[FEATURE] Allow configuring default paths for skills, rules, agents, and worktrees in settings.json

Currently, Claude Code looks for configuration files in hardcoded locations:

• Skills: ~/.claude/skills/ and .claude/skills/
• Rules (AGENTS.md, CLAUDE.md): ~/.claude/ and .claude/
• Agents: ~/.claude/agents/ and .claude/agents/
• Worktrees: .claude/worktrees/

Feature Request

Add settings.json options to override these default paths, allowing teams and users to:

• Store skills/rules/agents/worktrees in custom directories
• Align with team conventions (e.g., .worktree/ at repo root instead of .claude/worktrees/)
• Reduce clutter in the .claude/ directory
• Support monorepo structures with different conventions per subdirectory
• Support relative and absolute paths

Proposed settings

{
  "paths": {
    "skills": ".skills",
    "agents": ".agents",
    "worktrees": ".worktree",
    "rules": ".rules"
  }
}

This would apply to User, Project, and Local settings scopes.