fix: hash-check before deletion, track all files, fix overrides bug, update help text

- remove_tracked_files: always compare SHA-256 hash before deleting,
  even when called with explicit files dict; skip modified files unless
  --force is set (was unconditionally deleting all tracked files)
- finalize_setup: track ALL files from setup() (no agent-root filter);
  safe because removal now checks hashes
- list_all_agents: track embedded versions in separate dict so overrides
  always reference the correct embedded version, not a catalog/project
  pack that overwrote the seen dict
- --ai-skills help text: updated to say 'requires --ai or --agent'

src/specify_cli/__init__.py

@@ -1725,7 +1725,7 @@ def init(
     skip_tls: bool = typer.Option(False, "--skip-tls", help="Skip SSL/TLS verification (not recommended)"),
     debug: bool = typer.Option(False, "--debug", help="Show verbose diagnostic output for network and extraction failures"),
     github_token: str = typer.Option(None, "--github-token", help="GitHub token to use for API requests (or set GH_TOKEN or GITHUB_TOKEN environment variable)"),
-    ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
+    ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai or --agent)"),
     offline: bool = typer.Option(False, "--offline", help="Use assets bundled in the specify-cli package instead of downloading from GitHub (no network access required). Bundled assets will become the default in v0.6.0 and this flag will be removed."),
     preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
     branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, ...) or 'timestamp' (YYYYMMDD-HHMMSS)"),