feat(cli): add specify doctor command for project health validation

[mvanhorn]

Summary

Adds specify doctor - a CLI command that validates the internal health of a spec-kit project. Goes beyond specify check (which only validates external tool installations) to validate the project itself: templates, agent config, scripts, constitution, and feature artifacts.

Why this matters

Users hit confusing errors when their spec-kit project is misconfigured, and there's no diagnostic tool to help them.

Source	Evidence	Engagement
#1866	"specify commands do not work for Codex CLI" - users can't diagnose setup problems	6 comments
#1697	"/speckit.specify not available in CC" - agent config mismatch	1 comment with repro steps
#1705	"AGY projects don't get extension commands registered"	1 comment
#1833	"Vibe and Antigravity agents missing from CommandRegistrar" - config drift	0 comments

All of these share a common diagnostic gap: no way to validate the project's internal configuration without manually inspecting files.

Changes

• Added specify doctor command to the CLI (src/specify_cli/__init__.py)
• Five check functions: _check_templates(), _check_agent_config(), _check_scripts(), _check_constitution(), _check_features()
• Template check: verifies all 5 expected template files exist and have content
• Agent config check: reads .specify/init-options.json and verifies the agent directory and command files
• Script check: verifies bash scripts are executable and powershell scripts exist
• Constitution check: verifies constitution.md exists and has content
• Feature check: scans specs/NNN-*/ for complete artifact sets (spec, plan, tasks)
• Health score: 0-10 based on pass/(pass+warn+fail) ratio
• Options: --json (machine-readable CI output, exits 1 on failures), --fix (auto-fix script permissions), --verbose
• 16 unit tests in tests/test_doctor.py

Testing

$ .venv/bin/python -m pytest tests/test_doctor.py -v
16 passed in 0.18s

$ .venv/bin/python -m pytest tests/ -v
398 passed in 2.58s

Sample output:

Spec Kit Project Health Check

  Template Integrity
    ✓ spec-template.md: exists and valid
    ✓ plan-template.md: exists and valid
    ✓ tasks-template.md: exists and valid
    ✓ constitution-template.md: exists and valid
    ✓ checklist-template.md: exists and valid

  Agent Configuration (Claude Code)
    ✓ Claude Code directory: .claude/ exists
    ✓ command files: 6 command files found

  Scripts
    ✓ bash scripts: 5 scripts, all executable
    ✓ powershell scripts: 5 scripts present

  Constitution
    ✓ constitution: constitution.md exists (1,247 words)

  Active Features
    ✓ 003-user-auth: spec ✓ plan ✓ tasks ✓
    ⚠ 004-settings: spec ✓ plan ✓ tasks ✗

Health Score: 9/10 (1 warning)

This contribution was developed with AI assistance (Claude Code).

[mnriem]

Can you deliver this as an extension? See https://github.com/github/spec-kit/tree/main/extensions

[mvanhorn]

Got it - will repackage these as an extension. Closing these and will submit a PR with a bundled extension that provides resume, doctor, and validate as extension commands.