const empty = 20 - filled;
+  return chalk8.red("\u2588".repeat(Math.min(filled, 20))) + chalk8.gray("\u2591".repeat(Math.max(empty, 0)));
+}
+function formatTags(added, removed) {
+  const parts = [];
+  for (const p of added) parts.push(chalk8.green(`+${p}`));
+  for (const p of removed) parts.push(chalk8.red(`-${p}`));
+  return parts.slice(0, 4).join(" ");
+}
+function printBlameReport(result, mode, overallDrift) {
+  console.log();
+  console.log(chalk8.green.bold("RepoGenome Blame"));
+  console.log(SEP4);
+  console.log(chalk8.gray(`Overall Drift: ${overallDrift}%`));
+  console.log();
+  if (mode === "directory" || mode === "concept") {
+    if (mode === "directory") {
+      printDirectoryView(result.dirs, result.topDir);
+    } else {
+      printConceptView(result.conceptGroups);
+    }
+  } else {
+    printFileView(result.files);
+  }
+  if (result.topDir) {
+    console.log();
+    console.log(chalk8.gray(`  Tip: Run ${chalk8.white(`repogenome blame --by file`)} for file-level attribution.`));
+    console.log(chalk8.gray(`       Run ${chalk8.white(`repogenome blame --by concept`)} for concept grouping.`));
+  }
+  console.log();
+}
+function printDirectoryView(dirs, topDir) {
+  if (dirs.length === 0) {
+    console.log(chalk8.gray("  No drift attributed \u2014 genome is stable or no directories found."));
+    return;
+  }
+  console.log(chalk8.white.bold("Drift Attribution by Directory"));
+  console.log();
+  const nameWidth = Math.min(30, Math.max(...dirs.map((d) => d.name.length)) + 2);
+  for (const dir of dirs) {
+    const name = dir.name.padEnd(nameWidth);
+    const bar = driftBar(dir.contribution);
+    const pct = chalk8.white(`${dir.contribution.toFixed(1).padStart(5)}%`);
+    const tags = formatTags(dir.addedPatterns, dir.removedPatterns);
+    const marker = dir.name === topDir ? chalk8.yellow(" \u25C4") : "";
+    console.log(`  ${chalk8.cyan(name)} ${bar} ${pct}  ${tags}${marker}`);
+  }
+}
+function printConceptView(groups) {
+  if (groups.length === 0) {
+    console.log(chalk8.gray("  No concept groups found."));
+    return;
+  }
+  console.log(chalk8.white.bold("Drift Attribution by Concept"));
+  console.log();
+  for (const g of groups.slice(0, 10)) {
+    const label2 = g.concept.padEnd(20);
+    const bar = driftBar(g.totalContribution);
+    const pct = chalk8.white(`${g.totalContribution.toFixed(1).padStart(5)}%`);
+    const dirs = chalk8.gray(`(${g.directories.join(", ")})`);
+    console.log(`  ${chalk8.cyan(label2)} ${bar} ${pct}  ${dirs}`);
+  }
+}
+function printFileView(files) {
+  if (files.length === 0) {
+    console.log(chalk8.gray("  No file-level changes detected \u2014 drift may be in naming or concepts."));
+    return;
+  }
+  console.log(chalk8.white.bold("Top Changed Files"));
+  console.log();
+  const impactIcon = (impact) => {
+    if (impact === "high") return chalk8.red("[+]");
+    if (impact === "medium") return chalk8.yellow("[~]");
+    return chalk8.green("[\xB7]");
+  };
+  for (const entry of files.slice(0, 15)) {
+    const icon = impactIcon(entry.impact);
+    const file = chalk8.white(entry.file.padEnd(50));
+    const reason = chalk8.gray(entry.reason);
+    console.log(`  ${icon} ${file} ${reason}`);
+  }
+}
+
+// src/commands/blame.ts
+var _MUGM37 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+async function fileExists3(p) {
+  try {
+    await access3(p);
+    return true;
+  } catch {
+    return false;
+  }
+}
+function parseGenomeFile2(raw) {
+  try {
+    return JSON.parse(raw);
+  } catch {
+    console.error(chalk9.red("  Error: genome.json is corrupted or invalid JSON. Run `repogenome init` to regenerate it."));
+    process.exit(3);
+  }
+}
+function blameCommand() {
+  return new Command4("blame").description("Identify which directories and files are driving the most architectural drift").option("--by <mode>", "Attribution mode: directory | file | concept", "directory").option("--top <n>", "Show top N contributors", "10").option("--format <fmt>", "Output format: terminal | json", "terminal").option("--baseline <file>", "Path to a custom baseline genome file").action(async (options) => {
+    const rootPath = resolve4(".");
+    const repoDir = join10(rootPath, ".repogenome");
+    const baselineFile = options.baseline ? resolve4(options.baseline) : join10(repoDir, "genome.json");
+    if (!await fileExists3(baselineFile)) {
+      console.error(chalk9.red("  Error: No baseline found. Run `repogenome init` first."));
+      process.exit(2);
+    }
+    const mode = options.by ?? "directory";
+    const topN = parseInt(options.top ?? "10", 10);
+    const isJson = options.format === "json";
+    const spinner = isJson ? null : ora4({ text: chalk9.gray("Scanning current state\u2026"), color: "green" }).start();
+    try {
+      const baselineRaw = await readFile7(baselineFile, "utf-8");
+      const baseline = parseGenomeFile2(baselineRaw);
+      if (spinner) spinner.text = chalk9.gray("Analyzing current state\u2026");
+      const signals = await scan(rootPath);
+      if (signals.files.length === 0) {
+        spinner?.fail(chalk9.red("No supported files found."));
+        process.exit(3);
+      }
+      const current = await analyze(signals, rootPath);
+      const result = diff(baseline, current);
+      if (spinner) spinner.text = chalk9.gray("Scanning directories\u2026");
+      const dirScans = await scanDirectories(rootPath);
+      spinner?.stop();
+      const blameResult = runBlame(baseline, current, result, dirScans, topN);
+      if (isJson) {
+        printJson("blame", { overallDrift: result.overallDrift, blame: blameResult });
+      } else {
+        printBlameReport(blameResult, mode, result.overallDrift);
+      }
+    } catch (err) {
+      spinner?.stop();
+      console.error(chalk9.red(`  Error: ${err instanceof Error ? err.message : String(err)}`));
+      process.exit(3);
+    }
+  });
+}
+
+// src/cli.ts
+var _MUGM38 = Object.freeze({ b: 1299540065, g: "MuhammadUsmanGM" });
+var _require = createRequire2(import.meta.url);
+var { version: version2 } = _require("../package.json");
+var program = new Command5();
+var isMachineOutput = process.argv.includes("--format") && process.argv[process.argv.indexOf("--format") + 1] === "json";
+if (!isMachineOutput) printBanner();
+program.name("repogenome").description("Capture the architectural DNA of a codebase and track drift over time").version(version2);
+program.addCommand(initCommand());
+program.addCommand(auditCommand());
+program.addCommand(compareCommand());
+program.addCommand(blameCommand());
+program.parse();