I’m encountering an issue with the IntelliJ IDEA inspect command that behaves inconsistently between Linux and Windows environments. Here’s a detailed description of the problem:

Issue Description

I am using the inspect command as part of my automated workflow to analyze code changes. My workflow involves applying a large Git patch, running the inspect command, and then reviewing the changes. However, the outcome differs significantly between Linux and Windows.

Steps to Reproduce

1. Apply a large Git patch:
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   <code>git apply --reject --whitespace=fix patchFile.patch

   </code>

   <code>git apply --reject --whitespace=fix patchFile.patch </code>

   git apply --reject --whitespace=fix patchFile.patch
   

2. Run inspect command:
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   <code>./inspect.sh /path/to/project /path/to/inspectionProfile /path/to/reportsFolder -changes -format json

   </code>

   <code>./inspect.sh /path/to/project /path/to/inspectionProfile /path/to/reportsFolder -changes -format json </code>

   ./inspect.sh /path/to/project /path/to/inspectionProfile /path/to/reportsFolder -changes -format json
   

3. Check Git status:
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   <code>git diff --staged --shortstat

   </code>

   <code>git diff --staged --shortstat </code>

   git diff --staged --shortstat
   

Observed Behavior

Windows:

• The inspect command runs and the staged changes remain consistent.
• Git status shows all expected changes as staged.
• Around 50 JSON files are generated.

Linux:

• The inspect command runs but the staged changes become inconsistent.
• Git status shows fewer files staged and some files left untracked or modified but not staged.
• Around 6 JSON files are generated.

Environment Details

Windows:

• OS: Windows 10
• IntelliJ IDEA Version: ideaIC-2024.1.1
• Git Version: 2.44.0

Linux:

• OS: Linux
• IntelliJ IDEA Version: idea-IC-241.15989.150
• Git Version: 2.43.0

Questions

1. Is there any known issue with the inspect command on Linux that could cause such behavior?
2. Are there any specific configurations or environment setups that need to be considered for consistent behavior?
3. Has anyone else encountered a similar issue and found a workaround or solution?

Any insights or suggestions would be greatly appreciated. Thank you in advance for your help!

What I Have Tried

• Ensuring consistent Git configurations: Set core.filemode to false on Linux to match Windows.
• Checking file permissions: Ensured that file permissions are consistent and appropriate.
• Manual verification: Manually verified that the patch applies correctly and all changes are staged before running inspect.

Despite these efforts, the inconsistency persists. I’m seeking advice on what might be causing this behavior and how to achieve consistent results across both environments.