docs: Archive stale docs and create Atomizer-HQ agent documentation

Archive Management:
- Moved RALPH_LOOP, CANVAS, and dashboard implementation plans to archive/review/ for CEO review
- Moved completed restructuring plan and protocol v1 to archive/historical/
- Moved old session summaries to archive/review/

New HQ Documentation (docs/hq/):
- README.md: Overview of Atomizer-HQ multi-agent optimization team
- PROJECT_STRUCTURE.md: Standard KB-integrated project layout with Hydrotech reference
- KB_CONVENTIONS.md: Knowledge Base accumulation principles with generation tracking
- AGENT_WORKFLOWS.md: Project lifecycle phases and agent handoffs (OP_09 integration)
- STUDY_CONVENTIONS.md: Technical study execution standards and atomizer_spec.json format

Index Update:
- Reorganized docs/00_INDEX.md with HQ docs prominent
- Updated structure to reflect new agent-focused organization
- Maintained core documentation access for engineers

No files deleted, only moved to appropriate archive locations.

docs/00_INDEX.md

@@ -1,34 +1,77 @@
 # Atomizer Documentation Index
 
-**Last Updated**: 2026-01-24
+**Last Updated**: February 9, 2026  
-**Project Version**: 0.5.0 (AtomizerSpec v2.0 - Canvas Builder)
+**Project Version**: 0.5.0 (AtomizerSpec v2.0 + Atomizer-HQ Multi-Agent Team)
 
 ---
 
 ## Quick Start
 
-New to Atomizer? Start here:
+### For AI Agents (Atomizer-HQ Team)
+**Start here** if you're an AI agent working on client projects:
 
-1. **[README.md](../README.md)** - Project overview and philosophy
+1. **[HQ Overview](hq/README.md)** — What Atomizer-HQ is and how agents work together
-2. **[Getting Started](GETTING_STARTED.md)** - Installation, first study, dashboard
+2. **[Project Structure](hq/PROJECT_STRUCTURE.md)** — Standard project organization  
-3. **[Protocol System](protocols/README.md)** - How Atomizer is organized
+3. **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** — Who does what in the project lifecycle
-4. **[Example Studies](../studies/)** - Working examples
+4. **[Knowledge Base Conventions](hq/KB_CONVENTIONS.md)** — How to accumulate and share knowledge
+
+### For Engineers (Core Optimization)
+**Start here** if you're using Atomizer for FEA optimization:
+
+1. **[README.md](../README.md)** - Project overview and philosophy  
+2. **[Getting Started](GETTING_STARTED.md)** - Installation, first study, dashboard  
+3. **[Protocol System](protocols/README.md)** - How Atomizer is organized  
+4. **[Example Studies](../studies/)** - Working examples  
 
 ---
 
-## Documentation Structure
+## Atomizer-HQ Agent Documentation
 
-### Core Documentation
+The multi-agent optimization team that runs client FEA projects.
+
+### Essential HQ Docs
+
+| Document | Purpose | Target Agents |
+|----------|---------|---------------|
+| **[HQ Overview](hq/README.md)** | What Atomizer-HQ is, how to use these docs | All agents |
+| **[Project Structure](hq/PROJECT_STRUCTURE.md)** | Standard KB-integrated project layout | Manager, Technical Lead |  
+| **[KB Conventions](hq/KB_CONVENTIONS.md)** | Knowledge Base accumulation principles | All agents |
+| **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** | Project lifecycle and agent handoffs | All agents |
+| **[Study Conventions](hq/STUDY_CONVENTIONS.md)** | Technical study execution standards | Technical Lead, Optimizer |
+
+### Agent Roles Quick Reference
+
+| Agent | Role | Primary Phase | Key Responsibilities |
+|-------|------|---------------|---------------------|
+| 📋 **Secretary** | CEO interface | Intake | Client requirements, project initiation |
+| 🏗️ **Manager** | Coordination | Breakdown | Project structure, team coordination |
+| 🔧 **Technical Lead** | FEA expert | Introspection | Model setup, optimization planning |
+| ⚡ **Optimizer** | Study execution | Study | FEA optimization execution |
+| 📊 **Post-Processor** | Results analysis | Results | Performance analysis, insights |
+| 📝 **Reporter** | Documentation | Deliverables | Client reports, final packages |
+
+### Living Examples
+- **Reference Project**: [projects/hydrotech-beam/](../projects/hydrotech-beam/) — Complete project structure
+- **Project Structure**: Demonstrates KB-integrated organization and study flow
+- **Knowledge Accumulation**: Shows generation-tracked knowledge evolution
+
+---
+
+## Core Documentation
+
+Essential reference for understanding Atomizer's optimization framework.
+
+### Foundation Documents
 
 | Document | Purpose |
 |----------|---------|
 | **[GETTING_STARTED.md](GETTING_STARTED.md)** | Setup, first study, dashboard basics |
 | **[ARCHITECTURE.md](ARCHITECTURE.md)** | System architecture, hooks, data flow |
-| **[protocols/README.md](protocols/README.md)** | Protocol Operating System overview |
+| **[QUICK_REF.md](../QUICK_REF.md)** | Active reference guide |
 
 ### Protocol System
 
-The Protocol Operating System (POS) provides structured workflows:
+The Protocol Operating System (POS) provides structured workflows for optimization:
 
 ```
 protocols/
@@ -41,7 +84,8 @@ protocols/
 │   ├── OP_05_EXPORT_TRAINING_DATA.md
 │   ├── OP_06_TROUBLESHOOT.md
 │   ├── OP_07_DISK_OPTIMIZATION.md
-│   └── OP_08_GENERATE_REPORT.md
+│   ├── OP_08_GENERATE_REPORT.md
+│   └── OP_09_AGENT_COMMUNICATION.md
 ├── system/               # Technical specifications (SYS_10-18)
 │   ├── SYS_10_IMSO.md           # Intelligent optimization
 │   ├── SYS_11_MULTI_OBJECTIVE.md
@@ -59,22 +103,28 @@ protocols/
     └── EXT_04_CREATE_SKILL.md
 ```
 
-### User Guides
+---
 
-Located in `guides/`:
+## User Guides
 
-| Guide | Purpose |
+Practical guides for using Atomizer features (engineers + Claude Code era).
-|-------|---------|
-| **[CANVAS.md](guides/CANVAS.md)** | Visual study builder (AtomizerSpec v2.0) |
-| **[DASHBOARD.md](guides/DASHBOARD.md)** | Dashboard overview and features |
-| **[NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** | Neural acceleration guide |
-| **[NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** | Data → Training → Optimization |
-| **[hybrid_mode.md](guides/hybrid_mode.md)** | Hybrid FEA/NN optimization |
-| **[TRAINING_DATA_EXPORT_GUIDE.md](guides/TRAINING_DATA_EXPORT_GUIDE.md)** | Exporting data for neural training |
 
-### API Reference
+### Current User Guides
 
-Located in `api/`:
+| Guide | Purpose | Status |
+|-------|---------|--------|
+| **[CANVAS.md](guides/CANVAS.md)** | Visual study builder (AtomizerSpec v2.0) | Active |
+| **[DASHBOARD.md](guides/DASHBOARD.md)** | Dashboard overview and features | Active |
+| **[NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** | Neural acceleration guide | Active |
+| **[NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** | Data → Training → Optimization | Active |
+| **[hybrid_mode.md](guides/hybrid_mode.md)** | Hybrid FEA/NN optimization | Active |
+| **[TRAINING_DATA_EXPORT_GUIDE.md](guides/TRAINING_DATA_EXPORT_GUIDE.md)** | Exporting data for neural training | Active |
+
+---
+
+## API Reference
+
+Technical integration documentation for developers and advanced users.
 
 | Document | Purpose |
 |----------|---------|
@@ -83,18 +133,43 @@ Located in `api/`:
 | **[GNN_ARCHITECTURE.md](api/GNN_ARCHITECTURE.md)** | Graph Neural Network details |
 | **[NXOPEN_RESOURCES.md](api/NXOPEN_RESOURCES.md)** | NX Open documentation resources |
 
-### Physics Documentation
+---
 
-Located in `physics/`:
+## Domain Knowledge
+
+Physics and engineering domain documentation.
+
+### Physics Documentation
 
 | Document | Purpose |
 |----------|---------|
 | **[ZERNIKE_FUNDAMENTALS.md](physics/ZERNIKE_FUNDAMENTALS.md)** | Zernike polynomial basics |
 | **[ZERNIKE_OPD_METHOD.md](physics/ZERNIKE_OPD_METHOD.md)** | OPD method for mirror optimization |
 
-### Development
+---
 
-Located in `development/`:
+## Workflows and Operations
+
+Operational workflows for common tasks.
+
+### Standard Workflows
+
+| Document | Purpose |
+|----------|---------|
+| **[CREATE.md](WORKFLOWS/CREATE.md)** | Study creation workflow |
+| **[RUN.md](WORKFLOWS/RUN.md)** | Optimization execution workflow |
+| **[ANALYZE.md](WORKFLOWS/ANALYZE.md)** | Results analysis workflow |
+| **[DELIVER.md](WORKFLOWS/DELIVER.md)** | Deliverable creation workflow |
+| **[VALIDATE.md](WORKFLOWS/VALIDATE.md)** | Validation and verification workflow |
+| **[REPORT.md](WORKFLOWS/REPORT.md)** | Report generation workflow |
+
+---
+
+## Development and Architecture
+
+Technical development documentation.
+
+### Development Guides
 
 | Document | Purpose |
 |----------|---------|
@@ -102,9 +177,7 @@ Located in `development/`:
 | **[DEVELOPMENT_ROADMAP.md](development/DEVELOPMENT_ROADMAP.md)** | Future plans |
 | **[Philosophy.md](development/Philosophy.md)** | Design philosophy |
 
-### Diagrams
+### Architecture Documentation
-
-Located in `diagrams/`:
 
 | Document | Purpose |
 |----------|---------|
@@ -113,35 +186,57 @@ Located in `diagrams/`:
 
 ---
 
+## Archive
+
+Historical and review documents preserved for context and CEO review.
+
+### Archive Structure
+- **[archive/review/](archive/review/)** — Documents flagged for CEO review
+  - RALPH_LOOP implementation plans
+  - Dashboard implementation iterations  
+  - Superseded development plans
+  - Session summaries and old development notes
+- **[archive/historical/](archive/historical/)** — Historical but valuable documents
+  - Original protocol v1 monolithic document
+  - Foundational design documents
+  - Completed restructuring plans
+
+### Key Historical Documents
+- **[PROTOCOL_V1_MONOLITHIC.md](archive/historical/PROTOCOL_V1_MONOLITHIC.md)** — Original monolithic protocol (Nov 2025)
+- Various implementation plans and session summaries in review directories
+
+---
+
 ## Documentation by Task
 
-### Creating Studies
+### For Agents: Project Execution
+1. **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** — Project lifecycle and handoffs
+2. **[Project Structure](hq/PROJECT_STRUCTURE.md)** — How to organize projects  
+3. **[Study Conventions](hq/STUDY_CONVENTIONS.md)** — Technical execution standards
+4. **[KB Conventions](hq/KB_CONVENTIONS.md)** — Knowledge accumulation
 
-1. **[GETTING_STARTED.md](GETTING_STARTED.md)** - First study tutorial
+### For Engineers: Creating Studies
-2. **[OP_01_CREATE_STUDY.md](protocols/operations/OP_01_CREATE_STUDY.md)** - Detailed creation protocol
+1. **[GETTING_STARTED.md](GETTING_STARTED.md)** — First study tutorial
-3. **[guides/CANVAS.md](guides/CANVAS.md)** - Visual study builder
+2. **[OP_01_CREATE_STUDY.md](protocols/operations/OP_01_CREATE_STUDY.md)** — Detailed creation protocol
+3. **[guides/CANVAS.md](guides/CANVAS.md)** — Visual study builder
 
-### Running Optimizations
+### For Engineers: Running Optimizations
+1. **[OP_02_RUN_OPTIMIZATION.md](protocols/operations/OP_02_RUN_OPTIMIZATION.md)** — Run protocol
+2. **[SYS_10_IMSO.md](protocols/system/SYS_10_IMSO.md)** — Intelligent optimization
+3. **[SYS_15_METHOD_SELECTOR.md](protocols/system/SYS_15_METHOD_SELECTOR.md)** — Method selection
 
-1. **[OP_02_RUN_OPTIMIZATION.md](protocols/operations/OP_02_RUN_OPTIMIZATION.md)** - Run protocol
+### For Engineers: Neural Acceleration
-2. **[SYS_10_IMSO.md](protocols/system/SYS_10_IMSO.md)** - Intelligent optimization
+1. **[guides/NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** — Overview
-3. **[SYS_15_METHOD_SELECTOR.md](protocols/system/SYS_15_METHOD_SELECTOR.md)** - Method selection
+2. **[SYS_14_NEURAL_ACCELERATION.md](protocols/system/SYS_14_NEURAL_ACCELERATION.md)** — Technical spec
+3. **[guides/NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** — Step-by-step
 
-### Neural Acceleration
+### For Engineers: Analyzing Results
+1. **[OP_04_ANALYZE_RESULTS.md](protocols/operations/OP_04_ANALYZE_RESULTS.md)** — Analysis protocol
+2. **[SYS_17_STUDY_INSIGHTS.md](protocols/system/SYS_17_STUDY_INSIGHTS.md)** — Physics visualizations
 
-1. **[guides/NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** - Overview
+### For Everyone: Troubleshooting
-2. **[SYS_14_NEURAL_ACCELERATION.md](protocols/system/SYS_14_NEURAL_ACCELERATION.md)** - Technical spec
+1. **[OP_06_TROUBLESHOOT.md](protocols/operations/OP_06_TROUBLESHOOT.md)** — Troubleshooting guide
-3. **[guides/NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** - Step-by-step
+2. **[GETTING_STARTED.md#troubleshooting](GETTING_STARTED.md#troubleshooting)** — Common issues
-
-### Analyzing Results
-
-1. **[OP_04_ANALYZE_RESULTS.md](protocols/operations/OP_04_ANALYZE_RESULTS.md)** - Analysis protocol
-2. **[SYS_17_STUDY_INSIGHTS.md](protocols/system/SYS_17_STUDY_INSIGHTS.md)** - Physics visualizations
-
-### Troubleshooting
-
-1. **[OP_06_TROUBLESHOOT.md](protocols/operations/OP_06_TROUBLESHOOT.md)** - Troubleshooting guide
-2. **[GETTING_STARTED.md#troubleshooting](GETTING_STARTED.md#troubleshooting)** - Common issues
 
 ---
 
@@ -156,6 +251,7 @@ Located in `diagrams/`:
 | **OP_03** | Monitor Progress | Real-time monitoring |
 | **OP_04** | Analyze Results | Results analysis |
 | **OP_06** | Troubleshoot | Debugging issues |
+| **OP_09** | Agent Communication | HQ communication standards |
 | **SYS_10** | IMSO | Intelligent optimization |
 | **SYS_12** | Extractors | Physics extraction library |
 | **SYS_14** | Neural | Neural network acceleration |
@@ -166,10 +262,10 @@ Located in `diagrams/`:
 # Activate environment
 conda activate atomizer
 
-# Run optimization
+# Run optimization (engineers)
 python run_optimization.py --start --trials 50
 
-# Resume interrupted run
+# Resume interrupted run  
 python run_optimization.py --start --resume
 
 # Start dashboard
@@ -177,6 +273,9 @@ python launch_dashboard.py
 
 # Neural turbo mode
 python run_nn_optimization.py --turbo --nn-trials 5000
+
+# KB status check (agents)
+cad_kb.py status projects/[project]/kb
 ```
 
 ### Key Extractors
@@ -194,18 +293,6 @@ Full catalog: [SYS_12_EXTRACTOR_LIBRARY.md](protocols/system/SYS_12_EXTRACTOR_LI
 
 ---
 
-## Archive
-
-Historical documents are preserved in `archive/`:
-
-- `archive/historical/` - Legacy documents, old protocols
-- `archive/marketing/` - Briefings, presentations
-- `archive/session_summaries/` - Past development sessions
-- `archive/plans/` - Superseded plan documents (RALPH_LOOP V2/V3, CANVAS V3, etc.)
-- `archive/PROTOCOL_V1_MONOLITHIC.md` - Original monolithic protocol (Nov 2025)
-
----
-
 ## LLM Resources
 
 For Claude/AI integration:
@@ -218,5 +305,5 @@ For Claude/AI integration:
 
 ---
 
-**Last Updated**: 2026-01-24
+**Last Updated**: February 9, 2026  
-**Maintained By**: Antoine / Atomaste
+**Maintained By**: Atomizer-HQ Team (Manager, Technical Lead, Secretary) + Antoine

docs/hq/AGENT_WORKFLOWS.md

@@ -0,0 +1,450 @@
+# Agent Workflows
+
+**Version**: 1.0  
+**Created**: February 2026  
+**Reference**: OP_09 Communication Protocols
+
+---
+
+## Project Lifecycle Overview
+
+Every Atomizer-HQ project follows a structured workflow with clear phases and agent handoffs. Understanding who does what, when, and how ensures smooth project execution and quality deliverables.
+
+### Six-Phase Project Lifecycle
+
+```
+Intake → Breakdown → Introspection → Study → Results → Deliverables
+  ↓         ↓            ↓          ↓       ↓           ↓
+Secretary  Manager  Technical Lead  Optimizer  Post-Processor  Reporter
+```
+
+---
+
+## Phase 1: Intake (Secretary)
+
+**Responsibility**: Client interface, requirement capture, project initiation  
+**Duration**: 1-2 days  
+**Deliverable**: Project intake document
+
+### Secretary Tasks
+1. **Client Communication**
+   - Receive and clarify project requirements
+   - Identify scope, timeline, budget constraints
+   - Gather technical specifications and constraints
+   - Establish client communication preferences
+
+2. **Initial Assessment**
+   - Assess project complexity and feasibility
+   - Estimate required resources and timeline
+   - Identify potential technical challenges
+   - Flag any special requirements or risks
+
+3. **Project Initiation**
+   - Create initial project folder structure
+   - Document client requirements in structured format
+   - Create `project_metadata.json` with basic info
+   - Schedule handoff meeting with Manager
+
+### Secretary Deliverables
+- **Client Requirements Document** — Structured requirements capture
+- **Project Metadata** — `project_metadata.json` with client info
+- **Initial Risk Assessment** — Potential challenges identified
+- **Resource Estimate** — Preliminary timeline and effort estimate
+
+### Handoff to Manager
+**Communication**: Direct message with project summary  
+**Artifacts**: Requirements document, metadata file, risk assessment  
+**Meeting**: Handoff discussion to clarify any ambiguities
+
+---
+
+## Phase 2: Breakdown (Manager) 
+
+**Responsibility**: Project structuring, team coordination, workflow planning  
+**Duration**: 1-2 days  
+**Deliverable**: Complete project structure and execution plan
+
+### Manager Tasks
+1. **Project Structure Setup**
+   - Complete directory structure per `PROJECT_STRUCTURE.md`
+   - Initialize Knowledge Base framework
+   - Set up study planning structure
+   - Establish project documentation standards
+
+2. **Team Coordination**
+   - Assign Technical Lead and other team members
+   - Define agent responsibilities and interfaces
+   - Establish communication channels and schedules
+   - Plan handoff points and review gates
+
+3. **Execution Planning**
+   - Break down project into specific technical tasks
+   - Estimate timeline for each phase
+   - Identify dependencies and critical path
+   - Plan quality gates and review checkpoints
+
+4. **Risk Management**
+   - Review and refine initial risk assessment
+   - Plan mitigation strategies
+   - Identify decision points and escalation paths
+   - Establish contingency plans
+
+### Manager Deliverables
+- **Complete Project Structure** — Full directory hierarchy
+- **Execution Plan** — Timeline, milestones, dependencies
+- **Team Assignments** — Agent roles and responsibilities
+- **Communication Plan** — Channels, schedules, reporting structure
+
+### Handoff to Technical Lead
+**Communication**: Project kickoff meeting with full team  
+**Artifacts**: Complete project structure, execution plan, team assignments  
+**Review**: Executive summary of client requirements and constraints
+
+---
+
+## Phase 3: Introspection (Technical Lead)
+
+**Responsibility**: Technical analysis, model setup, optimization planning  
+**Duration**: 2-5 days  
+**Deliverable**: Technical foundation and study plan
+
+### Technical Lead Tasks
+1. **Technical Requirements Analysis**
+   - Review client requirements from engineering perspective
+   - Identify technical constraints and design criteria
+   - Establish performance metrics and success criteria
+   - Define technical scope and boundaries
+
+2. **Model Setup and Validation**
+   - Set up reference CAD and FEA models
+   - Validate baseline model performance
+   - Establish modeling conventions and assumptions
+   - Create model documentation and KB entries
+
+3. **Optimization Strategy Development**
+   - Define design variables and constraints
+   - Select optimization objectives and metrics
+   - Plan study sequence and progression
+   - Estimate computational requirements
+
+4. **Knowledge Base Initialization**
+   - Create initial component knowledge files
+   - Document material properties and constraints
+   - Establish FEA conventions and assumptions
+   - Initialize lessons learned framework
+
+### Technical Lead Deliverables
+- **Technical Requirements** — Engineering interpretation of client needs
+- **Reference Models** — Validated baseline CAD and FEA models  
+- **Study Plan** — Optimization strategy and study sequence
+- **Initial KB** — Component, material, and FEA knowledge foundation
+
+### Handoff to Optimizer
+**Communication**: Technical handoff meeting  
+**Artifacts**: Study plan, reference models, technical requirements  
+**Training**: Model setup, conventions, and optimization strategy
+
+---
+
+## Phase 4: Study Execution (Optimizer)
+
+**Responsibility**: FEA optimization execution, results generation  
+**Duration**: 3-10 days (depends on complexity)  
+**Deliverable**: Optimization results and raw data
+
+### Optimizer Tasks  
+1. **Study Setup**
+   - Create study directories per `STUDY_CONVENTIONS.md`
+   - Copy reference models to study workspace
+   - Configure optimization parameters and settings
+   - Validate model functionality and convergence
+
+2. **Optimization Execution**
+   - Execute optimization studies per study plan
+   - Monitor progress and convergence
+   - Troubleshoot any model or solver issues
+   - Adjust parameters as needed for convergence
+
+3. **Results Collection**
+   - Extract optimization results and performance data
+   - Document any issues or unexpected behaviors
+   - Create result summaries and best trial identification
+   - Archive study data and intermediate results
+
+4. **Knowledge Contribution**
+   - Document optimization insights and findings
+   - Update component behavior knowledge
+   - Note any modeling issues or improvements
+   - Record algorithmic performance observations
+
+### Optimizer Deliverables
+- **Study Results** — Complete optimization output data
+- **Best Designs** — Optimized model files and parameters
+- **Execution Log** — Study progression and issue documentation
+- **KB Contributions** — Optimization insights and lessons learned
+
+### Handoff to Post-Processor
+**Communication**: Results review meeting  
+**Artifacts**: Study results, best designs, execution documentation  
+**Context**: Any issues encountered, unexpected behaviors, recommendations
+
+---
+
+## Phase 5: Results Analysis (Post-Processor)
+
+**Responsibility**: Results analysis, validation, insight generation  
+**Duration**: 2-4 days  
+**Deliverable**: Analyzed results and engineering insights
+
+### Post-Processor Tasks
+1. **Results Validation** 
+   - Verify optimization results for engineering reasonableness
+   - Validate best designs against technical requirements
+   - Check constraint satisfaction and safety margins
+   - Perform sensitivity analysis on key parameters
+
+2. **Performance Analysis**
+   - Quantify performance improvements achieved
+   - Analyze trade-offs between competing objectives
+   - Identify design trends and behavioral patterns
+   - Compare results to baseline and requirements
+
+3. **Insight Generation**
+   - Extract engineering insights and design principles
+   - Identify key parameters and sensitivities
+   - Document unexpected findings and behaviors
+   - Generate recommendations for future work
+
+4. **Visualization and Documentation**
+   - Create plots, charts, and visual summaries
+   - Generate technical analysis documentation
+   - Prepare result summaries for stakeholder review
+   - Update Knowledge Base with analysis insights
+
+### Post-Processor Deliverables
+- **Results Analysis** — Comprehensive technical analysis
+- **Performance Summary** — Quantified improvements and metrics
+- **Engineering Insights** — Design principles and recommendations
+- **Visual Documentation** — Plots, charts, and graphical summaries
+
+### Handoff to Reporter  
+**Communication**: Analysis review meeting  
+**Artifacts**: Analysis results, performance summary, visual documentation  
+**Focus**: Key findings, recommendations, and client-relevant insights
+
+---
+
+## Phase 6: Deliverables (Reporter)
+
+**Responsibility**: Client-facing documentation, final report generation  
+**Duration**: 2-3 days  
+**Deliverable**: Complete client deliverable package
+
+### Reporter Tasks
+1. **Technical Report Generation**
+   - Synthesize all project work into cohesive technical report
+   - Translate engineering insights into client-relevant language
+   - Structure report for client technical and management audiences
+   - Include methodology, results, and recommendations
+
+2. **Deliverable Package Assembly**
+   - Organize optimized models and supporting data
+   - Create executive summary for management audience
+   - Prepare technical appendices and detailed data
+   - Package files for client delivery
+
+3. **Quality Review and Finalization**
+   - Review all deliverables for completeness and quality
+   - Ensure consistency across all documentation
+   - Validate technical accuracy and clarity
+   - Prepare final delivery package
+
+4. **Client Communication Support**
+   - Prepare presentation materials if requested
+   - Support client Q&A and follow-up discussions
+   - Document any post-delivery support requirements
+   - Plan potential follow-on work identification
+
+### Reporter Deliverables
+- **Technical Report** — Comprehensive project documentation
+- **Executive Summary** — Management-focused summary
+- **Optimized Models** — Final design files and supporting data
+- **Delivery Package** — Complete client deliverable set
+
+### Final Handoff to CEO
+**Communication**: Project completion review  
+**Artifacts**: Complete deliverable package, project summary  
+**Review**: Quality gate before CEO approval and client delivery
+
+---
+
+## Communication Protocols
+
+### Standard Communication Channels
+
+**Primary Coordination**: `#hq` channel  
+**Agent-to-Agent**: Direct messages via `sessions_send`  
+**Complex Tasks**: `sessions_spawn` for sub-agent delegation  
+**CEO Interface**: Secretary handles all CEO coordination
+
+### OP_09 Communication Standards
+
+All agent communications follow OP_09 protocols for clarity and traceability.
+
+**Message Format**:
+```
+TO: [Agent Name]
+FROM: [Agent Name]  
+RE: [Project Name] - [Phase] - [Specific Topic]
+PRIORITY: [High/Medium/Low]
+
+CONTEXT:
+[Brief context of the communication]
+
+REQUEST/INFORMATION:
+[Specific request or information being communicated]
+
+DELIVERABLES:
+[Expected deliverables and timeline]
+
+HANDOFF ARTIFACTS:
+[Specific files, data, or documentation being transferred]
+```
+
+### Handoff Protocols
+
+**Every Phase Transition**:
+1. **Handoff Meeting** — Direct agent-to-agent discussion
+2. **Artifact Transfer** — All relevant files and documentation  
+3. **Context Summary** — Key points, issues, decisions made
+4. **Success Criteria** — Clear definition of phase completion
+5. **Next Phase Kickoff** — Introduction and orientation for receiving agent
+
+---
+
+## Decision Logging
+
+### Project Decision Log
+Every project maintains a decision log tracking key decisions, rationale, and implications.
+
+**Decision Entry Format**:
+```markdown
+## Decision [ID]: [Title] ([Date])
+**Phase**: [Project Phase]  
+**Decision Maker**: [Agent Name]  
+**Participants**: [Other agents involved]
+
+### Context
+[Situation requiring decision]
+
+### Options Considered  
+[Alternative approaches evaluated]
+
+### Decision
+[What was decided]
+
+### Rationale
+[Why this decision was made]
+
+### Implications
+[Impact on project timeline, scope, approach]
+
+### Approval
+[Who approved this decision]
+```
+
+### Decision Categories
+- **Technical Approach** — Modeling, analysis methods
+- **Scope Changes** — Requirement modifications
+- **Resource Allocation** — Timeline, effort adjustments
+- **Quality Standards** — Acceptance criteria, review gates
+- **Client Interface** — Communication, expectation management
+
+---
+
+## Quality Gates and Reviews
+
+### Phase Review Gates
+Each phase includes a quality gate before handoff to the next agent.
+
+**Standard Review Criteria**:
+1. **Deliverable Completeness** — All required outputs produced
+2. **Quality Standards** — Meet technical and documentation standards
+3. **Success Criteria** — Phase objectives achieved
+4. **Knowledge Capture** — Insights documented in KB
+5. **Handoff Readiness** — Clear artifacts and communication for next phase
+
+### CEO Approval Gates
+Certain milestones require CEO (Antoine) approval before proceeding:
+
+**Required CEO Approvals**:
+- Project scope changes exceeding 20% effort increase
+- Technical approach changes affecting timeline or deliverables
+- Client communication regarding scope, timeline, or budget
+- Final deliverable package before client delivery
+- Project closure and lessons learned summary
+
+---
+
+## Agent Coordination Patterns
+
+### Daily Standups (When Active)
+**Format**: Brief status in `#hq` channel  
+**Frequency**: Daily during active project phases  
+**Content**: Yesterday's progress, today's plan, any blockers
+
+### Weekly Coordination
+**Format**: Project status meeting  
+**Participants**: Active project agents + Manager  
+**Agenda**: Progress review, issue resolution, next week planning
+
+### Cross-Project Learning
+**Format**: Lessons learned sharing  
+**Frequency**: Project completion + monthly review  
+**Purpose**: Share insights across projects, improve processes
+
+---
+
+## Escalation Procedures
+
+### Technical Issues
+1. **Agent-to-Agent** — Direct problem-solving collaboration
+2. **Technical Lead** — Complex technical decisions
+3. **Manager** — Resource or timeline impacts
+4. **CEO** — Client impact or scope changes
+
+### Process Issues  
+1. **Manager** — Workflow or coordination problems
+2. **Team Discussion** — Process improvement needs
+3. **CEO** — Systematic issues requiring policy changes
+
+### Client Issues
+1. **Secretary** — All client communication coordination
+2. **Manager** — Scope or expectation management
+3. **CEO** — Contract or relationship issues
+
+---
+
+## Continuous Improvement
+
+### Process Refinement
+- Document lessons learned in project KB
+- Identify workflow bottlenecks and inefficiencies
+- Propose process improvements based on experience
+- Update workflows based on successful patterns
+
+### Knowledge Sharing
+- Cross-pollinate insights between projects
+- Share successful techniques and approaches
+- Document common problems and solutions
+- Build institutional memory through KB accumulation
+
+### Team Development
+- Identify skill development opportunities
+- Share expertise across agents
+- Improve collaboration effectiveness
+- Enhance communication protocols
+
+---
+
+Last updated: February 2026

docs/hq/KB_CONVENTIONS.md

@@ -0,0 +1,476 @@
+# Knowledge Base Conventions
+
+**Version**: 1.0  
+**Created**: February 2026  
+**Scope**: Atomizer-HQ Knowledge Base Usage
+
+---
+
+## Core Principle: Accumulation, Never Replacement
+
+The Knowledge Base (KB) is the memory of Atomizer-HQ. Every insight, result, and lesson learned gets added to the KB. **Never replace or delete existing knowledge** — only append and refine.
+
+### Why Accumulation Matters
+- **Prevents re-work** — Don't rediscover the same constraints
+- **Tracks evolution** — See how understanding developed over time  
+- **Maintains context** — Know why decisions were made
+- **Enables learning** — Pattern recognition across projects
+
+---
+
+## Knowledge Base Structure
+
+### Two-Level KB System
+
+**1. Global KB** (`knowledge_base/`)
+- Cross-project insights
+- General FEA principles
+- Reusable component knowledge
+- Shared lessons learned
+
+**2. Project-Specific KB** (`projects/[project]/kb/`)
+- Project-specific findings
+- Component behavior in this application
+- Client-specific constraints
+- Study-specific insights
+
+### KB Directory Structure
+```
+kb/
+├── README.md                     # Navigation and conventions
+├── components/                   # Component-specific knowledge
+│   ├── [component-name].md      # Accumulated component insights
+│   └── manufacturing-constraints.md
+├── materials/                    # Material property knowledge  
+├── fea/                         # FEA-specific knowledge
+│   ├── models/                  # Modeling conventions
+│   ├── load-cases/              # Load case documentation
+│   └── results/                 # Results interpretation
+├── dev/                         # Development knowledge
+│   ├── lessons-learned.md       # Process insights
+│   ├── optimization-insights.md # What works/doesn't work
+│   └── process-improvements.md  # Workflow refinements
+└── [domain-specific]/           # Custom categories as needed
+```
+
+---
+
+## Generation Tracking System
+
+Every KB entry must track **when** and **why** knowledge was added. This creates a timeline of understanding evolution.
+
+### Generation Format
+```markdown
+## Generation N: [Descriptive Title] ([Date])
+**Context**: [What study/analysis led to this]  
+**Agent**: [Who contributed this knowledge]  
+**Confidence**: [High/Medium/Low]
+
+[Knowledge content...]
+
+### Key Insights
+- [Insight 1]
+- [Insight 2]
+
+### Implications
+- [How this affects future work]
+- [What should be investigated next]
+```
+
+### Example: Component Knowledge Evolution
+```markdown
+# hydraulic-cylinder-mount.md
+
+## Generation 1: Initial CAD Analysis (2026-02-01)
+**Context**: Baseline model review  
+**Agent**: Technical Lead  
+**Confidence**: High
+
+### Component Overview
+- Function: Mount hydraulic cylinder to main frame
+- Critical loads: 15kN axial, 5kN lateral
+- Material: Steel A36 (client requirement)
+- Manufacturing: Welded fabrication
+
+### Key Features
+- 4 bolt mounting pattern
+- Integrated gusset plates for lateral stability
+- Access clearance for maintenance
+
+## Generation 2: First FEA Results (2026-02-03)
+**Context**: Baseline validation study  
+**Agent**: Optimizer  
+**Confidence**: High
+
+### Stress Analysis Results
+- Maximum stress: 185 MPa at bolt interface
+- Critical location: Upper bolt hole edge
+- Safety factor: 1.45 (acceptable but tight)
+
+### Key Insights
+- Bolt pattern creates stress concentration
+- Current design marginal for peak loads
+- Fillet radius at gusset transition critical
+
+### Implications
+- Consider larger fillet radii in optimization
+- Investigate bolt pattern alternatives
+- Monitor fatigue potential at stress concentration
+
+## Generation 3: Optimization Insights (2026-02-05)
+**Context**: Stress minimization study results  
+**Agent**: Post-Processor  
+**Confidence**: Medium
+
+### Optimization Findings
+- Fillet radius optimization: 5mm → 8mm reduced stress 18%
+- Gusset thickness optimization: 12mm → 15mm reduced stress 12%
+- Combined effect: 28% stress reduction (185 → 133 MPa)
+
+### Unexpected Behaviors
+- Material redistribution created new stress concentration at base
+- Larger fillets improved stress but increased mass significantly
+- Sweet spot: 7mm fillet radius for stress-mass balance
+
+### Key Insights
+- Component responds well to local geometry changes
+- Global stiffness less important than local stress concentrators
+- Mass penalty acceptable for stress improvement
+
+### Implications
+- 7mm fillet radius recommended for similar mounts
+- Always check for new stress concentrations after optimization
+- Consider this component pattern for future hydraulic mounts
+```
+
+---
+
+## Component File Format
+
+Each component gets its own KB file with standardized sections.
+
+### Standard Component Template
+```markdown
+# [component-name].md
+
+## Component Overview
+**Function**: [Primary purpose]  
+**Critical Loads**: [Key loading conditions]  
+**Material**: [Current material choice]  
+**Manufacturing**: [Fabrication method]  
+
+## Behavioral Characteristics
+[How this component behaves under various conditions]
+
+## Design Sensitivities
+[What design parameters most affect performance]
+
+## Optimization Insights
+[What works well, what doesn't, from studies]
+
+## Constraints and Limitations
+[Manufacturing, geometric, material constraints]
+
+## Lessons Learned
+[Key insights that affect future designs]
+
+## Related Components
+[Links to other components that interact with this one]
+
+---
+[Then generations as above...]
+```
+
+---
+
+## FEA KB Structure
+
+FEA knowledge is organized by simulation aspect, not by study.
+
+### FEA Knowledge Categories
+
+**Models** (`fea/models/`):
+- Meshing conventions and best practices
+- Boundary condition approaches
+- Material model selection
+- Modeling assumptions and simplifications
+
+**Load Cases** (`fea/load-cases/`):
+- Operating condition definitions
+- Load magnitudes and distributions
+- Safety factors and design criteria
+- Dynamic vs. static considerations
+
+**Results** (`fea/results/`):
+- Stress criteria and failure modes
+- Results interpretation guidelines
+- Post-processing best practices
+- Validation methods
+
+### Example: FEA Models Knowledge
+```markdown
+# meshing-conventions.md
+
+## Generation 1: Initial Meshing Approach (2026-02-01)
+**Context**: Project setup  
+**Agent**: Technical Lead  
+**Confidence**: High
+
+### Standard Mesh Settings
+- Element type: Quadratic tetrahedral (10-node)
+- Element size: 5mm global, 2mm at stress concentrations
+- Mesh quality: Aspect ratio < 3, Jacobian > 0.6
+
+### Refinement Criteria
+- Refine at fillets, holes, geometric transitions
+- Use mesh convergence study for critical components
+- Target: <5% stress change with 50% size reduction
+
+## Generation 2: Mesh Sensitivity Findings (2026-02-03)
+**Context**: Baseline validation convergence study  
+**Agent**: Technical Lead  
+**Confidence**: High
+
+### Key Findings
+- Current mesh adequate for global stress (2% error vs. fine mesh)
+- Local stress concentrations require 1mm elements for convergence
+- Contact regions need special attention (0.5mm elements)
+
+### Updated Guidelines
+- Global: 5mm remains adequate
+- Stress concentrations: 1mm elements
+- Contact zones: 0.5mm elements
+- Always run convergence check on critical locations
+
+### Implications
+- Computational cost manageable with selective refinement
+- Focus refinement efforts on actual critical locations
+- Standard mesh appropriate for optimization studies
+```
+
+---
+
+## Material Knowledge Format
+
+Material knowledge tracks property validation and selection criteria.
+
+### Material Template
+```markdown
+# [material-type]-properties.md
+
+## Material Overview
+**Designation**: [Standard designation]  
+**Grade**: [Specific grade if applicable]  
+**Condition**: [Heat treatment, condition]  
+
+## Validated Properties
+[Properties confirmed through testing or analysis]
+
+## Design Allowables  
+[Properties used for design criteria]
+
+## Application History
+[Where and how this material has been used successfully]
+
+## Limitations and Considerations
+[When this material should/shouldn't be used]
+
+---
+[Then generations with specific validation results]
+```
+
+---
+
+## Agent Contribution Guidelines
+
+### All Agents: Basic KB Responsibilities
+1. **Read existing KB** before starting work (avoid duplicate effort)
+2. **Add findings** immediately after analysis (don't wait)
+3. **Use generation format** for all contributions
+4. **Link to source studies** when relevant
+
+### Specific Agent Roles
+
+**Technical Lead**: 
+- Component characterization
+- FEA modeling conventions
+- Material property validation
+- Engineering judgment and trade-offs
+
+**Optimizer**:
+- Optimization results and insights
+- Parameter sensitivity findings  
+- Algorithm performance notes
+- Convergence characteristics
+
+**Post-Processor**:
+- Results interpretation
+- Visualization insights
+- Analysis methodology
+- Validation approaches
+
+**Manager**:
+- Process lessons learned
+- Project management insights
+- Resource allocation learnings
+- Timeline and coordination notes
+
+---
+
+## Mario's Shared KB Skill Integration
+
+### Relationship to Global System
+The Atomizer KB system extends Mario's global Knowledge Base skill with domain-specific conventions.
+
+**Global KB Skill** (`/home/papa/clawd/skills/knowledge-base/SKILL.md`):
+- Core KB processing algorithms
+- CDR (Critical Design Review) generation
+- Knowledge extraction and summarization
+- Cross-project insight correlation
+
+**Atomizer Extension** (`/home/papa/atomizer/shared/skills/knowledge-base-atomizer-ext.md`):
+- FEA-specific knowledge patterns
+- Component behavior tracking
+- Optimization insight accumulation
+- Agent workflow integration
+
+### Extension File Format
+```markdown
+# knowledge-base-atomizer-ext.md
+
+## FEA Knowledge Patterns
+[Specific patterns for FEA knowledge organization]
+
+## Component Tracking Extensions
+[How to track component behavior across projects]
+
+## Optimization Insight Formats
+[Standardized formats for optimization results]
+
+## Agent Integration Points
+[How different agents contribute to KB]
+```
+
+### Using the Global KB CLI
+```bash
+# Check KB status for project
+cad_kb.py status projects/hydrotech-beam/kb
+
+# Generate project context summary
+cad_kb.py context projects/hydrotech-beam/kb --output summary.md
+
+# Create CDR content from accumulated knowledge
+cad_kb.py cdr projects/hydrotech-beam/kb --milestone "Design Optimization Complete"
+```
+
+---
+
+## Quality Standards
+
+### Knowledge Quality Criteria
+1. **Specific and Actionable** — "Increase fillet radius to 7mm" not "Make fillets bigger"
+2. **Context-Rich** — Explain why, not just what
+3. **Traceable** — Link to source studies, analyses, decisions
+4. **Timestamped** — Generation tracking for all entries
+5. **Validated** — Distinguish between hypothesis and confirmed results
+
+### Common Quality Issues
+❌ **Vague**: "Design performed well"  
+✅ **Specific**: "Stress reduced from 185 MPa to 133 MPa with 7mm fillet radius"
+
+❌ **No context**: "Use steel for this part"  
+✅ **Context**: "Steel A36 selected for cost; aluminum would reduce mass but exceed budget"
+
+❌ **Missing generation**: Old content with no timestamp  
+✅ **Generation tracked**: "Generation 3: Optimization Results (2026-02-05)"
+
+---
+
+## KB Maintenance and Review
+
+### Regular Maintenance Tasks
+
+**Weekly** (Manager):
+- Review new KB contributions for quality
+- Identify missing knowledge gaps
+- Ensure generation tracking compliance
+
+**Per Project** (Technical Lead):
+- Consolidate project-specific insights
+- Promote reusable knowledge to global KB
+- Archive completed project KB
+
+**Per Study** (All agents):
+- Document study-specific insights immediately
+- Update relevant component/material knowledge
+- Note any contradictions with existing knowledge
+
+### Knowledge Conflict Resolution
+When new knowledge contradicts existing knowledge:
+
+1. **Don't delete** the conflicting knowledge
+2. **Add new generation** with updated understanding
+3. **Explain the difference** — why did understanding change?
+4. **Flag for review** — may indicate systematic issue
+
+Example:
+```markdown
+## Generation 4: Revised Load Understanding (2026-02-10)
+**Context**: Additional client requirements revealed higher loads  
+**Agent**: Technical Lead  
+**Confidence**: High
+
+**NOTE**: This generation revises Generation 2 load assumptions.
+
+### Updated Load Requirements
+- Previous: 15kN axial (Generation 2)
+- Revised: 22kN axial (new client requirement)
+- Impact: Safety factor drops from 1.45 to 0.98 (inadequate)
+
+### Implications
+- Current design no longer adequate
+- Need significant reinforcement or redesign
+- All stress calculations in Generation 2-3 need updating
+```
+
+---
+
+## Examples and Templates
+
+### Component Knowledge Example
+See `projects/hydrotech-beam/kb/components/beam-support-bracket.md` for full example
+
+### Material Knowledge Example  
+See `projects/hydrotech-beam/kb/materials/steel-a36-properties.md` for full example
+
+### FEA Knowledge Example
+See `projects/hydrotech-beam/kb/fea/models/meshing-conventions.md` for full example
+
+---
+
+## Best Practices Summary
+
+### Writing Effective KB Entries
+1. **Write immediately** — Don't accumulate for later
+2. **Be specific** — Quantitative when possible  
+3. **Include context** — Why was this learned?
+4. **Link studies** — Reference source analysis
+5. **Use generations** — Track knowledge evolution
+6. **Update implications** — How does this affect future work?
+
+### Using Existing KB
+1. **Read before starting** — Don't duplicate effort
+2. **Search across projects** — Similar components may exist
+3. **Follow patterns** — Use established insights
+4. **Build on previous work** — Reference and extend
+5. **Question contradictions** — Flag inconsistencies
+
+### Maintaining KB Quality
+1. **Review contributions** — Ensure quality standards
+2. **Consolidate related entries** — Avoid fragmentation
+3. **Update implications** — Keep forward-looking guidance current
+4. **Archive completed projects** — Promote reusable insights to global
+
+---
+
+Last updated: February 2026

docs/hq/PROJECT_STRUCTURE.md

@@ -0,0 +1,377 @@
+# Standard Project Structure
+
+**Version**: 1.0  
+**Created**: February 2026  
+**Reference Implementation**: `projects/hydrotech-beam/`
+
+---
+
+## Overview
+
+All Atomizer-HQ projects follow a standardized Knowledge Base-integrated structure. This ensures consistent organization, efficient handoffs between agents, and proper accumulation of domain knowledge.
+
+**Key Principles**:
+- **Single Source of Truth** — Each project has one authoritative structure
+- **KB Integration** — Knowledge accumulates in structured format
+- **Study-Project Separation** — Studies are execution units, projects are business units
+- **Reference → Copy Flow** — Models flow from reference to study-specific copies
+
+---
+
+## Full Project Directory Structure
+
+```
+projects/[project-name]/
+│
+├── README.md                          # Project overview, status, contacts
+├── project_metadata.json              # Structured project info
+│
+├── deliverables/                      # Client-facing outputs
+│   ├── reports/                       # Technical reports, presentations
+│   ├── models/                        # Final optimized models
+│   └── data/                          # Results datasets, exports
+│
+├── images/                            # Visual assets (organized by type)
+│   ├── components/                    # Part/assembly images
+│   ├── studies/                       # Study result visualizations
+│   ├── analysis/                      # Analysis plots, graphs
+│   └── deliverables/                  # Client presentation images
+│
+├── kb/                                # Knowledge Base (THE CORE)
+│   ├── README.md                      # KB navigation and conventions
+│   ├── components/                    # Component-specific knowledge
+│   │   ├── [component-name].md        # Per-component accumulation
+│   │   └── manufacturing-constraints.md
+│   ├── materials/                     # Material property knowledge
+│   │   ├── steel-properties.md
+│   │   └── material-selection-criteria.md
+│   ├── fea/                          # FEA-specific knowledge
+│   │   ├── models/                    # Model setup knowledge
+│   │   │   ├── meshing-conventions.md
+│   │   │   ├── boundary-conditions.md
+│   │   │   └── modeling-assumptions.md
+│   │   ├── load-cases/                # Load case documentation
+│   │   │   ├── operational-loads.md
+│   │   │   └── safety-factors.md
+│   │   └── results/                   # Results interpretation
+│   │       ├── stress-criteria.md
+│   │       └── failure-modes.md
+│   ├── dev/                          # Development knowledge
+│   │   ├── lessons-learned.md         # Project-specific lessons
+│   │   ├── optimization-insights.md   # What worked, what didn't
+│   │   └── process-improvements.md    # Workflow refinements
+│   └── client/                       # Client-specific knowledge (optional)
+│       ├── requirements.md            # Client requirements evolution
+│       └── preferences.md             # Client preferences and constraints
+│
+├── models/                           # Reference models (READ-ONLY for studies)
+│   ├── reference/                    # Original/baseline models
+│   │   ├── [component].prt           # CAD models
+│   │   ├── [component].sim           # NX simulation setups
+│   │   └── [component].fem           # FEM files
+│   ├── variations/                   # Design variations
+│   └── optimized/                    # Final optimized models
+│
+└── studies/                          # Links to actual studies directory
+    ├── 01_baseline_validation/       # → ../../../studies/project_01_baseline/
+    ├── 02_stress_optimization/       # → ../../../studies/project_02_stress/
+    └── README.md                     # Study execution log
+```
+
+---
+
+## Directory Responsibilities
+
+### Core Directories
+
+| Directory | Owner | Purpose | Frequency |
+|-----------|-------|---------|-----------|
+| `README.md` | Manager | Project status, contacts | Updated weekly |
+| `project_metadata.json` | Secretary | Structured project data | Updated on changes |
+| `deliverables/` | Reporter | Client-facing outputs | End of phases |
+| `kb/` | **Everyone** | Accumulated knowledge | **Continuous** |
+| `models/reference/` | Technical Lead | Baseline models | Setup phase |
+| `studies/` | Optimizer | Study execution links | Per study |
+
+### KB Subdirectories
+
+| KB Directory | Primary Owner | Content |
+|--------------|---------------|---------|
+| `components/` | Technical Lead | Component behavior, constraints |
+| `materials/` | Technical Lead | Material properties, selection |
+| `fea/models/` | Technical Lead | Modeling conventions, assumptions |
+| `fea/load-cases/` | Technical Lead | Load cases, boundary conditions |
+| `fea/results/` | Post-Processor | Results interpretation, criteria |
+| `dev/` | All Agents | Process lessons, optimization insights |
+
+---
+
+## File Naming Conventions
+
+### General Rules
+- **Lowercase with hyphens**: `component-analysis.md`, not `Component_Analysis.md`
+- **Descriptive names**: `steel-yield-strength.md`, not `steel.md`
+- **No spaces**: Use hyphens, not spaces
+- **Consistent extensions**: `.md` for documentation, `.json` for data
+
+### Specific Conventions
+
+**Components**: `[component-type]-[specific-name].md`
+```
+beam-support-bracket.md
+hydraulic-cylinder-mount.md
+```
+
+**Materials**: `[material-type]-[property].md`
+```
+steel-properties.md
+aluminum-6061-characteristics.md
+```
+
+**Studies**: `[number]_[descriptive-name]`
+```
+01_baseline_validation
+02_stress_minimization
+03_mass_reduction_study
+```
+
+---
+
+## Model Flow Conventions
+
+### Reference → Study Copy Pattern
+
+1. **Reference Models** (`models/reference/`)
+   - Original/baseline models
+   - **READ-ONLY** for studies
+   - Version controlled
+   - Maintained by Technical Lead
+
+2. **Study Copies** (`studies/[study-name]/model/`)
+   - **Copied from reference** at study creation
+   - Modified during optimization
+   - Study-specific versions
+   - Managed by Optimizer
+
+3. **Optimized Models** (`models/optimized/`)
+   - Best results from studies
+   - **Copied from study results**
+   - Final deliverable candidates
+   - Curated by Technical Lead
+
+### Model Versioning
+```
+models/reference/bracket-v1.0.prt          # Initial design
+models/reference/bracket-v1.1.prt          # Design revision
+studies/stress-opt/model/bracket.prt       # Study working copy
+models/optimized/bracket-optimized-v2.0.prt # Final optimized
+```
+
+---
+
+## Project Creation Workflow
+
+### 1. Secretary: Project Intake
+```bash
+# Create project directory
+mkdir -p projects/[project-name]/{deliverables,images,kb,models,studies}
+
+# Create metadata
+# (See project_metadata.json template)
+```
+
+### 2. Manager: Structure Setup
+```bash
+# Copy template structure
+cp -r templates/project-template/* projects/[project-name]/
+
+# Create README from template
+# Update with project specifics
+```
+
+### 3. Technical Lead: KB Initialization
+```bash
+# Create component files
+touch projects/[project-name]/kb/components/[component].md
+
+# Initialize FEA knowledge structure
+mkdir -p projects/[project-name]/kb/fea/{models,load-cases,results}
+
+# Create reference models directory
+mkdir -p projects/[project-name]/models/reference
+```
+
+---
+
+## Study Integration
+
+### Study-Project Relationship
+- **Projects** = Business/client organizing unit
+- **Studies** = Technical execution unit
+- Studies reference project KB and models
+- Results flow back to project KB
+
+### Creating Project Studies
+```bash
+# Create study linked to project
+mkdir studies/project_01_baseline
+ln -s ../../../projects/[project]/studies studies/project_01_baseline/project_link
+
+# Copy reference models to study
+cp projects/[project]/models/reference/* studies/project_01_baseline/model/
+
+# Study inherits project KB context
+```
+
+### Results Flow Back
+1. **Study completes** → Results in `studies/[study]/results/`
+2. **Post-Processor analyzes** → Insights documented
+3. **KB accumulation** → Knowledge flows to `projects/[project]/kb/`
+4. **Model archival** → Best models to `projects/[project]/models/optimized/`
+
+---
+
+## KB Accumulation Principles
+
+### The Golden Rule: Add, Never Replace
+- **DO**: Append new insights, learnings, results
+- **DO NOT**: Overwrite existing knowledge
+- **Timestamp entries**: Generation tracking for all additions
+- **Version knowledge**: Track what was learned when
+
+### Component Knowledge Evolution
+```markdown
+# beam-support-analysis.md
+
+## Generation 1: Initial Analysis (2026-02-01)
+- Material: Steel A36
+- Critical stress location: Root of bracket
+- Baseline performance: 180 MPa max stress
+
+## Generation 2: First Optimization (2026-02-05) 
+- Discovered: Fillet radius critical to stress concentration
+- Optimized radius from 5mm → 8mm reduced stress by 15%
+- New critical location: Mounting bolt interface
+
+## Generation 3: Load Case Refinement (2026-02-08)
+- Added dynamic loading consideration
+- Peak stress now 220 MPa under dynamic conditions
+- Recommendation: Consider fatigue analysis
+```
+
+---
+
+## Templates
+
+### project_metadata.json Template
+```json
+{
+  "project_name": "project-name",
+  "client": "Client Name",
+  "project_manager": "agent-name",
+  "technical_lead": "agent-name",
+  "created": "2026-02-01",
+  "status": "active",
+  "phase": "introspection",
+  "description": "Brief project description",
+  "components": ["component1", "component2"],
+  "objectives": ["minimize stress", "reduce mass"],
+  "constraints": ["manufacturing feasibility"],
+  "studies": [
+    {
+      "name": "01_baseline_validation",
+      "status": "completed",
+      "study_link": "../../../studies/project_01_baseline"
+    }
+  ],
+  "deliverables": {
+    "interim_report": "deliverables/reports/interim-report.pdf",
+    "final_report": "deliverables/reports/final-report.pdf",
+    "optimized_models": "models/optimized/"
+  }
+}
+```
+
+### Project README Template
+```markdown
+# [Project Name]
+
+**Client**: [Client Name]  
+**Status**: [Active/Completed/On Hold]  
+**Phase**: [Intake/Breakdown/Introspection/Study/Results/Deliverables]  
+**Manager**: [Agent Name]  
+**Technical Lead**: [Agent Name]  
+
+## Objective
+[Brief description of what we're optimizing]
+
+## Components
+- [Component 1] — [Brief description]
+- [Component 2] — [Brief description]
+
+## Current Status
+[What's happening now, next steps]
+
+## Studies
+- [Study 1] — [Status] — [Brief outcome]
+- [Study 2] — [Status] — [Brief outcome]
+
+## Key Findings
+[Major insights, recommendations]
+
+## Deliverables
+- [X] Baseline analysis
+- [ ] Optimization study
+- [ ] Final report
+```
+
+---
+
+## Best Practices
+
+### Project Organization
+1. **One project per client deliverable**
+2. **Clear phase progression** (don't skip phases)
+3. **Regular KB updates** (not just at end)
+4. **Study naming consistency** (01_, 02_, etc.)
+
+### Knowledge Base Maintenance
+1. **Write as you work** — Don't accumulate at the end
+2. **Be specific** — "Fillet radius affects stress concentration" not "Design matters"
+3. **Include context** — Why was this learned? What led to this insight?
+4. **Link studies** — Reference which study generated the knowledge
+
+### Model Management
+1. **Protect reference models** — No direct modification
+2. **Study isolation** — Each study gets its own model copies
+3. **Version final models** — Clear naming for optimized versions
+4. **Archive intermediate** — Keep best intermediate results
+
+---
+
+## Living Example: Hydrotech Beam Project
+
+**Reference**: `projects/hydrotech-beam/`
+
+This project demonstrates the full structure in practice:
+- Complete KB with component, material, and FEA knowledge
+- Multiple studies linked and executed
+- Results flowing back to project KB
+- Deliverables organized for client handoff
+
+**Key Learnings from Hydrotech**:
+- KB accumulation prevented re-discovering constraints
+- Study-project linking maintained context
+- Reference model protection avoided corruption
+- Generation tracking showed knowledge evolution
+
+---
+
+## Questions and Updates
+
+- **Structure Questions**: Ask Manager or Technical Lead
+- **KB Conventions**: See `KB_CONVENTIONS.md`
+- **Study Execution**: See `STUDY_CONVENTIONS.md`
+- **Process Issues**: Document in project `kb/dev/lessons-learned.md`
+
+Last updated: February 2026

docs/hq/README.md

@@ -0,0 +1,117 @@
+# Atomizer-HQ Agent Documentation
+
+**Version**: 1.0  
+**Created**: February 2026  
+**Target Audience**: AI Agents (Manager, Secretary, Technical Lead, etc.)
+
+---
+
+## What is Atomizer-HQ?
+
+Atomizer-HQ is a multi-agent optimization team that runs FEA optimization projects for clients. Built on top of the Atomizer optimization framework, it provides a structured workflow from client intake through project delivery.
+
+**The Team**:
+- 📋 **Secretary** — CEO interface, admin, client intake
+- 🏗️ **Manager** — Project coordination, workflow orchestration  
+- 🔧 **Technical Lead** — FEA expertise, R&D leadership
+- ⚡ **Optimizer** — Study execution, optimization runs
+- 🔍 **Auditor** — Quality assurance, deliverable review
+- 📊 **Post-Processor** — Results analysis, visualization
+- 📝 **Reporter** — Technical documentation, client reports
+
+---
+
+## How to Use These Docs
+
+This documentation provides agent-specific guidance for:
+
+1. **Project Structure** — How projects are organized
+2. **Knowledge Base Usage** — Accumulating and sharing domain knowledge
+3. **Agent Workflows** — Who does what, when, and how
+4. **Study Conventions** — Technical study execution standards
+
+### Essential Reading for All Agents
+
+| Document | Purpose |
+|----------|---------|
+| **[PROJECT_STRUCTURE.md](PROJECT_STRUCTURE.md)** | Standard project layout and conventions |
+| **[KB_CONVENTIONS.md](KB_CONVENTIONS.md)** | Knowledge base usage and accumulation |
+| **[AGENT_WORKFLOWS.md](AGENT_WORKFLOWS.md)** | Project lifecycle and agent handoffs |
+
+### Role-Specific Guides
+
+| Document | Target Agents |
+|----------|---------------|
+| **[STUDY_CONVENTIONS.md](STUDY_CONVENTIONS.md)** | Technical Lead, Optimizer, Study Builder |
+
+---
+
+## Quick Reference
+
+### Project Phases
+1. **Intake** → Secretary handles client requirements
+2. **Breakdown** → Manager coordinates project setup  
+3. **Introspection** → Technical Lead analyzes requirements
+4. **Study** → Optimizer executes FEA optimization
+5. **Results** → Post-Processor analyzes outcomes
+6. **Deliverables** → Reporter generates client materials
+
+### Key Principles
+- **KB Accumulation**: Add knowledge, never replace
+- **Single Source of Truth**: Projects have one authoritative structure
+- **Quality Gates**: No deliverable goes to CEO without review
+- **Clear Handoffs**: Use OP_09 communication protocols
+
+### Living Examples
+- **Reference Project**: `projects/hydrotech-beam/` — Complete project structure
+- **Active Studies**: `studies/` — Study execution examples
+- **Knowledge Base**: `knowledge_base/` — Accumulated domain expertise
+
+---
+
+## Getting Started
+
+### New Agent Onboarding
+1. Read your role in `context-docs/01-AGENT-ROSTER.md`
+2. Review the project structure in `PROJECT_STRUCTURE.md`
+3. Understand KB conventions in `KB_CONVENTIONS.md`
+4. Check active projects in `projects/` for context
+
+### Starting a New Project
+1. Secretary creates project intake
+2. Manager sets up project structure (see `PROJECT_STRUCTURE.md`)
+3. Technical Lead performs introspection
+4. Follow workflows in `AGENT_WORKFLOWS.md`
+
+### Contributing to Documentation
+- These docs evolve based on agent experience
+- Update conventions when patterns emerge
+- Flag inconsistencies or missing guidance
+- CEO (Antoine) approves major changes
+
+---
+
+## Integration with Core Atomizer
+
+Atomizer-HQ builds on the core optimization framework:
+
+**Core Framework** (engineers + Claude Code):
+- `protocols/` — Operational and system protocols
+- `api/` — NX integration and technical APIs
+- `optimization_engine/` — Core FEA optimization algorithms
+
+**HQ Layer** (multi-agent team):
+- `projects/` — Client project workspaces
+- `knowledge_base/` — Accumulated domain expertise
+- Agent-specific workflows and conventions
+
+---
+
+## Support and Evolution
+
+- **Questions**: Ask in #hq channel or direct agent messages  
+- **Issues**: Flag problems in daily coordination
+- **Updates**: Documentation evolves with team experience
+- **Approval**: CEO (Antoine) reviews major changes
+
+Last updated: February 2026

docs/hq/STUDY_CONVENTIONS.md

@@ -0,0 +1,549 @@
+# Study Conventions
+
+**Version**: 1.0  
+**Created**: February 2026  
+**Target Audience**: Technical Lead, Optimizer, Study Builder  
+**References**: `studies/README.md`, `templates/HOW_TO_CREATE_A_STUDY.md`
+
+---
+
+## Overview
+
+Studies are the technical execution units of Atomizer-HQ. They represent specific FEA optimization runs that generate data, insights, and optimized designs. This document defines how studies are structured, executed, and integrated with the broader project workflow.
+
+### Study vs. Project Distinction
+- **Project** = Business/client organizing unit (`projects/[name]/`)
+- **Study** = Technical execution unit (`studies/[name]/`)
+- **Relationship**: Studies contribute results back to project KB and deliverables
+
+---
+
+## Study Directory Structure
+
+Every study follows a standardized structure for consistency and tool compatibility.
+
+### Standard Study Layout
+```
+studies/[study-name]/
+│
+├── README.md                      # Study purpose, configuration, results
+├── atomizer_spec.json             # Study configuration (AtomizerSpec v2.0)
+├── run_optimization.py            # Study execution script
+│
+├── model/                         # Study-specific model files
+│   ├── [component].prt            # NX CAD model (copied from project reference)
+│   ├── [component].sim            # NX simulation setup
+│   ├── [component].fem            # FEM file
+│   └── baseline_results/          # Initial validation results
+│
+├── introspection/                 # Pre-study analysis
+│   ├── model_analysis.md          # Model validation and setup notes
+│   ├── parameter_sensitivity.md   # Initial parameter studies
+│   └── optimization_plan.md       # Study-specific optimization strategy
+│
+├── results/                       # Generated by Atomizer (DO NOT COMMIT)
+│   ├── optimization.log           # High-level progress log
+│   ├── trial_logs/                # Detailed per-trial logs
+│   ├── history.json               # Complete trial history
+│   ├── history.csv                # CSV format for analysis
+│   ├── best_trial.json            # Best design summary
+│   ├── plots/                     # Auto-generated visualizations
+│   └── study_*.db                 # Optuna database files
+│
+└── project_link                   # Link to parent project (optional)
+```
+
+---
+
+## Study Naming Conventions
+
+Studies use a consistent naming pattern for organization and traceability.
+
+### Naming Pattern: `[project]_[number]_[descriptive_name]`
+
+**Examples**:
+- `hydrotech_01_baseline_validation`
+- `hydrotech_02_stress_optimization`  
+- `bracket_03_mass_reduction`
+- `mount_04_fatigue_analysis`
+
+### Naming Rules
+1. **Project prefix** — Links study to project context
+2. **Sequential numbering** — `01`, `02`, `03`, etc. (always two digits)
+3. **Descriptive name** — Clear purpose in underscore format
+4. **No spaces** — Use underscores throughout
+5. **Lowercase** — Consistent case convention
+
+---
+
+## atomizer_spec.json Format
+
+Studies use AtomizerSpec v2.0 as the single source of truth for configuration.
+
+### Complete atomizer_spec.json Example
+```json
+{
+  "study_name": "hydrotech_02_stress_optimization",
+  "description": "Minimize maximum stress in hydraulic cylinder mount",
+  "created": "2026-02-05T14:30:00Z",
+  "version": "2.0",
+  
+  "model": {
+    "sim_file": "model/cylinder_mount.sim",
+    "prt_file": "model/cylinder_mount.prt",
+    "fem_file": "model/cylinder_mount.fem",
+    "description": "Hydraulic cylinder mounting bracket with 4-bolt pattern"
+  },
+  
+  "design_variables": {
+    "bracket_thickness": {
+      "type": "continuous",
+      "min": 8.0,
+      "max": 20.0,
+      "initial": 12.0,
+      "units": "mm",
+      "description": "Main bracket plate thickness"
+    },
+    "fillet_radius": {
+      "type": "continuous", 
+      "min": 3.0,
+      "max": 12.0,
+      "initial": 5.0,
+      "units": "mm",
+      "description": "Fillet radius at gusset-bracket intersection"
+    },
+    "gusset_thickness": {
+      "type": "continuous",
+      "min": 6.0,
+      "max": 15.0,
+      "initial": 10.0,
+      "units": "mm",
+      "description": "Gusset plate thickness"
+    }
+  },
+  
+  "extractors": [
+    {
+      "name": "max_stress",
+      "function": "extract_stress",
+      "parameters": {
+        "result_type": "von_mises",
+        "metric": "max",
+        "units": "MPa"
+      },
+      "description": "Maximum von Mises stress in structure"
+    },
+    {
+      "name": "max_displacement", 
+      "function": "extract_displacement",
+      "parameters": {
+        "metric": "max",
+        "units": "mm"
+      },
+      "description": "Maximum displacement magnitude"
+    },
+    {
+      "name": "total_mass",
+      "function": "extract_mass",
+      "parameters": {
+        "units": "kg"
+      },
+      "description": "Total structural mass"
+    }
+  ],
+  
+  "objectives": [
+    {
+      "name": "minimize_stress",
+      "extractor": "max_stress",
+      "direction": "minimize",
+      "weight": 1.0,
+      "target": 150.0,
+      "units": "MPa"
+    }
+  ],
+  
+  "constraints": [
+    {
+      "name": "displacement_limit",
+      "extractor": "max_displacement", 
+      "type": "upper_bound",
+      "limit": 2.0,
+      "units": "mm",
+      "description": "Maximum allowable displacement"
+    },
+    {
+      "name": "mass_limit",
+      "extractor": "total_mass",
+      "type": "upper_bound", 
+      "limit": 5.0,
+      "units": "kg",
+      "description": "Maximum allowable mass"
+    }
+  ],
+  
+  "optimization_settings": {
+    "n_trials": 50,
+    "sampler": "TPE",
+    "n_startup_trials": 10,
+    "timeout": 7200,
+    "pruning": {
+      "enabled": true,
+      "patience": 5
+    }
+  },
+  
+  "post_processing": {
+    "generate_plots": true,
+    "plot_formats": ["png", "pdf"],
+    "cleanup_models": false,
+    "keep_top_n_models": 10
+  },
+  
+  "project": {
+    "name": "hydrotech-beam",
+    "phase": "stress_optimization", 
+    "kb_path": "../projects/hydrotech-beam/kb",
+    "deliverable_path": "../projects/hydrotech-beam/deliverables"
+  }
+}
+```
+
+---
+
+## Study Setup Process
+
+### 1. Technical Lead: Study Planning
+Before creating the study, the Technical Lead defines the optimization strategy.
+
+**Planning Tasks**:
+- Define study objectives and success criteria
+- Select design variables and ranges
+- Choose optimization strategy and settings
+- Plan model setup and validation approach
+
+**Planning Documentation** (`introspection/optimization_plan.md`):
+```markdown
+# Study Optimization Plan
+
+## Objective
+Minimize maximum stress while maintaining displacement and mass constraints
+
+## Design Variables
+- bracket_thickness: Primary structural parameter (8-20mm)
+- fillet_radius: Local stress concentrator (3-12mm)  
+- gusset_thickness: Secondary support (6-15mm)
+
+## Strategy
+1. Initial exploration: 20 trials to map design space
+2. Focused optimization: 30 additional trials on promising regions
+3. Validation: Verify best designs with mesh convergence
+
+## Expected Outcomes
+- Target: Reduce max stress from 185 MPa to <150 MPa
+- Maintain: Displacement <2mm, mass <5kg
+- Timeline: 2-3 days execution
+```
+
+### 2. Optimizer: Study Creation
+The Optimizer creates the study structure and configuration.
+
+**Creation Steps**:
+```bash
+# Create study directory
+mkdir -p studies/hydrotech_02_stress_optimization/{model,introspection,results}
+
+# Copy reference models from project
+cp projects/hydrotech-beam/models/reference/* \
+   studies/hydrotech_02_stress_optimization/model/
+
+# Create atomizer_spec.json from template
+# (Use existing study as template or create from scratch)
+
+# Create study README.md
+cp templates/study_README_template.md \
+   studies/hydrotech_02_stress_optimization/README.md
+```
+
+### 3. Optimizer: Model Validation  
+Validate the model setup before optimization begins.
+
+**Validation Checklist**:
+- [ ] Model loads and runs successfully in NX
+- [ ] Design variables update model geometry correctly
+- [ ] Extractors return valid results
+- [ ] Baseline results match expectations
+- [ ] Convergence criteria are met
+
+**Validation Documentation** (`introspection/model_analysis.md`):
+```markdown
+# Model Validation Results
+
+## Baseline Analysis
+- Max stress: 185.3 MPa at upper bolt interface
+- Max displacement: 1.42 mm at bracket tip
+- Total mass: 3.8 kg
+
+## Parameter Sensitivity
+- Thickness: 10% increase → 8% stress reduction
+- Fillet radius: 2mm increase → 12% stress reduction
+- Gusset thickness: Minimal effect on global stress
+
+## Model Quality
+- Mesh convergence: <5% change with 50% refinement
+- Solver convergence: 6 iterations typical
+- Extractor validation: Results consistent with NX postprocessor
+```
+
+---
+
+## Study Execution
+
+### Optimization Execution Workflow
+
+**1. Pre-Execution Check**:
+```bash
+# Validate configuration
+python optimization_engine/validate_spec.py studies/hydrotech_02_stress_optimization/atomizer_spec.json
+
+# Test model functionality  
+python optimization_engine/test_model.py studies/hydrotech_02_stress_optimization/
+```
+
+**2. Execute Study**:
+```bash
+# Navigate to Atomizer root
+cd /path/to/Atomizer
+
+# Run optimization
+python run_study.py --study studies/hydrotech_02_stress_optimization
+```
+
+**3. Monitor Progress**:
+```bash
+# Follow optimization log
+tail -f studies/hydrotech_02_stress_optimization/results/optimization.log
+
+# Check current status
+python optimization_engine/check_status.py studies/hydrotech_02_stress_optimization
+```
+
+### Progress Monitoring
+
+**Optimization Log Format**:
+```
+[14:35:22] Study START | Design variables: 3, Objectives: 1, Constraints: 2
+[14:35:22] Trial   0 START | bracket_thickness=12.0, fillet_radius=5.0, gusset_thickness=10.0
+[14:35:48] Trial   0 COMPLETE | max_stress=185.3, max_displacement=1.42, total_mass=3.8
+[14:35:51] Trial   1 START | bracket_thickness=15.2, fillet_radius=7.8, gusset_thickness=11.5
+[14:36:15] Trial   1 COMPLETE | max_stress=158.7, max_displacement=1.18, total_mass=4.2
+```
+
+---
+
+## Results Processing
+
+### Automatic Results Generation
+The optimization engine automatically generates:
+
+**Core Results**:
+- `history.json` — Complete trial data
+- `history.csv` — Analysis-friendly format  
+- `best_trial.json` — Optimal design summary
+- `optimization.log` — Human-readable progress
+
+**Visualizations** (if enabled):
+- Parameter correlation plots
+- Objective history plots
+- Constraint violation plots  
+- Pareto front plots (multi-objective)
+
+### Manual Results Analysis
+The Optimizer should create additional analysis as needed:
+
+**Custom Analysis** (`results/custom_analysis.md`):
+```markdown
+# Study Results Analysis
+
+## Best Design Summary
+- Optimal parameters: bracket_thickness=16.5mm, fillet_radius=9.2mm, gusset_thickness=12.1mm
+- Performance: max_stress=142.8 MPa (23% reduction from baseline)
+- Constraints: displacement=1.58mm (OK), mass=4.3kg (OK)
+
+## Key Insights
+- Fillet radius most influential parameter (40% of improvement)
+- Diminishing returns above 17mm bracket thickness
+- Gusset thickness has minimal effect within tested range
+
+## Validation Required
+- Mesh convergence check on optimal design
+- Fatigue analysis at reduced stress levels
+- Manufacturing feasibility of 9.2mm fillet radius
+```
+
+---
+
+## Results Integration with Projects
+
+### Knowledge Base Updates
+Study results flow back to the project KB immediately after completion.
+
+**KB Update Process**:
+1. **Component Knowledge** — Update component behavior insights
+2. **FEA Knowledge** — Document modeling insights and lessons
+3. **Optimization Knowledge** — Record algorithm performance and sensitivities
+4. **Lessons Learned** — Process improvements and unexpected findings
+
+**Example KB Update** (`projects/hydrotech-beam/kb/components/cylinder-mount.md`):
+```markdown
+## Generation 3: Stress Optimization Study (2026-02-05)
+**Context**: hydrotech_02_stress_optimization results  
+**Agent**: Optimizer  
+**Confidence**: High
+
+### Optimization Results
+- Achieved 23% stress reduction (185.3 → 142.8 MPa)
+- Optimal design: 16.5mm thickness, 9.2mm fillet, 12.1mm gusset
+- All constraints satisfied with margin
+
+### Key Sensitivities
+- Fillet radius: Most critical parameter (40% of improvement)
+- Bracket thickness: Diminishing returns >17mm  
+- Gusset thickness: Minimal effect in tested range (6-15mm)
+
+### Design Insights
+- Local geometry (fillet) more important than global (thickness)
+- Current constraint limits not binding (could push further)
+- Manufacturing implications: 9.2mm fillet requires machining
+
+### Implications
+- Focus future optimization on fillet and local geometry
+- Consider tighter mass constraints to drive efficiency
+- Investigate manufacturing cost of optimal fillet radius
+```
+
+### Model Archival  
+Best study models are promoted to project optimized models.
+
+**Model Promotion Process**:
+```bash
+# Copy optimal model to project
+cp studies/hydrotech_02_stress_optimization/results/best_trial/cylinder_mount_optimal.prt \
+   projects/hydrotech-beam/models/optimized/cylinder_mount_stress_optimized_v1.0.prt
+
+# Update model registry
+# (Document in project metadata and KB)
+```
+
+---
+
+## Study Quality Standards
+
+### Technical Quality Criteria
+1. **Model Validation** — Baseline results verified
+2. **Convergence** — Optimization converged appropriately  
+3. **Constraint Satisfaction** — All constraints respected
+4. **Result Validation** — Best designs verified for engineering reasonableness
+5. **Documentation** — Complete introspection and results documentation
+
+### Process Quality Criteria  
+1. **Planning** — Clear optimization strategy documented
+2. **Execution** — Followed standard execution workflow
+3. **Monitoring** — Progress tracked and issues documented
+4. **Integration** — Results properly integrated with project KB
+5. **Handoff** — Clear communication to Post-Processor
+
+### Documentation Standards
+Every study must include:
+
+**Required Documentation**:
+- [ ] `README.md` with study purpose and summary
+- [ ] `introspection/optimization_plan.md` with strategy
+- [ ] `introspection/model_analysis.md` with validation
+- [ ] `results/custom_analysis.md` with insights (if applicable)
+- [ ] KB updates with generation-tracked knowledge
+
+---
+
+## Common Study Patterns
+
+### 1. Baseline Validation Studies
+**Purpose**: Validate model setup and establish baseline performance  
+**Trials**: 3-5 (minimal optimization, focus on validation)  
+**Documentation**: Extensive model validation, minimal optimization insights
+
+### 2. Exploration Studies  
+**Purpose**: Map design space and identify promising regions  
+**Trials**: 20-50 (broad parameter ranges)  
+**Documentation**: Parameter sensitivities, design space characteristics
+
+### 3. Optimization Studies
+**Purpose**: Find optimal designs within known promising regions  
+**Trials**: 30-100 (focused parameter ranges)  
+**Documentation**: Convergence analysis, optimal design validation
+
+### 4. Validation Studies
+**Purpose**: Verify optimal designs and perform additional analysis  
+**Trials**: 5-10 (focused around optimal points)  
+**Documentation**: Mesh convergence, robustness analysis, manufacturing assessment
+
+---
+
+## Integration with Templates
+
+### Reference Documents
+- **`studies/README.md`** — Complete study directory overview
+- **`templates/HOW_TO_CREATE_A_STUDY.md`** — Detailed study creation guide
+- **`templates/study_template/`** — Template directory structure
+
+### Template Usage
+```bash
+# Create study from template
+cp -r templates/study_template studies/new_study_name
+
+# Customize for specific project
+# - Update atomizer_spec.json
+# - Copy reference models  
+# - Update README.md
+# - Create optimization plan
+```
+
+---
+
+## Troubleshooting Common Issues
+
+### Model Execution Problems
+**Symptoms**: Trials fail with model errors  
+**Solutions**:
+- Verify NX installation and licensing
+- Check model file paths in atomizer_spec.json
+- Validate design variable expressions exist in model
+- Test model manually in NX with parameter changes
+
+### Optimization Not Converging  
+**Symptoms**: No improvement over many trials  
+**Solutions**:
+- Check parameter ranges (too narrow/too wide?)
+- Verify objective scaling (similar magnitudes?)
+- Try different sampler (Random for exploration)
+- Increase trial count or adjust convergence criteria
+
+### Constraint Violations
+**Symptoms**: All or most trials violate constraints  
+**Solutions**:
+- Relax constraint limits (may be too tight)
+- Expand design variable bounds  
+- Adjust objective weights (prioritize feasibility)
+- Consider multi-stage optimization (feasibility first)
+
+### Results Don't Make Sense
+**Symptoms**: Optimal designs seem wrong or unrealistic  
+**Solutions**:
+- Verify extractor functions return correct values
+- Check units consistency across specification
+- Validate optimal design manually in NX
+- Review optimization log for anomalies
+
+---
+
+Last updated: February 2026