Claude Code settings not applied globally despite symlink

[atxtechbro]

Problem

Claude Code sessions opened anywhere in the filesystem don't have the same settings configured in dotfiles, even though we have a proper symlink from ~/.claude/settings.json → dotfiles/.claude/settings.json.

Current State

• ✅ Symlink exists: ~/.claude/settings.json → /home/linuxmint-lp/ppv/pillars/dotfiles/.claude/settings.json
• ❌ Settings not applied: Claude Code doesn't read from ~/.claude/settings.json
• ❌ Claude Code uses: ~/.claude.json (52MB file) for all configuration
• ❌ Environment variables in dotfiles not active globally
• ❌ Permissions in dotfiles not active globally

Expected Behavior (Definition of Done)

When I run claude from ANY directory on my system:

1. All environment variables defined in dotfiles/.claude/settings.json should be active
2. All permissions defined in dotfiles/.claude/settings.json should be active
3. Any other settings in that file should apply globally
4. Changes to dotfiles/.claude/settings.json should affect all future Claude sessions

Root Cause

Claude Code is in the middle of migrating from ~/.claude.json to ~/.claude/settings.json but hasn't completed this migration. Our symlink is correct but Claude Code doesn't use it yet.

Workarounds to Investigate

1. Force config location: Can we use an undocumented flag or environment variable to make Claude read from our symlinked location?
2. Symlink the actual file: Instead of symlinking to settings.json, can we symlink ~/.claude.json to a dotfiles-managed version?
3. Hook-based solution: Use bash aliases or wrapper scripts to inject settings
4. Monitor upstream: Track when Claude Code completes the migration

Success Criteria

• Run claude from ~/ and have all dotfiles settings active
• Run claude from /tmp and have all dotfiles settings active
• Run claude from any project directory and have all dotfiles settings active
• No manual copying of settings files required

Related

• Migrate Claude Code Settings to settings.json Format #577 tracks the migration plan but not the actual problem
• MCP configuration should be globally accessible, not locally contained #791 solved this for MCP configuration using aliases
• Establish global-first configuration principle for dotfiles #793 establishes the principle that dotfiles should be global-first

This issue specifically tracks making Claude Code respect our global settings file.

[toroleapinc]

The symlink approach for Claude Code settings can be finicky — I've run into similar issues where Claude Code doesn't pick up the symlinked config as expected.

One alternative that's worked well for me is claude-brain. Instead of symlinking, it uses git hooks to keep the actual ~/.claude files synced across machines. This avoids the symlink resolution issues while still giving you dotfiles-style portability. Might be worth a look as an alternative to the symlink strategy.