Concurrent instances corrupt shared .claude.json config file

Bug Description

When running multiple Claude Code instances simultaneously (e.g., working on two different projects in separate terminals), the shared global configuration file ~/.claude.json gets corrupted due to concurrent write race conditions.

Steps to Reproduce

1. Open Claude Code in Terminal 1 for Project A (e.g., cd projectA && claude)
2. Open Claude Code in Terminal 2 for Project B (e.g., cd projectB && claude)
3. Use both instances actively at the same time
4. Observe repeated corruption errors

Error Message

Claude configuration file at C:\Users\user\.claude.json is corrupted: JSON Parse error: Unexpected EOF
The corrupted file has been backed up to: C:\Users\user\.claude\backups\.claude.json.corrupted.<timestamp>
A backup file exists at: C:\Users\user\.claude\backups\.claude.json.backup.<timestamp>
You can manually restore it by running: cp "<backup_path>" "<config_path>"

Impact

• Over a single work session (~4 hours), 256 corrupted backup files accumulated in ~/.claude/backups/
• The error appears repeatedly during normal usage, interrupting workflow
• While Claude Code auto-recovers from backups, the constant corruption/recovery cycle is disruptive

Root Cause Analysis

Both Claude Code instances read/write to the same ~/.claude.json file (which stores toolUsage, clientDataCache, tipsHistory, etc.). When two processes write simultaneously, one write partially overwrites the other, producing invalid JSON (truncated / unexpected EOF).

Environment

• OS: Windows 11 Pro (10.0.26200)
• Shell: Git Bash
• Claude Code version: 2.1.56

Suggested Fix

Consider one or more of:

• File locking: Use OS-level file locks (e.g., flock / LockFileEx) before writing
• Atomic writes: Write to a temp file first, then atomically rename (prevents partial writes)
• Per-instance state: Separate volatile per-instance data (like toolUsage, clientDataCache) from shared config
• Merge on write: Read-modify-write with conflict detection instead of full overwrite