mycelium-hq/ai-brain-starter/health-doctor

health-doctor

The substrate has 41 tools + 5 skills + 2 auto-trigger hooks. None of it matters if the chain breaks silently. This skill is the surface for verifying the system is actually running.

Run /health doctor whenever:

• It's been a few days since you saw a workout in your calendar
• You want to know if yesterday's wearable data actually made it in
• You want to see which lab markers need a re-test
• You're setting up the auto-chain for the first time and want to confirm the wiring

What it reports

Six sections, each with a green / yellow / red flag:

1. Data freshness

For each enabled source:

• Apple Health: hours since last health_import_xml (yellow if > 14 days, red if > 28 days)
• Oura: hours since last health_import_oura (yellow if > 36h, red if > 7d)
• Fitbit: hours since last health_import_fitbit (yellow if > 36h, red if > 7d)
• Labs: days since last health_import_labs (yellow if any marker is > 180 days old or any out-of-range marker is > 90d without a re-test)

Pulled from the imports table via health_status().

2. Last prescription + completion

• Most recent prescription via health_coach_recent_prescriptions(days=7)
• Was it completed? (RPE + lift actuals logged via /coach log)
• Streak: how many days in a row had both a prescription AND a completion
• Missed days: prescriptions with no completion in the last 14 days

Yellow if completion rate < 60%. Red if completion rate < 40% or no prescriptions in 7 days.

3. Auto-trigger hooks installed

The default wired set is defined by hooks.json at the repo root (the file the installer actually writes into ~/.claude/settings.json, tested by services/health-mcp/tests/test_v05_hooks.py) — read it rather than assuming a fixed list, so this check can't drift from what installs. See docs/AUTOMATION.md for the full chain.

By default that's one hook:

• coach-auto-prescribe-on-journal.py on Stop (prescribes + backfills after /journal)

health-auto-sync.py (SessionStart wearable refresh) is opt-in, power-user only, and deliberately NOT wired by default — firing it on every SessionStart is wasteful for users with many sessions/day. Its absence from settings.json is expected, not a fault.

Red if the Stop hook (coach-auto-prescribe-on-journal.py) is not in settings.json. Yellow if the hook script file exists but isn't registered. Green if registered AND firing recently (check ~/.claude/hookify-blocks.log for the hook name in the last 48h). If health-auto-sync.py IS registered (the user opted in), report its freshness the same way, but never red for its absence.

4. Coach profile status

Reads <VAULT_ROOT>/Meta/coach-profile.yaml:

• Profile exists? Last updated?
• calendar_drop: true AND google-workspace MCP connected? (calendar drop won't fire otherwise)
• preferred_workout_clock set?
• days_per_week reasonable for level?
• started_iso set? (used by deload-week computation)

Yellow if any field missing. Red if no profile at all.

5. Lab status flags

Run health_lab_panel(today, lookback_days=180) and surface ANY marker with status: low or status: high:

• Marker, value, range, status
• Days since last test for that marker
• WHY this marker matters (pull from health_recommended_labs())
• Suggested re-test cadence (e.g. "re-test in 90 days after supplementation")

Yellow if any marker is out-of-range and last tested > 90 days ago. Red if any out-of-range marker is critical (low ferritin in menstruating users, elevated hs-CRP > 3.0, fasting insulin > 10, Vitamin D < 20).

6. Cycle phase + sleep regularity (women's substrate qualifier)

If menstrual flow records exist:

• Current phase + cycle day + irregularity flag from health_cycle_context(today)
• Cycle length variance over last 6 cycles
• Yellow if irregularity = "mild_irregular". Red if "irregular".

Plus health_sleep_regularity(last_14_days):

• Regularity score
• Bed-time stdev, wake-time stdev, mean sleep latency
• Yellow if regularity < 70. Red if < 50.

Output format

A markdown report with the six sections, each summarized to 3-5 lines with the flag, the data, and a one-line "what to do" if yellow or red.

Example:

# Health doctor — 2026-05-10
 
## 🟢 Data freshness
-Apple Health: 12 days ago (yellow threshold: 14d) — re-export soon
-Oura: 4 hours ago — fresh
-Fitbit: not configured
-Labs: ApoB tested 2026-05-01 (9 days), Vitamin D last 2026-05-01 (9 days)
 
## 🟡 Last prescription + completion
-Last prescription: 2026-05-09 lower_body_strength (diff 7/10)
-Completed: no
-7-day streak: 0 (missed yesterday's log)
-Action: /coach log yesterday's session to keep the progression chain accurate
 
## 🟢 Auto-trigger hooks
-SessionStart: health-auto-sync.py ✓ registered, last fired 4h ago
-Stop: coach-auto-prescribe-on-journal.py ✓ registered, last fired 14h ago
 
## 🟢 Coach profile
-/vault/Meta/coach-profile.yaml updated 2026-05-09
-calendar_drop: true (google-workspace MCP connected ✓)
-preferred_workout_clock: 07:00
-days_per_week: 4, level: intermediate, started_iso: 2026-05-09
 
## 🔴 Lab status flags
-Vitamin D 25-OH: 26 ng/mL (low, ref 30-100). Last tested 9 days ago.
  -Why: drives mood, immunity, recovery. Linked to chronic fatigue.
  -Suggested: 5000 IU/day; re-test in 90 days (target 2026-08-09)
 
## 🟡 Cycle + sleep regularity
-Cycle: luteal, day 22 (regular over last 6 cycles)
-Sleep regularity: 64/100 (yellow). Bed-time stdev 78min over last 14 days.
-Action: pick a wake time within a 30-min window for the next 14 days.

Tools called

• health_status() — top-level table counts + imports table
• health_coach_recent_prescriptions(days=7) — prescriptions + completion status
• health_coach_summary(days=28) — completion rate
• health_lab_panel(today, lookback_days=180) — most recent labs per marker
• health_recommended_labs() — the WHY for any flagged marker
• health_cycle_context(today) — current phase + irregularity
• health_sleep_regularity(today-14, today) — bed/wake variance

Plus:

• Read ~/.claude/settings.json to verify hooks are registered
• Read ~/.claude/hookify-blocks.log to verify hooks have fired recently
• Read <VAULT_ROOT>/Meta/coach-profile.yaml to verify profile state

When to surface unprompted

The hook system can surface specific flags WITHOUT the user running /health doctor explicitly:

• PostToolUse on any health-mcp call: if Apple Health is > 28 days stale, surface a one-line nudge ("Re-export Apple Health — last import 31 days ago")
• SessionStart: if any lab is out-of-range AND > 90 days old, surface re-test reminder
• Stop on coach-auto-prescribe: if today's prescription was created, surface the why_today line

These are hookify nudges, configured separately. The skill is the comprehensive surface; the nudges are the targeted catches.

Graceful failure

• health-mcp not registered → report "/health-setup first"
• DuckDB empty → report "/ingest-health first"
• No profile → report "/coach profile first"
• No journal entries → skip cycle / Floor sections silently

The doctor never blocks. It always returns a report, even if it's "this is what's missing to get started."

Voice

Direct. Color-coded flags (🟢 / 🟡 / 🔴) for fast scan. Each yellow / red has a specific "what to do" line, not a vague "consider reviewing." Reader should know exactly what to fix in 30 seconds of reading.