feat: enable file indexing by default

File indexing only adds ~3 seconds to the indexing process, so enable
it by default to make the get_file tool work out of the box.

- MCP index_revision tool now indexes files automatically
- CLI flag changed from --files to --no-files (opt-out)
- Update README examples

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

README.md

@@ -63,14 +63,14 @@ nixos-options serve
 **Index a nixpkgs revision:**
 
 ```bash
-# Index by channel name
+# Index by channel name (includes file contents by default)
 nixos-options index nixos-unstable
 
 # Index by git hash
 nixos-options index e6eae2ee2110f3d31110d5c222cd395303343b08
 
-# Index with file contents (enables get_file tool, slower)
-nixos-options index --files nixos-unstable
+# Index without file contents (faster, disables get_file tool)
+nixos-options index --no-files nixos-unstable
 ```
 
 **List indexed revisions:**