Allow customizing the .claude/ directory location

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

The .claude/ directory is currently hardcoded at the project root. Users cannot configure its location to match their preferred project structure or workflow.

Proposed Solution

Add a configuration option (e.g., in ~/.claude/settings.json or project-level settings.json) to specify a custom path for the .claude/ directory:

{
  "claudeDirectory": "/path/to/custom/.claude"
}

This would affect all contents currently stored under .claude/, including:

• worktrees/
• plans/
• agents/
• rules/

Alternative Solutions

_No response_

Priority

Medium - Would be very helpful

Feature Category

Configuration and settings

Use Case Example

• Some users prefer to keep tool-specific working files (worktrees, plans, agents) in a custom location rather than the project root
• In monorepo or multi-project setups, users may want to consolidate Claude Code working directories elsewhere
• Personal preference for organizing dotfiles and tool directories

Additional Context

_No response_