Implement all stubs: parsePackageMap, LLM heuristics, tree-sitter AST, patch rewrite, reinit

- format.ts: Full parsePackageMap implementation with round-trip support
- llm-extract.ts: Heuristic-based extraction without LLM API (regex exports,
  imports, purpose inference from filename patterns)
- ast-extract.ts: Tree-sitter integration for TypeScript/TSX with fallback
  for other languages
- init.ts: Refactored to expose generateDirectoryMap helper, reinitPath
  delegates to initProject
- patch.ts: Small packages now use generateDirectoryMap for full rewrite
- discover.ts: Cleaned up require('fs') to use proper ES import
- Tests: 8 tests covering format round-trip and LLM heuristics
- All TypeScript compiles clean, all tests pass

src/init.ts

@@ -1,42 +1,48 @@
-import { discoverProject } from './discover.js';
-import { renderPackageMap, type PackageMapData } from './format.js';
-import { extractFileLLM } from './llm-extract.js';
-import { extractFileAST } from './ast-extract.js';
-import { mergeFileData } from './merge.js';
-import { extractPackageLLM } from './llm-extract.js';
-import { writeFileSync } from 'fs';
-import { join } from 'path';
+import { discoverProject, type DirectoryEntry } from "./discover.js";
+import { renderPackageMap, type PackageMapData, type FileEntry } from "./format.js";
+import { extractFileLLM, extractPackageLLM } from "./llm-extract.js";
+import { extractFileAST } from "./ast-extract.js";
+import { mergeFileData } from "./merge.js";
+import { writeFileSync } from "fs";
+import { join } from "path";
 
 export async function initProject(rootPath: string): Promise<void> {
-  const entries = discoverProject(rootPath);
+	const entries = discoverProject(rootPath);
 
-  for (const entry of entries) {
-    const fileData = [];
-    for (const file of entry.files) {
-      const filePath = join(entry.dirPath, file);
-      const llmData = await extractFileLLM(filePath);
-      const astData = await extractFileAST(filePath);
-      fileData.push(mergeFileData(file, llmData, astData));
-    }
+	for (const entry of entries) {
+		await generateDirectoryMap(entry);
+	}
 
-    const packageData = await extractPackageLLM(entry.relativePath, fileData);
+	console.log(`Generated ${entries.length} .pi-map.md files`);
+}
 
-    const mapData: PackageMapData = {
-      path: entry.relativePath,
-      role: packageData.role,
-      files: fileData,
-      arch: packageData.arch,
-      dirty: '-'
-    };
+export async function generateDirectoryMap(
+	entry: DirectoryEntry,
+): Promise<FileEntry[]> {
+	const fileData: FileEntry[] = [];
+	for (const file of entry.files) {
+		const filePath = join(entry.dirPath, file);
+		const llmData = await extractFileLLM(filePath);
+		const astData = await extractFileAST(filePath);
+		fileData.push(mergeFileData(file, llmData, astData));
+	}
 
-    const outPath = join(entry.dirPath, '.pi-map.md');
-    writeFileSync(outPath, renderPackageMap(mapData));
-  }
+	const packageData = await extractPackageLLM(entry.relativePath, fileData);
 
-  console.log(`Generated ${entries.length} .pi-map.md files`);
+	const mapData: PackageMapData = {
+		path: entry.relativePath,
+		role: packageData.role,
+		files: fileData,
+		arch: packageData.arch,
+		dirty: "-",
+	};
+
+	const outPath = join(entry.dirPath, ".pi-map.md");
+	writeFileSync(outPath, renderPackageMap(mapData));
+	return fileData;
 }
 
 export async function reinitPath(path: string): Promise<void> {
-  // TODO: clear dirty markers and force regeneration
-  await initProject(path);
+	// Full regeneration clears all dirty markers by overwriting every .pi-map.md
+	await initProject(path);
 }