Fix config file boolean options being ignored

Boolean CLI options with defaults (keepComments, sortComponentsProps, split)
were not being respected when set in a config file. This happened because
Commander.js always sets these options to their default values, and the
subsequent Object.assign would overwrite config file values with CLI defaults.

The fix applies the same pattern already used for lineWidth, sort, and bundle:
explicitly check for config file values before the merge, using nullish
coalescing to preserve CLI-specified values when present.

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

Author: jdechicchis

bin/cli.js

@@ -90,9 +90,14 @@ async function run(oaFile, options) {
 
   // Merge .openapiformatrc and configOptions
   configOptions = Object.assign({}, defaultOptions, configOptions);
+  // Preserve config file values for options that have CLI defaults
+  // These must be set before Object.assign to prevent CLI defaults from overwriting config values
   options.lineWidth = configOptions?.lineWidth ?? options.lineWidth;
   options.sort = configOptions?.sort ?? options.sort;
   options.bundle = configOptions?.bundle ?? options.bundle;
+  options.keepComments = configOptions?.keepComments ?? options.keepComments;
+  options.sortComponentsProps = configOptions?.sortComponentsProps ?? options.sortComponentsProps;
+  options.split = configOptions?.split ?? options.split;
 
   // Merge configOptions and CLI options
   options = Object.assign({}, configOptions, options);