chore: polish for FOL contract delivery (CHANGELOG, CLI guardrails, metadata)

- Update CHANGELOG.md for 1.1.0 (date, refactoring, repository fixes)
- Add overwrite guardrails to imhotep-cli init — skips existing files
- Add bugs/homepage/keywords metadata to 5 public packages
- Mark imhotep-bench and imhotep-fixtures as private packages
- Add selector field to SourceReference interface (core types)
- Remove 7  casts from check-all.ts (folAst.position, cardinality results)
- Generate package-lock.json for reproducible installs

packages/imhotep-cli/src/cli.ts

@@ -50,8 +50,15 @@ function main(): void {
       : process.cwd();
     
     try {
-      initProject({ preset, targetDir });
+      const result = initProject({ preset, targetDir });
       console.log(`✓ Scaffolded ${preset} project in ${targetDir}`);
+
+      if (result.created.length > 0) {
+        console.log(`  Created: ${result.created.map(f => f.replace(targetDir, '.')).join(', ')}`);
+      }
+      if (result.skipped.length > 0) {
+        console.warn(`  Skipped (already exists): ${result.skipped.map(f => f.replace(targetDir, '.')).join(', ')}`);
+      }
       console.log(`  Run: cd ${targetDir} && npm install && npm test`);
     } catch (error: any) {
       console.error(`Error: ${error.message}`);

packages/imhotep-cli/src/index.ts

@@ -1,3 +1,3 @@
 // Public API exports for imhotep-cli
-export { initProject, type InitOptions } from './init.js';
+export { initProject, type InitOptions, type InitResult } from './init.js';
 export { presets, getPresetNames, getPreset, type PresetName } from './presets/index.js';

packages/imhotep-cli/src/init.ts

@@ -1,5 +1,5 @@
 // Core init logic for scaffolding Imhotep projects from presets
-import { mkdirSync, writeFileSync } from 'node:fs';
+import { mkdirSync, writeFileSync, existsSync } from 'node:fs';
 import { join } from 'node:path';
 import { getPreset } from './presets/index.js';
 
@@ -8,49 +8,59 @@ export interface InitOptions {
   targetDir: string;
 }
 
-export function initProject(options: InitOptions): void {
+export interface InitResult {
+  created: string[];
+  skipped: string[];
+}
+
+function safeWrite(filePath: string, content: string, results: { created: string[]; skipped: string[] }): void {
+  if (existsSync(filePath)) {
+    results.skipped.push(filePath)
+  } else {
+    writeFileSync(filePath, content, 'utf-8')
+    results.created.push(filePath)
+  }
+}
+
+export function initProject(options: InitOptions): InitResult {
   const { preset, targetDir } = options;
-  
-  // Resolve preset template
+  const results: InitResult = { created: [], skipped: [] };
+
   const template = getPreset(preset);
-  
-  // Create directory structure
+
   mkdirSync(targetDir, { recursive: true });
   mkdirSync(join(targetDir, 'tests'), { recursive: true });
   mkdirSync(join(targetDir, 'fixtures'), { recursive: true });
-  
-  // Write config file
-  writeFileSync(
+
+  safeWrite(
     join(targetDir, 'imhotep.config.js'),
     template.configFile,
-    'utf-8'
+    results
   );
-  
-  // Write test file
-  writeFileSync(
+
+  safeWrite(
     join(targetDir, 'tests', 'example.test.ts'),
     template.testFile,
-    'utf-8'
+    results
   );
-  
-  // Write fixture file
-  writeFileSync(
+
+  safeWrite(
     join(targetDir, 'fixtures', 'example.html'),
     template.fixtureFile,
-    'utf-8'
+    results
   );
-  
-  // Write package.json
-  writeFileSync(
+
+  safeWrite(
     join(targetDir, 'package.json'),
     JSON.stringify(template.packageJson, null, 2),
-    'utf-8'
+    results
   );
-  
-  // Write README
-  writeFileSync(
+
+  safeWrite(
     join(targetDir, 'README.md'),
     template.readme,
-    'utf-8'
+    results
   );
+
+  return results
 }