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>

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"))
 				},
 			},
 			{