docs: Major documentation overhaul - restructure folders, update tagline, add Getting Started guide

- Restructure docs/ folder (remove numeric prefixes):
  - 04_USER_GUIDES -> guides/
  - 05_API_REFERENCE -> api/
  - 06_PHYSICS -> physics/
  - 07_DEVELOPMENT -> development/
  - 08_ARCHIVE -> archive/
  - 09_DIAGRAMS -> diagrams/

- Replace tagline 'Talk, don't click' with 'LLM-driven optimization framework' in 9 files

- Create comprehensive docs/GETTING_STARTED.md:
  - Prerequisites and quick setup
  - Project structure overview
  - First study tutorial (Claude or manual)
  - Dashboard usage guide
  - Neural acceleration introduction

- Rewrite docs/00_INDEX.md with correct paths and modern structure

- Archive obsolete files:
  - 01_PROTOCOLS.md -> archive/historical/01_PROTOCOLS_legacy.md
  - 03_GETTING_STARTED.md -> archive/historical/
  - ATOMIZER_PODCAST_BRIEFING.md -> archive/marketing/

- Update timestamps to 2026-01-20 across all key files

- Update .gitignore to exclude docs/generated/

- Version bump: ATOMIZER_CONTEXT v1.8 -> v2.0
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# Execution Plan & Ralph Loop Generator
**Purpose**: Instructions for generating comprehensive execution plans with autonomous implementation prompts from any design document.
---
## When to Use
After completing a deep investigation that produced:
- A master design document (architecture, schemas, component designs)
- Clear understanding of what needs to be built
Use this to generate:
- Detailed task list with dependencies
- File-level implementation instructions
- Autonomous execution prompts (Ralph Loop)
- Quick reference guides
---
## Generator Prompt
```markdown
Based on the design document at [PATH_TO_DESIGN_DOC], create a comprehensive execution plan for autonomous implementation.
### Task Breakdown Requirements
1. **Granularity**: Break work into tasks that take 15-60 minutes each
2. **Atomic**: Each task should produce a testable/verifiable output
3. **Sequential IDs**: Use format P{phase}.{number} (e.g., P1.1, P1.2, P2.1)
4. **Dependencies**: Explicitly list which tasks must complete first
### For Each Task, Specify:
- **Task ID & Name**: P1.1 - Create TypeScript types from JSON Schema
- **File(s)**: Exact file path(s) to create or modify
- **Action**: Specific implementation instructions
- **Reference**: Section of design doc with details/examples
- **Dependencies**: List of prerequisite task IDs
- **Acceptance Criteria**: How to verify task is complete
### Structure the Plan As:
1. **Project Overview**: Goal, reference docs, success metrics
2. **Phase Structure**: Table showing phases, duration, focus areas
3. **Implementation Order**: Critical path diagram (text-based)
4. **Phase Sections**: Detailed tasks grouped by phase
5. **File Summary**: Tables of files to create and modify
6. **Success Criteria**: Checkboxes for each phase completion
7. **Risk Mitigation**: Known risks and how to handle them
### Also Generate:
1. **Ralph Loop Prompts**:
- Initial prompt to start autonomous execution
- Continuation prompt for resuming
- Phase-specific prompts
- Troubleshooting prompts
- Full task list for TodoWrite initialization
2. **Quick Start Guide**:
- TL;DR summary
- Copy-paste commands to start
- Phase summary table
- Key concepts glossary
- Success metrics checklist
### Output Files:
- `{PROJECT}_EXECUTION_PLAN.md` - Detailed task list
- `{PROJECT}_RALPH_PROMPT.md` - Autonomous execution prompts
- `{PROJECT}_QUICKSTART.md` - Quick reference guide
```
---
## Example Usage
### Input
```
Based on the design document at `docs/plans/UNIFIED_CONFIGURATION_ARCHITECTURE.md`,
create a comprehensive execution plan for autonomous implementation.
The project involves:
- Backend services (Python/FastAPI)
- Frontend components (React/TypeScript)
- MCP tools integration
- Database migrations
Generate the execution plan, Ralph Loop prompts, and quick start guide.
```
### Output Structure
```
docs/plans/
├── {PROJECT}_EXECUTION_PLAN.md # 50+ detailed tasks
├── {PROJECT}_RALPH_PROMPT.md # Autonomous prompts
└── {PROJECT}_QUICKSTART.md # TL;DR guide
```
---
## Task Template
Use this template for each task:
```markdown
### P{X}.{Y} - {Task Name}
- **File**: `path/to/file.ext`
- **Action**: {What to implement}
- **Reference**: {Design doc section} Section X.Y
- **Dependencies**: P{X}.{Z}, P{X}.{W}
- **Acceptance**: {How to verify completion}
```
---
## Phase Template
```markdown
## PHASE {N}: {Phase Name}
### P{N}.1 - {First Task}
- **File**: `path/to/file`
- **Action**: {Description}
- **Dependencies**: {None or list}
- **Acceptance**: {Criteria}
### P{N}.2 - {Second Task}
...
```
---
## Ralph Prompt Template
```markdown
# Ralph Loop Prompt: {Project Name}
## Claude CLI Command
\`\`\`bash
claude --dangerously-skip-permissions
\`\`\`
## Initial Prompt (Copy This)
\`\`\`
You are implementing {Project Description}.
## Project Context
Read these documents before starting:
1. `{path/to/design_doc}` - Master design document
2. `{path/to/execution_plan}` - Detailed task list
3. `{path/to/schema_or_types}` - Type definitions (if applicable)
## Your Mission
Implement the system following the execution plan. Work through tasks in order (P1.1 → P1.2 → ... → P{N}.{M}).
## Rules
1. **Follow the plan**: Execute tasks in order specified
2. **Check dependencies**: Don't start until prerequisites complete
3. **Use TodoWrite**: Track all tasks, mark progress
4. **Test as you go**: Verify acceptance criteria
5. **Commit regularly**: After each logical group
6. **Reference the design**: Use code examples from docs
7. **Ask if blocked**: Explain blockers clearly
Begin by reading the reference documents and loading tasks into TodoWrite.
\`\`\`
## Continuation Prompt
\`\`\`
Continue implementing {Project Name}.
Reference: `{path/to/execution_plan}`
Check current todo list, find last completed task, continue from there.
\`\`\`
## Full Task List for TodoWrite
\`\`\`
P1.1 - {Task name}
P1.2 - {Task name}
...
\`\`\`
```
---
## Quick Start Template
```markdown
# {Project Name} - Quick Start Guide
## TL;DR
**Goal**: {One sentence description}
**Effort**: ~{N} tasks across {M} phases (~{W} weeks)
**Key Files**:
- Design: `{path}`
- Tasks: `{path}`
- Prompts: `{path}`
---
## Start Autonomous Implementation
### 1. Open Claude CLI
\`\`\`bash
claude --dangerously-skip-permissions
\`\`\`
### 2. Paste Initial Prompt
\`\`\`
{Condensed version of initial prompt}
\`\`\`
### 3. Let It Run
---
## Phase Summary
| Phase | Tasks | Focus | Deliverables |
|-------|-------|-------|--------------|
| 1 | P1.1-P1.{N} | {Focus} | {Key outputs} |
| 2 | P2.1-P2.{N} | {Focus} | {Key outputs} |
...
---
## Success Metrics
- [ ] {Metric 1}
- [ ] {Metric 2}
...
```
---
## Quality Checklist
Before finalizing the execution plan, verify:
- [ ] Every task has a specific file path
- [ ] Every task has clear acceptance criteria
- [ ] Dependencies form a valid DAG (no cycles)
- [ ] Tasks are ordered so dependencies come first
- [ ] Phase boundaries make logical sense
- [ ] Commits points are identified (after groups of related tasks)
- [ ] Risk mitigations are documented
- [ ] Ralph prompts reference all necessary documents
- [ ] Quick start is actually quick (fits on one screen)
- [ ] Task list for TodoWrite is complete and copy-pasteable
---
## Complexity Guidelines
| Project Size | Tasks | Phases | Typical Duration |
|--------------|-------|--------|------------------|
| Small | 10-20 | 2 | 1-2 weeks |
| Medium | 20-50 | 3-4 | 3-6 weeks |
| Large | 50-100 | 4-6 | 6-12 weeks |
| Epic | 100+ | 6+ | 12+ weeks |
---
## Common Patterns
### Backend-First Pattern
```
Phase 1: Data models, validation, core service
Phase 2: REST API endpoints
Phase 3: Frontend integration
Phase 4: Testing & polish
```
### Full-Stack Feature Pattern
```
Phase 1: Schema/types, backend service, API
Phase 2: Frontend components, state management
Phase 3: Integration, real-time sync
Phase 4: Testing, documentation
```
### Migration Pattern
```
Phase 1: New system alongside old
Phase 2: Migration tooling
Phase 3: Gradual cutover
Phase 4: Deprecate old system
```
### Integration Pattern
```
Phase 1: Define contracts/interfaces
Phase 2: Implement adapters
Phase 3: Wire up connections
Phase 4: Testing, error handling
```
---
## Tips for Better Plans
1. **Start with the end**: Define success criteria first, then work backward
2. **Identify the critical path**: What's the minimum to get something working?
3. **Group related tasks**: Makes commits logical and rollback easier
4. **Front-load risky tasks**: Discover blockers early
5. **Include buffer**: Things always take longer than expected
6. **Make tasks testable**: "It works" is not acceptance criteria
7. **Reference existing code**: Point to similar patterns in codebase
8. **Consider parallelism**: Some phases can overlap if teams split work
---
*Use this template to generate execution plans for any project following a design document.*