Awesome-Agent-Skills-for-Empirical-Research doctor
git clone https://github.com/brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research
T=$(mktemp -d) && git clone --depth=1 https://github.com/brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/25-HosungYou-Diverga/skills/doctor" ~/.claude/skills/brycewang-stanford-awesome-agent-skills-for-empirical-research-doctor && rm -rf "$T"
skills/25-HosungYou-Diverga/skills/doctor/SKILL.mdDiverga Doctor
Version: 11.1.0 Trigger:
/diverga:doctor
Description
System diagnostics for the Diverga plugin. Checks plugin health, skill sync, hook enforcement, configuration validity, API keys, and project state. Reports issues with actionable fix commands.
Follows OpenClaw Check-Report-Fix pattern: every detected issue includes a fix recommendation.
Instructions
When user invokes
/diverga:doctor, execute all 7 diagnostic layers sequentially and display results.
Layer 1: Plugin Health
Check plugin registration:
- Read
~/.claude/plugins/installed_plugins.json - Verify
entry existsdiverga@diverga - Extract version and install date
Check config JSON validity:
- Read
~/.claude/plugins/diverga/config/diverga-config.json - Verify it parses as valid JSON
- Check required fields exist:
,version
,human_checkpointslanguage
Report format:
PLUGIN HEALTH Registration: [PASS - diverga@diverga v11.1.0 | FAIL - not found in installed_plugins.json] Config file: [PASS - valid JSON | FAIL - missing or invalid] Config fields: [PASS - all required fields present | WARN - missing: field1, field2]
Fix if FAIL:
- Registration missing: "Run: /plugin install diverga"
- Config missing: "Run: /diverga:setup to regenerate configuration"
- Config invalid JSON: "Config file is corrupted. Run: /diverga:setup to regenerate"
Layer 2: Skill Sync
Check skill counts match between plugin and local cache:
- Use Glob to count directories in
~/.claude/plugins/diverga/skills/*/SKILL.md - Use Glob to count directories in
(exclude~/.claude/skills/diverga-*/SKILL.md
prefix duplication — count unique skill names)diverga-diverga - Compare counts
Check for missing skills in local cache:
- For each skill in plugin directory, check if corresponding
exists in local skillsdiverga-{name} - List any missing skills
Report format:
SKILL SYNC Plugin skills: [count] skills in plugin directory Local skills: [count] skills in local cache Sync status: [PASS - all synced | WARN - X skills missing locally] Missing: [list of missing skill names, if any]
Fix if WARN:
- "Missing local skills. To resync, reinstall the plugin or manually copy:"
- For each missing skill: " cp -r ~/.claude/plugins/diverga/skills/{name} ~/.claude/skills/diverga-{name}"
Layer 3: Plugin Cache Sync
Check that the plugin cache matches the installed version:
- Read
→ extract~/.claude/plugins/diverga/plugin.jsonversion - Glob
→ list cached versions~/.claude/plugins/cache/diverga/diverga/*/plugin.json - Compare: cached version should match installed version
- Check if cached version has
hooks/hooks.json
Report format:
PLUGIN CACHE Installed version: [11.1.0 | FAIL - plugin.json missing] Cached version: [11.1.0 | WARN - stale cache: 8.0.1 | FAIL - no cache found] Cache has hooks: [PASS - hooks.json present | FAIL - hooks missing from cache] Cache has agents: [PASS - agents/ present | WARN - agents/ missing]
Fix if WARN/FAIL:
- Stale cache: "Plugin cache is outdated. Run in terminal:"
REPO="/Volumes/External SSD/Projects/Diverga/Diverga-core" CACHE="$HOME/.claude/plugins/cache/diverga/diverga/11.1.0" rm -rf "$HOME/.claude/plugins/cache/diverga/diverga/8.0.1" mkdir -p "$CACHE" cp -R "$REPO"/{skills,agents,config,hooks,mcp,CLAUDE.md,AGENTS.md,README.md} "$CACHE/" cp "$REPO/.claude-plugin/plugin.json" "$CACHE/" - No hooks in cache: "Copy hooks manually: cp -R ~/.claude/plugins/diverga/hooks/ $CACHE/hooks/"
- Restart Claude Code after cache update for changes to take effect
Layer 4: Hook Enforcement
Check hook configuration:
- Read
→ verify it exists and has~/.claude/plugins/diverga/hooks/hooks.json
entriesPreToolUse - Check matchers include "Agent" and "Skill" (not "Task" — known bug in pre-11.1.0)
- Read
→ check if hooks are also configured at global level~/.claude/settings.json - Test hook execution: Run
→ verify it returns valid JSON withecho '{"tool_name":"Skill","tool_input":{"skill":"diverga:c1"}}' | node ~/.claude/plugins/diverga/hooks/prereq-enforcer.mjs
fieldcontinue
Report format:
HOOK ENFORCEMENT Plugin hooks.json: [PASS - exists with Agent+Skill matchers | FAIL - missing or wrong matchers] Global hooks: [PASS - configured in settings.json | WARN - not in settings.json (relies on plugin)] Hook executable: [PASS - returns valid JSON | FAIL - execution error] Matcher check: [PASS - uses "Agent" | FAIL - uses stale "Task" matcher]
Fix if issues found:
- Wrong matcher: 'Change "Task" to "Agent" in hooks.json — Claude Code uses "Agent" as tool name'
- Not in settings.json: "Add hooks to ~/.claude/settings.json for reliable enforcement across sessions"
- Execution error: "Check that better-sqlite3 is installed: cd ~/.claude/plugins/diverga/mcp && npm install"
Layer 5: Config Validity
Deep validation of diverga-config.json:
- Read
~/.claude/plugins/diverga/config/diverga-config.json - Check
field matches "11.1.0"version - Check
object exists and hashuman_checkpoints
(boolean) andenabled
(array)required - Check
is one of: "en", "ko", "auto"language - Check
hasmodel_routing
,high
,medium
keys if presentlow
Report format:
CONFIG VALIDITY Version field: [PASS - 11.1.0 | WARN - version mismatch: found X.Y.Z] Checkpoints: [PASS - configured | FAIL - missing or malformed] Language: [PASS - "en" | WARN - unexpected value: "XX"] Model routing: [PASS - configured | SKIP - not set (using defaults)]
Fix if issues found:
- Version mismatch: "Config version X.Y.Z doesn't match plugin 11.1.0. Run: /diverga:setup to update"
- Checkpoints malformed: "Run: /diverga:setup to reconfigure checkpoints"
Layer 6: API Keys
Check 8 environment variables using Bash tool (
):echo $VAR_NAME
| Variable | Purpose | Required? |
|---|---|---|
| LLM screening (recommended) | Recommended |
| Claude API | Recommended |
| OpenAI screening | Optional |
| Gemini visualization | Optional |
| Paper retrieval | Optional |
| OpenAlex polite pool | Optional |
| Scopus access | Optional |
| Web of Science | Optional |
For each variable, use Bash:
echo "${VAR_NAME:+configured}" — if output is "configured", it's set; if empty, it's not set.
Report format:
API STATUS Groq: [configured | NOT SET -> export GROQ_API_KEY=your_key] Anthropic: [configured | NOT SET -> export ANTHROPIC_API_KEY=your_key] OpenAI: [configured | not set (optional)] Gemini: [configured | not set (optional)] Semantic Scholar: [configured | not set (optional)] OpenAlex: [configured | not set (optional)] Scopus: [configured | not set (optional)] Web of Science: [configured | not set (optional)]
Fix if NOT SET (recommended keys):
- Show
for each missing recommended keyexport VAR_NAME=your_key_here - For optional keys, just note "(optional)" — no urgent fix needed
Layer 7: Project State
Check for active research project:
- Use Glob to check if
exists in current working directory.research/project-state.yaml - If exists: Read it and validate YAML structure (has
,project_name
)current_stage - Also check if
directory exists with expected subdirectories.research/
Report format:
PROJECT STATE Active project: [project name | No active project] State file: [PASS - valid | WARN - invalid YAML | SKIP - no project] Research dir: [PASS - structure intact | WARN - missing subdirs | SKIP - no project]
Fix if issues:
- Invalid YAML: "Project state file is corrupted. Run: /diverga:setup in your project directory"
- Missing subdirs: "Run: /diverga:setup to reinitialize project structure"
- No project: "Start a new project with: /diverga:setup or describe your research topic"
Final Summary
After all 7 layers, display overall status:
══════════════════════════════════════════════ DIVERGA SYSTEM DIAGNOSTICS v11.1.0 ══════════════════════════════════════════════ [Layer 1-7 results as shown above] ------------------------------------------ OVERALL: [HEALTHY | X WARNING(S) | X ERROR(S)] [If issues found, numbered list:] 1. [Issue description] -> [Fix command] 2. [Issue description] -> [Fix command] ... [If healthy:] All systems operational. Diverga is ready to use. Run /diverga:help to see all 24 agents and commands. ══════════════════════════════════════════════
Implementation Notes
- Execute all Bash commands for API key checks in PARALLEL (single message, multiple Bash calls)
- Use Read tool for JSON/YAML file checks
- Use Glob tool for skill counting
- This skill is READ-ONLY — it does not modify any files
- If any individual check encounters an error (file not readable, etc.), show "UNABLE TO CHECK" rather than crashing
- Total execution target: under 10 seconds