Write tool overwrites uncommitted working tree changes without warning

Bug Description

Claude Code's Write tool overwrote a file that had uncommitted working tree changes (shown as M in git status at conversation start), destroying the user's in-progress work without preserving it.

Steps to Reproduce

1. Have a file with uncommitted modifications (unstaged changes visible in git status)
2. Ask Claude Code to modify that file
3. Claude Code uses the Write tool to completely replace the file contents with new code
4. The user's pre-existing uncommitted changes are permanently lost (no stash, no backup)

Expected Behavior

Before overwriting a file with uncommitted changes, Claude Code should either:

• Read and preserve the existing contents, building on top of the user's changes
• Warn the user that uncommitted changes exist and will be lost
• Use the Edit tool (which applies diffs) instead of the Write tool (which replaces entirely)

Actual Behavior

Claude Code used the Write tool to completely replace tracker/src/tracker/base.py, which had unstaged modifications ( M in git status). The pre-existing uncommitted work was destroyed with no way to recover it.

Context

• The git status at conversation start clearly showed the file was modified: M tracker/src/tracker/base.py
• Claude Code did read the file before writing, but did not compare against the committed version to identify and preserve the user's changes
• The file was not stashed, so recovery was impossible

Environment

• Claude Code CLI
• Model: claude-opus-4-6
• OS: Linux