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Reorganizing models and enabling "other" models #12

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56c0529
chore: Restructure RuleHub directories and update manifest categories
google-labs-jules[bot] Mar 31, 2026
b2ad06c
Merge pull request #1 from akutuva21/refactor-categories-635465190162…
akutuva21 Mar 31, 2026
9841cff
🔒 Fix Prototype Pollution in setNested
google-labs-jules[bot] Apr 13, 2026
68a03c2
🧪 [testing] add tests for parseScalar
google-labs-jules[bot] Apr 13, 2026
d3c87fc
Remove FIX comment for Autoinducer dynamics in quorum-sensing-circuit
google-labs-jules[bot] Apr 13, 2026
849a897
chore: Remove resolved FIX comment in eco_food_web_chaos_3sp.bngl
google-labs-jules[bot] Apr 13, 2026
b0a191c
perf(manifest): optimize setNested path handling
google-labs-jules[bot] Apr 13, 2026
6ce8215
🧪 testing: add tests for validateMetadataFile
google-labs-jules[bot] Apr 13, 2026
9237d2e
Add test suite for manifest generation script
google-labs-jules[bot] Apr 13, 2026
51efe26
Add tests for parseMetadataYaml in validate-metadata.js
google-labs-jules[bot] Apr 13, 2026
13d5659
refactor: implement 3rd harmonic using trigonometric identity
google-labs-jules[bot] Apr 13, 2026
58142f0
Refactor: Extract listModelFiles to utils module
google-labs-jules[bot] Apr 13, 2026
1fd3bf2
Merge pull request #4 from akutuva21/fix-autoinducer-dynamics-comment…
akutuva21 Apr 13, 2026
ca50992
Merge pull request #5 from akutuva21/fix/eco-food-web-chaos-comment-1…
akutuva21 Apr 13, 2026
6f0a3d7
test: make validate-metadata exports additive for branch compatibility
akutuva21 Apr 13, 2026
4fd9f8f
test: keep parseScalar export alongside validateMetadataFile
akutuva21 Apr 13, 2026
04a5512
test: export parse helpers and validator together
akutuva21 Apr 13, 2026
eceeae3
security: block dangerous nested keys across metadata parsers
akutuva21 Apr 13, 2026
c7882e1
Merge pull request #8 from akutuva21/add-manifest-generation-tests-11…
akutuva21 Apr 13, 2026
5f40077
Merge pull request #6 from akutuva21/perf-optimize-set-nested-1541902…
akutuva21 Apr 13, 2026
2304c63
Merge pull request #3 from akutuva21/testing-improvement-parse-scalar…
akutuva21 Apr 13, 2026
3fec483
Merge pull request #7 from akutuva21/add-validate-metadata-tests-1132…
akutuva21 Apr 13, 2026
0b5dd07
Merge pull request #11 from akutuva21/fix/extract-listmodelfiles-7277…
akutuva21 Apr 13, 2026
d2f9c22
Merge pull request #10 from akutuva21/fix-3rd-harmonic-identity-12548…
akutuva21 Apr 13, 2026
18e1ffc
Merge remote-tracking branch 'origin/master' into test-parse-metadata…
akutuva21 Apr 13, 2026
71ec28e
merge: resolve validate-metadata export conflict with master
akutuva21 Apr 13, 2026
5ec41e9
Merge pull request #9 from akutuva21/test-parse-metadata-yaml-7716385…
akutuva21 Apr 13, 2026
b891164
merge: resolve security branch conflicts after test/refactor merges
akutuva21 Apr 13, 2026
13a88be
Merge pull request #2 from akutuva21/security-fix-prototype-pollution…
akutuva21 Apr 13, 2026
c291b8f
Merge branch 'RuleWorld:master' into master
akutuva21 Apr 13, 2026
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Expand Up @@ -33,7 +33,6 @@ begin reaction rules
Autoinducer() + Gene(state~off) -> Gene(state~on) + Autoinducer() k_activate
Gene(state~on) -> Gene(state~on) + Protein() k_export
Protein() -> 0 k_import
# FIX: Add Autoinducer dynamics (was conserved)
Protein() -> Protein() + Autoinducer() 0.1 # Protein produces AI
Autoinducer() -> 0 0.05 # AI degradation
Autoinducer_env() -> 0 0.02 # Environmental AI clearance
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