@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 +1,681 @@
1
+ import { existsSync, mkdirSync, readdirSync, readFileSync, statSync, writeFileSync } from 'node:fs';
2
+ import { dirname, extname, isAbsolute, join, relative, resolve } from 'node:path';
3
+ import * as childProcess from 'node:child_process';
4
+ import { estimateTokens } from '../context/ContextBudget.js';
5
+ import { externalCommandExists, runExternalCommandSync } from '../core/ExternalCommand.js';
6
+ const SOURCE_EXTENSIONS = new Set([
7
+ '.ts', '.tsx', '.js', '.jsx', '.mjs', '.cjs',
8
+ '.go', '.java', '.py', '.rs', '.cs',
9
+ '.cpp', '.cc', '.cxx', '.c', '.h', '.hpp',
10
+ '.vue', '.svelte', '.sql',
11
+ ]);
12
+ const IGNORED_DIRS = new Set([
13
+ '.git',
14
+ '.scale',
15
+ 'node_modules',
16
+ 'dist',
17
+ 'coverage',
18
+ 'tmp',
19
+ '.worktrees',
20
+ ]);
21
+ const CODEGRAPH_SOURCE = 'https://github.com/colbymchenry/codegraph';
22
+ const CODEGRAPH_INSTALL_HINT = 'npx @colbymchenry/codegraph or npm i -g @colbymchenry/codegraph';
23
+ const CODEGRAPH_PROJECT_INIT_HINT = 'codegraph init -i';
24
+ const CODEGRAPH_SERVE_COMMAND = 'codegraph serve --mcp';
25
+ const GRAPHIFY_SOURCE = 'https://github.com/safishamsi/graphify';
26
+ const GRAPHIFY_INSTALL_HINT = 'uv tool install graphify && graphify install --platform codex';
27
+ const DEFAULT_CODEGRAPH_PROVIDER = {
28
+ id: 'codegraph',
29
+ type: 'external-cli',
30
+ enabled: true,
31
+ command: 'codegraph',
32
+ capabilities: ['symbols', 'callers', 'callees', 'impact', 'context', 'summary', 'module-map'],
33
+ source: CODEGRAPH_SOURCE,
34
+ installHint: CODEGRAPH_INSTALL_HINT,
35
+ projectInitHint: CODEGRAPH_PROJECT_INIT_HINT,
36
+ serveCommand: CODEGRAPH_SERVE_COMMAND,
37
+ };
38
+ const DEFAULT_GRAPHIFY_PROVIDER = {
39
+ id: 'graphify',
40
+ type: 'artifact',
41
+ enabled: true,
42
+ manifest: 'graphify-out/graph.json',
43
+ capabilities: ['symbols', 'callers', 'callees', 'impact', 'context', 'summary', 'module-map'],
44
+ source: GRAPHIFY_SOURCE,
45
+ installHint: GRAPHIFY_INSTALL_HINT,
46
+ };
47
+ let execFileSyncImpl = childProcess.execFileSync;
48
+ export function setCodeIntelligenceExecFileSyncForTesting(impl) {
49
+ execFileSyncImpl = impl ?? childProcess.execFileSync;
50
+ }
51
+ export function defaultCodeIntelligenceConfig() {
52
+ return {
53
+ version: '1.0',
54
+ providers: [
55
+ { ...DEFAULT_CODEGRAPH_PROVIDER },
56
+ { ...DEFAULT_GRAPHIFY_PROVIDER },
57
+ ],
58
+ fallback: {
59
+ enabled: true,
60
+ tools: ['internal-scan', 'rg', 'read'],
61
+ },
62
+ };
63
+ }
64
+ export function codeIntelligenceConfigPath(projectDir = process.cwd(), scaleDir = '.scale') {
65
+ return join(resolveScaleRoot(projectDir, scaleDir), 'code-intelligence.json');
66
+ }
67
+ export function writeCodeIntelligenceConfig(options = {}) {
68
+ const projectDir = resolve(options.projectDir ?? process.cwd());
69
+ const path = codeIntelligenceConfigPath(projectDir, options.scaleDir);
70
+ if (existsSync(path) && !options.force) {
71
+ return { path, written: false, config: loadCodeIntelligenceConfig(projectDir, options.scaleDir).config };
72
+ }
73
+ mkdirSync(dirname(path), { recursive: true });
74
+ const config = defaultCodeIntelligenceConfig();
75
+ writeFileSync(path, JSON.stringify(config, null, 2), 'utf-8');
76
+ return { path, written: true, config };
77
+ }
78
+ export function loadCodeIntelligenceConfig(projectDir = process.cwd(), scaleDir = '.scale') {
79
+ const path = codeIntelligenceConfigPath(projectDir, scaleDir);
80
+ if (!existsSync(path)) {
81
+ return { config: defaultCodeIntelligenceConfig(), path, exists: false };
82
+ }
83
+ try {
84
+ const parsed = JSON.parse(readFileSync(path, 'utf-8'));
85
+ return {
86
+ path,
87
+ exists: true,
88
+ config: {
89
+ version: parsed.version ?? '1.0',
90
+ providers: Array.isArray(parsed.providers)
91
+ ? parsed.providers.map(provider => hydrateProviderConfig(provider))
92
+ : [],
93
+ fallback: {
94
+ enabled: parsed.fallback?.enabled !== false,
95
+ tools: Array.isArray(parsed.fallback?.tools) ? parsed.fallback.tools.map(String) : ['internal-scan', 'rg', 'read'],
96
+ },
97
+ },
98
+ };
99
+ }
100
+ catch {
101
+ return { config: defaultCodeIntelligenceConfig(), path, exists: true };
102
+ }
103
+ }
104
+ export function inspectCodeIntelligence(options = {}) {
105
+ const projectDir = resolve(options.projectDir ?? process.cwd());
106
+ const loaded = loadCodeIntelligenceConfig(projectDir, options.scaleDir);
107
+ const projectIndexPath = codegraphProjectIndexPath(projectDir);
108
+ const projectIndexExists = existsSync(projectIndexPath);
109
+ const providers = loaded.config.providers.map(providerStatus(projectDir));
110
+ const availableProviderCount = providers.filter(provider => provider.available).length;
111
+ const fallbackAvailable = loaded.config.fallback.enabled;
112
+ return {
113
+ projectDir,
114
+ scaleDir: resolveScaleRoot(projectDir, options.scaleDir),
115
+ configPath: loaded.path,
116
+ configExists: loaded.exists,
117
+ projectIndexPath,
118
+ projectIndexExists,
119
+ providers,
120
+ fallback: {
121
+ enabled: loaded.config.fallback.enabled,
122
+ tools: loaded.config.fallback.tools,
123
+ available: fallbackAvailable,
124
+ reason: fallbackAvailable ? 'internal source scan fallback is available' : 'fallback is disabled by policy',
125
+ },
126
+ availableProviderCount,
127
+ recommendations: recommendations(loaded.exists, providers, fallbackAvailable, projectIndexExists),
128
+ };
129
+ }
130
+ export function queryCodeGraph(options) {
131
+ return runCodeGraphQuery({ ...options, mode: 'query' });
132
+ }
133
+ export function impactCodeGraph(options) {
134
+ return runCodeGraphQuery({
135
+ projectDir: options.projectDir,
136
+ scaleDir: options.scaleDir,
137
+ query: options.symbol,
138
+ mode: 'impact',
139
+ });
140
+ }
141
+ export function buildCodeGraphContext(options) {
142
+ const budget = options.budget ?? 2000;
143
+ const projectDir = resolve(options.projectDir ?? process.cwd());
144
+ const externalContext = queryExternalCodeGraphContext({
145
+ projectDir,
146
+ scaleDir: options.scaleDir,
147
+ query: options.symbol,
148
+ });
149
+ if (externalContext) {
150
+ let total = 0;
151
+ const contextFiles = [];
152
+ for (const file of externalContext.files) {
153
+ const absolute = resolve(projectDir, file);
154
+ const tokens = existsSync(absolute) && statSync(absolute).isFile()
155
+ ? estimateTokens(readFileSync(absolute, 'utf-8'))
156
+ : 0;
157
+ const included = total + tokens <= budget;
158
+ if (included)
159
+ total += tokens;
160
+ contextFiles.push({
161
+ path: file,
162
+ estimatedTokens: tokens,
163
+ included,
164
+ reason: included ? 'within codegraph context budget' : `omitted because it would exceed budget ${budget}`,
165
+ });
166
+ }
167
+ return {
168
+ projectDir,
169
+ generatedAt: new Date().toISOString(),
170
+ mode: 'context',
171
+ query: options.symbol,
172
+ provider: 'codegraph',
173
+ fallbackUsed: false,
174
+ hits: externalContext.hits,
175
+ files: externalContext.files,
176
+ symbols: externalContext.symbols,
177
+ confidence: confidence(externalContext.hits.length, false),
178
+ roi: roiMetrics(externalContext.hits.length, false, externalContext.files.length),
179
+ warnings: [`CodeGraph context summary: ${externalContext.summary}`],
180
+ budget,
181
+ totalEstimatedTokens: total,
182
+ contextFiles,
183
+ omitted: contextFiles.filter(file => !file.included),
184
+ };
185
+ }
186
+ const base = impactCodeGraph(options);
187
+ let total = 0;
188
+ const contextFiles = [];
189
+ for (const file of base.files) {
190
+ const absolute = resolve(options.projectDir ?? process.cwd(), file);
191
+ const tokens = existsSync(absolute) && statSync(absolute).isFile()
192
+ ? estimateTokens(readFileSync(absolute, 'utf-8'))
193
+ : 0;
194
+ const included = total + tokens <= budget;
195
+ if (included)
196
+ total += tokens;
197
+ contextFiles.push({
198
+ path: file,
199
+ estimatedTokens: tokens,
200
+ included,
201
+ reason: included ? 'within codegraph context budget' : `omitted because it would exceed budget ${budget}`,
202
+ });
203
+ }
204
+ return {
205
+ ...base,
206
+ mode: 'context',
207
+ budget,
208
+ totalEstimatedTokens: total,
209
+ contextFiles,
210
+ omitted: contextFiles.filter(file => !file.included),
211
+ };
212
+ }
213
+ export function createCodeGraphRoiReport(options) {
214
+ const report = options.symbol
215
+ ? impactCodeGraph({ projectDir: options.projectDir, scaleDir: options.scaleDir, symbol: options.symbol })
216
+ : queryCodeGraph({ projectDir: options.projectDir, scaleDir: options.scaleDir, query: options.query ?? '' });
217
+ return {
218
+ projectDir: report.projectDir,
219
+ generatedAt: new Date().toISOString(),
220
+ query: report.query,
221
+ provider: report.provider,
222
+ fallbackUsed: report.fallbackUsed,
223
+ metrics: report.roi,
224
+ recommendation: report.fallbackUsed ? 'needs-evidence' : 'keep-optional',
225
+ evidenceLevel: report.fallbackUsed ? 'estimated' : 'measured',
226
+ };
227
+ }
228
+ function runCodeGraphQuery(options) {
229
+ const projectDir = resolve(options.projectDir ?? process.cwd());
230
+ const query = options.query.trim();
231
+ const status = inspectCodeIntelligence({ projectDir, scaleDir: options.scaleDir });
232
+ const available = status.providers.find(provider => provider.available && provider.type === 'artifact');
233
+ const externalAvailable = status.providers.find(provider => provider.available && provider.type === 'external-cli');
234
+ const warnings = [];
235
+ let hits = [];
236
+ let provider;
237
+ let fallbackUsed = false;
238
+ if (available) {
239
+ const config = loadCodeIntelligenceConfig(projectDir, options.scaleDir).config;
240
+ const providerConfig = config.providers.find(item => item.id === available.id);
241
+ if (providerConfig) {
242
+ hits = queryArtifactProvider(projectDir, providerConfig, query, options.mode);
243
+ provider = providerConfig.id;
244
+ if (hits.length === 0)
245
+ warnings.push(`Provider ${providerConfig.id} returned no hits for "${query}".`);
246
+ }
247
+ }
248
+ else if (externalAvailable?.id === 'codegraph' && status.projectIndexExists && options.mode === 'query') {
249
+ const externalQuery = queryExternalCodeGraph(projectDir, query);
250
+ if (externalQuery) {
251
+ hits = externalQuery.hits;
252
+ provider = externalAvailable.id;
253
+ warnings.push(...externalQuery.warnings);
254
+ if (hits.length === 0)
255
+ warnings.push(`Provider ${externalAvailable.id} returned no hits for "${query}".`);
256
+ }
257
+ }
258
+ else if (externalAvailable) {
259
+ if (externalAvailable.id === 'codegraph' && !status.projectIndexExists) {
260
+ warnings.push('CodeGraph CLI is installed, but this project has no .codegraph/ index yet; run codegraph init -i to enable upstream graph queries.');
261
+ }
262
+ else {
263
+ warnings.push(`External provider ${externalAvailable.id} is available, but no command adapter is configured yet; using fallback unless an artifact provider is configured.`);
264
+ }
265
+ }
266
+ if (hits.length === 0 && status.fallback.enabled) {
267
+ fallbackUsed = true;
268
+ provider = undefined;
269
+ hits = fallbackSourceScan(projectDir, query);
270
+ warnings.push('Used internal source scan fallback because no graph provider produced hits.');
271
+ }
272
+ else if (hits.length === 0) {
273
+ warnings.push('Fallback is disabled by code-intelligence policy.');
274
+ }
275
+ const files = unique(hits.map(hit => hit.file).filter(Boolean));
276
+ const symbols = unique(hits.map(hit => hit.symbol).filter((value) => Boolean(value)));
277
+ const roi = roiMetrics(hits.length, fallbackUsed, files.length);
278
+ return {
279
+ projectDir,
280
+ generatedAt: new Date().toISOString(),
281
+ mode: options.mode,
282
+ query,
283
+ provider,
284
+ fallbackUsed,
285
+ hits,
286
+ files,
287
+ symbols,
288
+ confidence: confidence(hits.length, fallbackUsed),
289
+ roi,
290
+ warnings,
291
+ };
292
+ }
293
+ function providerStatus(projectDir) {
294
+ return provider => {
295
+ const enabled = provider.enabled !== false;
296
+ const capabilities = provider.capabilities ?? [];
297
+ const projectIndexExists = existsSync(codegraphProjectIndexPath(projectDir));
298
+ if (!enabled) {
299
+ return {
300
+ id: provider.id,
301
+ type: provider.type,
302
+ enabled,
303
+ available: false,
304
+ capabilities,
305
+ reason: 'provider disabled by policy',
306
+ source: provider.source,
307
+ installHint: provider.installHint,
308
+ projectInitHint: provider.projectInitHint,
309
+ serveCommand: provider.serveCommand,
310
+ };
311
+ }
312
+ if (provider.type === 'artifact') {
313
+ const manifest = provider.manifest ? resolveProjectPath(projectDir, provider.manifest) : '';
314
+ const available = Boolean(manifest && existsSync(manifest));
315
+ return {
316
+ id: provider.id,
317
+ type: provider.type,
318
+ enabled,
319
+ available,
320
+ capabilities,
321
+ reason: available ? `manifest found at ${provider.manifest}` : `manifest not found: ${provider.manifest ?? '(missing)'}`,
322
+ source: provider.source,
323
+ installHint: provider.installHint,
324
+ projectInitHint: provider.projectInitHint,
325
+ serveCommand: provider.serveCommand,
326
+ };
327
+ }
328
+ if (provider.type === 'external-cli') {
329
+ const available = provider.command ? commandExists(provider.command) : false;
330
+ const readinessSuffix = provider.id === 'codegraph'
331
+ ? projectIndexExists
332
+ ? '; project index found at .codegraph/'
333
+ : '; project index missing (.codegraph/)'
334
+ : '';
335
+ return {
336
+ id: provider.id,
337
+ type: provider.type,
338
+ enabled,
339
+ available,
340
+ capabilities,
341
+ reason: available ? `command available: ${provider.command}${readinessSuffix}` : `command not found: ${provider.command ?? '(missing)'}`,
342
+ source: provider.source,
343
+ installHint: provider.installHint,
344
+ projectInitHint: provider.projectInitHint,
345
+ serveCommand: provider.serveCommand,
346
+ };
347
+ }
348
+ return {
349
+ id: provider.id,
350
+ type: provider.type,
351
+ enabled,
352
+ available: false,
353
+ capabilities,
354
+ reason: 'unknown provider type',
355
+ source: provider.source,
356
+ installHint: provider.installHint,
357
+ projectInitHint: provider.projectInitHint,
358
+ serveCommand: provider.serveCommand,
359
+ };
360
+ };
361
+ }
362
+ function queryArtifactProvider(projectDir, provider, query, mode) {
363
+ if (!provider.manifest)
364
+ return [];
365
+ const manifest = resolveProjectPath(projectDir, provider.manifest);
366
+ if (!existsSync(manifest))
367
+ return [];
368
+ const content = readFileSync(manifest, 'utf-8');
369
+ if (extname(manifest).toLowerCase() === '.json') {
370
+ try {
371
+ return queryJsonManifest(projectDir, provider.id, content, query, mode);
372
+ }
373
+ catch {
374
+ return [];
375
+ }
376
+ }
377
+ return queryTextManifest(projectDir, provider.id, provider.manifest, content, query);
378
+ }
379
+ function queryJsonManifest(projectDir, provider, content, query, mode) {
380
+ const parsed = JSON.parse(content);
381
+ const symbols = Array.isArray(parsed.symbols) ? parsed.symbols : [];
382
+ const files = Array.isArray(parsed.files) ? parsed.files : [];
383
+ const symbolByName = new Map(symbols.map(symbol => [String(symbol.name), symbol]));
384
+ const hits = [];
385
+ const lower = query.toLowerCase();
386
+ for (const symbol of symbols) {
387
+ const name = String(symbol.name ?? '');
388
+ const file = normalizeManifestPath(symbol.file ?? symbol.path);
389
+ if (!name || !file)
390
+ continue;
391
+ if (name.toLowerCase().includes(lower) || file.toLowerCase().includes(lower)) {
392
+ hits.push({ provider, file, symbol: name, reason: 'symbol matched graph manifest', confidence: 0.86 });
393
+ if (mode === 'impact') {
394
+ for (const ref of relatedFiles(symbol, symbolByName)) {
395
+ hits.push({ provider, file: ref, symbol: name, reason: 'related caller/callee from graph manifest', confidence: 0.78 });
396
+ }
397
+ }
398
+ }
399
+ }
400
+ for (const file of files) {
401
+ const path = normalizeManifestPath(file.path ?? file.file);
402
+ if (!path)
403
+ continue;
404
+ const fileSymbols = stringifyList(file.symbols);
405
+ if (path.toLowerCase().includes(lower) || fileSymbols.toLowerCase().includes(lower)) {
406
+ hits.push({ provider, file: path, reason: 'file matched graph manifest', confidence: 0.7 });
407
+ }
408
+ }
409
+ return dedupeHits(hits.filter(hit => existsOrLooksLikePath(projectDir, hit.file)));
410
+ }
411
+ function queryTextManifest(projectDir, provider, manifestPath, content, query) {
412
+ const lower = query.toLowerCase();
413
+ return content.split(/\r?\n/).flatMap((line, index) => {
414
+ if (!line.toLowerCase().includes(lower))
415
+ return [];
416
+ return [{
417
+ provider,
418
+ file: normalizePath(manifestPath),
419
+ line: index + 1,
420
+ reason: 'text graph artifact matched query',
421
+ confidence: 0.45,
422
+ }];
423
+ }).filter(hit => existsOrLooksLikePath(projectDir, hit.file)).slice(0, 30);
424
+ }
425
+ function fallbackSourceScan(projectDir, query) {
426
+ if (!query)
427
+ return [];
428
+ const files = sourceFiles(projectDir);
429
+ const lower = query.toLowerCase();
430
+ const hits = [];
431
+ for (const file of files) {
432
+ const content = safeRead(file);
433
+ const lines = content.split(/\r?\n/);
434
+ for (let i = 0; i < lines.length; i += 1) {
435
+ if (!lines[i].toLowerCase().includes(lower))
436
+ continue;
437
+ hits.push({
438
+ provider: 'fallback-internal-scan',
439
+ file: normalizePath(relative(projectDir, file)),
440
+ line: i + 1,
441
+ reason: 'fallback source text match',
442
+ confidence: 0.35,
443
+ });
444
+ break;
445
+ }
446
+ if (hits.length >= 30)
447
+ break;
448
+ }
449
+ return hits;
450
+ }
451
+ function sourceFiles(projectDir) {
452
+ const files = [];
453
+ walk(projectDir, projectDir, files);
454
+ return files;
455
+ }
456
+ function walk(dir, projectDir, files) {
457
+ const base = normalizePath(relative(projectDir, dir)).split('/').pop() ?? '';
458
+ if (IGNORED_DIRS.has(base))
459
+ return;
460
+ for (const entry of readdirSync(dir, { withFileTypes: true })) {
461
+ const absolute = join(dir, entry.name);
462
+ if (entry.isDirectory()) {
463
+ if (!IGNORED_DIRS.has(entry.name))
464
+ walk(absolute, projectDir, files);
465
+ continue;
466
+ }
467
+ if (entry.isFile() && SOURCE_EXTENSIONS.has(extname(entry.name).toLowerCase()))
468
+ files.push(absolute);
469
+ }
470
+ }
471
+ function relatedFiles(symbol, symbolByName) {
472
+ const refs = [
473
+ ...stringifyArray(symbol.callers),
474
+ ...stringifyArray(symbol.callees),
475
+ ...stringifyArray(symbol.dependencies),
476
+ ...stringifyArray(symbol.dependents),
477
+ ];
478
+ return unique(refs.flatMap(ref => {
479
+ const asPath = normalizeManifestPath(ref);
480
+ if (asPath && hasFileExtension(asPath))
481
+ return [asPath];
482
+ const related = symbolByName.get(ref);
483
+ const relatedPath = normalizeManifestPath(related?.file ?? related?.path);
484
+ return relatedPath ? [relatedPath] : [];
485
+ }));
486
+ }
487
+ function stringifyArray(value) {
488
+ return Array.isArray(value) ? value.map(item => {
489
+ if (typeof item === 'string')
490
+ return item;
491
+ if (item && typeof item === 'object') {
492
+ const record = item;
493
+ return String(record.file ?? record.path ?? record.name ?? '');
494
+ }
495
+ return '';
496
+ }).filter(Boolean) : [];
497
+ }
498
+ function stringifyList(value) {
499
+ return stringifyArray(value).join(' ');
500
+ }
501
+ function normalizeManifestPath(value) {
502
+ if (!value)
503
+ return '';
504
+ return normalizePath(String(value).trim());
505
+ }
506
+ function existsOrLooksLikePath(projectDir, file) {
507
+ return hasFileExtension(file) || existsSync(resolve(projectDir, file));
508
+ }
509
+ function hasFileExtension(path) {
510
+ return Boolean(extname(path));
511
+ }
512
+ function roiMetrics(hitCount, fallbackUsed, fileCount) {
513
+ const baselineFileReads = Math.max(fileCount + 4, hitCount, 1);
514
+ const recommendedFileReads = fileCount;
515
+ return {
516
+ graphHits: fallbackUsed ? 0 : hitCount,
517
+ fallbackCount: fallbackUsed ? 1 : 0,
518
+ baselineFileReads,
519
+ recommendedFileReads,
520
+ fileReadsSaved: Math.max(0, baselineFileReads - recommendedFileReads),
521
+ toolCallsSaved: Math.max(0, (fallbackUsed ? 1 : 3) - 1),
522
+ };
523
+ }
524
+ function confidence(hitCount, fallbackUsed) {
525
+ if (hitCount === 0)
526
+ return 0;
527
+ return fallbackUsed ? 0.35 : Math.min(0.9, 0.55 + hitCount * 0.05);
528
+ }
529
+ function recommendations(configExists, providers, fallbackAvailable, projectIndexExists) {
530
+ const output = [];
531
+ const codegraph = providers.find(provider => provider.id === 'codegraph');
532
+ if (!configExists)
533
+ output.push('Run scale codegraph init to create .scale/code-intelligence.json.');
534
+ if (codegraph && !codegraph.available && codegraph.installHint) {
535
+ output.push(`Install CodeGraph from ${codegraph.source ?? CODEGRAPH_SOURCE}: ${codegraph.installHint}.`);
536
+ }
537
+ if (codegraph?.available && !projectIndexExists) {
538
+ output.push('Run codegraph init -i in the project root to build the local .codegraph/ index.');
539
+ }
540
+ if (providers.every(provider => !provider.available))
541
+ output.push('No graph provider is available; exploration will use explicit fallback.');
542
+ if (!fallbackAvailable)
543
+ output.push('Fallback is disabled; missing providers may leave code intelligence unavailable.');
544
+ return output;
545
+ }
546
+ function commandExists(command) {
547
+ return externalCommandExists(command, {
548
+ execFileSync: execFileSyncImpl,
549
+ spawnSync: childProcess.spawnSync,
550
+ });
551
+ }
552
+ function resolveScaleRoot(projectDir, scaleDir = '.scale') {
553
+ return isAbsolute(scaleDir) ? scaleDir : resolve(projectDir, scaleDir);
554
+ }
555
+ function resolveProjectPath(projectDir, path) {
556
+ return isAbsolute(path) ? path : resolve(projectDir, path);
557
+ }
558
+ function safeRead(path) {
559
+ try {
560
+ return readFileSync(path, 'utf-8');
561
+ }
562
+ catch {
563
+ return '';
564
+ }
565
+ }
566
+ function normalizePath(path) {
567
+ return path.replace(/\\/g, '/');
568
+ }
569
+ function unique(values) {
570
+ return Array.from(new Set(values.filter(Boolean).map(normalizePath)));
571
+ }
572
+ function dedupeHits(hits) {
573
+ const seen = new Set();
574
+ return hits.filter(hit => {
575
+ const key = `${hit.provider}:${hit.file}:${hit.symbol ?? ''}:${hit.line ?? ''}:${hit.reason}`;
576
+ if (seen.has(key))
577
+ return false;
578
+ seen.add(key);
579
+ return true;
580
+ });
581
+ }
582
+ function hydrateProviderConfig(provider) {
583
+ const defaults = provider.id === 'codegraph'
584
+ ? DEFAULT_CODEGRAPH_PROVIDER
585
+ : provider.id === 'graphify'
586
+ ? DEFAULT_GRAPHIFY_PROVIDER
587
+ : undefined;
588
+ return {
589
+ ...(defaults ?? {}),
590
+ ...provider,
591
+ capabilities: provider.capabilities ?? defaults?.capabilities,
592
+ source: provider.source ?? defaults?.source,
593
+ installHint: provider.installHint ?? defaults?.installHint,
594
+ projectInitHint: provider.projectInitHint ?? defaults?.projectInitHint,
595
+ serveCommand: provider.serveCommand ?? defaults?.serveCommand,
596
+ };
597
+ }
598
+ function codegraphProjectIndexPath(projectDir) {
599
+ return join(projectDir, '.codegraph');
600
+ }
601
+ function queryExternalCodeGraph(projectDir, query) {
602
+ try {
603
+ const output = runExternalCommandSync('codegraph', ['query', query, '-p', projectDir, '--json'], {
604
+ encoding: 'utf8',
605
+ stdio: ['ignore', 'pipe', 'pipe'],
606
+ }, {
607
+ execFileSync: execFileSyncImpl,
608
+ spawnSync: childProcess.spawnSync,
609
+ });
610
+ const parsed = JSON.parse(String(output));
611
+ const hits = parsed.flatMap((entry, index) => {
612
+ const file = normalizeManifestPath(entry.node?.filePath);
613
+ const symbol = String(entry.node?.qualifiedName ?? entry.node?.name ?? '').trim();
614
+ if (!file)
615
+ return [];
616
+ return [{
617
+ provider: 'codegraph',
618
+ file,
619
+ symbol: symbol || undefined,
620
+ line: entry.node?.startLine,
621
+ reason: `CodeGraph CLI symbol search match${entry.node?.kind ? ` (${entry.node.kind})` : ''}`,
622
+ confidence: Math.max(0.55, Math.min(0.95, 0.9 - index * 0.05)),
623
+ }];
624
+ });
625
+ return {
626
+ hits: dedupeHits(hits.filter(hit => existsOrLooksLikePath(projectDir, hit.file))),
627
+ warnings: [],
628
+ };
629
+ }
630
+ catch (error) {
631
+ return {
632
+ hits: [],
633
+ warnings: [`CodeGraph CLI query failed: ${error instanceof Error ? error.message : String(error)}`],
634
+ };
635
+ }
636
+ }
637
+ function queryExternalCodeGraphContext(options) {
638
+ const status = inspectCodeIntelligence({ projectDir: options.projectDir, scaleDir: options.scaleDir });
639
+ const provider = status.providers.find(item => item.id === 'codegraph' && item.available);
640
+ if (!provider || !status.projectIndexExists)
641
+ return null;
642
+ try {
643
+ const output = runExternalCommandSync('codegraph', ['context', options.query, '-p', options.projectDir, '--format', 'json', '--no-code'], {
644
+ encoding: 'utf8',
645
+ stdio: ['ignore', 'pipe', 'pipe'],
646
+ }, {
647
+ execFileSync: execFileSyncImpl,
648
+ spawnSync: childProcess.spawnSync,
649
+ });
650
+ const parsed = JSON.parse(String(output));
651
+ const hits = Array.isArray(parsed.entryPoints)
652
+ ? parsed.entryPoints.flatMap((entry, index) => {
653
+ const file = normalizeManifestPath(entry.filePath);
654
+ const symbol = String(entry.qualifiedName ?? entry.name ?? '').trim();
655
+ if (!file)
656
+ return [];
657
+ return [{
658
+ provider: 'codegraph',
659
+ file,
660
+ symbol: symbol || undefined,
661
+ line: entry.startLine,
662
+ reason: `CodeGraph CLI context entry point${entry.kind ? ` (${entry.kind})` : ''}`,
663
+ confidence: Math.max(0.55, Math.min(0.92, 0.88 - index * 0.05)),
664
+ }];
665
+ })
666
+ : [];
667
+ const files = unique((parsed.relatedFiles ?? []).map(file => normalizeManifestPath(file)).filter(Boolean));
668
+ if (hits.length === 0 && files.length === 0)
669
+ return null;
670
+ return {
671
+ summary: parsed.summary ?? 'CodeGraph returned related files and entry points.',
672
+ hits: dedupeHits(hits.filter(hit => existsOrLooksLikePath(options.projectDir, hit.file))),
673
+ files,
674
+ symbols: unique(hits.map(hit => hit.symbol).filter((value) => Boolean(value))),
675
+ };
676
+ }
677
+ catch {
678
+ return null;
679
+ }
680
+ }
681
+ //# sourceMappingURL=CodeIntelligence.js.map