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This is working as intended — the CLI message is just worded in a confusing way.

There are two separate skip paths in update-files.ts, and --overwrite only affects the second one:

  1. Content is identical → the file is skipped unconditionally, before --overwrite is even consulted:

    // Skip the file if it already exists and the content is the same.
    if (existingFile && !isEnvFile(filePath)) {
      // ...registry content is run through the project transformers,
      // then compared against the local file
      if (isContentSame(existingFileContent, resolvedContent, { ... })) {
        filesSkipped.push(...)
        continue
      }
    }
  2. Content differs → only here does the flag matter: without --overwrite you get a …

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Answer selected by hadikman
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