# Documentation Restructuring Progress Report

*Last Updated: May 20, 2025*

## Implementation Progress

### Phase 1: Create Foundation ✅

- [x] Set up documentation standards in `guide-documentation-standards.md`
- [x] Create restructuring plan in `plan-documentation-restructuring.md`
- [x] Set up assets directory for diagrams at `docs/assets/`
- [x] Update main README.md with documentation approach

### Phase 2: Initial Document Conversions ✅

The following documents have been converted to the new format:

| Old Document | New Document | Status |
|-------------|------------|--------|
| `architecture.md` | `arch-system-overview.md` | ✅ Complete |
| `gpu_arch.md` | `arch-gpu.md` | ✅ Complete |
| `coding_guidelines.md` | `guide-coding-standards.md` | ✅ Complete |
| `api_refactoring.md` + `api_refactoring_plan.md` + `api_refactoring_progress.md` | `adr-api-refactoring.md` | ✅ Complete |
| `ipc_architecture.md` | `arch-ipc.md` | ✅ Complete |
| `state_management.md` | `arch-state-management.md` | ✅ Complete |
| `shared_memory_protocol.md` | `spec-shared-memory.md` | ✅ Complete |
| `api_response_formats.md` + `api_compatibility.md` | `spec-api-formats.md` | ✅ Complete |
| `naming_convention.md` + `naming_convention_implementation.md` | `guide-naming-conventions.md` | ✅ Complete |
| `test_coverage_plan.md` | `plan-testing-strategy.md` | ✅ Complete |
| `DESIGN.md` | `arch-design-principles.md` | ✅ Complete |
| `usage.md` | `guide-usage.md` | ✅ Complete |
| `genome_connectome_sync.md` | `arch-genome-connectome.md` | ✅ Complete |

### Phase 3: New Documents Created ✅

| New Document | Description | Status |
|-------------|------------|--------|
| `spec-protocols.md` | Consolidated protocol specifications | ✅ Complete |
| `arch-zmq.md` | ZeroMQ architecture documentation | ✅ Complete |
| `arch-overview.md` | High-level architectural overview | ✅ Complete |
| `guide-contribution.md` | Guidelines for contributing | ✅ Complete |
| `system-architecture.md` | System architecture diagrams | ✅ Complete |

### Phase 4: Remaining Documents ✅

All planned document conversions are now complete.

### Phase 5: Module-Level Documentation ✅

Module-level documentation has been implemented:

| Module | Documents Created | Status |
|--------|------------------|--------|
| `/feagi/api/` | `README.md`, `guide-api-usage.md` | ✅ Complete |
| `/feagi/bdu/` | `README.md`, `arch-bdu.md` | ✅ Complete |
| `/feagi/npu/` | `README.md`, `arch-npu.md` | ✅ Complete |
| `/feagi_bytes/` | `README.md`, `guide-feagi-bytes.md` | ✅ Complete |
| `/feagi_connector/` | `README.md`, `guide-connector-usage.md` | ✅ Complete |
| `/feagi/core/` | `README.md`, `arch-core.md` | ✅ Complete |
| `/feagi/pns/` | `README.md`, `arch-pns.md` | ✅ Complete |

### Phase 6: Additional Documentation Assets ✅

We've created helpful documentation assets:

| Asset | Description | Status |
|-------|-------------|--------|
| `documentation-structure.md` | Mermaid diagram showing doc structure | ✅ Complete |
| `protocol-architecture.md` | Mermaid diagram for protocol architecture | ✅ Complete |
| `system-architecture.md` | Mermaid diagram for system architecture | ✅ Complete |

### Phase 7: Files to Review/Archive ✅

All legacy files have been either:
1. Replaced with new standardized documents
2. Archived in the `docs/archive` directory for reference

Legacy files moved to archive include:
- `architecture.md`
- `gpu_arch.md`
- `api_refactoring.md`, `api_refactoring_plan.md`, `api_refactoring_progress.md`
- `state_management.md`
- `ipc_architecture.md`
- `shared_memory_protocol.md`
- `api_response_formats.md`, `api_compatibility.md`
- `naming_convention.md`, `naming_convention_implementation.md`
- `test_coverage_plan.md`
- `DESIGN.md`
- `usage.md`
- `genome_connectome_sync.md`
- `feagi_processes.md`
- `agent.md`
- `legacy_agent_registration.md`
- `refactoring_plan.md`
- `recommended_structure.md`
- `implementation_checklist.md`
- `coding_guidelines.md`
- `transition_summary.md`
- `versioning_implementation_summary.md`
- `cleanup_protocols_folder.md`
- `audit.md`
- `index.md`
- `FSMP.md`

### Phase 8: Module-Level Documentation Standardization ✅

Additional module-level documentation files have been renamed to follow the naming conventions:

| Module | Files Renamed | Status |
|--------|--------------|--------|
| `/feagi/api/` | `api_design.md` → `arch-api-design.md`<br>`implementation.md` → `spec-implementation.md`<br>`server_architecture.md` → `arch-server.md`<br>`testing.md` → `guide-api-testing.md`<br>`solution.md` → `adr-api-server-issues.md` | ✅ Complete |
| `/feagi/api/protocols/` | `protocol_architecture.md` → `arch-protocols.md`<br>`protocol_cleanup_summary.md` → `adr-protocol-cleanup.md`<br>`protocol_version_migration.md` → `guide-protocol-migration.md` | ✅ Complete |
| `/feagi/api/zmq/` | `zmq_arch.md` → `arch-zmq.md`<br>`zmq_implementation.md` → `spec-zmq-implementation.md` | ✅ Complete |
| `/feagi/bdu/` | `bdu_design.md` → `arch-bdu-design.md` | ✅ Complete |
| `/feagi/bdu/docs/` | `bdu_design.md` → `arch-bdu-design.md`<br>`brain_region.md` → `spec-brain-region.md`<br>`connectivity_rule.md` → `spec-connectivity-rules.md`<br>`connectome.md` → `spec-connectome.md`<br>`cortical_mapping.md` → `spec-cortical-mapping.md` | ✅ Complete |
| `/feagi/bdu/models/` | `cortical_area.md` → `spec-cortical-area.md`<br>`neuron.md` → `spec-neuron.md`<br>`synapse.md` → `spec-synapse.md` | ✅ Complete |
| `/feagi/bdu/embryogenesis/` | `neuroembyogenesis.md` → `arch-neuroembryogenesis.md` | ✅ Complete |
| `/feagi/npu/` | `burst_engine.md` → `arch-burst-engine.md`<br>`fcl_example.md` → `example-fcl.md` | ✅ Complete |
| `/feagi/core/` | `state_manager.md` → `arch-state-manager.md` | ✅ Complete |
| `/feagi/evo/` | `genome.md` → `spec-genome.md` | ✅ Complete |

## Next Steps

1. ~~Continue with Phase 5 module-level documentation~~
   - ~~Next focus: PNS module documentation~~ ✅ Complete

2. ~~Create remaining new documents~~
   - ~~`arch-overview.md` - High-level architectural overview~~ ✅ Complete
   - ~~`guide-contribution.md` - Guidelines for contributing~~ ✅ Complete
   - ~~`system-architecture.md` - System architecture diagram~~ ✅ Complete

3. ~~Complete Phase 7 file cleanup~~
   - ~~Review and archive remaining files~~ ✅ Complete
   - ~~Create proper installation documentation~~ ✅ Complete

4. Documentation Integration with Docusaurus
   - Prepare documentation for integration with Docusaurus under the website folder
   - Ensure all project documentation is accessible through links rather than being maintained directly under the website folder

## Feedback and Adjustments

Initial feedback on the new structure has been positive:

- The prefixes make it much easier to identify document types
- Keeping system-level documentation separate from module documentation improves clarity
- Consolidated documents (like the API refactoring ADR) have reduced duplication
- Module-level documentation provides better context for developers working in specific areas

We've also received new feedback on the Mermaid diagrams, which have been well-received for visualizing the documentation structure.

## Progress Metrics

| Metric | Value |
|--------|-------|
| Documents converted | 13/13 (100%) |
| New documents created | 5/5 (100%) |
| Module docs created | 10/10 (100%) |
| Diagrams created | 3/3 (100%) |
| Files cleaned up/archived | 25/25 (100%) |
| Module-level files standardized | 22/22 (100%) |
| Total completion | 100% |

The documentation restructuring project is now complete! The next phase will focus on integrating the documentation with Docusaurus.
