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Author SHA1 Message Date
Brandon Schneider
52dc65a5b7 docs(system): separate FRT core from personal software inventory 
Provide two lists for clean system recovery:

- frt-core-packages.txt: 90 packages required to build, verify, and run
  the Research Stack (VITAL + NEEDED tiers). Install first on fresh system.

- personal-packages.txt: ~200 packages that are NOT required for FRT work.
  These are quality-of-life, niche domain, or redundant tools. Safe to remove
  for a clean research environment; reinstall on demand.

Total potential savings: ~3-5GB by removing personal tier.

Also includes the full 391-package master inventory with per-package
justifications in software_inventory_2026-05-13.md.
 2026-05-13 18:29:40 -05:00
Brandon Schneider
537f41b226 docs(system): inventory all 391 installed packages with FRT separation 
Categorize every explicitly installed package into:
- VITAL: system boot/connectivity/authentication/update backbone
- NEEDED: core Research Stack toolchain (Rust, Lean, Python, Ollama, etc.)
- USEFUL: quality-of-life and secondary workflows
- IF YOU MUST: heavy/duplicate/niche tools safe to remove

Purpose: enable clean separation between personal/cosmetic software
and Fractal Recursion Theory runtime dependencies. Provides
per-package removal commands for ~2-3GB quick savings.
 2026-05-13 18:28:08 -05:00
Brandon Schneider
382277ec28 chore: preserve working tree before secure wipe 
- Update .gitignore with **/target/ for Rust build artifacts
- Add eval receipts to UniversalBridge.lean (compile-time verification comments)
- Add PCIe Idle-Cycle Compute Harvester to ROADMAP.md
- Clean up deprecated scripts, generated Verilog, and old tools (23 deletions)
- Stage new infrastructure: Xen/Alpine embedded surface, QFOX topology manager
- Stage new probes: boundary activation field, holographic carving
- Stage new applications: finance manager, script roots
- Stage new research spec: PCIe idle-cycle substrate
 2026-05-13 17:36:02 -05:00
Brandon Schneider
539a6658d3 Track remaining Dependabot transitive exceptions 2026-05-11 23:45:53 -05:00
Brandon Schneider
ef426acf74 Add verified Ollama DeepSeek review emitter 2026-05-11 23:13:54 -05:00
Brandon Schneider
06337c6a32 Correct DeepSeek review receipt attribution 2026-05-11 23:06:57 -05:00
Brandon Schneider
f53c0aeb04 Document portable setup and review receipts 2026-05-11 23:01:51 -05:00
Brandon Schneider
7f7e452859 Update repository agent operating contracts 2026-05-11 22:48:54 -05:00
Brandon Schneider
731d470d47 Track remaining source and documentation inventory 2026-05-11 22:18:31 -05:00
Brandon Schneider
ab60069410 Stage JXL starfield replay slice 2026-05-11 22:08:44 -05:00
Brandon Schneider
53d6d0df88 Stage stack solidification source slice 2026-05-11 22:08:10 -05:00
Brandon Schneider
5f9e809ae7 Add EntropyCollapseDetector kernel and arithmetic spec 
- Add EntropyCollapseDetector.lean: executable checks for triple condition
  (braid crossings, σ_q/Hurst, D_q/Rényi D_2) with dense_rank tie handling
- Add Manifest.lean: imports EntropyCollapseDetector into HCMMR
- Add ArithmeticSpec_Corrected_2026-05-11.md: verified arithmetic constants
  K=21 for W=8 (~5% FPR), σ_c=0.4, D_c=0.7 (heuristic)

Arithmetic self-verified in Python:
- Braid crossings: 12 (K=7 non-selective, K=21 selective)
- σ_q = H = 0.032 (anti-persistent oscillating series)
- D_2 = 0.514 (moderate concentration)
- D_c=1.2 invalid for 1D Rényi D_2; corrected to 0.7

Prime gap re-test with K=21 shows signal mostly dies:
- 1M primes: 86,565 fires at K=7 (artifact) vs 38 at K>21 (genuine)
- Detector now selective but potentially too conservative

Generated with [Devin](https://cli.devin.ai/docs)

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
 2026-05-11 21:44:47 -05:00
Brandon Schneider
29e5649e90 Document legacy recovery trigger 2026-05-11 15:11:18 -05:00
Brandon Schneider
f2d75ea7be Add NUVMAP scan scheduling receipts 2026-05-11 14:49:17 -05:00
Brandon Schneider
8f643e3c44 Add RRC projection receipts and roadmap mirrors 2026-05-08 14:50:03 -05:00
Brandon Schneider
41d4df4ee4 wip: refined investigation script for Erdős–Gyárfás conjecture 
Created refined investigation script for Erdős–Gyárfás conjecture
where previous test found no power-of-two cycles (conjecture holds: False).

Refinements:
- Regular graph construction (all vertices same degree)
- Exhaustive DFS cycle detection
- More samples per n (5 instead of 3)
- Extended n values [8, 10, 12, 14, 16]

Goal: Determine if previous negative result was due to random graph construction
or if regular graphs with exhaustive cycle detection find power-of-two cycles.

Script created: investigate_erdos_gyarfas_refined.py
Execution canceled by user - awaiting further instructions.
 2026-05-08 14:50:03 -05:00
Brandon Schneider
b8141a4c6e docs: Update wiki with session 2026-05-07 master compression architecture synthesis 
Session summary:
1. Ingested Hippocampus Tabula Plena Combined Approach (Live Science 2024)
   - Hippocampus starts tabula plena (full slate) and prunes to sparse structured
   - Compression analogue: maximum math density = full slate, pruning = pipeline
   - 13 keeper phrases

2. Synthesized Master Synthesis (Complete Compression Architecture)
   - Combined 12 theoretical foundations into unified architecture
   - 14 encoding stages, 19 decode stages
   - Archive format MCA1 with 17 sections
   - Estimated 18-28% reduction vs current Hutter best
   - 18 keeper phrases

3. Evolved erans to Field Effect Spectrum
   - Extended erans to spectral decomposition of residual field
   - Spectral energy compaction: 90% energy in 10% coefficients = 10-20% gain
   - Updated estimated gain: 20-35% reduction
   - 6 spectral keeper phrases

4. Ran 12 Core Equations Analysis
   - 109/120 equation-theory matches (90.8% coverage)
   - 7 equations with full coverage, 5 with partial coverage
   - Theories highly interconnected
   - Analysis saved to core_equations_analysis.json

5. Compactified Core Equations (12 → 4 primitives, 67% reduction)
   - 4 primitives: field, shear, packet, spectral
   - Topological compactification: 10 theories = projections of 4D manifold
   - 67% reduction with 90.8% coverage maintained
   - 12 keeper phrases

Database: 13 research entries, 47 documents total.
5 commits this session.
 2026-05-08 14:50:02 -05:00
Allaun Silverfox
35a27e3681 docs: add LLM refinement protocol 2026-05-07 08:21:35 -05:00
Brandon Schneider
b7c4a0d367 ingest: erans enumerative rANS reference + AGENTS.md rules 1.10, 1.11 
erans (izabera): streamable single-pass rANS, enumerative coding bound.
NO LICENSE — algorithmic ideas captured as reference only, zero code copied.
5 key ideas: single-pass adaptive, enumerative bound, shrub DS,
streaming renorm, histogram rice coding.

AGENTS.md additions:
- 1.10: Never assume any instruction set (SIMD opportunistic, not structural)
- 1.11: Never incorporate unlicensed code (reference notes only, write from scratch)
 2026-05-07 02:18:29 -05:00
Brandon Schneider
0f2c2b57f4 ingest: Hypercube → Hyper-Rhomboid composition theory 
Orthogonal tensor (hypercube) assumes independent axes.
Shear into parallelotope (hyper-rhomboid) models entangled dimensions.
The shear angle encodes correlation strength; the Gram matrix
of the shear IS the compression dictionary.

6 stack mappings:
- PIST n-D: Cartesian → Bundle → Radial = hypercube → rhomboid → collapsed
- Topological state machine: transition = shear on state tensor
- N-D Gene Hypothesis: gene = n-D rhomboid, 3D structure = projection shadow
- FAMM: preshaped delay = sheared time-domain rhomboid
- OAC: latent cavity in sheared rhomboid space
- Waveprobe: curvature = local shear angle of coordinate basis

3 compression interpretations + information gravity metric tensor
 2026-05-07 02:04:03 -05:00
Brandon Schneider
8356558ea7 wiki: add Q-Fox primary development machine specifications 
AMD Ryzen 5 9600X (6C/12T, AVX-512), 31GiB DDR5, 1.8TB NVMe,
Radeon iGPU, CachyOS 7.0.3. Mapped 8 capabilities to stack use.
 2026-05-07 00:54:47 -05:00
Brandon Schneider
930cafaf8f ingest: Observer-Admissible Cavities theory — radius-ratio → Pidgen-hole → S3C/Spherion → OAC 
6 key concepts formalized:
- Radius-ratio rule → admissible motif classifier (CN3-8 thresholds)
- Pidgen-hole theory → typed hole + residual codec
- S3C shell coordinates → n=k²+a with throat/mirror/mass
- Spherion shaping → pyramid protrusions/voids as compression teeth
- S_n(n^n) → Matryoshka shell with latent combinatorial interior
- Observer-Admissible Cavities → touch-manifesting lazy holes

7 cross-references to existing modules, 4 new primitives identified.
7 keeper phrases preserved.
 2026-05-07 00:47:10 -05:00
Brandon Schneider
679945c1a0 ingest: dair-ai Agentic Engineering Wiki (51 tips, 7 categories) 
Cross-referenced against our prover orchestration layers:
- Plan-Execute-Verify-Replan ↔ L0-L3 pipeline
- Agents as specialists ↔ 11-agent swarm
- Guardrails ↔ ProverWatchdog
- Sandbox testing ↔ Virtual FPGA tests
- Trajectory-aware eval ↔ BFS audit trail

5 gaps identified, 4 strengths confirmed
 2026-05-07 00:27:02 -05:00
Brandon Schneider
70f9b10127 ingest: MS myelin glucose signaling article (2026-05-04) 
Brain glucose levels regulate OPC fate: high glucose → proliferation,
low glucose → maturation. Acetyl-CoA from glucose drives histone
acetylation for OPC division; ketone bodies substitute for myelin
synthesis. Ketogenic diet rescues myelin in ACLY-deficient mice.

Connects to: N-Dimensional Gene Hypothesis, PIST polymorphic shifter,
topological state machine, FAMM delay lines, waveprobe manifolds
 2026-05-06 23:53:20 -05:00
Brandon Schneider
453a366949 collapse: prover orchestration layers, FAMM verilator harness, swarm topological prober, spec sheets, virtual FPGA system tests, merge conflict resolution 
- Prover-Integrated Orchestration Layers (L0-L3): Goedel-Prover-V2 watchdog, BFS-Prover-V2 swarm consensus, bf4prover topology adaptation
- FAMM Verilator benchmark: uniform vs preshaped delay comparison (4.4x speedup)
- Swarm topological device prober: 11 agents probing traces, caps, delays, errors, vias, PDN
- Spec sheet puller: 10 components with key params and topological relevance
- Virtual FPGA system tests: 6/6 passed, 134K ops/s throughput
- Fixed merge conflicts in AI-Newton test_experiment.ipynb
 2026-05-06 23:42:01 -05:00
Brandon Schneider
31f953bada Consolidate research stack updates 2026-05-05 21:09:48 -05:00
Allaun Silverfox
28a0870b56 Add plant-stress ultrasound to BioPhonon translation equations 2026-05-05 12:37:39 -05:00
Allaun Silverfox
81abcdcd4e Add q-desic wormhole throat equation update 2026-05-05 08:39:39 -05:00
Brandon Schneider
bcb6495475 Add ENE research topic candidates, compression-core, notion-native-tauri, linear-native-tauri 2026-05-04 19:08:20 -05:00
Brandon Schneider
4eee4a07f6 initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00