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Goal: Remove outdated, wrong, or redundant information.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?

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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)

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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]

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Version History

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