[BUG] Skills and custom commands not loading - debug log shows incorrect error about duplicate inodes

Preflight Checklist

• [ ] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Skills and/or commands are failing to load without feedback to the user as to the cause.

Debug logging reveals these are being excluded as duplicates due to inode duplication, which is an error in the Claude Code harness.

I've loaded this bug as a pointer to help find the proper bug report for this.

The problem is caused due to the harness using fs.statSync() or similar; this is returning an IEEE 754 double, which can overflow the significant digit range on some file systems. This causes incorrect inode values to be read:

5764607523036429244 === 5764607523036429000
5764607523036429245 === 5764607523036429000

What Should Happen?

The harness should be using fs.statSync(filePath, { bigint: true }) or similar to load inode numbers, allowing full precision to be preserved.

Error Messages/Logs

Skipping duplicate skill 'csharp-modern' from projectSettings (same inode already loaded from projectSettings)
Skipping duplicate skill 'jira' from projectSettings (same inode already loaded from projectSettings)

Actual inode's are unique; truncated inode's are the same.

Steps to Reproduce

Have a sufficiently large file system with inode numbers exceeding 17 significant digits.
Try and load multiple skills with the same inode prefix
Use --debug to observe incorrect inode duplication error

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

2.0.70 potentially (problem is new to me, but may be due to regression in recent update)

Claude Code Version

2.0.71

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

Known to impact MacOS as well as Windows. Any 64-bit file table should be capable of being impacted once inodes get high enough.
Previous issue is @ https://github.com/anthropics/claude-code/issues/13893

I've loaded this as a duplicate to help people find the correct one.