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>

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{