Inconsistent Behavior of `inspect` Command on Linux and Windows

Hi IntelliJ Community,

I'm encountering an issue with the `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:
   git apply --reject --whitespace=fix patchFile.patch
2. Run `inspect` command:
   ./inspect.sh /path/to/project /path/to/inspectionProfile /path/to/reportsFolder -changes -format json
3. Check Git status:
   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

What I Have Tried:

1. Ensuring consistent Git configurations: Set `core.filemode` to `false` on Linux to match Windows.
2. Checking file permissions: Ensured that file permissions are consistent and appropriate.
3. 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.

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!