Previously, user filters completely replaced manifest filtering. Now:
1. Manifest patterns are applied first (defines what package provides)
2. User patterns are applied on top (narrows down further)
This means if a manifest excludes 10 extensions and user adds one more
exclusion, all 11 are excluded (not just the user's one).
- Manifest extensions/skills/prompts/themes arrays now support glob patterns
- Use !pattern for exclusions (e.g., '!**/deprecated/*')
- Enables packages to bundle dependencies and selectively include resources
- Support glob patterns and ! exclusions in package filter arrays
- Support glob patterns and ! exclusions in top-level settings arrays
- Add helper functions: isPattern, hasPatterns, collectFiles, collectSkillEntries, applyPatterns
- Add resolveLocalEntries for pattern-aware resolution of top-level arrays
- Add applyPackageFilter and collectAllPackageFiles for package filter patterns
- Add comprehensive tests for both top-level and package filter patterns
- Add progress callbacks to PackageManager for TUI status during install/remove/update
- Add extension conflict detection (tools, commands, flags with same names)
- Accept raw GitHub/GitLab URLs without git: prefix
- Add tests for package-manager.ts and resource-loader.ts
- Add empty fixture directories for skills tests
