Bug: .ignore file is ignored when customPatterns is defined in config

[yamadashy]

Description

When customPatterns is defined in the config file (~/.config/repomix/repomix.config.json or repomix.config.json), the .ignore file is completely ignored instead of being merged with the custom patterns.

Reproduction Steps

1. Create a .ignore file in your project root with a pattern (e.g., spec/data/)
2. Add customPatterns to your config file:

   {
     "ignore": {
       "customPatterns": ["bin/"]
     }
   }

3. Run repomix
4. Files matching the .ignore pattern are included in the output (should be excluded)

Expected Behavior

All ignore sources should be merged and applied together:

• Custom patterns from config
• .repomixignore
• .ignore
• .gitignore (if enabled)
• Default patterns (if enabled)

The priority order should only matter when rules conflict, not for whether sources are applied.

Current Behavior

When customPatterns is defined in the config, the .ignore file is completely ignored.

Additional Context

• Reported by @thomaswitt in Use .ignore file file content to ignore files. #937 (comment: Use .ignore file file content to ignore files. #937 (comment))
• Related to the .ignore support feature added in v1.9.0 (Use .ignore file file content to ignore files. #937)
• Similar tools like ripgrep and fd merge all ignore sources

Environment

• Repomix version: 1.9.0

[yamadashy]

I attempted to reproduce this issue with the current code (v1.9.1) but could not replicate the reported behavior. Both .ignore files and customPatterns are correctly merged and applied together.

Added comprehensive tests in #960. I'll continue investigating to identify the root cause.