allaun/Research-Stack
1
0
Fork 0
mirror of https://github.com/allaunthefox/Research-Stack.git synced 2026-07-31 03:05:21 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions
444 commits 18 branches 0 tags 425 MiB
Commit graph

60 commits

Author SHA1 Message Date
Brandon Schneider
3044f36df7 docs(agents): project-wide AGENTS.md audit — cross-refs, baseline, contracts 
Actions taken from 5-agent audit sweep (audit date 2026-05-26):

AGENTS.md / docs sync:
- root AGENTS.md: add scripts/qc-flag and lean_expert_agent to Nested Contracts
- All 6 nested AGENTS.md files: append Cross-References section pointing to
  root for Post-Interaction Workflow, Programming Choice Flow, Do Not Sweep,
  Git Remote Hygiene (Lean, Infra, text-to-cad, docs, qc-flag, lean_expert_agent)
- 6-Documentation/docs/AGENTS.md: cross-ref also lists AVMIsa.Emit sole output
  boundary and Compiler surface blessing

Lean build baseline:
- 0-Core-Formalism/lean/Semantics/AGENTS.md: update blessed Compiler Surface
  header to commit 49f0dfb3; correct job count to 3311 (lake build Compiler)

ARCHITECTURE.md:
- §7 repo table: add RRC.Emit, AVMIsa.Emit, RRC.Corpus278 to Lean/Semantics entry
- New §7.1 Compiler Surface: documents 3-root pipeline and sole output boundary
- §4 Data Flow: annotate output with AVMIsa.Emit sole-boundary note

TODO_MAP.md:
- Phase A6: add 3 new Lean deliverables (Corpus278, RRC.Emit, AVMIsa.Emit);
  update status/result with Compiler build baseline; refine next action

Build: Compiler 3311 jobs, 0 errors (no Lean changes).

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

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
 2026-05-26 22:34:46 -05:00
Allaun Silverfox
5579ffa046 chore(pending): quarantine python Notion+Linear MCP server (Lean-first unification) 2026-05-26 17:59:19 -05:00
Allaun Silverfox
f9778f3fb3 chore(pending): quarantine python MCP server (Lean-first unification) 2026-05-26 17:56:25 -05:00
Allaun Silverfox
ceb6a91d97 cleanup(ene): load node list from nodes.yaml instead of hardcoded hostnames 2026-05-26 17:16:02 -05:00
Allaun Silverfox
a5a10723ab cleanup(ene): use nodes.yaml inventory instead of hardcoded host resource map 2026-05-26 17:15:50 -05:00
Allaun Silverfox
87e5eb33a7 cleanup(ene): make obsidian shim provenance configurable and schema-complete 2026-05-26 16:54:12 -05:00
Allaun Silverfox
e36cff917b cleanup(ene): make provenance node/tailscale configurable via env vars and CLI arg 2026-05-26 16:42:03 -05:00
Allaun Silverfox
1181849cea cleanup(ene): make provenance node/tailscale configurable via env vars and CLI arg 2026-05-26 16:40:35 -05:00
Brandon Schneider
8f3d83745b Patch NoDupe qs vulnerability 2026-05-25 20:52:25 -05:00
Brandon Schneider
d4180194d7 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
073a70eb86 WIP: accumulated changes 2026-05-25 16:24:21 -05:00
dependabot[bot]
b61f14f6bc Bump dashmap 
Bumps the parquet-cargo-minor-patch group in /5-Applications/parquet_compressor with 1 update: [dashmap](https://github.com/xacrimon/dashmap).

Updates `dashmap` from 6.1.0 to 6.2.1
- [Release notes](https://github.com/xacrimon/dashmap/releases)
- [Commits](https://github.com/xacrimon/dashmap/compare/v6.1.0...v6.2.1)

---
updated-dependencies:
- dependency-name: dashmap
  dependency-version: 6.2.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: parquet-cargo-minor-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
(cherry picked from commit 6a5703df97d971e85fbb1fdf49b54617bda6100f)
 2026-05-20 23:03:27 -05:00
dependabot[bot]
ea7d3b94c3 Bump itertools in /5-Applications/parquet_compressor 
Bumps [itertools](https://github.com/rust-itertools/itertools) from 0.12.1 to 0.14.0.
- [Changelog](https://github.com/rust-itertools/itertools/blob/master/CHANGELOG.md)
- [Commits](https://github.com/rust-itertools/itertools/compare/v0.12.1...v0.14.0)

---
updated-dependencies:
- dependency-name: itertools
  dependency-version: 0.14.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
(cherry picked from commit b5d6ea5e7e9b4be35cf17b734bf9e21ae570a032)
 2026-05-20 23:03:27 -05:00
dependabot[bot]
fea92c6c9a Bump indicatif in /5-Applications/parquet_compressor 
Bumps [indicatif](https://github.com/console-rs/indicatif) from 0.17.11 to 0.18.4.
- [Release notes](https://github.com/console-rs/indicatif/releases)
- [Commits](https://github.com/console-rs/indicatif/compare/0.17.11...0.18.4)

---
updated-dependencies:
- dependency-name: indicatif
  dependency-version: 0.18.4
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
(cherry picked from commit 1b51e05db59c69a3d613e7a41eb76cbffc216400)
 2026-05-20 23:03:27 -05:00
dependabot[bot]
47964b85f2 Bump the notion-tauri-cargo-minor-patch group 
Bumps the notion-tauri-cargo-minor-patch group in /5-Applications/notion-native-tauri with 2 updates: [tauri](https://github.com/tauri-apps/tauri) and [tauri-build](https://github.com/tauri-apps/tauri).

Updates `tauri` from 2.11.1 to 2.11.2
- [Release notes](https://github.com/tauri-apps/tauri/releases)
- [Commits](https://github.com/tauri-apps/tauri/compare/tauri-v2.11.1...tauri-v2.11.2)

Updates `tauri-build` from 2.6.1 to 2.6.2
- [Release notes](https://github.com/tauri-apps/tauri/releases)
- [Commits](https://github.com/tauri-apps/tauri/compare/tauri-build-v2.6.1...tauri-build-v2.6.2)

---
updated-dependencies:
- dependency-name: tauri
  dependency-version: 2.11.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: notion-tauri-cargo-minor-patch
- dependency-name: tauri-build
  dependency-version: 2.6.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: notion-tauri-cargo-minor-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
(cherry picked from commit ca226eb8cbad60de00487216277d0257c642d700)
 2026-05-20 23:03:27 -05:00
dependabot[bot]
fcf2474fd1 Bump the linear-tauri-cargo-minor-patch group 
Bumps the linear-tauri-cargo-minor-patch group in /5-Applications/linear-native-tauri with 2 updates: [tauri](https://github.com/tauri-apps/tauri) and [tauri-build](https://github.com/tauri-apps/tauri).

Updates `tauri` from 2.11.1 to 2.11.2
- [Release notes](https://github.com/tauri-apps/tauri/releases)
- [Commits](https://github.com/tauri-apps/tauri/compare/tauri-v2.11.1...tauri-v2.11.2)

Updates `tauri-build` from 2.6.1 to 2.6.2
- [Release notes](https://github.com/tauri-apps/tauri/releases)
- [Commits](https://github.com/tauri-apps/tauri/compare/tauri-build-v2.6.1...tauri-build-v2.6.2)

---
updated-dependencies:
- dependency-name: tauri
  dependency-version: 2.11.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: linear-tauri-cargo-minor-patch
- dependency-name: tauri-build
  dependency-version: 2.6.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: linear-tauri-cargo-minor-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
(cherry picked from commit 58850d0106485de31fa48e0232407f0d8ce334b1)
 2026-05-20 23:03:27 -05:00
dependabot[bot]
a442e24081 Bump the cargo group across 3 directories with 1 update 
Bumps the cargo group with 1 update in the /2-Search-Space/search/stract directory: [openssl](https://github.com/rust-openssl/rust-openssl).
Bumps the cargo group with 1 update in the /2-Search-Space/search/stract/crates/leechy-py directory: [openssl](https://github.com/rust-openssl/rust-openssl).
Bumps the cargo group with 1 update in the /5-Applications/teleport-kanban directory: [openssl](https://github.com/rust-openssl/rust-openssl).

Updates `openssl` from 0.10.79 to 0.10.80
- [Release notes](https://github.com/rust-openssl/rust-openssl/releases)
- [Commits](https://github.com/rust-openssl/rust-openssl/compare/openssl-v0.10.79...openssl-v0.10.80)

Updates `openssl` from 0.10.79 to 0.10.80
- [Release notes](https://github.com/rust-openssl/rust-openssl/releases)
- [Commits](https://github.com/rust-openssl/rust-openssl/compare/openssl-v0.10.79...openssl-v0.10.80)

Updates `openssl` from 0.10.79 to 0.10.80
- [Release notes](https://github.com/rust-openssl/rust-openssl/releases)
- [Commits](https://github.com/rust-openssl/rust-openssl/compare/openssl-v0.10.79...openssl-v0.10.80)

---
updated-dependencies:
- dependency-name: openssl
  dependency-version: 0.10.80
  dependency-type: indirect
  dependency-group: cargo
- dependency-name: openssl
  dependency-version: 0.10.80
  dependency-type: indirect
  dependency-group: cargo
- dependency-name: openssl
  dependency-version: 0.10.80
  dependency-type: indirect
  dependency-group: cargo
...

Signed-off-by: dependabot[bot] <support@github.com>
(cherry picked from commit 4163e69bafc86fd27dc4535747c75e39db822f57)
 2026-05-20 23:02:48 -05:00
Brandon Schneider
a4a5a4027c feat(ene): replace legacy Python mesh with Rust crates 2026-05-20 18:46:18 -05:00
Brandon Schneider
fd863af6fd Expand devcontainer with full Python stack, add MCP servers (Notion/AWS), strengthen Lean theorems 
- .devcontainer/Dockerfile: add PostgreSQL client libs, OpenSSL/libffi headers, gfortran/BLAS for scipy, rclone; install full Python dependency set (boto3, psycopg2-binary, fastapi, uvicorn, notion-client, httpx, pytest, numpy, scipy, etc.) in uv-managed venv; add rclone S3 gateway init script as ENTRYPOINT
- .devcontainer/devcontainer.json: switch from build to pre-built image (localhost/research
 2026-05-19 01:52:14 -05:00
Brandon Schneider
c957fac96e Add EC2 recovery backup: NixOS config, AppFlowy compose/env template, credential server bootstrap, recovery guide 
- ec2-configuration.nix: full NixOS config for aws-nixos-node-1
- docker-compose.minimal.yml: AppFlowy Cloud compose with search_path fix
- .env.example: sanitized AppFlowy env template
- nixos-setup-cred-server.sh: credential server bootstrap
- RECOVERY.md: step-by-step rebuild instructions
- .gitignore: secrets dir excluded
- credential_provider.py reverted to repo HEAD (EC2 had hardcoded AWS creds)
- racknerd_root.txt removed from working tree
 2026-05-18 10:44:23 -05:00
Brandon Schneider
c5b6a31a8b 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
Allaun Silverfox
80a3d4f202 Add Anti-FAMM/Anti-BraidStorm adversary runner 2026-05-17 15:10:31 -05:00
Brandon Schneider
5a763468c9 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
Allaun Silverfox
0c085053cf Add Plasma Chiral Drag Witness runner 2026-05-17 10:11:38 -05:00
Allaun Silverfox
0d9b434357 Add BraidStorm Sidon Crossing Anti-Alias runner 2026-05-16 20:54:30 -05:00
Allaun Silverfox
64522343dc Add Golden Braid Centering Gate runner 2026-05-16 19:46:13 -05:00
Allaun Silverfox
6aba73e780 Add autonomous speedrun harness gate runner 2026-05-16 19:09:42 -05:00
Allaun Silverfox
683e931915 Add MarkovJunior 16D shim runner 2026-05-16 18:42:25 -05:00
Allaun Silverfox
ebd9ef82b2 Add Sidon FAMM map runner 2026-05-16 17:18:49 -05:00
Allaun Silverfox
32fd7f759e Add Builder-Judge-Warden geodesic cleanup runner 2026-05-16 16:59:26 -05:00
Allaun Silverfox
02471b9dde Add logogram chirality route gate runner 2026-05-16 16:31:01 -05:00
Allaun Silverfox
20fbc7a940 Add NUVMAP Delta-DAG graph coloring compressor 2026-05-16 16:13:58 -05:00
Allaun Silverfox
733c454d5d Add 16D Chaos Game field shrinker runner 2026-05-16 14:39:56 -05:00
Allaun Silverfox
f4a4ef30b0 Add Semantic Mass route plow runner 2026-05-16 13:41:51 -05:00
Allaun Silverfox
ac0f959cf6 Add Semantic Mass Z-domain accelerator runner 2026-05-16 13:24:51 -05:00
Allaun Silverfox
0f733d03ff Add FAMM empirical Hessian receipt runner 2026-05-16 13:14:33 -05:00
Brandon Schneider
a6311ed940 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
d14d6b4b25 Refactor provenance sources for open witness backends 2026-05-12 05:57:04 -05:00
Brandon Schneider
79546e5dc7 Quiet parquet compressor warnings 2026-05-11 23:48:42 -05:00
Brandon Schneider
d8616d2879 Track remaining Dependabot transitive exceptions 2026-05-11 23:45:53 -05:00
Brandon Schneider
eafd19a487 Remediate dependency alert residue 2026-05-11 23:26:12 -05:00
Brandon Schneider
d56ef67ec9 Add verified Ollama DeepSeek review emitter 2026-05-11 23:13:54 -05:00
Brandon Schneider
cb96c6bed2 Update repository agent operating contracts 2026-05-11 22:48:54 -05:00
Brandon Schneider
d440fa3f47 Scrub tracked API key material 2026-05-11 22:25:43 -05:00
Brandon Schneider
a99e839bab Track remaining source and documentation inventory 2026-05-11 22:18:31 -05:00
Brandon Schneider
1225404b72 Point ENE scripts at shared data 2026-05-11 22:10:55 -05:00
Brandon Schneider
29f9b78b6d Stage stack solidification source slice 2026-05-11 22:08:10 -05:00
Brandon Schneider
cabf709253 Ignore generated run outputs and scrub API key scripts 2026-05-11 22:06:39 -05:00
Brandon Schneider
c8ba00190e Add NUVMAP scan scheduling receipts 2026-05-11 14:49:17 -05:00
Brandon Schneider
eb50a316b4 Fix Dependabot dependency alerts 2026-05-08 15:04:30 -05:00