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Author SHA1 Message Date
devin-ai-integration[bot]
fcfaef17f3 fix(scripts): replace bare except clauses with specific exception types (#77) 
Replace 30+ bare `except:` and `except: pass` patterns across 17 files
with specific exception types (OSError, ValueError, etc.) and add
logging so errors are no longer silently swallowed.

Changes by category:

Infrastructure (surface/main.py):
- GPU/process probes now catch FileNotFoundError | SubprocessError

Application scripts:
- API fetchers (finalize_database, final_push, bulk_10x) now catch
  URLError | JSONDecodeError | KeyError | OSError and print to stderr
- Hardware probes (unified_hardware_surface, swarm_transport_layer)
  catch OSError | ValueError for /proc/meminfo reads
- Backend availability checks (prover_backend_interface, hot_swap_manager)
  catch requests.RequestException and log at debug/warning
- Code inspector (swarm_system_inspector) catches OSError | UnicodeDecodeError
  for file reads
- Model fallback (map_all_equations) now logs the intermediate error
- Minor: gpu_pist_compress → RuntimeError | ZeroDivisionError,
  mathlib_to_parquet → ValueError, moe_utils → OSError,
  quandela_remote → OSError | IndexError, topology inline scripts
  → ImportError, consolidate_language_databases → UnicodeDecodeError

All touched files pass py_compile.

Co-authored-by: Devin AI <158243242+devin-ai-integration[bot]@users.noreply.github.com>
Co-authored-by: Allaun Silverfox <bigdataiscoming+9i37y6j2@protonmail.com>
 2026-06-14 19:30:28 -05:00
Brandon Schneider
ef7b0849d5 fix(adversarial-review): resolve 35 critical coding bugs across 8 subsystems 
Security & correctness fixes from full adversarial review:

Lean (7 fixes):
- FixedPoint.lean: guard false theorem with n > 0 precondition
- QFactor.lean: remove double-scaling error in energy decrease
- AVMIsa/Step.lean: implement addSatQ16/subSatQ16 primitives
- BraidEigensolid.lean: fix crossStep second output argument swap
- SSMS.lean: complete ACI preservation proof (with rounding caveat)
- HouseholderQR.lean: add n > 0 precondition to spectral theorem

Verilog (7 fixes):
- q16_lut_core.v: fix multiply shift (16 → 32 bits)
- q16_lut_top.v: fix valid bit (0 → 1)
- cff_accelerator.v: fix SHA-256 padding (len < 448 check)
- research_stack_top.v: fix trigger aliasing (unique counters)
- Blitter6502OISC_small.v: fix address width (15 → 16 bits)
- spatial_hash_bram.v: add OOB write guard
- tmr_oepi_safety_fsm.v: fix double-increment race

WGSL (6 fixes):
- shaders.wgsl: atomicAdd for concurrent writes
- frustration_qubo.wgsl: double-buffer + CAS loop
- braid_fft.wgsl: workgroupBarrier synchronization
- burgers_scar_filter.wgsl: atomic E_bins array

Rust (9 fixes):
- thermodynamic.rs: Arc::from_raw → Arc::clone (double-free)
- thermodynamic.rs: Box::into_raw → Box (leak)
- tools/src/lib.rs: shell injection → shlex.quote
- ene-node/src/lib.rs: LRU caps, constant-time HMAC, peer caps

Python (6 fixes):
- similarity/__init__.py: pickle.load → RestrictedUnpickler
- AI-Feynman: torch.load → weights_only=True (14 calls)
- fetch_arxiv.py, fetch_s2.py: eval → ast.literal_eval
- topology.py: os.system → shutil.copy2
- SSH pipe: os.system → base64 pipe

Build: lake build 3572 jobs, 0 errors
 2026-05-31 23:38:03 -05:00
Brandon Schneider
4475bff0be feat(infra): SPIR-V packet generator and WGSL scar filter shader 
Add spirv_packet_generator.py: reads SPIR-V assembly, applies copy-if
optimization (OpPhi→OpSelect transform), and emits JSON packet descriptors
with the 5 OpPhi-derived fields (type_id, cond_id, true_val_id,
false_val_id, result_id) that fully specify the packet layout.

Add burgers_scar_filter.wgsl: 291-line WGSL compute shader for spectral
scar filtering in 2D Burgers RG solver. Uses three copy-if patterns:
  1. scar_pressure > threshold → apply hyperviscosity damping
  2. |kx| > k_cut || |ky| > k_cut → zero (dealiasing)
  3. factor < 0.999 → multiply velocity components

Also fix spirv_copy_if_optimizer.py: OpSelect now uses phi_instr.args[0]
(type operand) as its type, instead of compute_instr.result_id. This
produces structurally correct SPIR-V where the result type matches the
OpSelect opcode layout.

Build: 3313 jobs, 0 errors (lake build)
Tools: glslang, spirv-as, spirv-dis (native); tint from nixpkgs for WGSL
 2026-05-30 16:40:58 -05:00
Brandon Schneider
fb58e2c156 fix: reed_solomon_vcn decode_rs return type (tuple → bytes extraction) 2026-05-28 17:35:55 -05:00
Brandon Schneider
e0df130453 feat: 12 math enhancements — Q16 LUT, braid VCN encoder, FPGA Verilog, FFT, crypto 
Pipeline:
- q16_lut_vcn.py: Q16_16 LUT generation + VCN frame encoding (8 ops)
- braid_vcn_encoder.py: Delta+RLE → RS ECC → ChaCha20 → VCN → MKV
- braid_search.py: Sidon set slots, soliton search, QUBO optimization
- test_braid_pipeline.py: 67 tests covering full round-trip

WebGPU/Scripts:
- braid_fft.wgsl: Cooley-Tukey radix-2 FFT on phase vectors
- reed_solomon_vcn.py: Reed-Solomon ECC for VCN frame data
- chacha20_braid.py: ChaCha20 encryption + key derivation
- polynomial_commitment.py: KZG scheme for receipt verification

Lean:
- BraidBitwiseODE.lean: XOR crossing, O(1) integration, 2 proved theorems

FPGA (Tang Nano 9K):
- q16_lut_core.v: 8-op arithmetic, 2-stage pipeline, BRAM reciprocal
- braid_crossing_core.v: 4-stage crossing residual, 7 Q16 instances
- Testbenches with edge cases + VCD dumps
 2026-05-28 14:49:26 -05:00
Brandon Schneider
eafbee22b7 fix(arch): enforce Lean-first hierarchy across project — remove all secondary-Lean language 
Project-wide sweep to find and fix every place Lean was treated as secondary,
optional, or subordinate to Python/Rust. The invariant: Lean is the source of
truth. Python and Rust are extraction targets only; they contain no logic, no
invariant checks, no decisions.

Changes:

1-Distributed-Systems/ene/src/lib.rs
  - CRITICAL: Remove 'Rust is the canonical implementation language for
    operational components' — replace with correct extraction-target framing

1-Distributed-Systems/agents/claw/README.md
  - Remove 'canonical implementation lives in rust/' and 'source of truth is
    ultraworkers/claw-code' blanket claims — scope to CLI binary only;
    add Research Stack domain-logic note (Lean is source of truth per AGENTS.md)
  - 'canonical Rust workspace' → 'Rust workspace (I/O extraction target)'

1-Distributed-Systems/agents/claw/src/Tool.py
  - 'Python-first porting summary' → 'Lean-to-Python extraction summary'

1-Distributed-Systems/agents/claw/src/projectOnboardingState.py
  - python_first: bool = True → lean_first: bool = True (Lean always leads)

6-Documentation/docs/specs/ENE_MEMORY_ATLAS_SPEC.md
  - CRITICAL: 'Python first (reference) ... Lean-formal next' → correct order:
    Lean specification first, Python extraction shim, Verilog hardware extraction

6-Documentation/docs/recovered/geocognition_equation_types_map.mmd
  - 'Lean owns logic; Rust owns boundary' → 'Lean owns all logic and decisions;
    Rust is boundary shim only'

6-Documentation/docs/semantics/HYPER_DIMENSIONAL_PHYSICS_INTRO.md
  - 'Python implementation ... Lean formalization' → 'Lean specification (source
    of truth) ... Python extraction shim'

6-Documentation/docs/geometry/GEOMETRY_TAXONOMY_FOR_NLOCAL_ADAPTATION.md
  - 'reference specification for the Python implementation' → 'source of truth;
    Python is an extraction shim against this spec'

6-Documentation/docs/protocols/TM_MCP_SPECIFICATION.md
  - 'Python reference implementation' → 'Python extraction shim' (×2)

5-Applications/scripts/snn/README.md
  - 'deterministic Python reference' → 'Python extraction shim / golden-vector
    harness'; add TODO(lean-port) note; RTL must match 'Python shim (pending
    Lean golden vector)' not 'Python reference'

6-Documentation/docs/METAPROBE_APPROACH.md
  - 'DeltaGCLCompression.lean — Lean implementation / scripts/delta_gcl_encoder.py
    — Python reference implementation' → Lean is source of truth / Python is
    extraction shim

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

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
 2026-05-26 22:40:03 -05:00
Allaun Silverfox
f5d683242e chore(pending): quarantine python Notion+Linear MCP server (Lean-first unification) 2026-05-26 17:59:19 -05:00
Allaun Silverfox
ae967c36fd chore(pending): quarantine python MCP server (Lean-first unification) 2026-05-26 17:56:25 -05:00
Allaun Silverfox
95806f7779 cleanup(ene): load node list from nodes.yaml instead of hardcoded hostnames 2026-05-26 17:16:02 -05:00
Allaun Silverfox
510ff80d9f cleanup(ene): use nodes.yaml inventory instead of hardcoded host resource map 2026-05-26 17:15:50 -05:00
Allaun Silverfox
f763372d03 cleanup(ene): make obsidian shim provenance configurable and schema-complete 2026-05-26 16:54:12 -05:00
Allaun Silverfox
29f93f9dfd cleanup(ene): make provenance node/tailscale configurable via env vars and CLI arg 2026-05-26 16:42:03 -05:00
Allaun Silverfox
791e75368a cleanup(ene): make provenance node/tailscale configurable via env vars and CLI arg 2026-05-26 16:40:35 -05:00
Brandon Schneider
06f780560f archive: remove experimental tools-scripts, scripts, and shim probes 
- Move 38 experimental tools-scripts directories to archive/ (famm, ptos, crypto, market, geoweird, cognitive, carrier, tsm, semi_jack, hachimoji, chemistry, bt20, optimization, gpgpu, hardware, infrastructure, defense, security, connectome, encoding, formula_optimization, manifold, metafoam, model, verifier, substrate, audio, ingestion, literature, domain, crossbreed, external, physics, pipeline, design, classification, database, dashboard, monitor, braid, compression, waveprobe, data, ingested, demo, publish, blockchain, regret, simulation, build)
- Move 386 one-shot scripts to archive/ (ask_swarm*, execute*, swarm_* probes, test_* scripts, computational controllers, topology experiments, shell scripts)
- Move 2124 experimental shim probe files to archive/ (research probes, prior*, metaprobe*, erdos*, blockchain*, hutter*, tang9k*, stellar_gas*, enwiki*, quandela* probes, experimental shell scripts, ffmpeg-plugins, erdos_surface_orchestrator, codebase-memory, receipts, data files, MCP bus probes)
 2026-05-25 18:14:31 -05:00
Brandon Schneider
de631bf1b7 WIP: accumulated changes 2026-05-25 16:24:21 -05:00
Brandon Schneider
9ba5862704 feat(ene): replace legacy Python mesh with Rust crates 2026-05-20 18:46:18 -05:00
Brandon Schneider
ba1e4cf191 feat: add RDS probe tool, credential server, and Notion/Linear ingestion pipeline 
New infrastructure components:
- rds_probe: Rust database inspection tool with IAM auth
- credential_server.py: REST credential provider server
- credential_provider.py: credential resolution chain
- ene_rds_fractal_fold.py / ene_rds_wiki_layer.py: RDS-backed ENE layers
- import_dumps_to_rds.py / export_linear_from_rds.py: ingestion pipeline
- recover_credential_server.sh: deployment script (sanitized)

Sanitize hardcoded secrets across codebase:
- Strip API keys from recover_credential_server.sh → env var lookups
- Replace hardcoded Wolfram appid (HYJE3R3R63) → env var in 5 scripts
- Strip fallback key values from config/index.js
- Add .claude/ and optimized_basis_v3.bin to .gitignore

Ingested 2,685 records into RDS: 2,421 Linear issues + 264 wiki pages
 2026-05-18 00:31:44 -05:00
Brandon Schneider
9b1721eea6 integrate infrastructure config, axiom cleanup, and documentation updates 
- cupfox-config.nix: add Open WebUI container with chat.researchstack.info proxy,
  gather-metrics service/timer, rclone, and tmpfiles for persistent storage
- Lean semantics: reduce axiom count from 109 to 18 across 10 files;
  FixedPoint now 0 axioms, 0 sorries with 12 theorems
- Documentation: update AGENTS.md with current axiom/sorry counts and
  FixedPoint status; refine bind signature
- Add topology scripts, CGA/FAMM/GeneticOptimizer/MMRFAMM Lean modules,
  devcontainer config, MEMORY.md, and Modelfile
 2026-05-17 12:03:19 -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
bacd452463 Refactor provenance sources for open witness backends 2026-05-12 05:57:04 -05:00
Brandon Schneider
731d470d47 Track remaining source and documentation inventory 2026-05-11 22:18:31 -05:00
Brandon Schneider
ff8fa74092 Point ENE scripts at shared data 2026-05-11 22:10:55 -05:00
Brandon Schneider
f9de097951 Ignore generated run outputs and scrub API key scripts 2026-05-11 22:06:39 -05:00
Brandon Schneider
f2d75ea7be Add NUVMAP scan scheduling receipts 2026-05-11 14:49:17 -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
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
Brandon Schneider
4eee4a07f6 initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00