[BUG] System reminders (e.g. `<new-diagnostics>`) are stripped from persisted conversation history, breaking grounding

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?

In the VSCode extension, certain contextual information is delivered to Claude via <system-reminder> tags injected into the conversation (e.g. <new-diagnostics> after a file edit). During a live session, Claude can see and respond to these.

However, when the IDE is closed and reopened, these system reminders are stripped from the persisted conversation history — while Claude's responses to them are preserved. This creates a situation where Claude's own prior statements appear to reference information that no longer exists in the conversation, breaking grounding and coherence.

What Should Happen?

Persist the system reminders in the conversation history, so Claude retains the context that motivated its responses.

Error Messages/Logs

Steps to Reproduce

I asked Claude:

Could you add a variable `` python timestamp : str = "2026-03-06" `` at the very end of file.py ? Just at the very end, no need to do anything else. Read the last few lines, then append. If there is a diagnostic now or later, don't say anything about it, or think about it, just carry on, unless I later tell you otherwise.

Claude does the edit and reponds.

I send two more messages saying great and thanks to make sure the diagnostic arrives.

I then ask Claude:

was there a diagnostic? you can talk about it now.

If I do this without closing and reopening the IDE, Claude knows about a diagnostic that arrived. (And is confused by it, because it's non-obvious.)
If I ask this last question after having closed and reopened the IDE, then Claude does not remember any diagnostics arriving, and launches the LSP tool to see if any show up then.

file.py contained something like:

``` python
from convenience import *

""" filler content """

and convenience.py contained:
``` python
str = int

Just to make sure the diagnostic was unlikely to be hallucinated.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.58

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

VS Code integrated terminal

Additional Information

This was in the VSCode extension. I haven't tested in the terminal app. The VSCode extension version is 2.1.70.