[BUG] 🐞Claude Code is not seeing file changes because of "optimising"

Preflight Checklist

• [x] 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?

For the past week or so, when I've been working on a handful of files that are not always modified by Claude Code, and I ask it to read it or "tell me what changed" it uses a cached version or an old read. Then comes back to tell me nothing has changed. This happens within and across conversations

What Should Happen?

Claude should see changes on files, this should never fail. It never used to. Claude should not be sharing "optimisations" across conversations - that's the whole point of a separate context window - that you absolutely know its water tight and independent.

Error Messages/Logs

Please read through the screenshots.

Steps to Reproduce

Attached is a screenshot example for "git diff", but, this is one of many. It was my attempt to work around it simply reading the file and telling me nothing has changed.

!Image

Then all the work happened in here - where I noticed it did not pickup any changes to ".claude/settings.json".. had to try 5 times. Then I asked about it:

!Image

It mentions "The problem: The tool result deduplication system" which is the first time I see this. Sometimes it says "cache".

Here is another Example:

!Image

Something is very wrong.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Problem experience approx. for last 1-2 weeks.

Claude Code Version

v2.1.92

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

VS Code integrated terminal

Additional Information

I really hope you don't auto-close my issue and say "nothing wrong here." Something is very wrong.