# Toolchain Implementation Progress

**Plan**: See [Toolchain-Architecture.md](./Toolchain-Architecture.md)
**Started**: 2025-12-07
**Current Phase**: Phase 1 - Foundation + Variance Collection

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## Phase 1A: nyx-substrate Foundation ✅ COMPLETE

**Goal**: Build nyx-substrate package and database infrastructure

### ✅ Completed (2025-12-07)

- [x] Package structure (pyproject.toml, src/ layout)
- [x] PhoebeConnection class with connection pooling
- [x] Message protocol helpers (partnership messages)
- [x] VarianceProbeRun Pydantic schema
- [x] VarianceProbeDAO for database operations
- [x] variance_probe_runs table in phoebe
- [x] Installation and connection testing

**Files Created**: 9 new files
**Status**: 🟢 nyx-substrate v0.1.0 installed and tested

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## Phase 1B: nyx-probing Integration ✅ COMPLETE

**Goal**: Extend nyx-probing to use nyx-substrate for variance collection

### ✅ Completed (2025-12-07)

- [x] Add nyx-substrate dependency to nyx-probing/pyproject.toml
- [x] Create VarianceRunner class (nyx_probing/runners/variance_runner.py)
- [x] Add variance CLI commands (nyx_probing/cli/variance.py)
- [x] Register commands in main CLI
- [x] Integration test (imports and CLI verification)

**Files Created**: 3 new files
**Files Modified**: 2 files
**CLI Commands Added**: 4 (collect, batch, stats, analyze)
**Status**: 🟢 nyx-probing v0.1.0 with variance collection ready

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## Phase 1C: Baseline Variance Collection ⏸️ READY

**Goal**: Collect baseline variance data for depth-3 champions

### ⏳ Ready to Execute (on prometheus)

- [ ] Run 1000x variance for "Geworfenheit" (thrownness)
- [ ] Run 1000x variance for "Vernunft" (reason)
- [ ] Run 1000x variance for "Erkenntnis" (knowledge)
- [ ] Run 1000x variance for "Pflicht" (duty)
- [ ] Run 1000x variance for "Aufhebung" (sublation)
- [ ] Run 1000x variance for "Wille" (will)

**Next Actions**:
1. SSH to prometheus.eachpath.local (THE SPINE)
2. Install nyx-substrate and nyx-probing in venv
3. Run batch collection or individual terms
4. Analyze distributions and document baselines

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## Phase 1D: Corpus Extraction Pipeline ✅ COMPLETE

**Goal**: Extract vocabulary and co-occurrence metrics for RAG policy development

### ✅ Completed (2025-12-13)

- [x] Create extractors module in nyx-probing
- [x] Implement VocabExtractor (TF-IDF vocabulary)
- [x] Implement CoOccurrenceAnalyzer (PMI, Jaccard, Dice)
- [x] Generate anchor term signatures (20 anchors)
- [x] Generate chunking recommendations (5 clusters)
- [x] Run initial extraction on nimmerverse vault
- [x] Export glossary to CSV/JSON (5,243 terms)
- [x] Export co-occurrence analysis (18,169 pairs)

**Files Created**: 7 new files
- `nyx_probing/extractors/__init__.py`
- `nyx_probing/extractors/vocab_extractor.py` (~350 LOC)
- `nyx_probing/extractors/cooccurrence.py` (~400 LOC)
- `data/nimmerverse_glossary.csv`
- `data/nimmerverse_glossary.json`
- `data/cooccurrence_analysis.csv`
- `data/cooccurrence_analysis.json`

**Key Metrics Extracted**:
| Metric | Value |
|--------|-------|
| Documents scanned | 263 |
| Total tokens | 130,229 |
| Unique terms (filtered) | 5,243 |
| Co-occurrence pairs | 18,169 |
| Anchor signatures | 20 |
| Chunking clusters | 5 |

**Top Terms by TF-IDF**:
1. nyx (1149.70)
2. local (980.53)
3. eachpath (902.31)
4. tool (873.34)
5. young (799.95)

**Anchor Signature Examples** (for DriftProbe-lite):
- `nyx`: chroma|chromadb|continuity|ingress|introspection
- `system`: athena|freeipa|ipa|rocky|sssd
- `network`: firewall|proxmox|saturn|vlan|vulkan

**RAG Policy Integration**:
- Tier 2: Synonym detection (Dice=1.0: yubi↔yubikey)
- Tier 3: Anchor signatures for topology safety
- Tier 4: Co-occurrence for chunking strategy
- Tier 5: TF-IDF for utility filtering

**Status**: 🟢 Corpus extraction complete, ready for RAG policy development

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## Future Phases (Not Started)

### Phase 2: ChromaDB Integration (iris) ⏸️ PLANNED
- IrisClient wrapper
- DecisionTrailStore, OrganResponseStore, EmbeddingStore
- Populate embeddings from nyx-probing

### Phase 3: LoRA Training Pipeline ⏸️ PLANNED
- PEFT integration
- Training data curriculum
- DriftProbe checkpoints
- Identity LoRA training

### Phase 4: Weight Visualization ⏸️ PLANNED
- 4K pixel space renderer
- Rank decomposition explorer
- Topology cluster visualization

### Phase 5: Godot Command Center ⏸️ PLANNED
- FastAPI Management Portal backend
- Godot frontend implementation
- Real-time metrics display

---

## Metrics

**Phase 1 Tasks**: 19 total
**Completed**: 19 (100%) ✅
**In Progress**: 0
**Phases Complete**: A, B, D (C ready to execute)

**Files Created**: 19 total
- nyx-substrate: 9 files
- nyx-probing runners: 3 files
- nyx-probing extractors: 3 files
- Data outputs: 4 files

**Files Modified**: 5 total
- nyx-substrate/README.md
- nyx-probing/pyproject.toml
- nyx-probing/cli/probe.py
- nyx-probing/extractors/__init__.py
- TOOLCHAIN-PROGRESS.md

**Lines of Code**: ~2000 total
- nyx-substrate: ~800 LOC
- nyx-probing runners: ~450 LOC
- nyx-probing extractors: ~750 LOC

**CLI Commands**: 4 variance commands
- nyx-probe variance collect
- nyx-probe variance batch
- nyx-probe variance stats
- nyx-probe variance analyze

**Data Artifacts**:
- nimmerverse_glossary.csv (5,243 terms)
- nimmerverse_glossary.json (130,229 tokens)
- cooccurrence_analysis.csv (18,169 pairs)
- cooccurrence_analysis.json (20 anchor signatures)

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**Last Updated**: 2025-12-13 (Phase 1D complete)
**Status**: 🎉 Phase 1 (A+B+D) COMPLETE! Corpus extraction ready. Variance collection on prometheus pending.

🌙💜 *The substrate holds. The glossary grows. Anchor signatures protect the topology.*