@hongmaple0820/med-scale-research-os 0.43.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1104) hide show
  1. package/.scale/mcp-servers.yaml +144 -0
  2. package/.scale/skills.json +830 -0
  3. package/.scale/verification.json +52 -0
  4. package/LICENSE +15 -0
  5. package/README.en.md +156 -0
  6. package/README.md +156 -0
  7. package/dist/adapters/AiderAdapter.d.ts +22 -0
  8. package/dist/adapters/AiderAdapter.js +262 -0
  9. package/dist/adapters/AiderAdapter.js.map +1 -0
  10. package/dist/adapters/AntigravityAdapter.d.ts +4 -0
  11. package/dist/adapters/AntigravityAdapter.js +21 -0
  12. package/dist/adapters/AntigravityAdapter.js.map +1 -0
  13. package/dist/adapters/ClaudeCodeAdapter.d.ts +54 -0
  14. package/dist/adapters/ClaudeCodeAdapter.js +185 -0
  15. package/dist/adapters/ClaudeCodeAdapter.js.map +1 -0
  16. package/dist/adapters/ClineAdapter.d.ts +4 -0
  17. package/dist/adapters/ClineAdapter.js +20 -0
  18. package/dist/adapters/ClineAdapter.js.map +1 -0
  19. package/dist/adapters/CodexAdapter.d.ts +15 -0
  20. package/dist/adapters/CodexAdapter.js +160 -0
  21. package/dist/adapters/CodexAdapter.js.map +1 -0
  22. package/dist/adapters/CursorAdapter.d.ts +14 -0
  23. package/dist/adapters/CursorAdapter.js +171 -0
  24. package/dist/adapters/CursorAdapter.js.map +1 -0
  25. package/dist/adapters/DeepSeekTuiAdapter.d.ts +19 -0
  26. package/dist/adapters/DeepSeekTuiAdapter.js +263 -0
  27. package/dist/adapters/DeepSeekTuiAdapter.js.map +1 -0
  28. package/dist/adapters/DoubaoAdapter.d.ts +14 -0
  29. package/dist/adapters/DoubaoAdapter.js +184 -0
  30. package/dist/adapters/DoubaoAdapter.js.map +1 -0
  31. package/dist/adapters/GeminiAdapter.d.ts +14 -0
  32. package/dist/adapters/GeminiAdapter.js +163 -0
  33. package/dist/adapters/GeminiAdapter.js.map +1 -0
  34. package/dist/adapters/GenericProjectAgentAdapter.d.ts +29 -0
  35. package/dist/adapters/GenericProjectAgentAdapter.js +204 -0
  36. package/dist/adapters/GenericProjectAgentAdapter.js.map +1 -0
  37. package/dist/adapters/HermesAdapter.d.ts +14 -0
  38. package/dist/adapters/HermesAdapter.js +163 -0
  39. package/dist/adapters/HermesAdapter.js.map +1 -0
  40. package/dist/adapters/JCodeAdapter.d.ts +4 -0
  41. package/dist/adapters/JCodeAdapter.js +19 -0
  42. package/dist/adapters/JCodeAdapter.js.map +1 -0
  43. package/dist/adapters/KiloCodeAdapter.d.ts +4 -0
  44. package/dist/adapters/KiloCodeAdapter.js +20 -0
  45. package/dist/adapters/KiloCodeAdapter.js.map +1 -0
  46. package/dist/adapters/KimiAdapter.d.ts +14 -0
  47. package/dist/adapters/KimiAdapter.js +183 -0
  48. package/dist/adapters/KimiAdapter.js.map +1 -0
  49. package/dist/adapters/KiroAdapter.d.ts +14 -0
  50. package/dist/adapters/KiroAdapter.js +180 -0
  51. package/dist/adapters/KiroAdapter.js.map +1 -0
  52. package/dist/adapters/OpenClawAdapter.d.ts +14 -0
  53. package/dist/adapters/OpenClawAdapter.js +163 -0
  54. package/dist/adapters/OpenClawAdapter.js.map +1 -0
  55. package/dist/adapters/OpenCodeAdapter.d.ts +14 -0
  56. package/dist/adapters/OpenCodeAdapter.js +172 -0
  57. package/dist/adapters/OpenCodeAdapter.js.map +1 -0
  58. package/dist/adapters/QCoderAdapter.d.ts +14 -0
  59. package/dist/adapters/QCoderAdapter.js +159 -0
  60. package/dist/adapters/QCoderAdapter.js.map +1 -0
  61. package/dist/adapters/QoderAdapter.d.ts +4 -0
  62. package/dist/adapters/QoderAdapter.js +21 -0
  63. package/dist/adapters/QoderAdapter.js.map +1 -0
  64. package/dist/adapters/TraeAdapter.d.ts +14 -0
  65. package/dist/adapters/TraeAdapter.js +159 -0
  66. package/dist/adapters/TraeAdapter.js.map +1 -0
  67. package/dist/adapters/VSCAdapter.d.ts +14 -0
  68. package/dist/adapters/VSCAdapter.js +159 -0
  69. package/dist/adapters/VSCAdapter.js.map +1 -0
  70. package/dist/adapters/WindsurfAdapter.d.ts +14 -0
  71. package/dist/adapters/WindsurfAdapter.js +185 -0
  72. package/dist/adapters/WindsurfAdapter.js.map +1 -0
  73. package/dist/adapters/WorkBuddyAdapter.d.ts +14 -0
  74. package/dist/adapters/WorkBuddyAdapter.js +159 -0
  75. package/dist/adapters/WorkBuddyAdapter.js.map +1 -0
  76. package/dist/adapters/index.d.ts +32 -0
  77. package/dist/adapters/index.js +87 -0
  78. package/dist/adapters/index.js.map +1 -0
  79. package/dist/agents/AgentChannel.d.ts +43 -0
  80. package/dist/agents/AgentChannel.js +136 -0
  81. package/dist/agents/AgentChannel.js.map +1 -0
  82. package/dist/agents/AgentCoordinator.d.ts +29 -0
  83. package/dist/agents/AgentCoordinator.js +136 -0
  84. package/dist/agents/AgentCoordinator.js.map +1 -0
  85. package/dist/agents/AgentDispatcher.d.ts +24 -0
  86. package/dist/agents/AgentDispatcher.js +112 -0
  87. package/dist/agents/AgentDispatcher.js.map +1 -0
  88. package/dist/agents/AgentManager.d.ts +14 -0
  89. package/dist/agents/AgentManager.js +85 -0
  90. package/dist/agents/AgentManager.js.map +1 -0
  91. package/dist/agents/AgentPool.d.ts +59 -0
  92. package/dist/agents/AgentPool.js +192 -0
  93. package/dist/agents/AgentPool.js.map +1 -0
  94. package/dist/agents/AgentRegistry.d.ts +20 -0
  95. package/dist/agents/AgentRegistry.js +36 -0
  96. package/dist/agents/AgentRegistry.js.map +1 -0
  97. package/dist/agents/AgentSourceLoader.d.ts +73 -0
  98. package/dist/agents/AgentSourceLoader.js +103 -0
  99. package/dist/agents/AgentSourceLoader.js.map +1 -0
  100. package/dist/agents/IAgent.d.ts +53 -0
  101. package/dist/agents/IAgent.js +4 -0
  102. package/dist/agents/IAgent.js.map +1 -0
  103. package/dist/agents/LeadershipPresets.d.ts +16 -0
  104. package/dist/agents/LeadershipPresets.js +152 -0
  105. package/dist/agents/LeadershipPresets.js.map +1 -0
  106. package/dist/agents/definitions/debugger.d.ts +2 -0
  107. package/dist/agents/definitions/debugger.js +6 -0
  108. package/dist/agents/definitions/debugger.js.map +1 -0
  109. package/dist/agents/definitions/doc-writer.d.ts +2 -0
  110. package/dist/agents/definitions/doc-writer.js +6 -0
  111. package/dist/agents/definitions/doc-writer.js.map +1 -0
  112. package/dist/agents/definitions/implementer.d.ts +2 -0
  113. package/dist/agents/definitions/implementer.js +6 -0
  114. package/dist/agents/definitions/implementer.js.map +1 -0
  115. package/dist/agents/definitions/planner.d.ts +2 -0
  116. package/dist/agents/definitions/planner.js +6 -0
  117. package/dist/agents/definitions/planner.js.map +1 -0
  118. package/dist/agents/definitions/researcher.d.ts +2 -0
  119. package/dist/agents/definitions/researcher.js +6 -0
  120. package/dist/agents/definitions/researcher.js.map +1 -0
  121. package/dist/agents/definitions/reviewer.d.ts +2 -0
  122. package/dist/agents/definitions/reviewer.js +6 -0
  123. package/dist/agents/definitions/reviewer.js.map +1 -0
  124. package/dist/agents/definitions/security.d.ts +2 -0
  125. package/dist/agents/definitions/security.js +6 -0
  126. package/dist/agents/definitions/security.js.map +1 -0
  127. package/dist/agents/definitions/tester.d.ts +2 -0
  128. package/dist/agents/definitions/tester.js +6 -0
  129. package/dist/agents/definitions/tester.js.map +1 -0
  130. package/dist/agents/index.d.ts +23 -0
  131. package/dist/agents/index.js +44 -0
  132. package/dist/agents/index.js.map +1 -0
  133. package/dist/agents/profiles.d.ts +26 -0
  134. package/dist/agents/profiles.js +197 -0
  135. package/dist/agents/profiles.js.map +1 -0
  136. package/dist/agents/types.d.ts +262 -0
  137. package/dist/agents/types.js +4 -0
  138. package/dist/agents/types.js.map +1 -0
  139. package/dist/api/cli.d.ts +2 -0
  140. package/dist/api/cli.js +6678 -0
  141. package/dist/api/cli.js.map +1 -0
  142. package/dist/api/doctor.d.ts +83 -0
  143. package/dist/api/doctor.js +982 -0
  144. package/dist/api/doctor.js.map +1 -0
  145. package/dist/api/mcp.d.ts +32 -0
  146. package/dist/api/mcp.js +223 -0
  147. package/dist/api/mcp.js.map +1 -0
  148. package/dist/api/medscale.d.ts +2 -0
  149. package/dist/api/medscale.js +20 -0
  150. package/dist/api/medscale.js.map +1 -0
  151. package/dist/api/quickstart.d.ts +86 -0
  152. package/dist/api/quickstart.js +291 -0
  153. package/dist/api/quickstart.js.map +1 -0
  154. package/dist/artifact/fsm.d.ts +41 -0
  155. package/dist/artifact/fsm.js +221 -0
  156. package/dist/artifact/fsm.js.map +1 -0
  157. package/dist/artifact/fsmDefinitions.d.ts +18 -0
  158. package/dist/artifact/fsmDefinitions.js +296 -0
  159. package/dist/artifact/fsmDefinitions.js.map +1 -0
  160. package/dist/artifact/sqliteStore.d.ts +61 -0
  161. package/dist/artifact/sqliteStore.js +381 -0
  162. package/dist/artifact/sqliteStore.js.map +1 -0
  163. package/dist/artifact/store.d.ts +49 -0
  164. package/dist/artifact/store.js +116 -0
  165. package/dist/artifact/store.js.map +1 -0
  166. package/dist/artifact/types.d.ts +535 -0
  167. package/dist/artifact/types.js +74 -0
  168. package/dist/artifact/types.js.map +1 -0
  169. package/dist/bootstrap/DependencyBootstrap.d.ts +112 -0
  170. package/dist/bootstrap/DependencyBootstrap.js +1046 -0
  171. package/dist/bootstrap/DependencyBootstrap.js.map +1 -0
  172. package/dist/bootstrap/DependencyBootstrapRenderer.d.ts +3 -0
  173. package/dist/bootstrap/DependencyBootstrapRenderer.js +138 -0
  174. package/dist/bootstrap/DependencyBootstrapRenderer.js.map +1 -0
  175. package/dist/bridge/PythonBridge.d.ts +80 -0
  176. package/dist/bridge/PythonBridge.js +437 -0
  177. package/dist/bridge/PythonBridge.js.map +1 -0
  178. package/dist/bridge/index.d.ts +2 -0
  179. package/dist/bridge/index.js +7 -0
  180. package/dist/bridge/index.js.map +1 -0
  181. package/dist/bridge/medicalWorkflows.d.ts +29 -0
  182. package/dist/bridge/medicalWorkflows.js +156 -0
  183. package/dist/bridge/medicalWorkflows.js.map +1 -0
  184. package/dist/bridge/types.d.ts +381 -0
  185. package/dist/bridge/types.js +113 -0
  186. package/dist/bridge/types.js.map +1 -0
  187. package/dist/cache/ScanCache.d.ts +41 -0
  188. package/dist/cache/ScanCache.js +120 -0
  189. package/dist/cache/ScanCache.js.map +1 -0
  190. package/dist/capabilities/BrowserCapability.d.ts +30 -0
  191. package/dist/capabilities/BrowserCapability.js +73 -0
  192. package/dist/capabilities/BrowserCapability.js.map +1 -0
  193. package/dist/capabilities/BrowserQACapability.d.ts +165 -0
  194. package/dist/capabilities/BrowserQACapability.js +438 -0
  195. package/dist/capabilities/BrowserQACapability.js.map +1 -0
  196. package/dist/capabilities/CapabilityRegistry.d.ts +17 -0
  197. package/dist/capabilities/CapabilityRegistry.js +65 -0
  198. package/dist/capabilities/CapabilityRegistry.js.map +1 -0
  199. package/dist/capabilities/ComputerCapability.d.ts +28 -0
  200. package/dist/capabilities/ComputerCapability.js +40 -0
  201. package/dist/capabilities/ComputerCapability.js.map +1 -0
  202. package/dist/capabilities/InstalledSkillsIntegration.d.ts +69 -0
  203. package/dist/capabilities/InstalledSkillsIntegration.js +240 -0
  204. package/dist/capabilities/InstalledSkillsIntegration.js.map +1 -0
  205. package/dist/capabilities/SearchCapability.d.ts +46 -0
  206. package/dist/capabilities/SearchCapability.js +88 -0
  207. package/dist/capabilities/SearchCapability.js.map +1 -0
  208. package/dist/capabilities/index.d.ts +6 -0
  209. package/dist/capabilities/index.js +9 -0
  210. package/dist/capabilities/index.js.map +1 -0
  211. package/dist/capabilities/types.d.ts +92 -0
  212. package/dist/capabilities/types.js +7 -0
  213. package/dist/capabilities/types.js.map +1 -0
  214. package/dist/cli/autofixCommands.d.ts +22 -0
  215. package/dist/cli/autofixCommands.js +32 -0
  216. package/dist/cli/autofixCommands.js.map +1 -0
  217. package/dist/cli/cortexCommands.d.ts +71 -0
  218. package/dist/cli/cortexCommands.js +335 -0
  219. package/dist/cli/cortexCommands.js.map +1 -0
  220. package/dist/cli/costCommands.d.ts +13 -0
  221. package/dist/cli/costCommands.js +48 -0
  222. package/dist/cli/costCommands.js.map +1 -0
  223. package/dist/cli/evolutionCommands.d.ts +112 -0
  224. package/dist/cli/evolutionCommands.js +246 -0
  225. package/dist/cli/evolutionCommands.js.map +1 -0
  226. package/dist/cli/gateStatusCommands.d.ts +1 -0
  227. package/dist/cli/gateStatusCommands.js +52 -0
  228. package/dist/cli/gateStatusCommands.js.map +1 -0
  229. package/dist/cli/liteCommands.d.ts +81 -0
  230. package/dist/cli/liteCommands.js +148 -0
  231. package/dist/cli/liteCommands.js.map +1 -0
  232. package/dist/cli/orchCommands.d.ts +43 -0
  233. package/dist/cli/orchCommands.js +135 -0
  234. package/dist/cli/orchCommands.js.map +1 -0
  235. package/dist/cli/phaseCommands.d.ts +248 -0
  236. package/dist/cli/phaseCommands.js +1878 -0
  237. package/dist/cli/phaseCommands.js.map +1 -0
  238. package/dist/cli/promptCommands.d.ts +1 -0
  239. package/dist/cli/promptCommands.js +57 -0
  240. package/dist/cli/promptCommands.js.map +1 -0
  241. package/dist/cli/qaCommands.d.ts +22 -0
  242. package/dist/cli/qaCommands.js +84 -0
  243. package/dist/cli/qaCommands.js.map +1 -0
  244. package/dist/cli/quickstartCommands.d.ts +17 -0
  245. package/dist/cli/quickstartCommands.js +47 -0
  246. package/dist/cli/quickstartCommands.js.map +1 -0
  247. package/dist/cli/runCommand.d.ts +39 -0
  248. package/dist/cli/runCommand.js +113 -0
  249. package/dist/cli/runCommand.js.map +1 -0
  250. package/dist/cli/scoreCommands.d.ts +1 -0
  251. package/dist/cli/scoreCommands.js +112 -0
  252. package/dist/cli/scoreCommands.js.map +1 -0
  253. package/dist/cli/shieldCommands.d.ts +30 -0
  254. package/dist/cli/shieldCommands.js +212 -0
  255. package/dist/cli/shieldCommands.js.map +1 -0
  256. package/dist/cli/targetCommands.d.ts +552 -0
  257. package/dist/cli/targetCommands.js +3173 -0
  258. package/dist/cli/targetCommands.js.map +1 -0
  259. package/dist/cli/tuiCommands.d.ts +7 -0
  260. package/dist/cli/tuiCommands.js +33 -0
  261. package/dist/cli/tuiCommands.js.map +1 -0
  262. package/dist/cli/vibeCommands.d.ts +64 -0
  263. package/dist/cli/vibeCommands.js +221 -0
  264. package/dist/cli/vibeCommands.js.map +1 -0
  265. package/dist/codegraph/CodeIntelligence.d.ts +147 -0
  266. package/dist/codegraph/CodeIntelligence.js +681 -0
  267. package/dist/codegraph/CodeIntelligence.js.map +1 -0
  268. package/dist/config/profiles.d.ts +64 -0
  269. package/dist/config/profiles.js +223 -0
  270. package/dist/config/profiles.js.map +1 -0
  271. package/dist/context/AntiPatternRegistry.d.ts +38 -0
  272. package/dist/context/AntiPatternRegistry.js +203 -0
  273. package/dist/context/AntiPatternRegistry.js.map +1 -0
  274. package/dist/context/CavemanCompressor.d.ts +20 -0
  275. package/dist/context/CavemanCompressor.js +14 -0
  276. package/dist/context/CavemanCompressor.js.map +1 -0
  277. package/dist/context/ContextBudget.d.ts +128 -0
  278. package/dist/context/ContextBudget.js +423 -0
  279. package/dist/context/ContextBudget.js.map +1 -0
  280. package/dist/context/ContextBuilder.d.ts +71 -0
  281. package/dist/context/ContextBuilder.js +372 -0
  282. package/dist/context/ContextBuilder.js.map +1 -0
  283. package/dist/context/ContextCompiler.d.ts +34 -0
  284. package/dist/context/ContextCompiler.js +120 -0
  285. package/dist/context/ContextCompiler.js.map +1 -0
  286. package/dist/context/ProjectAnatomy.d.ts +18 -0
  287. package/dist/context/ProjectAnatomy.js +287 -0
  288. package/dist/context/ProjectAnatomy.js.map +1 -0
  289. package/dist/context/SessionStartSequence.d.ts +54 -0
  290. package/dist/context/SessionStartSequence.js +162 -0
  291. package/dist/context/SessionStartSequence.js.map +1 -0
  292. package/dist/core/ExternalCommand.d.ts +9 -0
  293. package/dist/core/ExternalCommand.js +70 -0
  294. package/dist/core/ExternalCommand.js.map +1 -0
  295. package/dist/core/GbrainRuntime.d.ts +25 -0
  296. package/dist/core/GbrainRuntime.js +270 -0
  297. package/dist/core/GbrainRuntime.js.map +1 -0
  298. package/dist/core/container.d.ts +14 -0
  299. package/dist/core/container.js +35 -0
  300. package/dist/core/container.js.map +1 -0
  301. package/dist/core/eventBus.d.ts +60 -0
  302. package/dist/core/eventBus.js +157 -0
  303. package/dist/core/eventBus.js.map +1 -0
  304. package/dist/core/logger.d.ts +5 -0
  305. package/dist/core/logger.js +51 -0
  306. package/dist/core/logger.js.map +1 -0
  307. package/dist/cortex/GovernanceMetrics.d.ts +66 -0
  308. package/dist/cortex/GovernanceMetrics.js +230 -0
  309. package/dist/cortex/GovernanceMetrics.js.map +1 -0
  310. package/dist/cortex/InstinctExtractor.d.ts +61 -0
  311. package/dist/cortex/InstinctExtractor.js +184 -0
  312. package/dist/cortex/InstinctExtractor.js.map +1 -0
  313. package/dist/cortex/InstinctStore.d.ts +54 -0
  314. package/dist/cortex/InstinctStore.js +266 -0
  315. package/dist/cortex/InstinctStore.js.map +1 -0
  316. package/dist/cortex/ReflexionEngine.d.ts +34 -0
  317. package/dist/cortex/ReflexionEngine.js +157 -0
  318. package/dist/cortex/ReflexionEngine.js.map +1 -0
  319. package/dist/cortex/SessionInjector.d.ts +44 -0
  320. package/dist/cortex/SessionInjector.js +127 -0
  321. package/dist/cortex/SessionInjector.js.map +1 -0
  322. package/dist/cortex/adapters/ClaudeAdapter.d.ts +17 -0
  323. package/dist/cortex/adapters/ClaudeAdapter.js +61 -0
  324. package/dist/cortex/adapters/ClaudeAdapter.js.map +1 -0
  325. package/dist/cortex/adapters/CodexAdapter.d.ts +10 -0
  326. package/dist/cortex/adapters/CodexAdapter.js +52 -0
  327. package/dist/cortex/adapters/CodexAdapter.js.map +1 -0
  328. package/dist/cortex/adapters/CursorAdapter.d.ts +10 -0
  329. package/dist/cortex/adapters/CursorAdapter.js +46 -0
  330. package/dist/cortex/adapters/CursorAdapter.js.map +1 -0
  331. package/dist/cortex/adapters/GeminiAdapter.d.ts +11 -0
  332. package/dist/cortex/adapters/GeminiAdapter.js +48 -0
  333. package/dist/cortex/adapters/GeminiAdapter.js.map +1 -0
  334. package/dist/dashboard/DashboardServer.d.ts +86 -0
  335. package/dist/dashboard/DashboardServer.js +380 -0
  336. package/dist/dashboard/DashboardServer.js.map +1 -0
  337. package/dist/dashboard/MedicalWorkflowData.d.ts +155 -0
  338. package/dist/dashboard/MedicalWorkflowData.js +664 -0
  339. package/dist/dashboard/MedicalWorkflowData.js.map +1 -0
  340. package/dist/dashboard/MetricsAggregator.d.ts +38 -0
  341. package/dist/dashboard/MetricsAggregator.js +99 -0
  342. package/dist/dashboard/MetricsAggregator.js.map +1 -0
  343. package/dist/dashboard/index.d.ts +4 -0
  344. package/dist/dashboard/index.js +3 -0
  345. package/dist/dashboard/index.js.map +1 -0
  346. package/dist/dashboard/server.d.ts +52 -0
  347. package/dist/dashboard/server.js +84 -0
  348. package/dist/dashboard/server.js.map +1 -0
  349. package/dist/env/EnvironmentDoctor.d.ts +66 -0
  350. package/dist/env/EnvironmentDoctor.js +581 -0
  351. package/dist/env/EnvironmentDoctor.js.map +1 -0
  352. package/dist/eval/BenchmarkPublisher.d.ts +25 -0
  353. package/dist/eval/BenchmarkPublisher.js +27 -0
  354. package/dist/eval/BenchmarkPublisher.js.map +1 -0
  355. package/dist/eval/WorkflowEval.d.ts +161 -0
  356. package/dist/eval/WorkflowEval.js +377 -0
  357. package/dist/eval/WorkflowEval.js.map +1 -0
  358. package/dist/evolution/AutoDefectCreator.d.ts +43 -0
  359. package/dist/evolution/AutoDefectCreator.js +157 -0
  360. package/dist/evolution/AutoDefectCreator.js.map +1 -0
  361. package/dist/evolution/BehaviorTracker.d.ts +46 -0
  362. package/dist/evolution/BehaviorTracker.js +67 -0
  363. package/dist/evolution/BehaviorTracker.js.map +1 -0
  364. package/dist/evolution/EvolutionEngine.d.ts +102 -0
  365. package/dist/evolution/EvolutionEngine.js +326 -0
  366. package/dist/evolution/EvolutionEngine.js.map +1 -0
  367. package/dist/evolution/EvolutionEvaluator.d.ts +61 -0
  368. package/dist/evolution/EvolutionEvaluator.js +118 -0
  369. package/dist/evolution/EvolutionEvaluator.js.map +1 -0
  370. package/dist/evolution/LessonValidator.d.ts +36 -0
  371. package/dist/evolution/LessonValidator.js +132 -0
  372. package/dist/evolution/LessonValidator.js.map +1 -0
  373. package/dist/evolution/PatternExtractor.d.ts +40 -0
  374. package/dist/evolution/PatternExtractor.js +83 -0
  375. package/dist/evolution/PatternExtractor.js.map +1 -0
  376. package/dist/evolution/RuleMaturity.d.ts +39 -0
  377. package/dist/evolution/RuleMaturity.js +70 -0
  378. package/dist/evolution/RuleMaturity.js.map +1 -0
  379. package/dist/evolution/SessionLearnings.d.ts +70 -0
  380. package/dist/evolution/SessionLearnings.js +217 -0
  381. package/dist/evolution/SessionLearnings.js.map +1 -0
  382. package/dist/evolution/SkillCreator.d.ts +75 -0
  383. package/dist/evolution/SkillCreator.js +219 -0
  384. package/dist/evolution/SkillCreator.js.map +1 -0
  385. package/dist/fsm/FSMAgentBridge.d.ts +59 -0
  386. package/dist/fsm/FSMAgentBridge.js +193 -0
  387. package/dist/fsm/FSMAgentBridge.js.map +1 -0
  388. package/dist/fsm/index.d.ts +2 -0
  389. package/dist/fsm/index.js +3 -0
  390. package/dist/fsm/index.js.map +1 -0
  391. package/dist/governance/GovernanceRoi.d.ts +30 -0
  392. package/dist/governance/GovernanceRoi.js +102 -0
  393. package/dist/governance/GovernanceRoi.js.map +1 -0
  394. package/dist/governance/ProgressiveGovernance.d.ts +22 -0
  395. package/dist/governance/ProgressiveGovernance.js +159 -0
  396. package/dist/governance/ProgressiveGovernance.js.map +1 -0
  397. package/dist/guardrails/ActiveRedTeam.d.ts +46 -0
  398. package/dist/guardrails/ActiveRedTeam.js +203 -0
  399. package/dist/guardrails/ActiveRedTeam.js.map +1 -0
  400. package/dist/guardrails/DependencyAuditor.d.ts +68 -0
  401. package/dist/guardrails/DependencyAuditor.js +378 -0
  402. package/dist/guardrails/DependencyAuditor.js.map +1 -0
  403. package/dist/guardrails/DetectorEnhanced.d.ts +111 -0
  404. package/dist/guardrails/DetectorEnhanced.js +202 -0
  405. package/dist/guardrails/DetectorEnhanced.js.map +1 -0
  406. package/dist/guardrails/GateEvaluator.d.ts +18 -0
  407. package/dist/guardrails/GateEvaluator.js +129 -0
  408. package/dist/guardrails/GateEvaluator.js.map +1 -0
  409. package/dist/guardrails/Gateway.d.ts +26 -0
  410. package/dist/guardrails/Gateway.js +56 -0
  411. package/dist/guardrails/Gateway.js.map +1 -0
  412. package/dist/guardrails/OWASPDetector.d.ts +58 -0
  413. package/dist/guardrails/OWASPDetector.js +508 -0
  414. package/dist/guardrails/OWASPDetector.js.map +1 -0
  415. package/dist/guardrails/ReviewEnforcer.d.ts +52 -0
  416. package/dist/guardrails/ReviewEnforcer.js +117 -0
  417. package/dist/guardrails/ReviewEnforcer.js.map +1 -0
  418. package/dist/guardrails/advancedDetectors.d.ts +38 -0
  419. package/dist/guardrails/advancedDetectors.js +188 -0
  420. package/dist/guardrails/advancedDetectors.js.map +1 -0
  421. package/dist/guardrails/detectors.d.ts +34 -0
  422. package/dist/guardrails/detectors.js +332 -0
  423. package/dist/guardrails/detectors.js.map +1 -0
  424. package/dist/guardrails/roles.d.ts +4 -0
  425. package/dist/guardrails/roles.js +54 -0
  426. package/dist/guardrails/roles.js.map +1 -0
  427. package/dist/hooks/BugPatternDetector.d.ts +36 -0
  428. package/dist/hooks/BugPatternDetector.js +207 -0
  429. package/dist/hooks/BugPatternDetector.js.map +1 -0
  430. package/dist/hooks/HookDeployer.d.ts +44 -0
  431. package/dist/hooks/HookDeployer.js +144 -0
  432. package/dist/hooks/HookDeployer.js.map +1 -0
  433. package/dist/hooks/HookGeneratorEnhanced.d.ts +67 -0
  434. package/dist/hooks/HookGeneratorEnhanced.js +641 -0
  435. package/dist/hooks/HookGeneratorEnhanced.js.map +1 -0
  436. package/dist/hooks/WorkflowHooksManager.d.ts +30 -0
  437. package/dist/hooks/WorkflowHooksManager.js +160 -0
  438. package/dist/hooks/WorkflowHooksManager.js.map +1 -0
  439. package/dist/hooks/index.d.ts +6 -0
  440. package/dist/hooks/index.js +5 -0
  441. package/dist/hooks/index.js.map +1 -0
  442. package/dist/i18n/Language.d.ts +9 -0
  443. package/dist/i18n/Language.js +38 -0
  444. package/dist/i18n/Language.js.map +1 -0
  445. package/dist/index.d.ts +101 -0
  446. package/dist/index.js +104 -0
  447. package/dist/index.js.map +1 -0
  448. package/dist/knowledge/CerebrumManager.d.ts +25 -0
  449. package/dist/knowledge/CerebrumManager.js +127 -0
  450. package/dist/knowledge/CerebrumManager.js.map +1 -0
  451. package/dist/knowledge/GraphifyKnowledgeBase.d.ts +38 -0
  452. package/dist/knowledge/GraphifyKnowledgeBase.js +409 -0
  453. package/dist/knowledge/GraphifyKnowledgeBase.js.map +1 -0
  454. package/dist/knowledge/KnowledgeBase.d.ts +51 -0
  455. package/dist/knowledge/KnowledgeBase.js +182 -0
  456. package/dist/knowledge/KnowledgeBase.js.map +1 -0
  457. package/dist/knowledge/SQLiteKnowledgeBase.d.ts +29 -0
  458. package/dist/knowledge/SQLiteKnowledgeBase.js +203 -0
  459. package/dist/knowledge/SQLiteKnowledgeBase.js.map +1 -0
  460. package/dist/knowledge/TfidfIndex.d.ts +50 -0
  461. package/dist/knowledge/TfidfIndex.js +177 -0
  462. package/dist/knowledge/TfidfIndex.js.map +1 -0
  463. package/dist/knowledge/UbiquitousLanguageManager.d.ts +49 -0
  464. package/dist/knowledge/UbiquitousLanguageManager.js +133 -0
  465. package/dist/knowledge/UbiquitousLanguageManager.js.map +1 -0
  466. package/dist/memory/MemoryBrain.d.ts +146 -0
  467. package/dist/memory/MemoryBrain.js +679 -0
  468. package/dist/memory/MemoryBrain.js.map +1 -0
  469. package/dist/memory/MemoryFabric.d.ts +130 -0
  470. package/dist/memory/MemoryFabric.js +317 -0
  471. package/dist/memory/MemoryFabric.js.map +1 -0
  472. package/dist/memory/MemoryIntelligence.d.ts +42 -0
  473. package/dist/memory/MemoryIntelligence.js +215 -0
  474. package/dist/memory/MemoryIntelligence.js.map +1 -0
  475. package/dist/memory/MemoryLearning.d.ts +62 -0
  476. package/dist/memory/MemoryLearning.js +209 -0
  477. package/dist/memory/MemoryLearning.js.map +1 -0
  478. package/dist/memory/MemoryProviders.d.ts +165 -0
  479. package/dist/memory/MemoryProviders.js +940 -0
  480. package/dist/memory/MemoryProviders.js.map +1 -0
  481. package/dist/memory/MemoryReview.d.ts +65 -0
  482. package/dist/memory/MemoryReview.js +260 -0
  483. package/dist/memory/MemoryReview.js.map +1 -0
  484. package/dist/memory/index.d.ts +6 -0
  485. package/dist/memory/index.js +7 -0
  486. package/dist/memory/index.js.map +1 -0
  487. package/dist/orchestration/EffectsWiring.d.ts +8 -0
  488. package/dist/orchestration/EffectsWiring.js +87 -0
  489. package/dist/orchestration/EffectsWiring.js.map +1 -0
  490. package/dist/orchestrator/OrchestratorDaemon.d.ts +44 -0
  491. package/dist/orchestrator/OrchestratorDaemon.js +150 -0
  492. package/dist/orchestrator/OrchestratorDaemon.js.map +1 -0
  493. package/dist/orchestrator/PolicyLoader.d.ts +80 -0
  494. package/dist/orchestrator/PolicyLoader.js +229 -0
  495. package/dist/orchestrator/PolicyLoader.js.map +1 -0
  496. package/dist/orchestrator/ReconciliationLoop.d.ts +71 -0
  497. package/dist/orchestrator/ReconciliationLoop.js +266 -0
  498. package/dist/orchestrator/ReconciliationLoop.js.map +1 -0
  499. package/dist/orchestrator/TrackerAdapter.d.ts +60 -0
  500. package/dist/orchestrator/TrackerAdapter.js +147 -0
  501. package/dist/orchestrator/TrackerAdapter.js.map +1 -0
  502. package/dist/orchestrator/WorkspaceManager.d.ts +66 -0
  503. package/dist/orchestrator/WorkspaceManager.js +257 -0
  504. package/dist/orchestrator/WorkspaceManager.js.map +1 -0
  505. package/dist/output/BrandThemeLoader.d.ts +54 -0
  506. package/dist/output/BrandThemeLoader.js +340 -0
  507. package/dist/output/BrandThemeLoader.js.map +1 -0
  508. package/dist/output/GovernanceDashboard.d.ts +59 -0
  509. package/dist/output/GovernanceDashboard.js +281 -0
  510. package/dist/output/GovernanceDashboard.js.map +1 -0
  511. package/dist/output/HTMLArtifactLayer.d.ts +97 -0
  512. package/dist/output/HTMLArtifactLayer.js +576 -0
  513. package/dist/output/HTMLArtifactLayer.js.map +1 -0
  514. package/dist/output/HTMLDocumentRenderer.d.ts +83 -0
  515. package/dist/output/HTMLDocumentRenderer.js +718 -0
  516. package/dist/output/HTMLDocumentRenderer.js.map +1 -0
  517. package/dist/output/UIPrototypeRenderer.d.ts +61 -0
  518. package/dist/output/UIPrototypeRenderer.js +500 -0
  519. package/dist/output/UIPrototypeRenderer.js.map +1 -0
  520. package/dist/output/index.d.ts +10 -0
  521. package/dist/output/index.js +8 -0
  522. package/dist/output/index.js.map +1 -0
  523. package/dist/prompts/PhasePromptRegistry.d.ts +53 -0
  524. package/dist/prompts/PhasePromptRegistry.js +517 -0
  525. package/dist/prompts/PhasePromptRegistry.js.map +1 -0
  526. package/dist/prompts/PromptOptimizer.d.ts +42 -0
  527. package/dist/prompts/PromptOptimizer.js +309 -0
  528. package/dist/prompts/PromptOptimizer.js.map +1 -0
  529. package/dist/prompts/VibeTemplateGallery.d.ts +25 -0
  530. package/dist/prompts/VibeTemplateGallery.js +295 -0
  531. package/dist/prompts/VibeTemplateGallery.js.map +1 -0
  532. package/dist/qa/BrowserDaemon.d.ts +23 -0
  533. package/dist/qa/BrowserDaemon.js +79 -0
  534. package/dist/qa/BrowserDaemon.js.map +1 -0
  535. package/dist/qa/E2ETestOrchestrator.d.ts +14 -0
  536. package/dist/qa/E2ETestOrchestrator.js +19 -0
  537. package/dist/qa/E2ETestOrchestrator.js.map +1 -0
  538. package/dist/review/CrossModelReviewer.d.ts +35 -0
  539. package/dist/review/CrossModelReviewer.js +75 -0
  540. package/dist/review/CrossModelReviewer.js.map +1 -0
  541. package/dist/review/ReviewAggregator.d.ts +13 -0
  542. package/dist/review/ReviewAggregator.js +28 -0
  543. package/dist/review/ReviewAggregator.js.map +1 -0
  544. package/dist/review/reviewCommands.d.ts +15 -0
  545. package/dist/review/reviewCommands.js +24 -0
  546. package/dist/review/reviewCommands.js.map +1 -0
  547. package/dist/routing/LocalModelProvider.d.ts +11 -0
  548. package/dist/routing/LocalModelProvider.js +21 -0
  549. package/dist/routing/LocalModelProvider.js.map +1 -0
  550. package/dist/routing/ModelRouter.d.ts +42 -0
  551. package/dist/routing/ModelRouter.js +94 -0
  552. package/dist/routing/ModelRouter.js.map +1 -0
  553. package/dist/routing/PromptCachePolicy.d.ts +37 -0
  554. package/dist/routing/PromptCachePolicy.js +97 -0
  555. package/dist/routing/PromptCachePolicy.js.map +1 -0
  556. package/dist/runtime/AiOsRuntime.d.ts +485 -0
  557. package/dist/runtime/AiOsRuntime.js +1846 -0
  558. package/dist/runtime/AiOsRuntime.js.map +1 -0
  559. package/dist/runtime/CostAnalyzer.d.ts +53 -0
  560. package/dist/runtime/CostAnalyzer.js +160 -0
  561. package/dist/runtime/CostAnalyzer.js.map +1 -0
  562. package/dist/runtime/CostOptimizer.d.ts +11 -0
  563. package/dist/runtime/CostOptimizer.js +21 -0
  564. package/dist/runtime/CostOptimizer.js.map +1 -0
  565. package/dist/runtime/ExecutionLedger.d.ts +46 -0
  566. package/dist/runtime/ExecutionLedger.js +71 -0
  567. package/dist/runtime/ExecutionLedger.js.map +1 -0
  568. package/dist/runtime/FinalReportGuard.d.ts +16 -0
  569. package/dist/runtime/FinalReportGuard.js +14 -0
  570. package/dist/runtime/FinalReportGuard.js.map +1 -0
  571. package/dist/runtime/ModelUsageLedger.d.ts +101 -0
  572. package/dist/runtime/ModelUsageLedger.js +296 -0
  573. package/dist/runtime/ModelUsageLedger.js.map +1 -0
  574. package/dist/runtime/RuntimeDoctor.d.ts +23 -0
  575. package/dist/runtime/RuntimeDoctor.js +151 -0
  576. package/dist/runtime/RuntimeDoctor.js.map +1 -0
  577. package/dist/runtime/RuntimeEvidenceLedger.d.ts +50 -0
  578. package/dist/runtime/RuntimeEvidenceLedger.js +89 -0
  579. package/dist/runtime/RuntimeEvidenceLedger.js.map +1 -0
  580. package/dist/runtime/SessionLedger.d.ts +53 -0
  581. package/dist/runtime/SessionLedger.js +104 -0
  582. package/dist/runtime/SessionLedger.js.map +1 -0
  583. package/dist/runtime/index.d.ts +7 -0
  584. package/dist/runtime/index.js +8 -0
  585. package/dist/runtime/index.js.map +1 -0
  586. package/dist/setup/SetupVerification.d.ts +42 -0
  587. package/dist/setup/SetupVerification.js +180 -0
  588. package/dist/setup/SetupVerification.js.map +1 -0
  589. package/dist/setup/SetupWizard.d.ts +45 -0
  590. package/dist/setup/SetupWizard.js +216 -0
  591. package/dist/setup/SetupWizard.js.map +1 -0
  592. package/dist/shield/PolicyCompiler.d.ts +70 -0
  593. package/dist/shield/PolicyCompiler.js +540 -0
  594. package/dist/shield/PolicyCompiler.js.map +1 -0
  595. package/dist/shield/ProtectedPaths.d.ts +39 -0
  596. package/dist/shield/ProtectedPaths.js +179 -0
  597. package/dist/shield/ProtectedPaths.js.map +1 -0
  598. package/dist/shield/ShieldProtocol.d.ts +50 -0
  599. package/dist/shield/ShieldProtocol.js +103 -0
  600. package/dist/shield/ShieldProtocol.js.map +1 -0
  601. package/dist/skills/ExternalSkills.d.ts +3 -0
  602. package/dist/skills/ExternalSkills.js +27 -0
  603. package/dist/skills/ExternalSkills.js.map +1 -0
  604. package/dist/skills/GrillingSessionSkill.d.ts +65 -0
  605. package/dist/skills/GrillingSessionSkill.js +113 -0
  606. package/dist/skills/GrillingSessionSkill.js.map +1 -0
  607. package/dist/skills/GrillingTemplates.d.ts +7 -0
  608. package/dist/skills/GrillingTemplates.js +38 -0
  609. package/dist/skills/GrillingTemplates.js.map +1 -0
  610. package/dist/skills/RoleSkills.d.ts +20 -0
  611. package/dist/skills/RoleSkills.js +154 -0
  612. package/dist/skills/RoleSkills.js.map +1 -0
  613. package/dist/skills/SkillCatalog.d.ts +13 -0
  614. package/dist/skills/SkillCatalog.js +184 -0
  615. package/dist/skills/SkillCatalog.js.map +1 -0
  616. package/dist/skills/SkillDiscovery.d.ts +84 -0
  617. package/dist/skills/SkillDiscovery.js +402 -0
  618. package/dist/skills/SkillDiscovery.js.map +1 -0
  619. package/dist/skills/SkillDoctor.d.ts +37 -0
  620. package/dist/skills/SkillDoctor.js +267 -0
  621. package/dist/skills/SkillDoctor.js.map +1 -0
  622. package/dist/skills/SkillExecutor.d.ts +38 -0
  623. package/dist/skills/SkillExecutor.js +237 -0
  624. package/dist/skills/SkillExecutor.js.map +1 -0
  625. package/dist/skills/SkillFrontmatter.d.ts +28 -0
  626. package/dist/skills/SkillFrontmatter.js +152 -0
  627. package/dist/skills/SkillFrontmatter.js.map +1 -0
  628. package/dist/skills/SkillInstaller.d.ts +40 -0
  629. package/dist/skills/SkillInstaller.js +117 -0
  630. package/dist/skills/SkillInstaller.js.map +1 -0
  631. package/dist/skills/SkillMdStandard.d.ts +33 -0
  632. package/dist/skills/SkillMdStandard.js +88 -0
  633. package/dist/skills/SkillMdStandard.js.map +1 -0
  634. package/dist/skills/SkillRadar.d.ts +83 -0
  635. package/dist/skills/SkillRadar.js +404 -0
  636. package/dist/skills/SkillRadar.js.map +1 -0
  637. package/dist/skills/SkillRegistry.d.ts +112 -0
  638. package/dist/skills/SkillRegistry.js +161 -0
  639. package/dist/skills/SkillRegistry.js.map +1 -0
  640. package/dist/skills/SkillRepository.d.ts +71 -0
  641. package/dist/skills/SkillRepository.js +435 -0
  642. package/dist/skills/SkillRepository.js.map +1 -0
  643. package/dist/skills/TriggerEngine.d.ts +43 -0
  644. package/dist/skills/TriggerEngine.js +142 -0
  645. package/dist/skills/TriggerEngine.js.map +1 -0
  646. package/dist/skills/coreSkills.d.ts +6 -0
  647. package/dist/skills/coreSkills.js +41 -0
  648. package/dist/skills/coreSkills.js.map +1 -0
  649. package/dist/skills/index.d.ts +10 -0
  650. package/dist/skills/index.js +12 -0
  651. package/dist/skills/index.js.map +1 -0
  652. package/dist/skills/interop/GStackInterop.d.ts +15 -0
  653. package/dist/skills/interop/GStackInterop.js +34 -0
  654. package/dist/skills/interop/GStackInterop.js.map +1 -0
  655. package/dist/skills/interop/OMCInterop.d.ts +15 -0
  656. package/dist/skills/interop/OMCInterop.js +34 -0
  657. package/dist/skills/interop/OMCInterop.js.map +1 -0
  658. package/dist/skills/routing/SkillGate.d.ts +12 -0
  659. package/dist/skills/routing/SkillGate.js +117 -0
  660. package/dist/skills/routing/SkillGate.js.map +1 -0
  661. package/dist/skills/routing/SkillPlanner.d.ts +8 -0
  662. package/dist/skills/routing/SkillPlanner.js +179 -0
  663. package/dist/skills/routing/SkillPlanner.js.map +1 -0
  664. package/dist/skills/routing/SkillPolicy.d.ts +6 -0
  665. package/dist/skills/routing/SkillPolicy.js +336 -0
  666. package/dist/skills/routing/SkillPolicy.js.map +1 -0
  667. package/dist/skills/routing/SkillRoutingTypes.d.ts +89 -0
  668. package/dist/skills/routing/SkillRoutingTypes.js +2 -0
  669. package/dist/skills/routing/SkillRoutingTypes.js.map +1 -0
  670. package/dist/skills/routing/TaskIntentClassifier.d.ts +6 -0
  671. package/dist/skills/routing/TaskIntentClassifier.js +79 -0
  672. package/dist/skills/routing/TaskIntentClassifier.js.map +1 -0
  673. package/dist/skills/routing/index.d.ts +5 -0
  674. package/dist/skills/routing/index.js +6 -0
  675. package/dist/skills/routing/index.js.map +1 -0
  676. package/dist/tasks/IssueTriageFSM.d.ts +26 -0
  677. package/dist/tasks/IssueTriageFSM.js +107 -0
  678. package/dist/tasks/IssueTriageFSM.js.map +1 -0
  679. package/dist/tasks/TaskEngine.d.ts +97 -0
  680. package/dist/tasks/TaskEngine.js +289 -0
  681. package/dist/tasks/TaskEngine.js.map +1 -0
  682. package/dist/testing/DiffTestSelector.d.ts +22 -0
  683. package/dist/testing/DiffTestSelector.js +114 -0
  684. package/dist/testing/DiffTestSelector.js.map +1 -0
  685. package/dist/testing/index.d.ts +1 -0
  686. package/dist/testing/index.js +3 -0
  687. package/dist/testing/index.js.map +1 -0
  688. package/dist/tools/CommandOutputCompressor.d.ts +28 -0
  689. package/dist/tools/CommandOutputCompressor.js +242 -0
  690. package/dist/tools/CommandOutputCompressor.js.map +1 -0
  691. package/dist/tools/CommandRunLedger.d.ts +77 -0
  692. package/dist/tools/CommandRunLedger.js +111 -0
  693. package/dist/tools/CommandRunLedger.js.map +1 -0
  694. package/dist/tools/RtkRuntime.d.ts +9 -0
  695. package/dist/tools/RtkRuntime.js +43 -0
  696. package/dist/tools/RtkRuntime.js.map +1 -0
  697. package/dist/tools/SafeCommandRunner.d.ts +16 -0
  698. package/dist/tools/SafeCommandRunner.js +83 -0
  699. package/dist/tools/SafeCommandRunner.js.map +1 -0
  700. package/dist/tools/ToolCapabilityRegistry.d.ts +51 -0
  701. package/dist/tools/ToolCapabilityRegistry.js +295 -0
  702. package/dist/tools/ToolCapabilityRegistry.js.map +1 -0
  703. package/dist/tools/ToolEvidenceGate.d.ts +39 -0
  704. package/dist/tools/ToolEvidenceGate.js +117 -0
  705. package/dist/tools/ToolEvidenceGate.js.map +1 -0
  706. package/dist/tools/ToolEvidenceStore.d.ts +58 -0
  707. package/dist/tools/ToolEvidenceStore.js +129 -0
  708. package/dist/tools/ToolEvidenceStore.js.map +1 -0
  709. package/dist/tools/ToolOrchestrator.d.ts +67 -0
  710. package/dist/tools/ToolOrchestrator.js +252 -0
  711. package/dist/tools/ToolOrchestrator.js.map +1 -0
  712. package/dist/tools/ToolPolicy.d.ts +33 -0
  713. package/dist/tools/ToolPolicy.js +172 -0
  714. package/dist/tools/ToolPolicy.js.map +1 -0
  715. package/dist/tools/index.d.ts +7 -0
  716. package/dist/tools/index.js +8 -0
  717. package/dist/tools/index.js.map +1 -0
  718. package/dist/tui/TuiDashboard.d.ts +3 -0
  719. package/dist/tui/TuiDashboard.js +120 -0
  720. package/dist/tui/TuiDashboard.js.map +1 -0
  721. package/dist/version.d.ts +3 -0
  722. package/dist/version.js +15 -0
  723. package/dist/version.js.map +1 -0
  724. package/dist/workflow/AdaptiveWorkflowRouter.d.ts +38 -0
  725. package/dist/workflow/AdaptiveWorkflowRouter.js +214 -0
  726. package/dist/workflow/AdaptiveWorkflowRouter.js.map +1 -0
  727. package/dist/workflow/CommitDiscipline.d.ts +68 -0
  728. package/dist/workflow/CommitDiscipline.js +328 -0
  729. package/dist/workflow/CommitDiscipline.js.map +1 -0
  730. package/dist/workflow/ContextGovernance.d.ts +51 -0
  731. package/dist/workflow/ContextGovernance.js +233 -0
  732. package/dist/workflow/ContextGovernance.js.map +1 -0
  733. package/dist/workflow/CrossRepoOrchestrator.d.ts +92 -0
  734. package/dist/workflow/CrossRepoOrchestrator.js +408 -0
  735. package/dist/workflow/CrossRepoOrchestrator.js.map +1 -0
  736. package/dist/workflow/DiagnosticLoop.d.ts +40 -0
  737. package/dist/workflow/DiagnosticLoop.js +105 -0
  738. package/dist/workflow/DiagnosticLoop.js.map +1 -0
  739. package/dist/workflow/EngineeringStandards.d.ts +212 -0
  740. package/dist/workflow/EngineeringStandards.js +1113 -0
  741. package/dist/workflow/EngineeringStandards.js.map +1 -0
  742. package/dist/workflow/EvidenceStore.d.ts +20 -0
  743. package/dist/workflow/EvidenceStore.js +48 -0
  744. package/dist/workflow/EvidenceStore.js.map +1 -0
  745. package/dist/workflow/EvolutionShadowPromoter.d.ts +46 -0
  746. package/dist/workflow/EvolutionShadowPromoter.js +73 -0
  747. package/dist/workflow/EvolutionShadowPromoter.js.map +1 -0
  748. package/dist/workflow/GateCatalog.d.ts +63 -0
  749. package/dist/workflow/GateCatalog.js +268 -0
  750. package/dist/workflow/GateCatalog.js.map +1 -0
  751. package/dist/workflow/GovernanceLock.d.ts +35 -0
  752. package/dist/workflow/GovernanceLock.js +58 -0
  753. package/dist/workflow/GovernanceLock.js.map +1 -0
  754. package/dist/workflow/GovernanceRoi.d.ts +52 -0
  755. package/dist/workflow/GovernanceRoi.js +204 -0
  756. package/dist/workflow/GovernanceRoi.js.map +1 -0
  757. package/dist/workflow/GovernanceTemplatePacks.d.ts +24 -0
  758. package/dist/workflow/GovernanceTemplatePacks.js +2134 -0
  759. package/dist/workflow/GovernanceTemplatePacks.js.map +1 -0
  760. package/dist/workflow/GovernanceTemplates.d.ts +19 -0
  761. package/dist/workflow/GovernanceTemplates.js +1291 -0
  762. package/dist/workflow/GovernanceTemplates.js.map +1 -0
  763. package/dist/workflow/McpGovernance.d.ts +63 -0
  764. package/dist/workflow/McpGovernance.js +198 -0
  765. package/dist/workflow/McpGovernance.js.map +1 -0
  766. package/dist/workflow/OutOfScopeStore.d.ts +37 -0
  767. package/dist/workflow/OutOfScopeStore.js +164 -0
  768. package/dist/workflow/OutOfScopeStore.js.map +1 -0
  769. package/dist/workflow/PhaseMarkerTracker.d.ts +63 -0
  770. package/dist/workflow/PhaseMarkerTracker.js +291 -0
  771. package/dist/workflow/PhaseMarkerTracker.js.map +1 -0
  772. package/dist/workflow/ResourceGovernance.d.ts +120 -0
  773. package/dist/workflow/ResourceGovernance.js +531 -0
  774. package/dist/workflow/ResourceGovernance.js.map +1 -0
  775. package/dist/workflow/ReviewAnalyzer.d.ts +80 -0
  776. package/dist/workflow/ReviewAnalyzer.js +438 -0
  777. package/dist/workflow/ReviewAnalyzer.js.map +1 -0
  778. package/dist/workflow/ReviewStore.d.ts +36 -0
  779. package/dist/workflow/ReviewStore.js +42 -0
  780. package/dist/workflow/ReviewStore.js.map +1 -0
  781. package/dist/workflow/SecurityAudit.d.ts +27 -0
  782. package/dist/workflow/SecurityAudit.js +294 -0
  783. package/dist/workflow/SecurityAudit.js.map +1 -0
  784. package/dist/workflow/SessionCoordinator.d.ts +103 -0
  785. package/dist/workflow/SessionCoordinator.js +401 -0
  786. package/dist/workflow/SessionCoordinator.js.map +1 -0
  787. package/dist/workflow/SessionPreamble.d.ts +19 -0
  788. package/dist/workflow/SessionPreamble.js +130 -0
  789. package/dist/workflow/SessionPreamble.js.map +1 -0
  790. package/dist/workflow/SessionStateTracker.d.ts +74 -0
  791. package/dist/workflow/SessionStateTracker.js +270 -0
  792. package/dist/workflow/SessionStateTracker.js.map +1 -0
  793. package/dist/workflow/ShipPipeline.d.ts +30 -0
  794. package/dist/workflow/ShipPipeline.js +366 -0
  795. package/dist/workflow/ShipPipeline.js.map +1 -0
  796. package/dist/workflow/TaskArtifactScaffolder.d.ts +69 -0
  797. package/dist/workflow/TaskArtifactScaffolder.js +333 -0
  798. package/dist/workflow/TaskArtifactScaffolder.js.map +1 -0
  799. package/dist/workflow/TaskDependencyGraph.d.ts +73 -0
  800. package/dist/workflow/TaskDependencyGraph.js +245 -0
  801. package/dist/workflow/TaskDependencyGraph.js.map +1 -0
  802. package/dist/workflow/TaskLevelDetector.d.ts +41 -0
  803. package/dist/workflow/TaskLevelDetector.js +219 -0
  804. package/dist/workflow/TaskLevelDetector.js.map +1 -0
  805. package/dist/workflow/TaskMetricsStore.d.ts +49 -0
  806. package/dist/workflow/TaskMetricsStore.js +149 -0
  807. package/dist/workflow/TaskMetricsStore.js.map +1 -0
  808. package/dist/workflow/TaskScoreEngine.d.ts +42 -0
  809. package/dist/workflow/TaskScoreEngine.js +181 -0
  810. package/dist/workflow/TaskScoreEngine.js.map +1 -0
  811. package/dist/workflow/TddLoop.d.ts +49 -0
  812. package/dist/workflow/TddLoop.js +78 -0
  813. package/dist/workflow/TddLoop.js.map +1 -0
  814. package/dist/workflow/UpgradeManager.d.ts +178 -0
  815. package/dist/workflow/UpgradeManager.js +665 -0
  816. package/dist/workflow/UpgradeManager.js.map +1 -0
  817. package/dist/workflow/VerificationCommands.d.ts +36 -0
  818. package/dist/workflow/VerificationCommands.js +123 -0
  819. package/dist/workflow/VerificationCommands.js.map +1 -0
  820. package/dist/workflow/VerificationProfile.d.ts +67 -0
  821. package/dist/workflow/VerificationProfile.js +241 -0
  822. package/dist/workflow/VerificationProfile.js.map +1 -0
  823. package/dist/workflow/VerificationSchema.d.ts +46 -0
  824. package/dist/workflow/VerificationSchema.js +97 -0
  825. package/dist/workflow/VerificationSchema.js.map +1 -0
  826. package/dist/workflow/WorkflowArtifactWriter.d.ts +113 -0
  827. package/dist/workflow/WorkflowArtifactWriter.js +242 -0
  828. package/dist/workflow/WorkflowArtifactWriter.js.map +1 -0
  829. package/dist/workflow/WorkflowEngine.d.ts +83 -0
  830. package/dist/workflow/WorkflowEngine.js +183 -0
  831. package/dist/workflow/WorkflowEngine.js.map +1 -0
  832. package/dist/workflow/WorkflowGuidance.d.ts +30 -0
  833. package/dist/workflow/WorkflowGuidance.js +204 -0
  834. package/dist/workflow/WorkflowGuidance.js.map +1 -0
  835. package/dist/workflow/WorkflowOpenTasks.d.ts +16 -0
  836. package/dist/workflow/WorkflowOpenTasks.js +37 -0
  837. package/dist/workflow/WorkflowOpenTasks.js.map +1 -0
  838. package/dist/workflow/WorkflowOrchestrator.d.ts +59 -0
  839. package/dist/workflow/WorkflowOrchestrator.js +326 -0
  840. package/dist/workflow/WorkflowOrchestrator.js.map +1 -0
  841. package/dist/workflow/WorkflowTemplates.d.ts +38 -0
  842. package/dist/workflow/WorkflowTemplates.js +371 -0
  843. package/dist/workflow/WorkflowTemplates.js.map +1 -0
  844. package/dist/workflow/WorkspaceLifecycle.d.ts +71 -0
  845. package/dist/workflow/WorkspaceLifecycle.js +401 -0
  846. package/dist/workflow/WorkspaceLifecycle.js.map +1 -0
  847. package/dist/workflow/WorkspacePolicy.d.ts +46 -0
  848. package/dist/workflow/WorkspacePolicy.js +141 -0
  849. package/dist/workflow/WorkspacePolicy.js.map +1 -0
  850. package/dist/workflow/WorkspaceSafety.d.ts +9 -0
  851. package/dist/workflow/WorkspaceSafety.js +49 -0
  852. package/dist/workflow/WorkspaceSafety.js.map +1 -0
  853. package/dist/workflow/WorkspaceTopology.d.ts +58 -0
  854. package/dist/workflow/WorkspaceTopology.js +176 -0
  855. package/dist/workflow/WorkspaceTopology.js.map +1 -0
  856. package/dist/workflow/autofix/AutoFixEngine.d.ts +37 -0
  857. package/dist/workflow/autofix/AutoFixEngine.js +169 -0
  858. package/dist/workflow/autofix/AutoFixEngine.js.map +1 -0
  859. package/dist/workflow/autonomous/AutonomousDevLoop.d.ts +88 -0
  860. package/dist/workflow/autonomous/AutonomousDevLoop.js +381 -0
  861. package/dist/workflow/autonomous/AutonomousDevLoop.js.map +1 -0
  862. package/dist/workflow/autonomous/BackgroundHunter.d.ts +74 -0
  863. package/dist/workflow/autonomous/BackgroundHunter.js +220 -0
  864. package/dist/workflow/autonomous/BackgroundHunter.js.map +1 -0
  865. package/dist/workflow/autonomous/WorklogManager.d.ts +50 -0
  866. package/dist/workflow/autonomous/WorklogManager.js +264 -0
  867. package/dist/workflow/autonomous/WorklogManager.js.map +1 -0
  868. package/dist/workflow/autonomous/index.d.ts +3 -0
  869. package/dist/workflow/autonomous/index.js +5 -0
  870. package/dist/workflow/autonomous/index.js.map +1 -0
  871. package/dist/workflow/cognitive/AmbiguityScorer.d.ts +17 -0
  872. package/dist/workflow/cognitive/AmbiguityScorer.js +107 -0
  873. package/dist/workflow/cognitive/AmbiguityScorer.js.map +1 -0
  874. package/dist/workflow/cognitive/ConsensusPlanner.d.ts +26 -0
  875. package/dist/workflow/cognitive/ConsensusPlanner.js +141 -0
  876. package/dist/workflow/cognitive/ConsensusPlanner.js.map +1 -0
  877. package/dist/workflow/cognitive/SocraticQuestioner.d.ts +33 -0
  878. package/dist/workflow/cognitive/SocraticQuestioner.js +276 -0
  879. package/dist/workflow/cognitive/SocraticQuestioner.js.map +1 -0
  880. package/dist/workflow/evolution/LessonExtractor.d.ts +90 -0
  881. package/dist/workflow/evolution/LessonExtractor.js +317 -0
  882. package/dist/workflow/evolution/LessonExtractor.js.map +1 -0
  883. package/dist/workflow/evolution/SelfImproveEngine.d.ts +156 -0
  884. package/dist/workflow/evolution/SelfImproveEngine.js +361 -0
  885. package/dist/workflow/evolution/SelfImproveEngine.js.map +1 -0
  886. package/dist/workflow/execution/RalphEngine.d.ts +54 -0
  887. package/dist/workflow/execution/RalphEngine.js +145 -0
  888. package/dist/workflow/execution/RalphEngine.js.map +1 -0
  889. package/dist/workflow/execution/UltraworkEngine.d.ts +43 -0
  890. package/dist/workflow/execution/UltraworkEngine.js +135 -0
  891. package/dist/workflow/execution/UltraworkEngine.js.map +1 -0
  892. package/dist/workflow/gates/EnhancedGates.d.ts +74 -0
  893. package/dist/workflow/gates/EnhancedGates.js +653 -0
  894. package/dist/workflow/gates/EnhancedGates.js.map +1 -0
  895. package/dist/workflow/gates/GateSystem.d.ts +180 -0
  896. package/dist/workflow/gates/GateSystem.js +1279 -0
  897. package/dist/workflow/gates/GateSystem.js.map +1 -0
  898. package/dist/workflow/gates/MetaGovernanceGates.d.ts +70 -0
  899. package/dist/workflow/gates/MetaGovernanceGates.js +617 -0
  900. package/dist/workflow/gates/MetaGovernanceGates.js.map +1 -0
  901. package/dist/workflow/gates/VisualGate.d.ts +41 -0
  902. package/dist/workflow/gates/VisualGate.js +174 -0
  903. package/dist/workflow/gates/VisualGate.js.map +1 -0
  904. package/dist/workflow/index.d.ts +45 -0
  905. package/dist/workflow/index.js +47 -0
  906. package/dist/workflow/index.js.map +1 -0
  907. package/dist/workflow/qa/E2ETestRunner.d.ts +102 -0
  908. package/dist/workflow/qa/E2ETestRunner.js +227 -0
  909. package/dist/workflow/qa/E2ETestRunner.js.map +1 -0
  910. package/dist/workflow/quality/HonestDelivery.d.ts +19 -0
  911. package/dist/workflow/quality/HonestDelivery.js +77 -0
  912. package/dist/workflow/quality/HonestDelivery.js.map +1 -0
  913. package/dist/workflow/quality/KarpathyEvaluator.d.ts +18 -0
  914. package/dist/workflow/quality/KarpathyEvaluator.js +76 -0
  915. package/dist/workflow/quality/KarpathyEvaluator.js.map +1 -0
  916. package/dist/workflow/types.d.ts +151 -0
  917. package/dist/workflow/types.js +4 -0
  918. package/dist/workflow/types.js.map +1 -0
  919. package/dist/workflows/DAGBuilder.d.ts +52 -0
  920. package/dist/workflows/DAGBuilder.js +169 -0
  921. package/dist/workflows/DAGBuilder.js.map +1 -0
  922. package/dist/workflows/GateParser.d.ts +55 -0
  923. package/dist/workflows/GateParser.js +73 -0
  924. package/dist/workflows/GateParser.js.map +1 -0
  925. package/dist/workflows/WorkflowExecutor.d.ts +56 -0
  926. package/dist/workflows/WorkflowExecutor.js +143 -0
  927. package/dist/workflows/WorkflowExecutor.js.map +1 -0
  928. package/dist/workflows/WorkflowOrchestrator.d.ts +81 -0
  929. package/dist/workflows/WorkflowOrchestrator.js +337 -0
  930. package/dist/workflows/WorkflowOrchestrator.js.map +1 -0
  931. package/dist/workflows/index.d.ts +2 -0
  932. package/dist/workflows/index.js +5 -0
  933. package/dist/workflows/index.js.map +1 -0
  934. package/dist/workflows/presets.d.ts +34 -0
  935. package/dist/workflows/presets.js +224 -0
  936. package/dist/workflows/presets.js.map +1 -0
  937. package/docs/README.md +105 -0
  938. package/docs/guides/DEVELOPMENT_WORKFLOW.md +99 -0
  939. package/docs/guides/GETTING_STARTED.md +93 -0
  940. package/docs/guides/MEDICAL_AGENT_OPERATING_GUIDE.md +61 -0
  941. package/docs/guides/MEDICAL_RESEARCH_DELIVERY.md +217 -0
  942. package/docs/guides/MIGRATION.md +119 -0
  943. package/docs/reference/cli.md +2921 -0
  944. package/docs/start/README.md +79 -0
  945. package/docs/start/agent-governance-demo.md +107 -0
  946. package/docs/start/artifact-lifecycle.md +326 -0
  947. package/docs/start/quickstart.md +191 -0
  948. package/docs/start/workflow-upgrade.md +198 -0
  949. package/docs/workflow/GATES_AND_SCORE.md +89 -0
  950. package/docs/workflow/PROMPT_OPTIMIZATION.md +44 -0
  951. package/docs/workflow/README.md +123 -0
  952. package/docs/workflow/node-library.md +52 -0
  953. package/docs/workflow/templates/api-contract.md +29 -0
  954. package/docs/workflow/templates/architecture-review.md +23 -0
  955. package/docs/workflow/templates/db-change-plan.md +20 -0
  956. package/docs/workflow/templates/docs-impact.md +17 -0
  957. package/docs/workflow/templates/e2e-plan.md +20 -0
  958. package/docs/workflow/templates/explore.md +16 -0
  959. package/docs/workflow/templates/github-actions-scale-preflight.yml +32 -0
  960. package/docs/workflow/templates/mini-prd.md +16 -0
  961. package/docs/workflow/templates/plan.md +37 -0
  962. package/docs/workflow/templates/pre-push-scale-preflight.sh +8 -0
  963. package/docs/workflow/templates/product-smoke.md +61 -0
  964. package/docs/workflow/templates/reality-check.md +28 -0
  965. package/docs/workflow/templates/resource-cleanup.md +17 -0
  966. package/docs/workflow/templates/resource-impact.md +25 -0
  967. package/docs/workflow/templates/review.md +12 -0
  968. package/docs/workflow/templates/runtime.md +23 -0
  969. package/docs/workflow/templates/security-review.md +26 -0
  970. package/docs/workflow/templates/skill-evidence.md +33 -0
  971. package/docs/workflow/templates/skill-plan.md +39 -0
  972. package/docs/workflow/templates/spec.md +17 -0
  973. package/docs/workflow/templates/standards-impact.md +28 -0
  974. package/docs/workflow/templates/summary.md +16 -0
  975. package/docs/workflow/templates/tasks.md +8 -0
  976. package/docs/workflow/templates/ui-spec.md +29 -0
  977. package/docs/workflow/templates/verification.md +20 -0
  978. package/docs/workflow/templates/visual-review.md +20 -0
  979. package/docs/zh/quickstart.md +108 -0
  980. package/examples/demo-projects/agent-governance-demo/CONTEXT.md +14 -0
  981. package/examples/demo-projects/agent-governance-demo/README.md +48 -0
  982. package/examples/demo-projects/agent-governance-demo/docs/CONTEXT-MAP.md +14 -0
  983. package/examples/demo-projects/agent-governance-demo/package.json +22 -0
  984. package/examples/demo-projects/agent-governance-demo/src/oauth-state.ts +39 -0
  985. package/examples/demo-projects/agent-governance-demo/tests/oauth-state.test.ts +52 -0
  986. package/mcp-configs/_INDEX.md +55 -0
  987. package/mcp-configs/context7/config.json +9 -0
  988. package/mcp-configs/fetch/config.json +9 -0
  989. package/mcp-configs/filesystem/config.json +9 -0
  990. package/mcp-configs/github/config.json +11 -0
  991. package/mcp-configs/memory/config.json +9 -0
  992. package/mcp-configs/neon/config.json +11 -0
  993. package/mcp-configs/playwright/config.json +9 -0
  994. package/mcp-configs/postgres/config.json +11 -0
  995. package/mcp-configs/puppeteer/config.json +9 -0
  996. package/mcp-configs/sequential-thinking/config.json +9 -0
  997. package/package.json +113 -0
  998. package/scripts/workflow/lib/gbrain-runtime.mjs +185 -0
  999. package/scripts/workflow/lib/report-output.mjs +107 -0
  1000. package/scripts/workflow/medscale-release-smoke.mjs +338 -0
  1001. package/scripts/workflow/provider-rehearsal.mjs +597 -0
  1002. package/scripts/workflow/setup-smoke.mjs +433 -0
  1003. package/target-research-platform/bridge_runner.py +310 -0
  1004. package/target-research-platform/config.yaml +148 -0
  1005. package/target-research-platform/data/immune_infiltration/ACC.csv +201 -0
  1006. package/target-research-platform/data/immune_infiltration/BLCA.csv +201 -0
  1007. package/target-research-platform/data/immune_infiltration/BRCA.csv +201 -0
  1008. package/target-research-platform/data/immune_infiltration/CESC.csv +201 -0
  1009. package/target-research-platform/data/immune_infiltration/CHOL.csv +201 -0
  1010. package/target-research-platform/data/immune_infiltration/COAD.csv +201 -0
  1011. package/target-research-platform/data/immune_infiltration/DLBC.csv +201 -0
  1012. package/target-research-platform/data/immune_infiltration/ESCA.csv +201 -0
  1013. package/target-research-platform/data/immune_infiltration/GBM.csv +201 -0
  1014. package/target-research-platform/data/immune_infiltration/HNSC.csv +201 -0
  1015. package/target-research-platform/data/immune_infiltration/KICH.csv +201 -0
  1016. package/target-research-platform/data/immune_infiltration/KIRC.csv +201 -0
  1017. package/target-research-platform/data/immune_infiltration/KIRP.csv +201 -0
  1018. package/target-research-platform/data/immune_infiltration/LAML.csv +201 -0
  1019. package/target-research-platform/data/immune_infiltration/LGG.csv +201 -0
  1020. package/target-research-platform/data/immune_infiltration/LIHC.csv +201 -0
  1021. package/target-research-platform/data/immune_infiltration/LUAD.csv +201 -0
  1022. package/target-research-platform/data/immune_infiltration/LUSC.csv +201 -0
  1023. package/target-research-platform/data/immune_infiltration/MESO.csv +201 -0
  1024. package/target-research-platform/data/immune_infiltration/OV.csv +201 -0
  1025. package/target-research-platform/data/immune_infiltration/PAAD.csv +201 -0
  1026. package/target-research-platform/data/immune_infiltration/PCPG.csv +201 -0
  1027. package/target-research-platform/data/immune_infiltration/PRAD.csv +201 -0
  1028. package/target-research-platform/data/immune_infiltration/READ.csv +201 -0
  1029. package/target-research-platform/data/immune_infiltration/SARC.csv +201 -0
  1030. package/target-research-platform/data/immune_infiltration/SKCM.csv +201 -0
  1031. package/target-research-platform/data/immune_infiltration/STAD.csv +201 -0
  1032. package/target-research-platform/data/immune_infiltration/TGCT.csv +201 -0
  1033. package/target-research-platform/data/immune_infiltration/THCA.csv +201 -0
  1034. package/target-research-platform/data/immune_infiltration/THYM.csv +201 -0
  1035. package/target-research-platform/data/immune_infiltration/UCEC.csv +201 -0
  1036. package/target-research-platform/data/immune_infiltration/UCS.csv +201 -0
  1037. package/target-research-platform/data/immune_infiltration/UVM.csv +201 -0
  1038. package/target-research-platform/docs/JSON_SCHEMA.md +352 -0
  1039. package/target-research-platform/docs/PROGRESS_2026-06-09.md +140 -0
  1040. package/target-research-platform/main.py +755 -0
  1041. package/target-research-platform/pyproject.toml +54 -0
  1042. package/target-research-platform/requirements.txt +9 -0
  1043. package/target-research-platform/run_dashboard.py +5 -0
  1044. package/target-research-platform/run_real_medical_workflow.py +28 -0
  1045. package/target-research-platform/scripts/demo_report.py +481 -0
  1046. package/target-research-platform/scripts/generate_evidence_package.py +75 -0
  1047. package/target-research-platform/scripts/prepare_immune_data.py +386 -0
  1048. package/target-research-platform/src/__init__.py +4 -0
  1049. package/target-research-platform/src/analysis/__init__.py +3 -0
  1050. package/target-research-platform/src/analysis/stage1_expression/__init__.py +12 -0
  1051. package/target-research-platform/src/analysis/stage1_expression/immune_correlation.py +366 -0
  1052. package/target-research-platform/src/analysis/stage1_expression/pipeline.py +579 -0
  1053. package/target-research-platform/src/analysis/stage1_expression/survival_analysis.py +382 -0
  1054. package/target-research-platform/src/analysis/stage2_screening/__init__.py +12 -0
  1055. package/target-research-platform/src/analysis/stage2_screening/differential_expression.py +451 -0
  1056. package/target-research-platform/src/analysis/stage2_screening/druggability_score.py +477 -0
  1057. package/target-research-platform/src/analysis/stage2_screening/pipeline.py +822 -0
  1058. package/target-research-platform/src/analysis/stage3_deep_research/__init__.py +12 -0
  1059. package/target-research-platform/src/analysis/stage3_deep_research/competitive_landscape.py +479 -0
  1060. package/target-research-platform/src/analysis/stage3_deep_research/pipeline.py +763 -0
  1061. package/target-research-platform/src/analysis/stage3_deep_research/target_function.py +290 -0
  1062. package/target-research-platform/src/analysis/stage4_business/__init__.py +12 -0
  1063. package/target-research-platform/src/analysis/stage4_business/business_plan.py +816 -0
  1064. package/target-research-platform/src/analysis/stage4_business/milestone_planner.py +844 -0
  1065. package/target-research-platform/src/analysis/stage4_business/pipeline.py +284 -0
  1066. package/target-research-platform/src/api_clients/__init__.py +29 -0
  1067. package/target-research-platform/src/api_clients/aminer_client.py +163 -0
  1068. package/target-research-platform/src/api_clients/base_client.py +186 -0
  1069. package/target-research-platform/src/api_clients/clinicaltrials_client.py +411 -0
  1070. package/target-research-platform/src/api_clients/geo_client.py +1420 -0
  1071. package/target-research-platform/src/api_clients/gtex_client.py +209 -0
  1072. package/target-research-platform/src/api_clients/hpa_client.py +170 -0
  1073. package/target-research-platform/src/api_clients/immune_data_manager.py +247 -0
  1074. package/target-research-platform/src/api_clients/openalex_client.py +86 -0
  1075. package/target-research-platform/src/api_clients/opentargets_client.py +558 -0
  1076. package/target-research-platform/src/api_clients/pubmed_client.py +361 -0
  1077. package/target-research-platform/src/api_clients/tcga_client.py +712 -0
  1078. package/target-research-platform/src/api_clients/timer_client.py +169 -0
  1079. package/target-research-platform/src/dashboard/app.py +2283 -0
  1080. package/target-research-platform/src/dashboard/deliverables.py +710 -0
  1081. package/target-research-platform/src/dashboard/static/artifactPreview.js +96 -0
  1082. package/target-research-platform/src/dashboard/static/index.html +1292 -0
  1083. package/target-research-platform/src/dashboard/status_tracker.py +237 -0
  1084. package/target-research-platform/src/output/__init__.py +42 -0
  1085. package/target-research-platform/src/output/agent_llm_provider.py +171 -0
  1086. package/target-research-platform/src/output/chart_generator.py +550 -0
  1087. package/target-research-platform/src/output/data_exporter.py +215 -0
  1088. package/target-research-platform/src/output/delivery_packager.py +791 -0
  1089. package/target-research-platform/src/output/evidence_package.py +230 -0
  1090. package/target-research-platform/src/output/journal_templates.py +193 -0
  1091. package/target-research-platform/src/output/literature_enricher.py +395 -0
  1092. package/target-research-platform/src/output/literature_reviewer.py +420 -0
  1093. package/target-research-platform/src/output/manuscript_fact_checker.py +279 -0
  1094. package/target-research-platform/src/output/manuscript_generator.py +1189 -0
  1095. package/target-research-platform/src/output/manuscript_quality.py +401 -0
  1096. package/target-research-platform/src/output/medical_skills_bridge.py +140 -0
  1097. package/target-research-platform/src/output/report_generator.py +542 -0
  1098. package/target-research-platform/src/output/usage_envelope.py +193 -0
  1099. package/target-research-platform/src/utils/__init__.py +1 -0
  1100. package/target-research-platform/src/utils/config.py +125 -0
  1101. package/target-research-platform/src/utils/logger.py +71 -0
  1102. package/target-research-platform/src/validators/__init__.py +13 -0
  1103. package/target-research-platform/src/validators/cross_validator.py +394 -0
  1104. package/target-research-platform/src/validators/data_provenance.py +298 -0
@@ -0,0 +1,641 @@
1
+ // SCALE Engine - Hook Generator Enhanced (v0.10.0)
2
+ // Generates JavaScript hooks from rules, templates, and detectors.
3
+ import { writeFileSync, mkdirSync, existsSync, readFileSync } from 'node:fs';
4
+ import { join } from 'node:path';
5
+ import { logger } from '../core/logger.js';
6
+ // ============================================================================
7
+ // Built-in templates
8
+ // ============================================================================
9
+ const BUILTIN_TEMPLATES = [
10
+ {
11
+ id: 'tmpl-file-size-guard',
12
+ name: 'File Size Guard',
13
+ hookType: 'PreToolUse',
14
+ matcherPattern: 'Write',
15
+ description: 'Prevent writing files larger than a threshold',
16
+ templateBody: 'const MAX_LINES = {{maxLines}}; const input = JSON.parse(process.argv[2] || {}); const content = input.tool_input?.content || ""; const lines = content.split("\\n").length; if (lines > MAX_LINES) { console.error("[BLOCKED] File exceeds limit"); process.exit(2); } console.log("[PASS]"); process.exit(0);',
17
+ variables: [{ name: 'maxLines', type: 'number', required: true, defaultValue: 800, description: 'Maximum lines' }]
18
+ },
19
+ {
20
+ id: 'tmpl-dangerous-command-guard',
21
+ name: 'Dangerous Command Guard',
22
+ hookType: 'PreToolUse',
23
+ matcherPattern: 'Bash',
24
+ description: 'Block dangerous bash commands',
25
+ templateBody: 'const BLOCKED = ["rm -rf", "DROP", "TRUNCATE"]; const input = JSON.parse(process.argv[2] || {}); const cmd = input.tool_input?.command || ""; for (const p of BLOCKED) { if (cmd.includes(p)) { console.error("[BLOCKED] Dangerous: " + p); process.exit(2); } } console.log("[PASS]"); process.exit(0);',
26
+ variables: []
27
+ },
28
+ {
29
+ id: 'tmpl-test-verification',
30
+ name: 'Test Verification',
31
+ hookType: 'Stop',
32
+ matcherPattern: '',
33
+ description: 'Ensure tests pass before session ends',
34
+ templateBody: 'console.log("[CHECK] Test verification"); console.log("[PASS]"); process.exit(0);',
35
+ variables: [{ name: 'testCommand', type: 'string', required: true, defaultValue: 'bun test', description: 'Test command' }]
36
+ },
37
+ {
38
+ id: 'tmpl-console-log-detector',
39
+ name: 'Console.log Detector',
40
+ hookType: 'PostToolUse',
41
+ matcherPattern: 'Write|Edit',
42
+ description: 'Detect console.log statements',
43
+ templateBody: 'console.log("[CHECK] Console detection"); console.log("[PASS]"); process.exit(0);',
44
+ variables: []
45
+ },
46
+ // ========== Workflow Integration Hooks (v0.10.0) ==========
47
+ {
48
+ id: 'tmpl-karpathy-k1-think',
49
+ name: 'Karpathy K1-THINK Check',
50
+ hookType: 'PreToolUse',
51
+ matcherPattern: 'Write|Edit',
52
+ description: 'Ensure hypotheses are listed before coding',
53
+ templateBody: String.raw `const input = JSON.parse(process.argv[2] || "{}"); const content = input.tool_input?.content || ""; const lines = content.split("\n").length; if (lines > 20) { const hasThinking = content.includes("// @thinking") || content.includes("// Hypothesis") || content.includes("<!-- THINKING") || content.includes("Hypothesis:") || content.includes("Think:"); if (!hasThinking) { console.error("[WARN] K1-THINK: Consider listing hypotheses before coding"); console.log("[PASS-WITH-WARNING]"); process.exit(0); } } console.log("[PASS]"); process.exit(0);`,
54
+ variables: []
55
+ },
56
+ {
57
+ id: 'tmpl-karpathy-k2-simple',
58
+ name: 'Karpathy K2-SIMPLE Check',
59
+ hookType: 'PreToolUse',
60
+ matcherPattern: 'Write|Edit',
61
+ description: 'Warn about speculative future features',
62
+ templateBody: String.raw `const input = JSON.parse(process.argv[2] || "{}"); const content = input.tool_input?.content || ""; const extraFeatures = ["TODO:", "FIXME:", "Note:", "refactor", "enhance", "improve"]; const warnings = extraFeatures.filter(f => content.includes(f) && content.includes("future")); if (warnings.length > 0) { console.error("[WARN] K2-SIMPLE: Potential extra features: " + warnings.join(",")); } console.log("[PASS]"); process.exit(0);`,
63
+ variables: []
64
+ },
65
+ {
66
+ id: 'tmpl-hardcoded-secret-guard',
67
+ name: 'Hardcoded Secret Guard (G7)',
68
+ hookType: 'PreToolUse',
69
+ matcherPattern: 'Write|Edit',
70
+ description: 'Block hardcoded secrets or credentials',
71
+ templateBody: String.raw `const input = JSON.parse(process.argv[2] || "{}"); const content = input.tool_input?.content || ""; const patterns = [/(password|passwd|pwd)\s*[=:]\s*["'][^"']{8,}/i, /(api[_-]?key|apikey)\s*[=:]\s*["'][^"']{20,}/i, /(secret|token|auth)\s*[=:]\s*["'][^"']{20,}/i, /(aws|azure|gcp)[_-]?(key|secret|token)\s*[=:]/i]; for (const pattern of patterns) { if (pattern.test(content)) { console.error("[BLOCKED] G7-Security: Hardcoded secret detected"); process.exit(2); } } console.log("[PASS]"); process.exit(0);`,
72
+ variables: []
73
+ },
74
+ {
75
+ id: 'tmpl-empty-catch-guard',
76
+ name: 'Empty Catch Guard',
77
+ hookType: 'PostToolUse',
78
+ matcherPattern: 'Write|Edit',
79
+ description: 'Block empty catch blocks',
80
+ templateBody: String.raw `const input = JSON.parse(process.argv[2] || "{}"); const content = input.tool_input?.content || ""; const emptyCatchPattern = /catch\s*\([^)]*\)\s*\{\s*\}/; if (emptyCatchPattern.test(content)) { console.error("[BLOCKED] Silent failure: Empty catch block"); process.exit(2); } console.log("[PASS]"); process.exit(0);`,
81
+ variables: []
82
+ },
83
+ {
84
+ id: 'tmpl-unverified-check',
85
+ name: 'Unverified Check (HonestDelivery)',
86
+ hookType: 'Stop',
87
+ matcherPattern: '',
88
+ description: 'Check for unverified claims before session ends',
89
+ templateBody: String.raw `const fs = require("fs"); const path = require("path"); const scaleDir = process.env.SCALE_DIR || ".scale"; const dbPath = path.join(scaleDir, "scale.db"); if (!fs.existsSync(dbPath)) { console.log("[PASS]"); process.exit(0); } console.log("[CHECK] HonestDelivery: Verify test evidence"); console.log("[PASS]"); process.exit(0);`,
90
+ variables: []
91
+ },
92
+ {
93
+ id: 'tmpl-mutation-guard',
94
+ name: 'Mutation Guard',
95
+ hookType: 'PostToolUse',
96
+ matcherPattern: 'Write|Edit',
97
+ description: 'Warn about direct mutations',
98
+ templateBody: String.raw `const input = JSON.parse(process.argv[2] || "{}"); const content = input.tool_input?.content || ""; const patterns = [/[^=!<>]=[^=]/, /\.push\(/, /\.splice\(/, /delete\s+/]; const hasMutation = patterns.some(pattern => pattern.test(content)); if (hasMutation) { console.log("[INFO] Consider immutable patterns"); } console.log("[PASS]"); process.exit(0);`,
99
+ variables: []
100
+ },
101
+ {
102
+ id: 'tmpl-ai-slop-detector',
103
+ name: 'AI Slop Detector',
104
+ hookType: 'PostToolUse',
105
+ matcherPattern: 'Write',
106
+ description: 'Detect AI-generated code patterns',
107
+ templateBody: String.raw `const input = JSON.parse(process.argv[2] || "{}"); const content = input.tool_input?.content || ""; const patterns = [/"\s*\+\s*"/, /linear-gradient\(.*purple.*blue/i, /grid.*3.*columns/i, /hero.*gradient/i]; const detected = patterns.filter(pattern => pattern.test(content)); if (detected.length > 2) { console.log("[WARN] AI Slop detected: Review for human-like code"); } console.log("[PASS]"); process.exit(0);`,
108
+ variables: []
109
+ },
110
+ // ========== Phase Completion Check (v0.10.0) ==========
111
+ {
112
+ id: 'tmpl-phase-completion-check',
113
+ name: 'Phase Completion Check',
114
+ hookType: 'Stop',
115
+ matcherPattern: '',
116
+ description: 'Verify all SCALE Engine phases are complete before stopping',
117
+ templateBody: String.raw `const fs = require("fs"); const path = require("path"); const scaleDir = process.env.SCALE_DIR || ".scale"; const stateFile = path.join(scaleDir, "phases", ".phase-state"); if (!fs.existsSync(stateFile)) { console.error("[STOP] SCALE Engine: No phase state found. All phases must complete."); console.error("Missing: DEFINE, PLAN, EXECUTE, VERIFY, REVIEW, SHIP"); process.exit(2); } try { const state = JSON.parse(fs.readFileSync(stateFile, "utf-8")); const required = ["DEFINE", "PLAN", "EXECUTE", "VERIFY", "REVIEW", "SHIP"]; const missing = required.filter(p => !state[p] || state[p].completed !== true); if (missing.length > 0) { console.error("[STOP] SCALE Engine: Incomplete phases: " + missing.join(", ")); process.exit(2); } console.log("[PASS] All SCALE Engine phases complete"); process.exit(0); } catch (e) { console.error("[STOP] SCALE Engine: Failed to read phase state"); process.exit(2); }`,
118
+ variables: []
119
+ },
120
+ // ========== Workflow Execution Hooks (v0.11.0) ==========
121
+ {
122
+ id: 'tmpl-explore-check',
123
+ name: 'Explore Phase Check',
124
+ hookType: 'PreToolUse',
125
+ matcherPattern: 'Write|Edit',
126
+ description: 'Check if exploration phase completed before writing code (warning, not blocking)',
127
+ templateBody: String.raw `const fs = require("fs"); const path = require("path"); const scaleDir = process.env.SCALE_DIR || ".scale"; const exploreFile = path.join(scaleDir, "state", "explore.json"); if (!fs.existsSync(exploreFile)) { console.error("[WORKFLOW] Exploration not completed. Run: scale define <title> --description <desc>"); console.error("[WORKFLOW] Or create .scale/state/explore.json manually"); process.exit(0); } try { const explore = JSON.parse(fs.readFileSync(exploreFile, "utf-8")); if (explore.fileCount < 3) { console.error("[WORKFLOW] Explored only " + explore.fileCount + " files (minimum 3 recommended)"); } if (!explore.mainContradiction) { console.error("[WORKFLOW] No main contradiction identified in exploration"); } } catch (e) { console.error("[WORKFLOW] Failed to read explore artifact"); } console.log("[PASS]"); process.exit(0);`,
128
+ variables: []
129
+ },
130
+ {
131
+ id: 'tmpl-next-step-reminder',
132
+ name: 'Next Step Reminder',
133
+ hookType: 'Stop',
134
+ matcherPattern: '',
135
+ description: 'Remind AI of the next workflow step when stopping',
136
+ templateBody: String.raw `const fs = require("fs"); const path = require("path"); const scaleDir = process.env.SCALE_DIR || ".scale"; const phases = ["DEFINE", "PLAN", "EXECUTE", "VERIFY", "REVIEW", "SHIP"]; const phaseMap = {DEFINE:"define",PLAN:"plan",EXECUTE:"build",VERIFY:"verify",REVIEW:"review",SHIP:"ship"}; const missing = []; for (const phase of phases) { const marker = path.join(scaleDir, "phases", ".phase-" + phase.toLowerCase()); if (!fs.existsSync(marker)) { missing.push(phase); } } const stateFile = path.join(scaleDir, "state", "explore.json"); const hasExplore = fs.existsSync(stateFile); if (missing.length > 0) { const next = missing[0]; const cmd = phaseMap[next] || next.toLowerCase(); console.log("[NEXT] Remaining: " + missing.join(" -> ")); console.log("[NEXT] Next step: scale " + cmd); } else { console.log("[DONE] All phases complete"); } process.exit(0);`,
137
+ variables: []
138
+ },
139
+ // ========== Anatomy Hooks (OpenWolf-inspired) ==========
140
+ {
141
+ id: 'tmpl-anatomy-pre-read',
142
+ name: 'Anatomy Pre-Read',
143
+ hookType: 'PreToolUse',
144
+ matcherPattern: 'Read',
145
+ description: 'Look up file description from anatomy.md before Claude reads it',
146
+ templateBody: String.raw `
147
+ const fs = require("fs");
148
+ const path = require("path");
149
+ const scaleDir = process.env.SCALE_DIR || ".scale";
150
+ const input = JSON.parse(process.argv[2] || "{}");
151
+ const filePath = input.tool_input?.file_path || input.tool_input?.path || "";
152
+ if (!filePath) { console.log("[PASS]"); process.exit(0); }
153
+ const anatomyPath = path.join(scaleDir, "anatomy.md");
154
+ if (!fs.existsSync(anatomyPath)) { console.log("[PASS]"); process.exit(0); }
155
+ try {
156
+ const content = fs.readFileSync(anatomyPath, "utf-8");
157
+ const basename = path.basename(filePath);
158
+ const lines = content.split("\n");
159
+ for (const line of lines) {
160
+ if (!line.startsWith("- ")) continue;
161
+ if (line.indexOf(basename) === -1) continue;
162
+ var tokMatch = line.match(/\(~(\d+)\s+tok\)/);
163
+ var tokens = tokMatch ? tokMatch[1] : "?";
164
+ var descPart = line.split(" - ")[1];
165
+ var desc = descPart ? descPart.split("(")[0].trim() : "no description";
166
+ console.error("[ANATOMY] " + basename + " - " + desc + " (~" + tokens + " tok)");
167
+ break;
168
+ }
169
+ } catch (error) {
170
+ console.error("[ANATOMY] Lookup skipped: " + (error && error.message ? error.message : String(error)));
171
+ }
172
+ console.log("[PASS]");
173
+ process.exit(0);`,
174
+ variables: []
175
+ },
176
+ {
177
+ id: 'tmpl-anatomy-post-write',
178
+ name: 'Anatomy Post-Write',
179
+ hookType: 'PostToolUse',
180
+ matcherPattern: 'Write|Edit',
181
+ description: 'Update anatomy.md after file write/edit',
182
+ templateBody: String.raw `
183
+ const fs = require("fs");
184
+ const path = require("path");
185
+ const scaleDir = process.env.SCALE_DIR || ".scale";
186
+ const projectDir = process.env.SCALE_PROJECT_DIR || process.cwd();
187
+ const input = JSON.parse(process.argv[2] || "{}");
188
+ const filePath = input.tool_input?.file_path || input.tool_input?.path || "";
189
+ if (!filePath) { console.log("[PASS]"); process.exit(0); }
190
+ const baseName = path.basename(filePath);
191
+ if (baseName === ".env" || baseName.startsWith(".env.")) { console.log("[PASS]"); process.exit(0); }
192
+ if (filePath.includes(scaleDir)) { console.log("[PASS]"); process.exit(0); }
193
+ try {
194
+ const content = input.tool_input?.content || input.tool_input?.new_string || "";
195
+ if (!content) { console.log("[PASS]"); process.exit(0); }
196
+ const tokens = Math.ceil(content.length / 4);
197
+ const relPath = path.relative(projectDir, filePath).replace(/\\\\/g, "/");
198
+ const dir = path.dirname(relPath);
199
+ const sectionKey = dir === "." ? "./" : dir + "/";
200
+ console.log("[ANATOMY-UPDATE] " + relPath + " (~" + tokens + " tok)");
201
+ } catch (error) {
202
+ console.error("[ANATOMY-UPDATE] Skipped: " + (error && error.message ? error.message : String(error)));
203
+ }
204
+ console.log("[PASS]");
205
+ process.exit(0);`,
206
+ variables: []
207
+ },
208
+ {
209
+ id: 'tmpl-anatomy-session-start',
210
+ name: 'Anatomy Session Start',
211
+ hookType: 'SessionStart',
212
+ matcherPattern: '',
213
+ description: 'Show project overview from anatomy.md at session start',
214
+ templateBody: String.raw `
215
+ const fs = require("fs");
216
+ const path = require("path");
217
+ const scaleDir = process.env.SCALE_DIR || ".scale";
218
+ const anatomyPath = path.join(scaleDir, "anatomy.md");
219
+ if (!fs.existsSync(anatomyPath)) { console.log("[PASS]"); process.exit(0); }
220
+ try {
221
+ const content = fs.readFileSync(anatomyPath, "utf-8");
222
+ const header = content.match(/> Files: (\d+) \| Total: ~([\d,]+) tokens/);
223
+ if (header) {
224
+ console.error("[ANATOMY] Project map: " + header[1] + " files, ~" + header[2] + " tokens");
225
+ }
226
+ const age = (Date.now() - fs.statSync(anatomyPath).mtimeMs) / (1000 * 60 * 60 * 24);
227
+ if (age > 7) {
228
+ console.error("[ANATOMY] anatomy.md is " + Math.floor(age) + " days old. Consider: scale scan");
229
+ }
230
+ } catch (error) {
231
+ console.error("[ANATOMY] Session summary skipped: " + (error && error.message ? error.message : String(error)));
232
+ }
233
+ console.log("[PASS]");
234
+ process.exit(0);`,
235
+ variables: []
236
+ },
237
+ // ========== Cerebrum Pre-Write Check ==========
238
+ {
239
+ id: 'tmpl-cerebrum-pre-write',
240
+ name: 'Cerebrum Pre-Write Check',
241
+ hookType: 'PreToolUse',
242
+ matcherPattern: 'Write|Edit',
243
+ description: 'Check Do-Not-Repeat rules before writing code',
244
+ templateBody: String.raw `
245
+ const fs = require("fs");
246
+ const path = require("path");
247
+ const input = JSON.parse(process.argv[2] || "{}");
248
+ const content = input.tool_input?.content || input.tool_input?.new_string || "";
249
+ if (!content) { console.log("[PASS]"); process.exit(0); }
250
+ const scaleDir = process.env.SCALE_DIR || ".scale";
251
+ const cerebrumPath = path.join(scaleDir, "cerebrum.md");
252
+ if (!fs.existsSync(cerebrumPath)) { console.log("[PASS]"); process.exit(0); }
253
+ try {
254
+ const cerebrum = fs.readFileSync(cerebrumPath, "utf-8");
255
+ const dnrSection = cerebrum.split("## Do Not Repeat")[1]?.split("## ")[0] || "";
256
+ const rules = dnrSection.match(/- \*\*(.+?)\*\*\s+-\s+(.+)/g) || [];
257
+ const contentLower = content.toLowerCase();
258
+ for (const rule of rules) {
259
+ const m = rule.match(/- \*\*(.+?)\*\*\s+-\s+(.+)/);
260
+ if (!m) continue;
261
+ const pattern = m[1].toLowerCase();
262
+ const desc = m[2];
263
+ const words = pattern.split(/\s+/).filter(w => w.length > 2);
264
+ const hits = words.filter(w => contentLower.includes(w));
265
+ if (hits.length > 0 && hits.length >= Math.ceil(words.length * 0.4)) {
266
+ console.error("[CEREBRUM] Do-Not-Repeat: \"" + m[1] + "\" - " + desc);
267
+ }
268
+ }
269
+ } catch (error) {
270
+ console.error("[CEREBRUM] Check skipped: " + (error && error.message ? error.message : String(error)));
271
+ }
272
+ console.log("[PASS]");
273
+ process.exit(0);`,
274
+ variables: []
275
+ },
276
+ // ========== Cerebrum Session Start ==========
277
+ {
278
+ id: 'tmpl-cerebrum-session-start',
279
+ name: 'Cerebrum Session Start',
280
+ hookType: 'SessionStart',
281
+ matcherPattern: '',
282
+ description: 'Show cerebrum status at session start',
283
+ templateBody: String.raw `
284
+ const fs = require("fs");
285
+ const path = require("path");
286
+ const scaleDir = process.env.SCALE_DIR || ".scale";
287
+ const cerebrumPath = path.join(scaleDir, "cerebrum.md");
288
+ if (!fs.existsSync(cerebrumPath)) { console.log("[PASS]"); process.exit(0); }
289
+ try {
290
+ const content = fs.readFileSync(cerebrumPath, "utf-8");
291
+ const dnrCount = (content.match(/- \*\*.+?\*\*/g) || []).length;
292
+ const prefCount = (content.match(/^- [^-]/gm) || []).length - dnrCount;
293
+ console.error("[CEREBRUM] " + dnrCount + " do-not-repeat rules, preferences loaded");
294
+ const age = (Date.now() - fs.statSync(cerebrumPath).mtimeMs) / (1000 * 60 * 60 * 24);
295
+ if (age > 14) {
296
+ console.error("[CEREBRUM] cerebrum.md is " + Math.floor(age) + " days old. Learning may be stale.");
297
+ }
298
+ } catch (error) {
299
+ console.error("[CEREBRUM] Session summary skipped: " + (error && error.message ? error.message : String(error)));
300
+ }
301
+ console.log("[PASS]");
302
+ process.exit(0);`,
303
+ variables: []
304
+ },
305
+ // ========== Bug Capture (PostToolUse Edit) ==========
306
+ {
307
+ id: 'tmpl-bug-capture',
308
+ name: 'Bug Pattern Capture',
309
+ hookType: 'PostToolUse',
310
+ matcherPattern: 'Edit',
311
+ description: 'Auto-detect bug fix patterns from Edit operations and log to buglog.json',
312
+ templateBody: String.raw `
313
+ const fs = require("fs");
314
+ const path = require("path");
315
+ const input = JSON.parse(process.argv[2] || "{}");
316
+ const oldStr = input.tool_input?.old_string || "";
317
+ const newStr = input.tool_input?.new_string || "";
318
+ const filePath = input.tool_input?.file_path || "";
319
+ if (!oldStr || !newStr || oldStr === newStr) { console.log("[PASS]"); process.exit(0); }
320
+
321
+ function detectPattern(old, nw) {
322
+ if (/catch\s*\(/.test(nw) && !/catch\s*\(/.test(old)) return "error-handling";
323
+ if (/\?\./.test(nw) && !/\?\./.test(old)) return "null-safety";
324
+ if (/\?\?/.test(nw) && !/\?\?/.test(old)) return "null-safety";
325
+ if (/if\s*\([^)]+\)\s*(return|throw)/.test(nw) && !/if\s*\([^)]+\)\s*(return|throw)/.test(old)) return "guard-clause";
326
+ if (/^import\s+/m.test(nw) && !/^import\s+/m.test(old)) return "missing-import";
327
+ if (/\bawait\b/.test(nw) && !/\bawait\b/.test(old)) return "async-fix";
328
+ if (/===/.test(nw) && /==[^=]/.test(old) && !/===/.test(old)) return "operator-fix";
329
+ if (/!==/.test(nw) && /!=[^=]/.test(old) && !/!==/.test(old)) return "operator-fix";
330
+ if (/:\s*(string|number|boolean|any)\b/.test(nw) && !/:\s*(string|number|boolean|any)\b/.test(old) && /\.(ts|tsx)$/.test(filePath)) return "type-fix";
331
+ if (old.split("\n").length === 1 && nw.split("\n").length === 1) {
332
+ var oldIds = (old.match(/\b[a-zA-Z_]\w*\b/g) || []);
333
+ var newIds = (nw.match(/\b[a-zA-Z_]\w*\b/g) || []);
334
+ var diff = oldIds.filter(function(i) { return newIds.indexOf(i) < 0; });
335
+ var added = newIds.filter(function(i) { return oldIds.indexOf(i) < 0; });
336
+ if (diff.length === 1 && added.length === 1) return "wrong-reference";
337
+ }
338
+ return null;
339
+ }
340
+
341
+ var pattern = detectPattern(oldStr, newStr);
342
+ if (!pattern) { console.log("[PASS]"); process.exit(0); }
343
+
344
+ var scaleDir = process.env.SCALE_DIR || ".scale";
345
+ var buglogPath = path.join(scaleDir, "buglog.json");
346
+ try {
347
+ var buglog = { version: 1, bugs: [] };
348
+ if (fs.existsSync(buglogPath)) {
349
+ buglog = JSON.parse(fs.readFileSync(buglogPath, "utf-8"));
350
+ }
351
+ var existing = buglog.bugs.find(function(b) { return b.file === filePath && b.pattern === pattern; });
352
+ if (existing) {
353
+ existing.occurrences = (existing.occurrences || 1) + 1;
354
+ existing.timestamp = new Date().toISOString();
355
+ } else {
356
+ buglog.bugs.push({
357
+ id: "bug-" + String(buglog.bugs.length + 1).padStart(3, "0"),
358
+ timestamp: new Date().toISOString(),
359
+ file: filePath,
360
+ pattern: pattern,
361
+ oldSnippet: oldStr.slice(0, 200),
362
+ newSnippet: newStr.slice(0, 200),
363
+ tags: ["auto-detected", pattern],
364
+ occurrences: 1
365
+ });
366
+ }
367
+ fs.mkdirSync(scaleDir, { recursive: true });
368
+ fs.writeFileSync(buglogPath, JSON.stringify(buglog, null, 2));
369
+ console.error("[BUG-CAPTURE] Detected " + pattern + " fix in " + path.basename(filePath));
370
+ } catch (e) {
371
+ console.error("[BUG-CAPTURE] Failed to log: " + e.message);
372
+ }
373
+ console.log("[PASS]");
374
+ process.exit(0);`,
375
+ variables: []
376
+ },
377
+ // ========== Bug Recall (PreToolUse Edit) ==========
378
+ {
379
+ id: 'tmpl-bug-recall',
380
+ name: 'Bug Recall Before Edit',
381
+ hookType: 'PreToolUse',
382
+ matcherPattern: 'Edit',
383
+ description: 'Check buglog.json for past bugs in the same file before editing',
384
+ templateBody: String.raw `
385
+ const fs = require("fs");
386
+ const path = require("path");
387
+ const input = JSON.parse(process.argv[2] || "{}");
388
+ const filePath = input.tool_input?.file_path || "";
389
+ if (!filePath) { console.log("[PASS]"); process.exit(0); }
390
+ const scaleDir = process.env.SCALE_DIR || ".scale";
391
+ const buglogPath = path.join(scaleDir, "buglog.json");
392
+ if (!fs.existsSync(buglogPath)) { console.log("[PASS]"); process.exit(0); }
393
+ try {
394
+ const buglog = JSON.parse(fs.readFileSync(buglogPath, "utf-8"));
395
+ const fileBugs = buglog.bugs.filter(b => b.file === filePath || b.file.endsWith(path.basename(filePath)));
396
+ if (fileBugs.length > 0) {
397
+ const summary = fileBugs.slice(0, 3).map(b => b.pattern + " (" + (b.timestamp || "").slice(0, 10) + ")").join(", ");
398
+ console.error("[BUG-RECALL] " + fileBugs.length + " past bugs in " + path.basename(filePath) + ": " + summary);
399
+ }
400
+ } catch (error) {
401
+ console.error("[BUG-RECALL] Skipped: " + (error && error.message ? error.message : String(error)));
402
+ }
403
+ console.log("[PASS]");
404
+ process.exit(0);`,
405
+ variables: []
406
+ },
407
+ // ========== Document Standards Check (G8) ==========
408
+ {
409
+ id: 'tmpl-doc-standards-check',
410
+ name: 'Document Standards Check (G8)',
411
+ hookType: 'PostToolUse',
412
+ matcherPattern: 'Write|Edit',
413
+ description: 'Check markdown files comply with DOCUMENT_STANDARDS.md',
414
+ templateBody: String.raw `
415
+ const input = JSON.parse(process.argv[2] || "{}");
416
+ const filePath = input.tool_input?.file_path || "";
417
+ if (!filePath.endsWith(".md")) { console.log("[PASS]"); process.exit(0); }
418
+ const content = input.tool_input?.content || "";
419
+ const issues = [];
420
+ // Check version header
421
+ if (!content.includes("Version:")) { issues.push("Missing version header"); }
422
+ // Check localhost links
423
+ if (/localhost[:\\/]/.test(content)) { issues.push("Contains localhost links"); }
424
+ // Check hardcoded secrets
425
+ if (/(password|secret|token|api_key)\\s*[:=]\\s*['"][^'"]{8,}/i.test(content)) { issues.push("Possible hardcoded secret"); }
426
+ // Check code blocks without language
427
+ const codeBlockPattern = /\`\`\`\\s*$/gm;
428
+ const matches = content.match(codeBlockPattern);
429
+ if (matches && matches.length > 0) { issues.push("Code blocks without language annotation"); }
430
+ if (issues.length > 0) { console.error("[WARN] G8-DocStandards: " + issues.join("; ")); }
431
+ console.log("[PASS]");
432
+ process.exit(0);`,
433
+ variables: []
434
+ }
435
+ ];
436
+ // ============================================================================
437
+ // HookGeneratorEnhanced implementation
438
+ // ============================================================================
439
+ export class HookGeneratorEnhanced {
440
+ constructor(eventBus) {
441
+ this.eventBus = eventBus;
442
+ this.templates = new Map();
443
+ this.generatedHooks = [];
444
+ for (const tmpl of BUILTIN_TEMPLATES) {
445
+ this.templates.set(tmpl.id, tmpl);
446
+ }
447
+ }
448
+ generateFromRule(rule, hooksDir) {
449
+ if (!rule.approved)
450
+ return null;
451
+ const suitableTemplate = this.findSuitableTemplate(rule);
452
+ if (!suitableTemplate && rule.enforcement !== 'hook')
453
+ return null;
454
+ mkdirSync(hooksDir, { recursive: true });
455
+ const hookId = 'HOOK-' + Date.now() + '-' + rule.id;
456
+ const scriptPath = join(hooksDir, hookId + '.cjs');
457
+ const variables = this.extractVariablesFromRule(rule);
458
+ const hookContent = suitableTemplate
459
+ ? this.renderTemplate(suitableTemplate, variables)
460
+ : this.generateRuleBasedHook(rule);
461
+ writeFileSync(scriptPath, hookContent, 'utf-8');
462
+ const hook = {
463
+ id: hookId,
464
+ ruleId: rule.id,
465
+ hookType: (suitableTemplate?.hookType === 'SessionStart' ? 'PreToolUse' : suitableTemplate?.hookType) ?? this.inferHookType(rule.pattern),
466
+ matcher: suitableTemplate?.matcherPattern ?? this.inferMatcher(rule.pattern),
467
+ scriptPath,
468
+ createdAt: Date.now(),
469
+ templateId: suitableTemplate?.id,
470
+ language: 'javascript',
471
+ checkBody: hookContent,
472
+ timeout: 5000,
473
+ retryable: false,
474
+ };
475
+ this.generatedHooks.push(hook);
476
+ this.eventBus.emit('hook.generated', { hookId, ruleId: rule.id, hookType: hook.hookType, scriptPath });
477
+ logger.info({ hookId, ruleId: rule.id }, 'Enhanced hook generated');
478
+ return hook;
479
+ }
480
+ generateFromTemplate(template, variables, hooksDir) {
481
+ mkdirSync(hooksDir, { recursive: true });
482
+ const hookId = 'HOOK-' + Date.now() + '-' + template.id;
483
+ const scriptPath = join(hooksDir, hookId + '.cjs');
484
+ const hookContent = this.renderTemplate(template, variables);
485
+ writeFileSync(scriptPath, hookContent, 'utf-8');
486
+ const hook = {
487
+ id: hookId,
488
+ hookType: template.hookType === 'SessionStart' ? 'PreToolUse' : template.hookType,
489
+ matcher: template.matcherPattern,
490
+ scriptPath,
491
+ createdAt: Date.now(),
492
+ templateId: template.id,
493
+ language: 'javascript',
494
+ checkBody: hookContent,
495
+ timeout: 5000,
496
+ retryable: false,
497
+ };
498
+ this.generatedHooks.push(hook);
499
+ this.eventBus.emit('hook.generated', { hookId, templateId: template.id, scriptPath });
500
+ logger.info({ hookId, templateId: template.id }, 'Hook generated from template');
501
+ return hook;
502
+ }
503
+ generateFromDetector(detectorType, pattern, hooksDir) {
504
+ mkdirSync(hooksDir, { recursive: true });
505
+ const hookId = 'HOOK-' + Date.now() + '-detector-' + detectorType;
506
+ const scriptPath = join(hooksDir, hookId + '.cjs');
507
+ const hookContent = this.generateDetectorHook(detectorType, pattern);
508
+ writeFileSync(scriptPath, hookContent, 'utf-8');
509
+ const hook = {
510
+ id: hookId,
511
+ hookType: this.inferHookTypeFromDetector(detectorType),
512
+ matcher: this.inferMatcherFromDetector(detectorType),
513
+ scriptPath,
514
+ createdAt: Date.now(),
515
+ detectorType,
516
+ language: 'javascript',
517
+ checkBody: hookContent,
518
+ timeout: 5000,
519
+ retryable: false,
520
+ };
521
+ this.generatedHooks.push(hook);
522
+ this.eventBus.emit('hook.generated', { hookId, detectorType, scriptPath });
523
+ logger.info({ hookId, detectorType }, 'Hook generated from detector');
524
+ return hook;
525
+ }
526
+ getTemplates() { return Array.from(this.templates.values()); }
527
+ registerTemplate(template) {
528
+ this.templates.set(template.id, template);
529
+ logger.info({ templateId: template.id }, 'Template registered');
530
+ }
531
+ async validateHook(hookPath) {
532
+ if (!existsSync(hookPath))
533
+ return { valid: false, errors: ['Hook file does not exist'] };
534
+ const errors = [];
535
+ try {
536
+ const content = readFileSync(hookPath, 'utf-8');
537
+ if (!content.includes('process.exit'))
538
+ errors.push('Hook must call process.exit()');
539
+ try {
540
+ new Function(content);
541
+ }
542
+ catch (e) {
543
+ errors.push('Syntax: ' + e.message);
544
+ }
545
+ }
546
+ catch (e) {
547
+ errors.push('Read error: ' + e.message);
548
+ }
549
+ return { valid: errors.length === 0, errors };
550
+ }
551
+ // ============================================================================
552
+ // Private methods
553
+ // ============================================================================
554
+ findSuitableTemplate(rule) {
555
+ const pattern = rule.pattern.toLowerCase();
556
+ if (pattern.includes('file') && pattern.includes('size'))
557
+ return this.templates.get('tmpl-file-size-guard') ?? null;
558
+ if (pattern.includes('dangerous') || pattern.includes('rm -rf'))
559
+ return this.templates.get('tmpl-dangerous-command-guard') ?? null;
560
+ if (pattern.includes('test') && pattern.includes('pass'))
561
+ return this.templates.get('tmpl-test-verification') ?? null;
562
+ if (pattern.includes('console.log'))
563
+ return this.templates.get('tmpl-console-log-detector') ?? null;
564
+ // ========== Workflow Hooks ==========
565
+ if (pattern.includes('karpathy') && pattern.includes('think'))
566
+ return this.templates.get('tmpl-karpathy-k1-think') ?? null;
567
+ if (pattern.includes('karpathy') && pattern.includes('simple'))
568
+ return this.templates.get('tmpl-karpathy-k2-simple') ?? null;
569
+ if (pattern.includes('secret') || pattern.includes('credential') || pattern.includes('hardcoded'))
570
+ return this.templates.get('tmpl-hardcoded-secret-guard') ?? null;
571
+ if (pattern.includes('empty') && pattern.includes('catch'))
572
+ return this.templates.get('tmpl-empty-catch-guard') ?? null;
573
+ if (pattern.includes('mutation') || pattern.includes('immutable'))
574
+ return this.templates.get('tmpl-mutation-guard') ?? null;
575
+ if (pattern.includes('ai') && pattern.includes('slop'))
576
+ return this.templates.get('tmpl-ai-slop-detector') ?? null;
577
+ if (pattern.includes('unverified') || pattern.includes('honest'))
578
+ return this.templates.get('tmpl-unverified-check') ?? null;
579
+ return null;
580
+ }
581
+ renderTemplate(template, variables) {
582
+ let content = template.templateBody;
583
+ for (const varDef of template.variables) {
584
+ const value = variables[varDef.name] ?? varDef.defaultValue;
585
+ const formatted = Array.isArray(value) ? JSON.stringify(value) : String(value);
586
+ content = content.replace('{{' + varDef.name + '}}', formatted);
587
+ }
588
+ return content;
589
+ }
590
+ extractVariablesFromRule(rule) {
591
+ const variables = {};
592
+ const pattern = rule.pattern.toLowerCase();
593
+ const lineMatch = pattern.match(/(\d+)\s*lines/);
594
+ if (lineMatch)
595
+ variables.maxLines = parseInt(lineMatch[1], 10);
596
+ const coverageMatch = pattern.match(/(\d+)%?\s*coverage/);
597
+ if (coverageMatch)
598
+ variables.minCoverage = parseInt(coverageMatch[1], 10);
599
+ return variables;
600
+ }
601
+ generateRuleBasedHook(rule) {
602
+ return '// Auto-generated hook from Rule: ' + rule.id + '\\nconst input = JSON.parse(process.argv[2] || {}); console.log("[PASS]"); process.exit(0);';
603
+ }
604
+ generateDetectorHook(detectorType, _pattern) {
605
+ const scripts = {
606
+ 'brute-retry': 'const input = JSON.parse(process.argv[2] || {}); console.log("[CHECK] Brute retry"); console.log("[PASS]"); process.exit(0);',
607
+ 'idle-tool': 'const input = JSON.parse(process.argv[2] || {}); console.log("[CHECK] Idle tool"); console.log("[PASS]"); process.exit(0);',
608
+ 'premature-done': 'const input = JSON.parse(process.argv[2] || {}); if (!input.tests_run) { console.error("[BLOCKED] Tests not run"); process.exit(2); } console.log("[PASS]"); process.exit(0);',
609
+ };
610
+ return scripts[detectorType] || 'const input = JSON.parse(process.argv[2] || {}); console.log("[PASS]"); process.exit(0);';
611
+ }
612
+ inferHookType(pattern) {
613
+ if (/test|verify|lint|build/i.test(pattern))
614
+ return 'Stop';
615
+ if (/before|pre|block|dangerous/i.test(pattern))
616
+ return 'PreToolUse';
617
+ if (/after|post|detect|console/i.test(pattern))
618
+ return 'PostToolUse';
619
+ return 'PreToolUse';
620
+ }
621
+ inferMatcher(pattern) {
622
+ if (/bash|command/i.test(pattern))
623
+ return 'Bash';
624
+ if (/edit|write|file/i.test(pattern))
625
+ return 'Edit|Write';
626
+ return '';
627
+ }
628
+ inferHookTypeFromDetector(detectorType) {
629
+ if (detectorType === 'premature-done')
630
+ return 'Stop';
631
+ if (detectorType === 'idle-tool')
632
+ return 'PreToolUse';
633
+ return 'PostToolUse';
634
+ }
635
+ inferMatcherFromDetector(detectorType) {
636
+ if (detectorType === 'brute-retry')
637
+ return 'Bash';
638
+ return '';
639
+ }
640
+ }
641
+ //# sourceMappingURL=HookGeneratorEnhanced.js.map