health

Academic Writer — Health Check

Run a comprehensive health check on every component of the Academic Writer system. Report status clearly so the researcher knows what's working and what needs attention.

1. Profile Check

if [ -f .academic-helper/profile.md ]; then
  cat .academic-helper/profile.md
else
  echo "MISSING"
fi

If missing: report FAIL and suggest /academic-writer:init.

If found, validate:

• Has fieldOfStudy? ✓/✗
• Has citationStyle? ✓/✗
• Has styleFingerprint? ✓/✗
• Fingerprint format: is it the expanded (nested) format or the old flat format?
  • If flat format: suggest re-running /academic-writer:init to get the expanded 25-dimension fingerprint
• Has tools object? ✓/✗
• Has sources array? ✓/✗ (and count)
• createdAt / updatedAt timestamps

---

2. Past Articles

ls past-articles/ 2>/dev/null | head -20

Report:

• Folder exists? ✓/✗
• Number of files found
• File types (PDF, DOCX, other)
• If empty: "Add 5–10 published articles for style analysis, then re-run /academic-writer:init."

---

3. Agentic-Search-Vectorless

Skip if tools.agentic-search-vectorless.enabled is false. Report as "Disabled (enable with /academic-writer:update-tools)".

Check port 8000 first (default):

curl -s --max-time 3 http://localhost:8000/health 2>/dev/null && echo "RUNNING" || echo "NOT_RUNNING"

• If RUNNING: service is available. ✓
• If NOT_RUNNING: check if a custom port is saved in profile.tools.agentic-search-vectorless.port. If a custom port is stored, retry with that port:

  curl -s --max-time 3 http://localhost:<CUSTOM_PORT>/health 2>/dev/null && echo "RUNNING" || echo "NOT_RUNNING"
  

• If still not running: ask the researcher: "Agentic-Search-Vectorless is not responding on port 8000. What port is it running on? (Or press Enter to skip this check.)"
  • If they provide a port: retry the curl with that port, then save it to profile.tools.agentic-search-vectorless.port
  • If they skip: report as ✗ Not running

Report:

• Service responding? ✓/✗
• Port used

---

4. Candlekeep

Skip if tools.candlekeep.enabled is false. Report as "Disabled (enable with /academic-writer:update-tools)".

command -v ck >/dev/null 2>&1 && echo "CLI: INSTALLED" || echo "CLI: NOT_FOUND"

If installed:

ck items list 2>&1 | head -20

Report:

• CLI installed? ✓/✗
• Can connect? ✓/✗
• Number of items in library
• If error: show the error message

---

5. Cognetivy

Skip if tools.cognetivy.enabled is false. Report as "Disabled".

command -v cognetivy >/dev/null 2>&1 && echo "CLI: INSTALLED" || echo "CLI: NOT_FOUND"

If installed:

ls .cognetivy/ 2>/dev/null && echo "DIR_EXISTS" || echo "DIR_MISSING"

cognetivy workflow list 2>&1 | head -10

cognetivy run list --workflow wf_academic_writer 2>&1 | head -10

Report:

• CLI installed? ✓/✗
• .cognetivy/ directory exists? ✓/✗
• Workspace initialized? ✓/✗
• Workflow wf_academic_writer registered? ✓/✗
• Number of past runs

If CLI not installed, show this setup guide:

How to set up Cognetivy:

1. Install the CLI:

   npm install -g cognetivy
   

   Or if you use bun:

   bun install -g cognetivy
   

2. Initialize the workspace in this project folder:

   timeout 5 cognetivy init --workspace-only
   

   (The timeout is needed because cognetivy init starts a studio server that blocks.)

3. Register Academic Writer workflows:

   cognetivy workflow set --file plugins/academic-writer/workflows/wf_write_article.json
   cognetivy workflow set --file plugins/academic-writer/workflows/wf_edit_article.json
   cognetivy workflow set --file plugins/academic-writer/workflows/wf_setup.json
   

4. Re-run /academic-writer:health to verify.

If CLI is installed but workspace not initialized:

"Cognetivy is installed but not initialized in this project. Run:

timeout 5 cognetivy init --workspace-only

Then re-run /academic-writer:health."

---

6. NotebookLM

Skip if tools.notebooklm.enabled is false. Report as "Disabled (enable with /academic-writer:update-tools)".

command -v nlm >/dev/null 2>&1 && echo "CLI: INSTALLED" || echo "CLI: NOT_FOUND"

If installed:

nlm login --check 2>&1

nlm notebook list 2>&1 | head -5

Report:

• CLI installed? ✓/✗
• Authenticated? ✓/✗
• Can list notebooks? ✓/✗ (and count)
• If error: show the error message

If CLI not installed, show this setup guide:

How to set up NotebookLM:

1. Install the CLI:

   npm install -g notebooklm-mcp-cli
   

2. Authenticate:

   nlm login
   

3. Re-run /academic-writer:health to verify.

---

7. Agent Files

ls .claude/agents/*.md 2>/dev/null

Verify all required agent files exist:

• .claude/agents/deep-reader.md ✓/✗
• .claude/agents/architect.md ✓/✗
• .claude/agents/section-writer.md ✓/✗
• .claude/agents/auditor.md ✓/✗
• .claude/agents/synthesizer.md ✓/✗

---

Present Results

Show a clean summary table:

Academic Writer — Health Report

Component	Status	Details
Profile	✓ OK / ✗ MISSING	Field: [field], Citation: [style], Sources: [N]
Style Fingerprint	✓ Expanded / ⚠ Legacy / ✗ Missing	[N] dimensions
Past Articles	✓ [N] files / ✗ Empty	PDF: [n], DOCX: [n]
Agentic-Search-Vectorless	✓ Running / ✗ Not running / — Disabled	Port: [port]
Candlekeep	✓ Connected / ✗ Error / — Disabled	[N] items

| Cognetivy | ✓ Ready / ✗ Not initialized / — Disabled | Run timeout 5 cognetivy init --workspace-only if not initialized | | NotebookLM | ✓ Connected / ✗ Not found / — Disabled | [N] notebooks | | Agent Files | ✓ All present / ✗ Missing [list] | 5/5 |

Overall: [N]/[total] checks passed

If there are issues, provide specific fix instructions:

To fix:

1. [Issue] → [specific command or action]
2. [Issue] → [specific command or action]