feat: Add MLP surrogate with Turbo Mode for 100x faster optimization
Neural Acceleration (MLP Surrogate): - Add run_nn_optimization.py with hybrid FEA/NN workflow - MLP architecture: 4-layer (64->128->128->64) with BatchNorm/Dropout - Three workflow modes: - --all: Sequential export->train->optimize->validate - --hybrid-loop: Iterative Train->NN->Validate->Retrain cycle - --turbo: Aggressive single-best validation (RECOMMENDED) - Turbo mode: 5000 NN trials + 50 FEA validations in ~12 minutes - Separate nn_study.db to avoid overloading dashboard Performance Results (bracket_pareto_3obj study): - NN prediction errors: mass 1-5%, stress 1-4%, stiffness 5-15% - Found minimum mass designs at boundary (angle~30deg, thick~30mm) - 100x speedup vs pure FEA exploration Protocol Operating System: - Add .claude/skills/ with Bootstrap, Cheatsheet, Context Loader - Add docs/protocols/ with operations (OP_01-06) and system (SYS_10-14) - Update SYS_14_NEURAL_ACCELERATION.md with MLP Turbo Mode docs NX Automation: - Add optimization_engine/hooks/ for NX CAD/CAE automation - Add study_wizard.py for guided study creation - Fix FEM mesh update: load idealized part before UpdateFemodel() New Study: - bracket_pareto_3obj: 3-objective Pareto (mass, stress, stiffness) - 167 FEA trials + 5000 NN trials completed - Demonstrates full hybrid workflow 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Antoine
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docs/protocols/extensions/EXT_03_CREATE_PROTOCOL.md
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docs/protocols/extensions/EXT_03_CREATE_PROTOCOL.md
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# EXT_03: Create New Protocol
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<!--
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PROTOCOL: Create New Protocol Document
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LAYER: Extensions
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VERSION: 1.0
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STATUS: Active
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LAST_UPDATED: 2025-12-05
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PRIVILEGE: admin
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LOAD_WITH: []
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-->
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## Overview
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This protocol guides you through creating new protocol documents for the Atomizer Protocol Operating System (POS). Use this when adding significant new system capabilities.
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**Privilege Required**: admin
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---
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## When to Use
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| Trigger | Action |
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|---------|--------|
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| Adding major new system capability | Follow this protocol |
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| "create protocol", "new protocol" | Follow this protocol |
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| Need to document architectural pattern | Follow this protocol |
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---
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## Protocol Types
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| Layer | Prefix | Purpose | Example |
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|-------|--------|---------|---------|
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| Operations | OP_ | How-to guides | OP_01_CREATE_STUDY |
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| System | SYS_ | Core specifications | SYS_10_IMSO |
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| Extensions | EXT_ | Extensibility guides | EXT_01_CREATE_EXTRACTOR |
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---
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## Step-by-Step Guide
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### Step 1: Determine Protocol Type
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- **Operations (OP_)**: User-facing procedures
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- **System (SYS_)**: Technical specifications
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- **Extensions (EXT_)**: Developer guides
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### Step 2: Assign Protocol Number
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**Operations**: Sequential (OP_01, OP_02, ...)
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**System**: By feature area (SYS_10=optimization, SYS_11=multi-obj, etc.)
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**Extensions**: Sequential (EXT_01, EXT_02, ...)
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Check existing protocols to avoid conflicts.
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### Step 3: Create Protocol File
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Use the template from `templates/protocol_template.md`:
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```markdown
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# {LAYER}_{NUMBER}_{NAME}.md
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<!--
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PROTOCOL: {Full Name}
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LAYER: {Operations|System|Extensions}
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VERSION: 1.0
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STATUS: Active
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LAST_UPDATED: {YYYY-MM-DD}
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PRIVILEGE: {user|power_user|admin}
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LOAD_WITH: [{dependencies}]
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-->
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## Overview
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{1-3 sentence description of what this protocol does}
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---
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## When to Use
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| Trigger | Action |
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|---------|--------|
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| {keyword or condition} | Follow this protocol |
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---
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## Quick Reference
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{Tables with key parameters, commands, or mappings}
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---
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## Detailed Specification
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### Section 1: {Topic}
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{Content}
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### Section 2: {Topic}
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{Content}
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---
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## Examples
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### Example 1: {Scenario}
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{Complete working example}
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---
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## Troubleshooting
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| Symptom | Cause | Solution |
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|---------|-------|----------|
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| {error} | {why} | {fix} |
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---
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## Cross-References
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- **Depends On**: [{protocol}]({path})
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- **Used By**: [{protocol}]({path})
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- **See Also**: [{related}]({path})
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---
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## Version History
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| Version | Date | Changes |
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|---------|------|---------|
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| 1.0 | {DATE} | Initial release |
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```
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### Step 4: Write Content
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**Required Sections**:
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1. Overview - What does this protocol do?
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2. When to Use - Trigger conditions
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3. Quick Reference - Fast lookup
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4. Detailed Specification - Full content
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5. Examples - Working examples
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6. Troubleshooting - Common issues
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7. Cross-References - Related protocols
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8. Version History - Changes over time
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**Writing Guidelines**:
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- Front-load important information
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- Use tables for structured data
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- Include complete code examples
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- Provide troubleshooting for common issues
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### Step 5: Update Navigation
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**docs/protocols/README.md**:
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```markdown
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| {NUM} | {Name} | [{Layer}]({layer}/{filename}) |
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```
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**.claude/skills/01_CHEATSHEET.md**:
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```markdown
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| {task} | {LAYER}_{NUM} | {key info} |
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```
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**.claude/skills/02_CONTEXT_LOADER.md**:
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Add loading rules if needed.
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### Step 6: Update Cross-References
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Add references in related protocols:
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- "Depends On" in new protocol
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- "Used By" or "See Also" in existing protocols
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### Step 7: Validate
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```bash
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# Check markdown syntax
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# Verify all links work
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# Test code examples
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# Ensure consistent formatting
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```
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---
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## Protocol Metadata
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### Header Comment Block
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```markdown
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<!--
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PROTOCOL: Full Protocol Name
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LAYER: Operations|System|Extensions
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VERSION: Major.Minor
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STATUS: Active|Draft|Deprecated
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LAST_UPDATED: YYYY-MM-DD
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PRIVILEGE: user|power_user|admin
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LOAD_WITH: [SYS_10, SYS_11]
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-->
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```
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### Status Values
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| Status | Meaning |
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|--------|---------|
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| Draft | In development, not ready for use |
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| Active | Production ready |
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| Deprecated | Being phased out |
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### Privilege Levels
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| Level | Who Can Use |
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|-------|-------------|
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| user | All users |
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| power_user | Developers who can extend |
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| admin | Full system access |
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---
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## Versioning
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### Semantic Versioning
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- **Major (X.0)**: Breaking changes
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- **Minor (1.X)**: New features, backward compatible
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- **Patch (1.0.X)**: Bug fixes (usually omit for docs)
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### Version History Format
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```markdown
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| Version | Date | Changes |
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|---------|------|---------|
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| 2.0 | 2025-12-15 | Redesigned architecture |
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| 1.1 | 2025-12-05 | Added neural support |
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| 1.0 | 2025-11-20 | Initial release |
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```
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---
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## Troubleshooting
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| Issue | Cause | Solution |
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|-------|-------|----------|
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| Protocol not found | Wrong path | Check location and README |
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| LLM not loading | Missing from context loader | Update 02_CONTEXT_LOADER.md |
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| Broken links | Path changed | Update cross-references |
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---
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## Cross-References
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- **Template**: `templates/protocol_template.md`
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- **Navigation**: `docs/protocols/README.md`
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- **Context Loading**: `.claude/skills/02_CONTEXT_LOADER.md`
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---
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## Version History
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| Version | Date | Changes |
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|---------|------|---------|
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| 1.0 | 2025-12-05 | Initial release |
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