docs: add Phase 1 toolchain architecture and progress tracking

Document the modular toolchain architecture design and track
implementation progress for Phase 1 (nyx-substrate foundation
and variance collection automation).

New Files:
- Toolchain-Architecture.md: Complete Phase 1 design document
  - Modular architecture vision (5 phases)
  - Repository structure and dependency graph
  - Phase 1 deliverables (nyx-substrate + nyx-probing)
  - Success criteria and testing plan
  - Future phases: ChromaDB, LoRA training, visualization, Godot

- TOOLCHAIN-PROGRESS.md: Implementation progress tracker
  - Phase 1A: nyx-substrate foundation (✅ COMPLETE)
  - Phase 1B: nyx-probing integration (✅ COMPLETE)
  - Phase 1C: Baseline variance collection (⏸️ READY)
  - Metrics: 11/11 tasks (100%), 12 files, ~1250 LOC
  - Status updates and completion tracking

Architecture:
  nyx-probing ────────┐
  nyx-training ───────┼──> nyx-substrate ──> phoebe (PostgreSQL)
  nyx-visualization ──┤                   └─> iris (ChromaDB)
  management-portal ──┘

Philosophy: Modular tools, clean interfaces, data-first design

Status: Phase 1 complete, ready for baseline collection on prometheus

🌙💜 Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

TOOLCHAIN-PROGRESS.md

@@ -0,0 +1,125 @@
+# Toolchain Implementation Progress
+
+**Plan**: See [Toolchain-Architecture.md](Toolchain-Architecture.md)
+**Started**: 2025-12-07
+**Current Phase**: Phase 1 - Foundation + Variance Collection
+
+---
+
+## 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
+
+---
+
+## 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
+
+---
+
+## 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
+
+---
+
+## 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 (A+B) Tasks**: 11 total
+**Completed**: 11 (100%) ✅
+**In Progress**: 0
+**Remaining**: 0
+
+**Files Created**: 12 total
+- nyx-substrate: 9 files
+- nyx-probing: 3 files
+
+**Files Modified**: 4 total
+- nyx-substrate/README.md
+- nyx-probing/pyproject.toml
+- nyx-probing/cli/probe.py
+- TOOLCHAIN-PROGRESS.md
+
+**Lines of Code**: ~1250 total
+- nyx-substrate: ~800 LOC
+- nyx-probing: ~450 LOC
+
+**CLI Commands**: 4 new commands
+- nyx-probe variance collect
+- nyx-probe variance batch
+- nyx-probe variance stats
+- nyx-probe variance analyze
+
+---
+
+**Last Updated**: 2025-12-07 17:00 CET
+**Status**: 🎉 Phase 1 (A+B) COMPLETE! Ready for baseline collection on prometheus.
+
+🌙💜 *The substrate holds. Progress persists. The toolchain grows.*