[BUG] System reminders for modified files repeat excessively, consuming context

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?

Description:

When files are modified during a session (by Claude or externally), <system-reminder> blocks about those modifications are injected after every subsequent tool call, not just when relevant.

Observed behavior:

Same 3 file modification reminders repeated 20+ times in one session
Reminders sent after unrelated tools (git push, pip install, MCP queries)
Each reminder ~300-500 bytes × 3 files × 20+ times = ~30KB+ wasted context
Expected behavior:

Send reminder once when modification detected
Only re-send when about to edit that specific file
Clear after file is committed or explicitly acknowledged
Example from session:

<system-reminder>
Note: d:\work\...\__init__.py was modified...
</system-reminder>
This appeared after: git push, pip install, speckitadv --version, MCP index_status(), and every other tool call.

Impact:

Context fills ~2-3x faster than expected
Reduces effective working context for actual tasks
Users report "context reaching 100% very fast compared to 1 month back"
Environment:

Claude Code VSCode extension
Model: Claude Opus 4.5

What Should Happen?

Expected behavior:

Send reminder once when modification detected
Only re-send when about to edit that specific file
Clear after file is committed or explicitly acknowledged

Error Messages/Logs

<system-reminder>
Note: d:\work\spec-kit-adv\scripts\python\speckit\__init__.py was modified, either by the user or by a linter. This change was intentional, so make sure to take it into account as you proceed (ie. don't revert it unless the user asks you to). Don't tell the user this, since they are already aware. Here are the relevant changes (shown with line numbers):
     1→"""
     2→Spec Kit Advanced - Zero-Prompt Architecture CLI
...
</system-reminder>

<!-- This SAME block repeats after EVERY tool call: git push, pip install, MCP queries, --version, etc. -->
<!-- In one session: 3 files × 20+ tool calls = 60+ identical reminder blocks -->

Steps to Reproduce

Steps to Reproduce:

Open Claude Code in VSCode
Edit any file (e.g., change a version number)
Run an unrelated command: git status
Observe <system-reminder> about the modified file
Run another unrelated command: pip install something
Observe the same <system-reminder> repeated
Run any tool (MCP query, bash command, etc.)
Observe reminder repeats every single time
Check context usage - fills much faster than expected
Additional context:

Reminders don't clear after commit
Reminders appear even for read-only operations
Same content repeated verbatim, not deduplicated

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.23

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_