@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 +1,679 @@
1
+ import Database from 'better-sqlite3';
2
+ import { createHash, randomUUID } from 'node:crypto';
3
+ import { existsSync, mkdirSync, readFileSync, readdirSync, writeFileSync } from 'node:fs';
4
+ import { dirname, isAbsolute, join, relative, resolve } from 'node:path';
5
+ import { WorkflowEvalStore } from '../eval/WorkflowEval.js';
6
+ import { RuntimeEvidenceLedger } from '../runtime/RuntimeEvidenceLedger.js';
7
+ import { redactEvidenceText, redactEvidenceValue } from '../tools/ToolEvidenceStore.js';
8
+ const SCHEMA = `
9
+ CREATE TABLE IF NOT EXISTS memory_nodes (
10
+ id TEXT PRIMARY KEY,
11
+ type TEXT NOT NULL,
12
+ title TEXT NOT NULL,
13
+ summary TEXT NOT NULL,
14
+ entities TEXT NOT NULL DEFAULT '[]',
15
+ source TEXT NOT NULL,
16
+ evidence_paths TEXT NOT NULL DEFAULT '[]',
17
+ confidence REAL NOT NULL,
18
+ scope TEXT NOT NULL,
19
+ status TEXT NOT NULL,
20
+ created_at TEXT NOT NULL,
21
+ updated_at TEXT NOT NULL,
22
+ last_verified_at TEXT,
23
+ metadata TEXT NOT NULL DEFAULT '{}',
24
+ fingerprint TEXT NOT NULL
25
+ );
26
+
27
+ CREATE INDEX IF NOT EXISTS idx_memory_nodes_type ON memory_nodes(type);
28
+ CREATE INDEX IF NOT EXISTS idx_memory_nodes_status ON memory_nodes(status);
29
+ CREATE INDEX IF NOT EXISTS idx_memory_nodes_scope ON memory_nodes(scope);
30
+ CREATE INDEX IF NOT EXISTS idx_memory_nodes_fingerprint ON memory_nodes(fingerprint);
31
+
32
+ CREATE TABLE IF NOT EXISTS memory_meta (
33
+ key TEXT PRIMARY KEY,
34
+ value TEXT NOT NULL
35
+ );
36
+
37
+ INSERT OR IGNORE INTO memory_meta (key, value) VALUES ('schema_version', '1');
38
+ `;
39
+ export class MemoryBrain {
40
+ constructor(options = {}) {
41
+ this.projectDir = resolve(options.projectDir ?? process.cwd());
42
+ this.scaleRoot = resolveScaleRoot(this.projectDir, options.scaleDir);
43
+ this.dbPath = options.dbPath ?? join(this.scaleRoot, 'memory', 'brain.sqlite');
44
+ this.now = options.now ?? (() => new Date());
45
+ mkdirSync(dirname(this.dbPath), { recursive: true });
46
+ this.db = new Database(this.dbPath);
47
+ this.db.pragma('journal_mode = WAL');
48
+ this.db.pragma('busy_timeout = 5000');
49
+ this.db.exec(SCHEMA);
50
+ this.writeManifest();
51
+ }
52
+ addNode(input) {
53
+ const now = this.now().toISOString();
54
+ const candidate = sanitizeNode({
55
+ id: input.id ?? `MEM-${Date.now()}-${randomUUID().slice(0, 8)}`,
56
+ type: input.type,
57
+ title: input.title,
58
+ summary: input.summary,
59
+ entities: unique(input.entities ?? inferEntities(`${input.title}\n${input.summary}`)),
60
+ source: input.source,
61
+ evidencePaths: unique(input.evidencePaths ?? []),
62
+ confidence: clampConfidence(input.confidence ?? 0.55),
63
+ scope: input.scope ?? 'project',
64
+ status: input.status ?? 'candidate',
65
+ createdAt: input.createdAt ?? now,
66
+ updatedAt: now,
67
+ lastVerifiedAt: input.lastVerifiedAt,
68
+ metadata: input.metadata ?? {},
69
+ });
70
+ assertNode(candidate);
71
+ this.upsert(candidate);
72
+ return candidate;
73
+ }
74
+ ingest(options) {
75
+ if (options.from === 'candidate')
76
+ return this.ingestCandidate(options);
77
+ if (options.from === 'failure')
78
+ return this.ingestFailureReplay(options);
79
+ return this.ingestEvidence(options);
80
+ }
81
+ query(query, options = {}) {
82
+ const terms = tokenize(query);
83
+ const nodes = this.list({ status: options.status })
84
+ .map(node => ({ node, score: scoreNode(node, terms) }))
85
+ .filter(item => item.score > 0)
86
+ .sort((a, b) => b.score - a.score || b.node.confidence - a.node.confidence)
87
+ .slice(0, options.limit ?? 8)
88
+ .map(item => item.node);
89
+ return {
90
+ query,
91
+ count: nodes.length,
92
+ nodes,
93
+ };
94
+ }
95
+ contradictions() {
96
+ const contradictions = detectContradictions(this.list({ status: 'active' }));
97
+ return {
98
+ ok: contradictions.length === 0,
99
+ count: contradictions.length,
100
+ contradictions,
101
+ };
102
+ }
103
+ dream() {
104
+ const nodes = this.list();
105
+ const duplicateGroups = duplicateGroupsFor(nodes);
106
+ const contradictions = detectContradictions(nodes.filter(node => node.status === 'active' || node.status === 'candidate'));
107
+ const missingEvidence = nodes.filter(node => node.status === 'active' && node.evidencePaths.length === 0);
108
+ const staleCandidates = nodes
109
+ .filter(node => node.status === 'active' && isStale(node))
110
+ .map(node => ({ id: node.id, title: node.title, reason: 'last verification is older than 30 days or missing' }));
111
+ const promotionCandidates = nodes
112
+ .filter(node => node.status === 'candidate' && node.evidencePaths.length > 0 && node.confidence >= 0.7)
113
+ .map(node => ({ id: node.id, title: node.title, confidence: node.confidence, evidencePaths: node.evidencePaths }));
114
+ return {
115
+ ok: missingEvidence.length === 0,
116
+ generatedAt: this.now().toISOString(),
117
+ summary: {
118
+ total: nodes.length,
119
+ active: nodes.filter(node => node.status === 'active').length,
120
+ candidate: nodes.filter(node => node.status === 'candidate').length,
121
+ stale: staleCandidates.length,
122
+ missingEvidence: missingEvidence.length,
123
+ duplicateGroups: duplicateGroups.length,
124
+ contradictions: contradictions.length,
125
+ },
126
+ promotionCandidates,
127
+ staleCandidates,
128
+ duplicateGroups,
129
+ contradictions,
130
+ suggestedDocs: suggestDocs(nodes, contradictions),
131
+ };
132
+ }
133
+ promote(id, options = {}) {
134
+ let node = this.get(id) ?? this.getMemoryNodeForCandidate(id);
135
+ const warnings = [];
136
+ if (!node) {
137
+ const candidate = this.readLearningCandidate(id);
138
+ if (!candidate) {
139
+ return { ok: false, warnings: [`Memory node or learning candidate not found: ${id}`] };
140
+ }
141
+ const report = this.ingestCandidate({ from: 'candidate', candidateId: id, scope: options.scope });
142
+ node = report.nodes[0];
143
+ warnings.push(...report.warnings);
144
+ }
145
+ if (!node)
146
+ return { ok: false, warnings: [`Unable to promote: ${id}`] };
147
+ if (node.evidencePaths.length === 0) {
148
+ return { ok: false, node, warnings: [...warnings, 'Active memory requires at least one evidence path.'] };
149
+ }
150
+ const promoted = {
151
+ ...node,
152
+ status: 'active',
153
+ scope: options.scope ?? node.scope,
154
+ confidence: Math.max(node.confidence, 0.75),
155
+ updatedAt: this.now().toISOString(),
156
+ lastVerifiedAt: this.now().toISOString(),
157
+ };
158
+ assertNode(promoted);
159
+ this.upsert(promoted);
160
+ return { ok: true, node: promoted, warnings };
161
+ }
162
+ updateStatus(id, status, options = {}) {
163
+ let node = this.get(id) ?? this.getMemoryNodeForCandidate(id);
164
+ const warnings = [];
165
+ if (!node) {
166
+ const candidate = this.readLearningCandidate(id);
167
+ if (!candidate) {
168
+ return { ok: false, warnings: [`Memory node or learning candidate not found: ${id}`] };
169
+ }
170
+ const report = this.ingestCandidate({ from: 'candidate', candidateId: id, scope: options.scope });
171
+ node = report.nodes[0];
172
+ warnings.push(...report.warnings);
173
+ }
174
+ if (!node)
175
+ return { ok: false, warnings: [`Unable to update memory status: ${id}`] };
176
+ const previousStatus = node.status;
177
+ const updated = {
178
+ ...node,
179
+ status,
180
+ scope: options.scope ?? node.scope,
181
+ updatedAt: this.now().toISOString(),
182
+ lastVerifiedAt: status === 'candidate' ? undefined : node.lastVerifiedAt,
183
+ metadata: {
184
+ ...(node.metadata ?? {}),
185
+ reviewedAt: this.now().toISOString(),
186
+ },
187
+ };
188
+ assertNode(updated);
189
+ this.upsert(updated);
190
+ return { ok: true, node: updated, previousStatus, warnings };
191
+ }
192
+ exportJsonl() {
193
+ return this.list().map(node => JSON.stringify(node)).join('\n') + '\n';
194
+ }
195
+ importJsonl(filePath) {
196
+ const warnings = [];
197
+ let imported = 0;
198
+ let skipped = 0;
199
+ const text = readFileSync(filePath, 'utf-8');
200
+ for (const line of text.split(/\r?\n/).filter(Boolean)) {
201
+ try {
202
+ const node = sanitizeNode(JSON.parse(line));
203
+ assertNode(node);
204
+ this.upsert(node);
205
+ imported += 1;
206
+ }
207
+ catch (error) {
208
+ skipped += 1;
209
+ warnings.push(`Skipped line: ${error.message}`);
210
+ }
211
+ }
212
+ return { ok: warnings.length === 0, imported, skipped, warnings };
213
+ }
214
+ list(filter = {}) {
215
+ let sql = 'SELECT * FROM memory_nodes';
216
+ const where = [];
217
+ const params = {};
218
+ if (filter.status) {
219
+ where.push('status = @status');
220
+ params.status = filter.status;
221
+ }
222
+ if (filter.scope) {
223
+ where.push('scope = @scope');
224
+ params.scope = filter.scope;
225
+ }
226
+ if (where.length)
227
+ sql += ` WHERE ${where.join(' AND ')}`;
228
+ sql += ' ORDER BY updated_at DESC';
229
+ return this.db.prepare(sql).all(params).map(rowToNode);
230
+ }
231
+ get(id) {
232
+ const row = this.db.prepare('SELECT * FROM memory_nodes WHERE id = ?').get(id);
233
+ return row ? rowToNode(row) : null;
234
+ }
235
+ getMemoryNodeForCandidate(id) {
236
+ return id.startsWith('MEM-') ? null : this.get(`MEM-${id}`);
237
+ }
238
+ close() {
239
+ this.db.close();
240
+ }
241
+ ingestEvidence(options) {
242
+ const ledger = new RuntimeEvidenceLedger({
243
+ projectDir: this.projectDir,
244
+ scaleDir: this.scaleRoot,
245
+ createDirs: false,
246
+ });
247
+ const records = ledger.list({ taskId: options.taskId, sessionId: options.sessionId, limit: Number.MAX_SAFE_INTEGER });
248
+ const warnings = [];
249
+ const nodes = [];
250
+ let skipped = 0;
251
+ for (const record of records) {
252
+ if (record.status === 'skipped') {
253
+ skipped += 1;
254
+ continue;
255
+ }
256
+ const node = this.addNode(nodeFromEvidence(record, {
257
+ projectDir: this.projectDir,
258
+ scaleRoot: this.scaleRoot,
259
+ type: options.type,
260
+ scope: options.scope,
261
+ }));
262
+ nodes.push(node);
263
+ }
264
+ if (records.length === 0)
265
+ warnings.push('No runtime evidence matched the requested task/session scope.');
266
+ return {
267
+ ok: nodes.length > 0,
268
+ source: 'evidence',
269
+ created: nodes.length,
270
+ skipped,
271
+ nodes,
272
+ warnings,
273
+ };
274
+ }
275
+ ingestCandidate(options) {
276
+ const candidate = this.readLearningCandidate(options.candidateId);
277
+ if (!candidate) {
278
+ return {
279
+ ok: false,
280
+ source: 'candidate',
281
+ created: 0,
282
+ skipped: 0,
283
+ nodes: [],
284
+ warnings: [`Learning candidate not found: ${options.candidateId ?? '<latest>'}`],
285
+ };
286
+ }
287
+ const node = this.addNode(nodeFromCandidate(candidate, {
288
+ projectDir: this.projectDir,
289
+ scaleRoot: this.scaleRoot,
290
+ type: options.type,
291
+ scope: options.scope,
292
+ }));
293
+ return {
294
+ ok: true,
295
+ source: 'candidate',
296
+ created: 1,
297
+ skipped: 0,
298
+ nodes: [node],
299
+ warnings: candidate.promotable ? [] : ['Learning candidate is not marked promotable; keep it as candidate until more evidence is recorded.'],
300
+ };
301
+ }
302
+ ingestFailureReplay(options) {
303
+ const store = new WorkflowEvalStore({
304
+ projectDir: this.projectDir,
305
+ scaleDir: this.scaleRoot,
306
+ });
307
+ const failures = options.failureId
308
+ ? [store.getFailure(options.failureId)].filter((failure) => Boolean(failure))
309
+ : store.listFailures({ taskId: options.taskId });
310
+ const warnings = [];
311
+ const nodes = [];
312
+ let skipped = 0;
313
+ for (const failure of failures) {
314
+ if (failure.status === 'closed' || failure.status === 'accepted-risk') {
315
+ skipped += 1;
316
+ continue;
317
+ }
318
+ const node = this.addNode(nodeFromFailureReplay(failure, {
319
+ projectDir: this.projectDir,
320
+ scaleRoot: this.scaleRoot,
321
+ type: options.type,
322
+ scope: options.scope,
323
+ }));
324
+ nodes.push(node);
325
+ }
326
+ if (failures.length === 0)
327
+ warnings.push(`Failure replay not found: ${options.failureId ?? options.taskId ?? '<latest>'}`);
328
+ return {
329
+ ok: nodes.length > 0,
330
+ source: 'failure',
331
+ created: nodes.length,
332
+ skipped,
333
+ nodes,
334
+ warnings,
335
+ };
336
+ }
337
+ readLearningCandidate(candidateId) {
338
+ const dir = join(this.scaleRoot, 'memory', 'learning-candidates');
339
+ if (!existsSync(dir))
340
+ return null;
341
+ const file = candidateId
342
+ ? join(dir, `${safePathSegment(candidateId)}.json`)
343
+ : readdirSync(dir)
344
+ .filter(name => name.endsWith('.json'))
345
+ .map(name => join(dir, name))
346
+ .sort()
347
+ .at(-1);
348
+ if (!file || !existsSync(file))
349
+ return null;
350
+ try {
351
+ return JSON.parse(readFileSync(file, 'utf-8').replace(/^\uFEFF/, ''));
352
+ }
353
+ catch {
354
+ return null;
355
+ }
356
+ }
357
+ upsert(node) {
358
+ const fingerprint = fingerprintFor(node);
359
+ this.db.prepare(`
360
+ INSERT INTO memory_nodes (
361
+ id, type, title, summary, entities, source, evidence_paths, confidence, scope, status,
362
+ created_at, updated_at, last_verified_at, metadata, fingerprint
363
+ ) VALUES (
364
+ @id, @type, @title, @summary, @entities, @source, @evidencePaths, @confidence, @scope, @status,
365
+ @createdAt, @updatedAt, @lastVerifiedAt, @metadata, @fingerprint
366
+ )
367
+ ON CONFLICT(id) DO UPDATE SET
368
+ type = excluded.type,
369
+ title = excluded.title,
370
+ summary = excluded.summary,
371
+ entities = excluded.entities,
372
+ source = excluded.source,
373
+ evidence_paths = excluded.evidence_paths,
374
+ confidence = excluded.confidence,
375
+ scope = excluded.scope,
376
+ status = excluded.status,
377
+ updated_at = excluded.updated_at,
378
+ last_verified_at = excluded.last_verified_at,
379
+ metadata = excluded.metadata,
380
+ fingerprint = excluded.fingerprint
381
+ `).run({
382
+ id: node.id,
383
+ type: node.type,
384
+ title: node.title,
385
+ summary: node.summary,
386
+ entities: JSON.stringify(node.entities),
387
+ source: node.source,
388
+ evidencePaths: JSON.stringify(node.evidencePaths),
389
+ confidence: node.confidence,
390
+ scope: node.scope,
391
+ status: node.status,
392
+ createdAt: node.createdAt,
393
+ updatedAt: node.updatedAt,
394
+ lastVerifiedAt: node.lastVerifiedAt ?? null,
395
+ metadata: JSON.stringify(node.metadata ?? {}),
396
+ fingerprint,
397
+ });
398
+ }
399
+ writeManifest() {
400
+ const manifestPath = join(this.scaleRoot, 'memory', 'brain-manifest.json');
401
+ mkdirSync(dirname(manifestPath), { recursive: true });
402
+ writeFileSync(manifestPath, JSON.stringify({
403
+ version: '1.0',
404
+ dbPath: normalizeProjectPath(this.projectDir, this.dbPath),
405
+ scope: 'project',
406
+ activeMemoryRequiresEvidence: true,
407
+ generatedAt: this.now().toISOString(),
408
+ }, null, 2), 'utf-8');
409
+ }
410
+ }
411
+ function nodeFromEvidence(record, input) {
412
+ const evidencePath = normalizeProjectPath(input.projectDir, join(input.scaleRoot, 'evidence', 'runtime', `${record.id}.json`));
413
+ return {
414
+ id: `MEM-${record.id}`,
415
+ type: input.type ?? (record.status === 'failed' ? 'incident' : 'fact'),
416
+ title: record.title,
417
+ summary: record.summary,
418
+ entities: inferEntities(`${record.title}\n${record.summary}\n${record.command ?? ''}`),
419
+ source: 'runtime-evidence',
420
+ evidencePaths: unique([evidencePath, ...(record.artifacts ?? [])]),
421
+ confidence: record.status === 'passed' ? 0.72 : 0.58,
422
+ scope: input.scope ?? 'project',
423
+ status: 'candidate',
424
+ metadata: {
425
+ taskId: record.taskId,
426
+ sessionId: record.sessionId,
427
+ evidenceId: record.id,
428
+ evidenceStatus: record.status,
429
+ command: record.command,
430
+ exitCode: record.exitCode,
431
+ },
432
+ };
433
+ }
434
+ function nodeFromCandidate(candidate, input) {
435
+ const candidatePath = normalizeProjectPath(input.projectDir, join(input.scaleRoot, 'memory', 'learning-candidates', `${candidate.id}.json`));
436
+ const artifactPaths = (candidate.artifactPaths ?? [])
437
+ .map(path => normalizeProjectPath(input.projectDir, path))
438
+ .filter(Boolean);
439
+ return {
440
+ id: `MEM-${candidate.id}`,
441
+ type: input.type ?? 'decision',
442
+ title: candidate.title,
443
+ summary: candidate.summary,
444
+ entities: inferEntities(`${candidate.title}\n${candidate.summary}\n${candidate.tags.join(' ')}`),
445
+ source: 'task-artifact',
446
+ evidencePaths: unique([
447
+ candidatePath,
448
+ ...artifactPaths,
449
+ ...candidate.graphRefs.map(path => normalizeProjectPath(input.projectDir, path)),
450
+ ...candidate.evidenceIds.map(id => join('.scale', 'evidence', 'runtime', `${id}.json`)),
451
+ ]),
452
+ confidence: candidate.promotable ? 0.72 : 0.5,
453
+ scope: input.scope ?? 'project',
454
+ status: 'candidate',
455
+ metadata: {
456
+ taskId: candidate.taskId,
457
+ sessionId: candidate.sessionId,
458
+ candidateId: candidate.id,
459
+ recommendedAction: candidate.recommendedAction,
460
+ tags: candidate.tags,
461
+ },
462
+ };
463
+ }
464
+ function nodeFromFailureReplay(failure, input) {
465
+ const failurePath = normalizeProjectPath(input.projectDir, join(input.scaleRoot, 'evals', 'failures', `${safePathSegment(failure.id)}.json`));
466
+ const summary = [
467
+ failure.wrongTurn,
468
+ `Prevention: ${failure.prevention}`,
469
+ `Correction: ${failure.correction}`,
470
+ ].join(' ');
471
+ return {
472
+ id: `MEM-${failure.id}`,
473
+ type: input.type ?? 'incident',
474
+ title: `Failure replay: ${failure.category} in ${failure.caseId}`,
475
+ summary,
476
+ entities: inferEntities(`${failure.category}\n${failure.phase}\n${failure.task}\n${failure.prevention}`),
477
+ source: 'task-artifact',
478
+ evidencePaths: [failurePath],
479
+ confidence: failure.status === 'promoted' ? 0.7 : 0.62,
480
+ scope: input.scope ?? 'project',
481
+ status: 'candidate',
482
+ metadata: {
483
+ taskId: failure.taskId,
484
+ suiteId: failure.suiteId,
485
+ caseId: failure.caseId,
486
+ failureId: failure.id,
487
+ category: failure.category,
488
+ phase: failure.phase,
489
+ failureStatus: failure.status,
490
+ replayCommand: failure.replayCommand,
491
+ redactionApplied: failure.redactionApplied,
492
+ },
493
+ };
494
+ }
495
+ function detectContradictions(nodes) {
496
+ const contradictions = [];
497
+ const pairs = new Set();
498
+ for (let i = 0; i < nodes.length; i += 1) {
499
+ for (let j = i + 1; j < nodes.length; j += 1) {
500
+ const left = nodes[i];
501
+ const right = nodes[j];
502
+ const shared = left.entities.filter(entity => right.entities.includes(entity));
503
+ if (shared.length === 0)
504
+ continue;
505
+ if (!polaritiesConflict(left, right))
506
+ continue;
507
+ const key = [left.id, right.id].sort().join(':');
508
+ if (pairs.has(key))
509
+ continue;
510
+ pairs.add(key);
511
+ contradictions.push({
512
+ id: `CON-${hash(key).slice(0, 10)}`,
513
+ title: `Contradiction around ${shared.slice(0, 3).join(', ')}`,
514
+ summary: `${left.title} conflicts with ${right.title}.`,
515
+ nodeIds: [left.id, right.id],
516
+ entities: shared,
517
+ evidencePaths: unique([...left.evidencePaths, ...right.evidencePaths]),
518
+ confidence: Math.min(0.9, Math.max(left.confidence, right.confidence)),
519
+ });
520
+ }
521
+ }
522
+ return contradictions;
523
+ }
524
+ function polaritiesConflict(left, right) {
525
+ const l = polarity(`${left.title}\n${left.summary}`);
526
+ const r = polarity(`${right.title}\n${right.summary}`);
527
+ if (l.enabled && r.disabled)
528
+ return true;
529
+ if (l.disabled && r.enabled)
530
+ return true;
531
+ if (l.exists && r.missing)
532
+ return true;
533
+ if (l.missing && r.exists)
534
+ return true;
535
+ if (l.allowed && r.blocked)
536
+ return true;
537
+ if (l.blocked && r.allowed)
538
+ return true;
539
+ return false;
540
+ }
541
+ function polarity(text) {
542
+ const lower = text.toLowerCase();
543
+ return {
544
+ enabled: /\b(enabled|enable|available|works|passed|active|on)\b/.test(lower),
545
+ disabled: /\b(disabled|disable|unavailable|not available|failed|inactive|off)\b/.test(lower),
546
+ exists: /\b(exists|present|configured|found)\b/.test(lower),
547
+ missing: /\b(missing|absent|not configured|not found)\b/.test(lower),
548
+ allowed: /\b(allowed|permitted|safe)\b/.test(lower),
549
+ blocked: /\b(blocked|forbidden|unsafe|denied)\b/.test(lower),
550
+ };
551
+ }
552
+ function duplicateGroupsFor(nodes) {
553
+ const groups = new Map();
554
+ for (const node of nodes) {
555
+ const key = fingerprintFor(node);
556
+ groups.set(key, [...(groups.get(key) ?? []), node]);
557
+ }
558
+ return [...groups.entries()]
559
+ .filter(([, group]) => group.length > 1)
560
+ .map(([fingerprint, group]) => ({
561
+ fingerprint,
562
+ nodeIds: group.map(node => node.id),
563
+ title: group[0].title,
564
+ }));
565
+ }
566
+ function suggestDocs(nodes, contradictions) {
567
+ const suggestions = new Set();
568
+ if (nodes.some(node => node.type === 'decision'))
569
+ suggestions.add('docs/architecture/');
570
+ if (nodes.some(node => node.type === 'incident'))
571
+ suggestions.add('docs/worklog/metrics.md');
572
+ if (contradictions.length > 0)
573
+ suggestions.add('docs/workflow/README.md');
574
+ return [...suggestions];
575
+ }
576
+ function isStale(node) {
577
+ const date = node.lastVerifiedAt ?? node.updatedAt;
578
+ const ageMs = Date.now() - Date.parse(date);
579
+ return Number.isFinite(ageMs) && ageMs > 30 * 24 * 60 * 60 * 1000;
580
+ }
581
+ function scoreNode(node, terms) {
582
+ if (terms.length === 0)
583
+ return 1;
584
+ const haystack = `${node.title}\n${node.summary}\n${node.entities.join(' ')}\n${node.evidencePaths.join(' ')}`.toLowerCase();
585
+ return terms.reduce((score, term) => score + (haystack.includes(term) ? 1 : 0), 0);
586
+ }
587
+ function rowToNode(row) {
588
+ const value = row;
589
+ return {
590
+ id: String(value.id),
591
+ type: value.type,
592
+ title: String(value.title),
593
+ summary: String(value.summary),
594
+ entities: parseJsonArray(value.entities),
595
+ source: value.source,
596
+ evidencePaths: parseJsonArray(value.evidence_paths),
597
+ confidence: Number(value.confidence),
598
+ scope: value.scope,
599
+ status: value.status,
600
+ createdAt: String(value.created_at),
601
+ updatedAt: String(value.updated_at),
602
+ lastVerifiedAt: value.last_verified_at ? String(value.last_verified_at) : undefined,
603
+ metadata: parseJsonObject(value.metadata),
604
+ };
605
+ }
606
+ function assertNode(node) {
607
+ if (node.status === 'active' && node.evidencePaths.length === 0) {
608
+ throw new Error('Active memory requires at least one evidence path.');
609
+ }
610
+ if (node.scope === 'global-candidate' && node.status === 'active') {
611
+ throw new Error('Global candidate memory cannot be activated inside a project brain.');
612
+ }
613
+ }
614
+ function sanitizeNode(node) {
615
+ const redacted = redactEvidenceValue(node).value;
616
+ const redact = (value) => redactEvidenceText(value).value;
617
+ return {
618
+ ...redacted,
619
+ title: redact(redacted.title),
620
+ summary: redact(redacted.summary),
621
+ entities: unique((redacted.entities ?? []).map(entity => redact(String(entity))).filter(Boolean)),
622
+ evidencePaths: unique((redacted.evidencePaths ?? []).map(path => String(path)).filter(Boolean)),
623
+ confidence: clampConfidence(redacted.confidence),
624
+ metadata: redacted.metadata ?? {},
625
+ };
626
+ }
627
+ function tokenize(text) {
628
+ return unique(text.toLowerCase().split(/[^a-z0-9._/-]+/).filter(term => term.length >= 2));
629
+ }
630
+ function inferEntities(text) {
631
+ const matches = text.match(/[A-Za-z][A-Za-z0-9._/-]{2,}/g) ?? [];
632
+ return unique(matches.map(item => item.toLowerCase()).filter(item => !STOP_WORDS.has(item))).slice(0, 12);
633
+ }
634
+ const STOP_WORDS = new Set(['the', 'and', 'for', 'with', 'from', 'this', 'that', 'task', 'tests', 'passed', 'failed', 'summary']);
635
+ function fingerprintFor(node) {
636
+ return hash(`${node.type}:${node.scope}:${node.title.toLowerCase().replace(/\s+/g, ' ').trim()}`);
637
+ }
638
+ function hash(value) {
639
+ return createHash('sha1').update(value).digest('hex');
640
+ }
641
+ function parseJsonArray(value) {
642
+ try {
643
+ const parsed = JSON.parse(String(value));
644
+ return Array.isArray(parsed) ? parsed.map(String) : [];
645
+ }
646
+ catch {
647
+ return [];
648
+ }
649
+ }
650
+ function parseJsonObject(value) {
651
+ try {
652
+ const parsed = JSON.parse(String(value));
653
+ return parsed && typeof parsed === 'object' && !Array.isArray(parsed) ? parsed : {};
654
+ }
655
+ catch {
656
+ return {};
657
+ }
658
+ }
659
+ function clampConfidence(value) {
660
+ if (!Number.isFinite(value))
661
+ return 0.5;
662
+ return Math.round(Math.max(0.05, Math.min(0.95, value)) * 100) / 100;
663
+ }
664
+ function safePathSegment(value) {
665
+ return value.replace(/[^a-zA-Z0-9._-]/g, '-').slice(0, 120) || 'memory-learning';
666
+ }
667
+ function resolveScaleRoot(projectDir, scaleDir) {
668
+ return isAbsolute(scaleDir ?? '') ? scaleDir : join(projectDir, scaleDir ?? '.scale');
669
+ }
670
+ function normalizeProjectPath(projectDir, filePath) {
671
+ const rel = relative(projectDir, filePath);
672
+ return rel && !rel.startsWith('..') && !isAbsolute(rel)
673
+ ? rel.replace(/\\/g, '/')
674
+ : filePath;
675
+ }
676
+ function unique(items) {
677
+ return [...new Set(items)];
678
+ }
679
+ //# sourceMappingURL=MemoryBrain.js.map