| name | manage-thinking-topics |
| description | Manage the incubation loop topic lifecycle — seed new questions, review status, crystallize converged conclusions, and retire stale topics |
| automation | manual |
| allowed-tools | Read, Write, Edit, Grep, Glob, Bash |
| user-invocable | true |
| argument-hint | [seed|review|crystallize|retire] [topic-slug] |
Manage Thinking Topics
Human-in-the-loop manager for the incubation loop topic registry. Handles the full lifecycle: seeding new questions into analysis, reviewing current status, graduating converged conclusions to permanent notes, and retiring topics no longer worth pursuing.
Companion skill: .claude/skills/incubation-loop/SKILL.md — the analytical engine that processes active topics.
State Dependencies
| Source | Location | Read | Write | Description |
|---|
| Thinking Registry | Brain/05-Meta/Thinking/THINKING-REGISTRY.md | ✓ | ✓ | Master list of all topics + status |
| Topic Files | Brain/05-Meta/Thinking/[topic-slug].md | ✓ | ✓ | Per-topic reasoning journal |
| Permanent Notes | Brain/02-Permanent/ | | ✓ | Atomic crystallized conclusions (graph-integrated, future-reasoning substrate) |
| Synthesis Reports | Brain/05-Meta/Reports/ | | ✓ | Terminal crystallized conclusions (decision-input snapshots, excluded from LBS index) |
| AI Extracted Notes | Brain/AI Extracted Notes/ | | ✓ | Alternative destination for crystallized notes |
Modes
Invoke with one of four modes. If no mode is provided, default to review.
Mode: review
Purpose: Show the full topic landscape at a glance - what's active, what needs crystallization, what's done.
Step 1: Read Registry
date '+%Y-%m-%d'
Read Brain/05-Meta/Thinking/THINKING-REGISTRY.md.
Step 2: For Each Active Topic - Load Summary
For each topic with status: active, read its thinking file. Extract:
run_count - how many iterations completedlast_run - date of last iteration- Current leading hypothesis + confidence score
- Next move in rotation (run_count mod 6)
- Any open questions flagged
Step 3: For Each Converged Topic - Load Summary
For each topic with status: converged, read its thinking file. Extract:
- The converged conclusion (Current Best Answer from last run)
- Confidence score at convergence
- Run count at convergence
Step 4: Present Status Report
Output a structured report:
## Thinking Topics: Status Review [DATE]
### Active Topics (N)
| Topic | Runs | Last Run | Leading Hypothesis | Confidence | Next Move |
|-------|------|----------|-------------------|------------|-----------|
### Converged — Ready for Crystallization (N)
| Topic | Runs | Conclusion Summary | Confidence |
|-------|------|-------------------|------------|
### Crystallized — Done (N)
| Topic | Permanent Note | Crystallized |
|-------|---------------|-------------|
### Summary
- [N] topics in active analysis
- [N] topics ready for crystallization (action needed)
- [N] topics fully crystallized
- Next incubation-loop run: processes all active topics
If there are converged topics, highlight: "[N] topics ready for crystallization — run /manage-thinking-topics crystallize [slug] to graduate each one."
Mode: seed
Purpose: Add a new question to the incubation loop.
Argument: topic slug (e.g., agent-memory-architecture)
Step 1: Gather Requirements
If the topic slug is not provided, ask for it. Then gather:
- Central question - The exact question being analyzed. Precise framing matters - vague questions stay vague.
- Why it matters - 1-2 sentences on stakes or relevance.
- Initial hypotheses - At least 2 competing hypotheses with rough initial confidence percentages (must sum to ~100%).
- Known evidence - Any notes or sources already known to be relevant (optional).
- Constraints/assumptions - What's taken as given? What's out of scope? (optional)
Step 2: Validate Slug
Check that Brain/05-Meta/Thinking/[topic-slug].md does NOT already exist. If it does, warn and stop.
Check that the slug is not already in the registry. If it is, warn and stop.
Step 3: Create Topic File
date '+%Y-%m-%d'
Create Brain/05-Meta/Thinking/[topic-slug].md:
---
created: YYYY-MM-DD
updated: YYYY-MM-DD
created_by: claude-sonnet-4-6
updated_by: claude-sonnet-4-6
agent_version: 01.25
topic: "[exact question being analyzed]"
run_count: 0
last_run: null
status: active
---
# Thinking: [Topic Title]
## Central Question
[The exact question. Precise framing matters - ambiguous questions stay ambiguous.]
## Why This Question Matters
[1-2 sentences on stakes or relevance]
## Initial Hypotheses
| Hypothesis | Initial Confidence | Basis |
|-----------|-------------------|-------|
| H1: [statement] | X% | [prior knowledge or intuition] |
| H2: [statement] | X% | [prior knowledge or intuition] |
## Known Evidence (Pre-Run)
[Any notes or sources already known to be relevant, or "None identified yet."]
## Constraints and Assumptions
[What are you taking as given? What's out of scope?]
---
*Analytical runs will be appended below by the incubation loop*
Step 4: Add to Registry
Read Brain/05-Meta/Thinking/THINKING-REGISTRY.md.
Add a row to the Active Topics table:
| [topic-slug] | [central question] | active | 0 | null |
Update updated and updated_by in frontmatter.
Step 5: Confirm
Report:
- Topic file created at
Brain/05-Meta/Thinking/[topic-slug].md
- Registry updated - topic is now active
- First incubation-loop run will apply: ACH Audit (move 0)
- Estimated convergence: 4-6 runs (~4-6 days at daily schedule)
Mode: crystallize
Purpose: Graduate a converged topic — either as an atomic permanent note (Brain/02-Permanent/, graph-integrated) or as a terminal synthesis report (Brain/05-Meta/Reports/, excluded from semantic indexing). Choose based on whether the conclusion is generative (future reasoning will reuse it) or terminal (snapshot of what was concluded).
Argument: topic slug of a converged topic
If no slug is provided: read the registry, present the converged topics (with one-line conclusions), and ask which to crystallize before proceeding. If prior session context points at a specific topic or pair (e.g., a just-completed analysis that named them), recommend it as the first option. Accept common misspellings of the mode name (e.g., "crystalize").
Step 1: Load Converged Topic
Read Brain/05-Meta/Thinking/[topic-slug].md.
Verify status: converged. If not converged, warn and stop.
Extraction strategy (prefer the canonical block, fall back gracefully):
-
First, look for ## Final Synthesis - a canonical block appended when the loop transitions a topic to converged. If present, this is the authoritative source. Extract from it:
- Conclusion (the substantive answer)
- Confidence and leading hypothesis
- Key evidence (already curated)
- Remaining uncertainty
- Related topics (if any)
-
If no Final Synthesis block exists (legacy topics from before the standardized format), read only the last 200 lines of the file rather than the full thinking journal (some are 5,000+ lines). Extract:
- The central question (from frontmatter)
- The most recent "Current Best Answer" section
- The most recent "Updated Hypotheses" table for confidence scores
- Any "Open Questions" flagged in the final run
-
Read the full file only if the last 200 lines do not contain a "Current Best Answer" or equivalent conclusion.
Step 2: Search for Existing Notes
python3 resources/local-brain-search/search.py "[central question keywords]" --limit 5 --mode spreading 2>/dev/null
Check if a permanent note already exists covering this conclusion. If so, note the overlap and ask whether to update it or create a new note.
Step 3: Choose Destination
Before drafting, decide the destination based on the nature of the conclusion:
| Signal | Destination |
|---|
| Conclusion is one atomic insight that future reasoning will cite | Brain/02-Permanent/ (permanent note) |
| Conclusion has multiple co-equal findings that belong together (e.g., a four-stage architecture, a stratified framework) | Brain/05-Meta/Reports/ (synthesis report) |
| Conclusion is a snapshot of a moment (geopolitical assessment, project-stack analysis) — decision-input, not future-reasoning substrate | Brain/05-Meta/Reports/ (synthesis report) |
| Conclusion captures a generative principle that will be reasoned FROM in other contexts | Brain/02-Permanent/ (permanent note) |
| Topic is transitory — relevant for current decisions, unlikely to be revisited | Brain/05-Meta/Reports/ (synthesis report) |
[APPROVAL GATE] Propose the destination and ask the user to confirm or override:
"Recommend: [destination] because [reason]. Confirm, or override to [other destination]?"
Synthesis reports do not participate in connection-finder or semantic search (the Reports/ folder is excluded from LBS indexing). They are visible in Obsidian and can link OUT to permanent notes via [[wiki-links]], but permanent notes should rarely link IN to reports.
Step 4: Draft Content
Adapt the draft to the chosen destination:
If permanent note (Brain/02-Permanent/):
- Written in the user's voice, not as a report
- Leads with the conclusion, not the process
- Cites the key evidence that drove the conclusion
- Notes remaining uncertainty or caveats
- Atomic — one main insight, ~50-100 lines
If synthesis report (Brain/05-Meta/Reports/):
- Long-form is appropriate — can be 200-600+ lines
- Lead with executive summary, then layered detail
- Multiple findings organized by section (each finding need not be atomic)
- Cite full evidence base with sources/URLs where applicable
- Wiki-link OUT to relevant permanent notes; reports are terminal
Propose the draft to the user for review before writing.
[APPROVAL GATE] Present the draft. Ask: "Write this to [chosen destination path]? (Yes / revise the draft / skip crystallization)"
Step 5: Write to Destination
On approval, write the file with proper frontmatter:
---
created: YYYY-MM-DD
updated: YYYY-MM-DD
created_by: claude-sonnet-4-6
updated_by: claude-sonnet-4-6
agent_version: 01.25
provenance: ai-inferred
---
Provenance (mandatory): Crystallized conclusions are agent-synthesized, so default provenance: ai-inferred. Per CLAUDE.md's guarded boundary, this only becomes endorsed or originated through an explicit endorsement act by the user at the [APPROVAL GATE] above - never set it automatically. If the user states the conclusion is his own thinking, set provenance: endorsed (or originated if it is purely his idea the loop merely formalized).
For synthesis reports, kebab-case the filename; add a date suffix if the report is a dated snapshot (e.g., trinity-production-architecture-2026-05-26.md).
Step 6: Update Topic File
Edit Brain/05-Meta/Thinking/[topic-slug].md:
- Set
status: crystallized
- Update
updated and updated_by
- Append a final note (adapt to destination):
---
**CRYSTALLIZED [DATE]** → [[Destination Note or Report Name]]
*Conclusion graduated to [permanent knowledge base | synthesis reports]. Thinking file archived.*
Step 7: Update Registry
In Brain/05-Meta/Thinking/THINKING-REGISTRY.md:
- Remove the row from Converged table
- Add a row to Crystallized table:
| [topic-slug] | [[Destination Note or Report Name]] | YYYY-MM-DD |
If the existing Crystallized table column header is still "Permanent Note", update it to "Destination" so it accommodates both atomic notes and synthesis reports.
Update updated and updated_by in frontmatter.
Step 8: Confirm
Report:
- File written at
[full destination path]
- Topic marked crystallized
- Registry updated
Mode: retire
Purpose: Remove a topic from active analysis without crystallizing it (topic no longer relevant, question was wrong, superseded by new evidence).
Argument: topic slug
Step 1: Load Topic
Read Brain/05-Meta/Thinking/[topic-slug].md. Show:
- Current status
- Run count
- Current leading hypothesis and confidence
Step 2: Confirm Retirement
[APPROVAL GATE] Ask:
"Retiring '[topic-slug]' will stop it from being processed by the incubation loop. The thinking file will be kept for reference but marked retired. Reason for retiring? (or type 'cancel')"
Capture the reason.
Step 3: Update Topic File
Edit Brain/05-Meta/Thinking/[topic-slug].md:
- Set
status: retired
- Update
updated and updated_by
- Append:
---
**RETIRED [DATE]**
*Reason: [reason given]*
*Topic removed from active analysis. Thinking file kept for reference.*
Step 4: Update Registry
In Brain/05-Meta/Thinking/THINKING-REGISTRY.md:
- Remove the row from whichever table it was in (Active or Converged)
- Do NOT add to Crystallized table (it wasn't graduated)
Optionally add a Retired section if one doesn't exist:
## Retired
| Topic Slug | Reason | Retired On |
|------------|--------|------------|
Update updated and updated_by in frontmatter.
Step 5: Confirm
Report:
- Topic marked retired in
Brain/05-Meta/Thinking/[topic-slug].md
- Removed from registry active/converged table
- Thinking file preserved at full path for future reference
Move Rotation Reference
When seeding or reviewing, the next analytical move is determined by run_count mod 6:
| run_count % 6 | Move |
|---|
| 0 | ACH Audit — eliminate weak hypotheses |
| 1 | Bayesian Update — explicit confidence tracking |
| 2 | Steelman Opposition — dialectical challenge |
| 3 | Cross-Domain Bridge — consilience from another field |
| 4 | Implication Check — falsificationism |
| 5 | Assumption Audit — find load-bearing shaky premises |
Convergence Criteria (Reference)
A topic converges when ALL:
run_count >= 4- Same hypothesis has led for 3+ consecutive runs
- Confidence delta between last two runs < 5 percentage points
- No major open questions flagged in last run
The incubation-loop skill checks this automatically after each run.
Error Handling
| Error | Recovery |
|---|
| Registry missing | Stop; inform user to seed registry via incubation-loop skill |
| Topic file missing for registry entry | Log warning; continue with other topics |
| Slug already exists (seed mode) | Stop; show existing file path |
| Topic not converged (crystallize mode) | Stop with current run count and status |
| KB search returns empty | Skip search step; note in output |
Self-Improvement
After completing this skill's primary task, consider tactical improvements:
