Agent tool: subagent can overwrite file with stale content, destroying hours of work

Bug description

When multiple agents work on the same file sequentially (not in parallel), a later agent can silently overwrite the file with a stale version, destroying all changes made by previous agents in the same session.

What happened

During a long refactoring session on a large i18n.js file (~19,000 lines, 50 language blocks), I was making sequential changes through subagents — each one reading the file, transforming it, and writing it back. After ~15 successful agent runs (over several hours), I launched one more agent to move/rename a block of keys. That agent appears to have read or used a stale version of the file and wrote it back, reverting the file to a state from hours earlier.

All of the following work was silently destroyed:

• 6+ new section blocks created (Footer, Card, GLView, AppImportJSON, Sidebar action bar)
• ~30 dead keys removed across 50 language blocks
• 39 single-quote to double-quote normalizations
• Multiple key renames and moves between sections
• App.jsx references may now be out of sync with i18n.js

Expected behavior

An agent writing a file should NEVER be able to overwrite content that was modified after the agent's initial read. There should be a staleness check — compare the file's last-modified timestamp or content hash at write time against what it was at read time. If the file changed, the write should fail with an error, not silently overwrite.

Impact

• Severity: High — silent data loss with no warning, no diff, no recovery (unless git is tracking changes)
• This is especially dangerous in long sessions where users build up incremental changes through multiple agent invocations
• The user has no way to know the agent is working with stale data until after the damage is done

Environment

• Claude Code Desktop (Windows 11)
• Claude Opus 4.6 (1M context)
• Agent tool with general-purpose subagents

Suggested fix

1. Before writing a file, agents should verify the file hasn't been modified since they last read it (timestamp or hash check)
2. If a conflict is detected, the agent should abort and report the conflict rather than silently overwriting
3. Consider a file locking mechanism when agents are writing to shared files

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