refactor: migrate from Bun.Glob to npm glob package

Replace Bun.Glob usage with a new Glob utility wrapper around the npm 'glob' package.
This moves us off Bun-specific APIs toward standard Node.js compatible solutions.

Changes:
- Add new src/util/glob.ts utility module with scan(), scanSync(), and match()
- Default include option is 'file' (only returns files, not directories)
- Add symlink option (default: false) to control symlink following
- Migrate all 12 files using Bun.Glob to use the new Glob utility
- Add comprehensive tests for the glob utility

Breaking changes:
- Removed support for include: 'dir' option (use include: 'all' and filter manually)
- symlink now defaults to false (was true in most Bun.Glob usages)

Files migrated:
- src/util/log.ts
- src/util/filesystem.ts
- src/tool/truncation.ts
- src/session/instruction.ts
- src/storage/json-migration.ts
- src/storage/storage.ts
- src/project/project.ts
- src/cli/cmd/tui/context/theme.tsx
- src/config/config.ts
- src/tool/registry.ts
- src/skill/skill.ts
- src/file/ignore.ts

package.json

@@ -70,6 +70,7 @@
     "@actions/artifact": "5.0.1",
     "@tsconfig/bun": "catalog:",
     "@types/mime-types": "3.0.1",
+    "glob": "13.0.5",
     "husky": "9.1.7",
     "prettier": "3.6.2",
     "semver": "^7.6.0",