feat: enhance doctor command with comprehensive health checks

[sametcelikbicak]

Summary

Enhances rolecraft doctor with comprehensive system health checks beyond the basic scan.

New checks

Check	Description
Node.js location	Shows process.execPath
Platform	OS and kernel release
Git / npm availability	Detects required tooling
~/.agents permissions	Directory permission string
Lockfile schema	Validates global lockfile format (version, structure)
Disk usage	Total size and count of installed skills
Agent detection ratio	Shows X/86 supported agents detected instead of just count
Per-agent permissions	Directory permissions per detected agent
Orphaned skill dirs	Directories in skills path not tracked in any lockfile
Broken symlinks	Detected as part of integrity check
MCP servers	Counts configured MCP servers (deduplicated by config path)
--json flag	Structured JSON output for scripting
--network flag	Optional GitHub connectivity test

Agent count clarification

Previous doctor showed 49 agent(s) found without context. Now shows 49/86 supported agents detected, making clear that 86 are supported but only 49 are installed on the system.

Docs

Updated:

• docs/commands/doctor.md — new output examples, --json/--network flags
• docs/reference.md — doctor entry with flag details

Tests

6 new tests added (25 total for doctor): platform, node location, lockfile schema validation, orphaned dirs, MCP check, --json output. All 736 tests pass.