Support .claude/ directory for CLAUDE.md and MCP config (.claude.json)

Currently Claude Code scatters related configuration files across the home directory:

• ~/.claude.json — MCP server configuration
• ~/CLAUDE.md — Global instructions file
• ~/.claude/ — Settings, sessions, memory, projects

Request: Consolidate all Claude-related files under ~/.claude/:

• ~/.claude/CLAUDE.md instead of ~/CLAUDE.md
• ~/.claude/config.json instead of ~/.claude.json

This would keep the home directory clean and make it obvious where all Claude-related files live. Users currently have to know that Claude files are split between ~/.claude.json, ~/CLAUDE.md, and ~/.claude/ — which is confusing.

Backwards compatibility could be maintained by falling back to the current locations if the new ones don't exist.