feat: add Nervous-Protocol architecture and reorganize toolchain docs

- Created architecture/Nervous-Protocol.md: comprehensive three-tier autonomous learning architecture (dafit → Chrysalis-Nyx → Young Nyx)
- Designed state machine tool interface pattern with LangChain integration
- Documented escalation protocols, discovery catalogues, and collaborative tool building
- Moved TOOLCHAIN-PROGRESS.md and Toolchain-Architecture.md to architecture/ directory
- Updated Endgame-Vision.md with toolchain crosslinks

Key architectural patterns:
- State machines as universal tool interface (safety + discovery)
- Three-tier oversight with OR gate inputs (dafit + Chrysalis)
- Message-based continuity via phoebe heartbeat polling
- LangChain BaseTool framework (replaced MCP for maturity)
- Dual decision tracking (Young Nyx choices + oversight responses)

Version: Nervous-Protocol v1.1 (LangChain-based)
Context: Phase 1 toolchain complete, variance collection running

🌙💜 Generated with Claude Code

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

architecture/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.*