[BUG] V1 apply_patch silently overwrites external file changes (missing stale-content check) #31776

Description

packages/opencode/src/tool/apply_patch.ts does not check for stale content before applying file changes. Between the verification phase (reading files, computing diffs) and the application phase (writing changes), the file content can change. If the file was modified by an external process or another tool call, apply_patch silently overwrites those changes.

Root Cause

The verification phase reads files at line 115, stores old content, and computes the new content. The application phase writes files at line 231, but never re-reads to check if the file changed between these two phases. There's a large TOCTOU window because the permission prompt runs between reading and writing.

Compare with the V2 core apply-patch.ts (packages/core/src/tool/apply-patch.ts) which correctly uses files.writeIfUnchanged() for conditional writes.

Steps to reproduce

1. Have a file open in another editor
2. AI calls apply_patch to modify the file
3. During the permission prompt, the user (or another process) modifies the same file
4. apply_patch applies its changes on top of the modified file, overwriting external edits
5. No error is raised - the external changes are silently lost

OpenCode version

1.17.3