Atomizer/hq/skills/atomizer-protocols/protocols/OP_11_DIGESTION.md

# OP_11 — Digestion Protocol

## Purpose
Enforce a structured learning cycle after each project phase — modeled on human sleep consolidation. We store what matters, discard noise, sort knowledge, repair gaps, and evolve our processes.

> "I really want you to enforce digestion, and learning, like what we do (human) while dreaming, we store, discard unnecessary, sort things, repair etc. I want you to do the same. In the end, I want you to evolve and document yourself as well."
> — Antoine Letarte, CEO (2026-02-11)

## Triggers

| Trigger | Scope | Who Initiates |
|---------|-------|---------------|
| **Phase completion** | Full digestion | Manager, after study phase closes |
| **Milestone hit** | Focused digestion | Manager or lead agent |
| **Weekly heartbeat** | Incremental housekeeping | Automated (cron/heartbeat) |
| **Project close** | Deep digestion + retrospective | Manager |

## The Six Operations

### 1. 📥 STORE — Extract & Persist
**Goal:** Capture what we learned that's reusable beyond this session.

**Actions:**
- Extract key findings from daily logs into `MEMORY.md` (per agent)
- Promote project-specific insights to `knowledge_base/projects/<project>/`
- Record new solver quirks, expression names, NX behaviors → domain KB
- Log performance data: what algorithm/settings worked, convergence rates
- Capture Antoine's corrections as **ground truth** (highest priority)

**Output:** Updated MEMORY.md, project CONTEXT.md, domain KB entries

### 2. 🗑️ DISCARD — Prune & Clean
**Goal:** Remove outdated, wrong, or redundant information.

**Actions:**
- Identify contradictions in memory files (e.g., mass=11.33 vs 1133)
- Remove stale daily logs older than 30 days (archive summary to MEMORY.md first)
- Flag and remove dead references (deleted files, renamed paths, obsolete configs)
- Clear TODO items that are done — mark complete, don't just leave them
- Remove verbose/redundant entries (compress repeated patterns into single lessons)

**Anti-pattern to catch:** Information that was corrected but the wrong version still lives somewhere.

### 3. 📂 SORT — Organize Hierarchically
**Goal:** Put knowledge at the right level of abstraction.

**Levels:**
| Level | Location | Example |
|-------|----------|---------|
| **Session** | `memory/YYYY-MM-DD.md` | "Fixed FEM lookup to exclude _i parts" |
| **Project** | `knowledge_base/projects/<project>/` | "Hydrotech beam uses CQUAD4 thin shells, SOL 101" |
| **Domain** | `knowledge_base/domain/` or skills | "NX integer expressions need unit=Constant" |
| **Company** | `atomizer-protocols`, `MEMORY.md` | "Always resolve paths with .resolve(), not .absolute()" |

**Actions:**
- Review session notes → promote recurring patterns up one level
- Check if project-specific knowledge is actually domain-general
- Ensure company-level lessons are in protocols or QUICK_REF, not buried in daily logs

### 4. 🔧 REPAIR — Fix Gaps & Drift
**Goal:** Reconcile what we documented vs what's actually true.

**Actions:**
- Cross-reference CONTEXT.md with actual code/config (do they match?)
- Verify file paths in docs still exist
- Check if protocol descriptions match actual practice (drift detection)
- Run through open gaps (G1, G2, etc.) — are any now resolved but not marked?
- Validate agent SOUL.md and AGENTS.md reflect current capabilities and team composition

**Key question:** "If a brand-new agent read our docs cold, would they be able to do the work?"

### 5. 🧬 EVOLVE — Improve Processes
**Goal:** Get smarter, not just busier.

**Actions:**
- **What slowed us down?** → Fix the process, not just the symptom
- **What did we repeat?** → Automate it or create a template
- **What did we get wrong?** → Add a check, update a protocol
- **What did Antoine correct?** → That's the highest-signal feedback. Build it in.
- **Agent performance:** Did any agent struggle? Needs better context? Different model?
- Propose protocol updates (new OP/SYS or amendments to existing)
- Update QUICK_REF.md if new shortcuts or patterns emerged

**Output:** Protocol amendment proposals, agent config updates, new templates

### 6. 📝 SELF-DOCUMENT — Update the Mirror
**Goal:** Our docs should reflect who we are *now*, not who we were at launch.

**Actions:**
- Update AGENTS.md with current team composition and active channels
- Update SOUL.md if role understanding has evolved
- Update IDENTITY.md if capabilities changed
- Refresh TOOLS.md with newly discovered tools or changed workflows
- Update project README files with actual status
- Ensure QUICK_REF.md reflects current best practices

**Test:** Read your own docs. Do they describe *you* today?

---

## Execution Format

### Phase Completion Digestion (Full)
Run all 6 operations. Manager coordinates, each agent digests their own workspace.

```
🧠 **Digestion Cycle — [Project] Phase [N] Complete**

**Trigger:** [Phase completion / Milestone / Weekly]
**Scope:** [Full / Focused / Incremental]

### STORE
- [What was captured and where]

### DISCARD  
- [What was pruned/removed]

### SORT
- [What was promoted/reorganized]

### REPAIR
- [What was fixed/reconciled]

### EVOLVE
- [Process improvements proposed]

### SELF-DOCUMENT
- [Docs updated]

**Commits:** [list of commits]
**Next:** [What happens after digestion]
```

### Weekly Heartbeat Digestion (Incremental)
Lighter pass — focus on DISCARD and REPAIR. Run by Manager during weekly heartbeat.

**Checklist:**
- [ ] Any contradictions in memory files?
- [ ] Any stale TODOs that are actually done?
- [ ] Any file paths that no longer exist?
- [ ] Any corrections from Antoine not yet propagated?
- [ ] Any process improvements worth capturing?

### Project Close Digestion (Deep)
Full pass + retrospective. Captures the complete project learning.

**Additional steps:**
- Write project retrospective: `knowledge_base/projects/<project>/RETROSPECTIVE.md`
- Extract reusable components → propose for shared skills
- Update LAC (Lessons and Corrections) if applicable
- Archive project memory (compress daily logs into single summary)

---

## Responsibilities

| Agent | Digests |
|-------|---------|
| **Manager** | Orchestrates cycle, digests own workspace, coordinates cross-agent |
| **Technical Lead** | Domain knowledge, model insights, solver quirks |
| **Optimizer** | Algorithm performance, strategy effectiveness |
| **Study Builder** | Code patterns, implementation lessons, reusable components |
| **Auditor** | Quality patterns, common failure modes, review effectiveness |
| **Secretary** | Communication patterns, Antoine preferences, admin workflows |

## Quality Gate

After digestion, Manager reviews:
1. Were all 6 operations addressed?
2. Were Antoine's corrections captured as ground truth?
3. Are docs consistent with reality?
4. Any proposed changes needing CEO approval?

If changes affect protocols or company-level knowledge:
> ⚠️ **Needs CEO approval:** [summary of proposed changes]

---

## Version History

| Version | Date | Changes |
|---------|------|---------|
| 1.0.0 | 2026-02-11 | Initial protocol, per CEO directive |