Files with identical names in different subdirectories are being skipped/ignored

Description

I encountered an issue where Repomix fails to include a file if there is another file with the same name elsewhere in the project (specifically in the config directory). Example: Having both config/database.php and config/lunar/database.php causes the second one to be ignored. Renaming the file (e.g., to config/lunar/database_lunar.php) fixes the issue, which suggests a path/name collision during globbing/collection.

Steps to reproduce:

1. 复制

   Have a project structure with a file config/database.php.

2. 复制

   Have another file with the same name in a subdirectory, e.g., config/lunar/database.php.

3. 复制

   Configure repomix.config.json to include both or the folder containing both.

4. 复制

   Run npx repomix.

5. 复制

   The file config/lunar/database.php is missing from the output.

Expected behavior: All files matching the include patterns should be included, regardless of whether there are other files with the same name in the repository.

Environment:

OS: Ubuntu 22.04

Additional context: I tried using npx repomix --verbose, but the file was silently excluded. Renaming the file to a unique name solved the problem, confirming it's a name collision issue.

Usage Context

Repomix CLI

Repomix Version

1.13.1

Node.js Version

v20.20.2