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

[tylerdurdenpin-cmyk]

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

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

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

4. Run npx repomix.
   

5. 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

[Rakshat28]

tried to make a minimum reproducible example (MRE) from scratch. I was unable to reproduce the bug in a clean environment.

I tested this with a fully tracked Git repository to see if Git tracking caused the issue, but Repomix correctly included both identically named files.

made a clean directory and its structure :

mkdir repomix-repro-1503
cd repomix-repro-1503
git init
mkdir -p config/lunar
echo "<?php // Content of ROOT database.php" > config/database.php
echo "<?php // Content of LUNAR database.php" > config/lunar/database.php

created the config files

cat <<EOF > repomix.config.json
{
  "include": ["config/**/*.php"]
}
EOF

git commit and ran repomix

git add .
git commit -m "Initial commit"
npx repomix

to verify the output

grep -q "Content of ROOT database.php" repomix-output.xml && echo " ROOT file INCLUDED" || echo " ROOT file MISSING"
grep -q "Content of LUNAR database.php" repomix-output.xml && echo " SUBDIRECTORY file INCLUDED" || echo " SUBDIRECTORY file MISSING"

and got this :

ROOT file INCLUDED
SUBDIRECTORY file INCLUDED

I am currently checking if an aggressive .gitignore rule, an untracked git status, or a .repomixignore pattern is accidentally catching the subdirectory.

[Samsen879]

I tried to reproduce this on the current main with the structure from the issue:

config/database.php
config/lunar/database.php

Using a single root with include: ["config/**/*.php"], both files are included in XML/Markdown/plain/JSON output. I also checked several include variants (config, config/**, config/**/database.php, **/database.php, and explicit paths), and both files are included except for config/*.php, which only matches direct children as expected.

I did find a related multi-root case: running with overlapping roots such as config config/lunar --include "**/*.php" can cause the root database.php content to be overwritten in JSON output on current main. That appears to be the same root-aware path issue addressed by #1618.

If this issue still happens with a single root, the missing piece is likely in local config/ignore/security behavior rather than basename collision. Could you share the exact repomix.config.*, .repomixignore / .gitignore entries, output style, and whether the security check reports any excluded files?