.gitignore patterns are ignored when using repomix <directory> command #776

Description

Bug Report

MRE Repository: https://github.com/Danipulok/repomix-ignore-bug

Issue:
When running repomix src, files listed in .gitignore are not ignored and appear in the output.

Expected behavior:
Files matching .gitignore patterns should be excluded from the output.

Actual behavior:
All files are included in the output, ignoring .gitignore patterns.

Test case:

# This command ignores .gitignore patterns (BUG)
repomix src --output src-command-output.md

# This command respects .gitignore patterns (WORKS)
repomix --include "src/**" --output include-command-output.md

Environment:

• Repomix version: 1.3.0
• Config: "useGitignore": true is explicitly set

Files structure:

• .gitignore contains: should_ignore1.py and src/should_ignore2.py
• src/ contains: valid.py, should_ignore1.py, should_ignore2.py

Result:

• repomix src includes all 3 files (should exclude 2)
• repomix --include "src/**" includes only 1 file (correct behavior)

The bug occurs specifically when targeting a subdirectory with repomix <directory> instead of using include patterns from the root.

Usage Context

Repomix CLI

Repomix Version

1.3.0

Node.js Version

v22.16.0