Expand MCP server with init, status, and focused generate tools

[ldraney]

Context

The MCP server currently has a single sop_generate tool that does everything at once. As discussed in #19, the generator now respects existing .claude/ directories and merges .mcp.json intelligently. The next step is making the MCP server a proper interface.

Current state

One tool: sop_generate — generates .claude/ and .mcp.json from sop/.

Proposed tools

sop_init

• Scaffold .claude/ with safe defaults (sop.json, engine.sh, settings.json)
• Never overwrites existing files
• Entry point for new projects

sop_status

• Report current configuration state
• sop.json present? How many rules, skills, agents, MCP servers?
• Which files are generated vs user-edited?
• Useful for sop-expert agent to understand what's configured

sop_generate (refined)

• Reads .claude/sop.json (not sop/sop.json — consolidate into .claude/)
• Only generates settings.json and merges .mcp.json
• Does not touch user-edited files (skills, agents, validators)

Design principles

• Individual-first: .claude/ is gitignored, config is personal
• Safe defaults: init gives a working setup out of the box
• Never overwrite: existing files are preserved unless explicitly requested
• MCP is the hands, sop-expert is the brain: tools do actions, agent provides guidance

User flow

User adds dev-sop-engine MCP to any project
  → sop_init: creates .claude/ with safe defaults
  → sop_status: "you have 0 rules, 0 skills, 1 MCP server"
  → User says "add a lint rule" → sop-expert agent guides them
  → sop_generate: wires up settings.json + merges .mcp.json

Also requires

• Refactor generator to read from .claude/sop.json instead of sop/sop.json
• Remove need for separate sop/ directory (consolidate into .claude/)

Relates to #19, #20