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

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

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/

This creates issues for teams and users who want to:

• Align with different directory conventions (e.g., use .worktree/ at repo root instead of .claude/worktrees/)
• Reduce clutter in the .claude/ directory
• Support monorepo structures with different conventions per subdirectory
• Store these files in locations that match their project organization

Proposed Solution

Add a paths configuration object in settings.json to override default locations:

```json
{
"paths": {
"skills": "{project}/.skills",
"agents": ".agents",
"worktrees": ".worktree",
"rules": ".rules"
}
}

  - Support both relative paths (relative to project root) and absolute paths
  - Apply to User (~/.claude/settings.json), Project (.claude/settings.json), and Local (.claude/settings.local.json) scopes
  - When not specified, use current hardcoded defaults for backward compatibility

### Alternative Solutions

Currently there are no workarounds:
  - Users must accept the hardcoded directory structure
  - Teams can't standardize on custom conventions
  - Monorepos can't have different configurations per directory

### Priority

Medium - Would be very helpful

### Feature Category

Configuration and settings

### Use Case Example

_No response_

### Additional Context

_No response_