[BUG] CLAUDE_CONFIG_DIR

Environment

• Platform (select one):
• [ ] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [x] Other: Claude Code
• Claude CLI version: 0.2.102
• Operating System: macOS 15.3.1
• Terminal: Ghostty

Bug Description

Setting CLAUDE_CONFIG_DIR does correctly create the configuration files in the new location but it creates identical files/folders for __store.db and statsig in the default location .claude.

Steps to Reproduce

1. rm .claude
2. export CLAUDE_CONFIG_DIR="${HOME}/.config/claude"
3. run claude, authenticate.
4. tree ~/.config/claude all new claude config files correctly found
5. ls -la a newly created .claude directory is created in the root with __store.db and statsig which is already in the new CLAUDE_CONFIG_DIR.

Expected Behavior

Setting CLAUDE_CONFIG_DIR should correctly move all configuration files to this new location and not produce identical files in two locations.