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:**

cmd/nixos-options/main.go

@@ -43,15 +43,15 @@ func main() {
 				ArgsUsage: "<revision>",
 				Flags: []cli.Flag{
 					&cli.BoolFlag{
-						Name:  "files",
-						Usage: "Also index file contents (slower, enables get_file tool)",
+						Name:  "no-files",
+						Usage: "Skip indexing file contents (faster, disables get_file tool)",
 					},
 				},
 				Action: func(c *cli.Context) error {
 					if c.NArg() < 1 {
 						return fmt.Errorf("revision argument required")
 					}
-					return runIndex(c, c.Args().First(), c.Bool("files"))
+					return runIndex(c, c.Args().First(), !c.Bool("no-files"))
 				},
 			},
 			{

internal/mcp/handlers.go

@@ -217,12 +217,19 @@ func (s *Server) makeIndexHandler(indexer *nixos.Indexer) ToolHandler {
 			return ErrorContent(fmt.Errorf("indexing failed: %w", err)), nil
 		}
 
+		// Index files by default
+		fileCount, err := indexer.IndexFiles(ctx, result.Revision.ID, result.Revision.GitHash)
+		if err != nil {
+			s.logger.Printf("Warning: file indexing failed: %v", err)
+		}
+
 		var sb strings.Builder
 		sb.WriteString(fmt.Sprintf("Indexed revision: %s\n", result.Revision.GitHash))
 		if result.Revision.ChannelName != "" {
 			sb.WriteString(fmt.Sprintf("Channel: %s\n", result.Revision.ChannelName))
 		}
 		sb.WriteString(fmt.Sprintf("Options: %d\n", result.OptionCount))
+		sb.WriteString(fmt.Sprintf("Files: %d\n", fileCount))
 		sb.WriteString(fmt.Sprintf("Duration: %s\n", result.Duration.Round(time.Millisecond)))
 
 		return CallToolResult{