mirror of
https://github.com/allaunthefox/Research-Stack.git
synced 2026-07-31 03:05:21 +00:00
allaun
779f4fe413
Add concept extraction/orchestration scripts under scripts/ and infra metadata in infra.json. Generated extraction outputs live under extraction/ and are regenerated from scripts; add extraction/ to .gitignore.
288 lines
7.7 KiB
Text
288 lines
7.7 KiB
Text
.env
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.env.*
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.claude/
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optimized_basis_v3.bin
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4-Infrastructure/deploy/
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# Virtual environments (root-level)
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.venv/
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.venv-*/
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# Third-party research repos (vendored, not authored here)
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ai-math-discovery-systems/
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# Scratch tests at root
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Agda_Test.agda
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test.lean
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**/node_modules/
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**/__pycache__/
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*.db
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*.log
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.DS_Store
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.windsurf/
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__pycache__/
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*.pyc
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*.pyo
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*.bak
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*.tmp
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*.old
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*.pid
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# Local-only generated/refill artifacts
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artifacts/
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Obdisidan connector/
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String-Star-Manifold/
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String-Star-Manifold-*.zip
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CompressionApproachViaTopology/
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*.perfect_balance_backup_*.gz
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# Large binary/tool installations
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**/ComfyUI/
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**/searxng/
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**/ObsidianConnector/
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**/mcp-researcher/
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tools/bin/
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tools/build/
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tools/search/
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**/archive/temp_junk/
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scripts/venv_unsloth/
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# Virtual environments (should never be committed)
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**/hutter_venv/
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**/venv_proxy/
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**/venv_wgpu/
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**/*.venv/
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**/venv/
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.venv-science/
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# API Keys and credentials (NEVER track in git)
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API KEYS/
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Security\ &\ Passwords/
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# Large data files (exceed GitHub 100MB limit)
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data/germane/research/*.zip
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data/germane/research/SOVEREIGN_MATH_MODEL_DATABASE_ITD.jsonl
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data/germane/research/SOVEREIGN_MATH_MODEL_DATABASE.jsonl
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data/germane/research/SOVEREIGN_MATH_MODEL_DATABASE_V2.json
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data/germane/research/SOVEREIGN_ITD_MANIFOLD.jsonl
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data/germane/research/MATHLIB_NLAB_MANIFOLD.jsonl
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data/manifest_selective_v5_xeno.jsonl
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data/manifest_selective_v5_xeno_FLAGGED.jsonl
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data/manifest.jsonl
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data/manifest_FLAGGED.jsonl
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data/s3c_sine_440Hz_1.0s_results.json
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data/*.iso
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# Lean build artifacts
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**/.lake/
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*.trace
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.changes/
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**/_build/
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**/__pycache__/
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# Rust build artifacts
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**/target/
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**/*.rs.bk
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# Agda build artifacts
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*.agdai
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# Local formal scratch/WIP that is not part of the clean build surface.
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0-Core-Formalism/Agda_Test.agda
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0-Core-Formalism/lean/Semantics/Ancillary/LegacyQuarantine/
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0-Core-Formalism/otom/tools/
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2-Search-Space/FAMM/FAMM_FSDU.lean
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2-Search-Space/FAMM/FAMM_hyperheuristic.lean
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2-Search-Space/FAMM/FAMM_minimal.lean
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4-Infrastructure/hardware/test.lean
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# Hardware/FPGA build artifacts
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**/obj_dir/
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**/hardware/sparkle/tangnano9k/*.fs
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**/hardware/sparkle/tangnano9k/*.pnr.json
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**/hardware/sparkle/tangnano9k/*.history
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**/hardware/sparkle/tangnano9k/sparkle_tangnano9k.json
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4-Infrastructure/hardware/tangnano9k/
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4-Infrastructure/hardware/tangnano9k_*.fs
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4-Infrastructure/hardware/tangnano9k_*.json
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4-Infrastructure/hardware/tangnano9k_*_pnr.json
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*.vcd
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*_tb.v
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*_test_vectors.json
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# Large data and archives (Offloaded to Gdrive via rclone)
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shared-data/
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6-Documentation/archive/
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5-Applications/out/
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5-Applications/scripts/models/
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**/shared-data/
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**/archive/
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*.zip
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*.tar.gz
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*.parquet
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# Rust build artifacts
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**/target/
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tools/servo-fetch/
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# Local runtime sandboxes
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**/.sandbox-home/
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**/.sandbox-tmp/
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# JavaScript build artifacts
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**/node_modules/
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# Downloaded external tool caches
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5-Applications/tools-scripts/external/openclaw/
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5-Applications/tools-scripts/external/mcp/
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5-Applications/tools-scripts/external/quantum/
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5-Applications/tools-scripts/external/typst-cli/
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# Local/generated mirrors that should not be ordinary staging surfaces.
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# Force-add a specific artifact when it is promoted into repository evidence.
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extensions/
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6-Documentation/typst/
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6-Documentation/tiddlywiki-local/wiki/tiddlers/*.tid
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6-Documentation/wiki/Obsidian-connector/Connector Gap Fill *.md
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# Downloaded third-party research trees and paper caches.
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2-Search-Space/AI-Feynman/
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2-Search-Space/AI-Newton/
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2-Search-Space/Goedel-Prover-V2/
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2-Search-Space/PINNs/
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2-Search-Space/alphageometry/
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2-Search-Space/neural-conservation-law/
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2-Search-Space/search/stract/crates/optics/testcases/samples/
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6-Documentation/papers/Downloads_from_internet/
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6-Documentation/papers/downloads/
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6-Documentation/papers/facebook_pdfs/
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6-Documentation/papers/literature/
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6-Documentation/papers/supporting-materials/
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# Generated benchmark corpora and run outputs.
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3-Mathematical-Models/dna_benchmark/**/corpus/
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3-Mathematical-Models/dna_benchmark/results/
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3-Mathematical-Models/dna_benchmark/**/compressor_manifold.json
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3-Mathematical-Models/dna_benchmark/**/eigenvalue_survey.json
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3-Mathematical-Models/equations_parquet_tagged/*_curriculum.jsonl
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3-Mathematical-Models/equations_parquet_tagged/*_receipt.json
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3-Mathematical-Models/equations_parquet_tagged/*_table.csv
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3-Mathematical-Models/unified_surface/cache/
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# Generated shim/app run bundles.
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4-Infrastructure/shim/erdos_surface_orchestrator/out/
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4-Infrastructure/shim/*_after.json
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4-Infrastructure/shim/*_benchmarks.csv
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4-Infrastructure/shim/*_before.json
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4-Infrastructure/shim/*_bit.json
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4-Infrastructure/shim/*_checkpoint.json
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4-Infrastructure/shim/*_compression.json
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4-Infrastructure/shim/*_curriculum.jsonl
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4-Infrastructure/shim/*_eigenvectors.json
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4-Infrastructure/shim/*_lut.json
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4-Infrastructure/shim/*_manifest.jsonl
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4-Infrastructure/shim/*_packages.json
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4-Infrastructure/shim/*_packets.jsonl
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4-Infrastructure/shim/*_pull.json
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4-Infrastructure/shim/*_receipt.json
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4-Infrastructure/shim/*_receipt_*.json
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4-Infrastructure/shim/*_report.json
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4-Infrastructure/shim/*_responses.jsonl
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4-Infrastructure/shim/*_results.json
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4-Infrastructure/shim/*_sft.jsonl
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4-Infrastructure/shim/*_smoke.json
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4-Infrastructure/shim/*_stream.bin
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4-Infrastructure/shim/finance_claim_remote_bundle/
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4-Infrastructure/shim/finance_claim_lut_fixtures/claim-*/
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4-Infrastructure/shim/finance_claim_lut_fixtures/*.pdf
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4-Infrastructure/shim/full_gambit_runs/
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4-Infrastructure/shim/h200_encode_dry_run/
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4-Infrastructure/shim/offload_receipts/
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4-Infrastructure/shim/parallel_metaprobe_runs/
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4-Infrastructure/shim/tang9k_pbacs_receipts/
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5-Applications/linear-native-tauri/gen/
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# AI tool editor hooks (generated, not authored)
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.cursor/
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.devin/
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.kilocode/
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.roo/
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# Scratch experiments and exploration
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scratch/
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woo.md
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find_minimum_energy.py
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verify_math_wolfram.py
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# Scratch Lean files (not part of the build surface)
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0-Core-Formalism/lean/Semantics/Semantics/Scratch.lean
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0-Core-Formalism/lean/Semantics/Semantics/Test.lean
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0-Core-Formalism/lean/Semantics/scratch_cofactor.lean
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# Shim scripts (not yet part of the clean surface)
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4-Infrastructure/shim/arxiv_crossref_stream.py
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4-Infrastructure/shim/default.nix
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4-Infrastructure/shim/Dockerfile.lean-corpus
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4-Infrastructure/shim/download_lean_corpus.py
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4-Infrastructure/shim/eigensolid_lean_bridge.py
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4-Infrastructure/shim/erdos_discrepancy_probe_simd.py
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4-Infrastructure/shim/erdos_e8_rrc_projection.py
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4-Infrastructure/shim/erdos_e8_rrc_refined.py
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4-Infrastructure/shim/q16_16_optimization_core.py
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4-Infrastructure/shim/Q16_16_OPTIMIZATION_DOCUMENTATION.md
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4-Infrastructure/shim/shell.nix
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4-Infrastructure/shim/verify_optimization_core.py
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# Downloaded lean corpus (third-party, not authored)
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4-Infrastructure/shim/lean_corpus/
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# Exploration docs (not part of the clean surface)
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docs/conjectures/
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0-Core-Formalism/otom/docs/conjectures/
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# Exploration prompt docs
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6-Documentation/docs/NUTBREAKER_*.md
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# Generated receipts
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pyrochlore_sidon_receipt.json
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# Generated hardware probe products.
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4-Infrastructure/hardware/batch_results/
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4-Infrastructure/hardware/*_receipt.json
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4-Infrastructure/hardware/*.png
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4-Infrastructure/hardware/*.pdf
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4-Infrastructure/hardware/metamanifold_prover.json
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# Local documentation exports and downloaded references.
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6-Documentation/chat-log-dumps/
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6-Documentation/docs/reference-videos/
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6-Documentation/docs/x86_64_specs/*.pdf
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6-Documentation/docs/x86_64_specs/*.txt
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6-Documentation/reports/jupyter-books/
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6-Documentation/reports/typst/*.pdf
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5-Applications/text-to-cad/models/.*/
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# Kernel module build artifacts
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*.ko
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*.mod
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*.mod.c
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*.order
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*.symvers
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Module.symvers
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# Symlinks for local dev convenience
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5-Applications/scripts/config/
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data
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result
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# Rust build artifacts
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**/target/
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# Recovery secrets backup - DO NOT COMMIT
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4-Infrastructure/infra/secrets/
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typescript
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# Generated concept extraction outputs (re-generate from scripts/)
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extraction/
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