@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
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  253. package/dist/cli/shieldCommands.d.ts +30 -0
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  256. package/dist/cli/targetCommands.d.ts +552 -0
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  259. package/dist/cli/tuiCommands.d.ts +7 -0
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  262. package/dist/cli/vibeCommands.d.ts +64 -0
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  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
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  274. package/dist/context/CavemanCompressor.d.ts +20 -0
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  277. package/dist/context/ContextBudget.d.ts +128 -0
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  280. package/dist/context/ContextBuilder.d.ts +71 -0
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  286. package/dist/context/ProjectAnatomy.d.ts +18 -0
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  289. package/dist/context/SessionStartSequence.d.ts +54 -0
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  292. package/dist/core/ExternalCommand.d.ts +9 -0
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  295. package/dist/core/GbrainRuntime.d.ts +25 -0
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  298. package/dist/core/container.d.ts +14 -0
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  307. package/dist/cortex/GovernanceMetrics.d.ts +66 -0
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  310. package/dist/cortex/InstinctExtractor.d.ts +61 -0
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  319. package/dist/cortex/SessionInjector.d.ts +44 -0
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  322. package/dist/cortex/adapters/ClaudeAdapter.d.ts +17 -0
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  325. package/dist/cortex/adapters/CodexAdapter.d.ts +10 -0
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  328. package/dist/cortex/adapters/CursorAdapter.d.ts +10 -0
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  337. package/dist/dashboard/MedicalWorkflowData.d.ts +155 -0
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  343. package/dist/dashboard/index.d.ts +4 -0
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  346. package/dist/dashboard/server.d.ts +52 -0
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  349. package/dist/env/EnvironmentDoctor.d.ts +66 -0
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  1061. package/target-research-platform/src/analysis/stage3_deep_research/target_function.py +290 -0
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  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
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  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 +1,129 @@
1
+ import { randomUUID } from 'node:crypto';
2
+ import { existsSync, mkdirSync, readFileSync, readdirSync, writeFileSync } from 'node:fs';
3
+ import { isAbsolute, join, resolve } from 'node:path';
4
+ const SENSITIVE_KEY_PATTERN = /(?:password|passwd|pwd|token|secret|authorization|cookie|credential|api[_-]?key|private[_-]?key)/i;
5
+ const REDACTED = '[REDACTED]';
6
+ export class ToolEvidenceStore {
7
+ constructor(options = {}) {
8
+ this.sequence = 0;
9
+ const projectDir = resolve(options.projectDir ?? process.cwd());
10
+ const scaleRoot = isAbsolute(options.scaleDir ?? '')
11
+ ? options.scaleDir
12
+ : join(projectDir, options.scaleDir ?? '.scale');
13
+ this.rootDir = join(scaleRoot, 'evidence', 'tool-runs');
14
+ this.now = options.now ?? (() => new Date());
15
+ if (!existsSync(this.rootDir))
16
+ mkdirSync(this.rootDir, { recursive: true });
17
+ }
18
+ save(input) {
19
+ const startedAt = this.now().toISOString();
20
+ const inputRedaction = redactUnknown(input.sanitizedInput);
21
+ const commandRedaction = redactText(input.command ?? '');
22
+ const summaryRedaction = redactText(input.outputSummary);
23
+ const versionRedaction = redactText(input.version ?? '');
24
+ const evidence = {
25
+ ...input,
26
+ id: `TOOL-${Date.now()}-${randomUUID().slice(0, 8)}`,
27
+ startedAt,
28
+ completedAt: this.now().toISOString(),
29
+ sequence: ++this.sequence,
30
+ sanitizedInput: inputRedaction.value,
31
+ command: input.command ? commandRedaction.value : undefined,
32
+ version: input.version ? versionRedaction.value : undefined,
33
+ outputSummary: summaryRedaction.value,
34
+ redactionApplied: inputRedaction.redacted || commandRedaction.redacted || summaryRedaction.redacted || versionRedaction.redacted,
35
+ };
36
+ const dir = this.taskDir(input.taskId);
37
+ if (!existsSync(dir))
38
+ mkdirSync(dir, { recursive: true });
39
+ writeFileSync(join(dir, `${evidence.id}.json`), JSON.stringify(evidence, null, 2), 'utf-8');
40
+ return evidence;
41
+ }
42
+ list(taskId) {
43
+ const dir = this.taskDir(taskId);
44
+ if (!existsSync(dir))
45
+ return [];
46
+ return readdirSync(dir)
47
+ .filter(file => file.endsWith('.json'))
48
+ .map(file => readEvidenceFile(join(dir, file)))
49
+ .filter((record) => Boolean(record))
50
+ .sort((a, b) => {
51
+ const time = Date.parse(b.completedAt) - Date.parse(a.completedAt);
52
+ if (time !== 0)
53
+ return time;
54
+ return b.sequence - a.sequence;
55
+ });
56
+ }
57
+ get(taskId, id) {
58
+ return readEvidenceFile(join(this.taskDir(taskId), `${id}.json`));
59
+ }
60
+ summary(taskId) {
61
+ const records = this.list(taskId);
62
+ const passed = records.filter(record => record.status === 'passed').length;
63
+ const failed = records.filter(record => record.status === 'failed').length;
64
+ const skipped = records.filter(record => record.status === 'skipped').length;
65
+ return {
66
+ taskId,
67
+ total: records.length,
68
+ passed,
69
+ failed,
70
+ skipped,
71
+ ok: failed === 0,
72
+ };
73
+ }
74
+ taskDir(taskId) {
75
+ return join(this.rootDir, safePathSegment(taskId));
76
+ }
77
+ }
78
+ export function redactEvidenceValue(value) {
79
+ return redactUnknown(value);
80
+ }
81
+ export function redactEvidenceText(text) {
82
+ return redactText(text);
83
+ }
84
+ function readEvidenceFile(file) {
85
+ try {
86
+ return JSON.parse(readFileSync(file, 'utf-8'));
87
+ }
88
+ catch {
89
+ return null;
90
+ }
91
+ }
92
+ function redactUnknown(value, key = '') {
93
+ if (SENSITIVE_KEY_PATTERN.test(key))
94
+ return { value: REDACTED, redacted: true };
95
+ if (typeof value === 'string')
96
+ return redactText(value);
97
+ if (Array.isArray(value)) {
98
+ let redacted = false;
99
+ const list = value.map(item => {
100
+ const result = redactUnknown(item);
101
+ redacted = redacted || result.redacted;
102
+ return result.value;
103
+ });
104
+ return { value: list, redacted };
105
+ }
106
+ if (value && typeof value === 'object') {
107
+ let redacted = false;
108
+ const output = {};
109
+ for (const [childKey, childValue] of Object.entries(value)) {
110
+ const result = redactUnknown(childValue, childKey);
111
+ redacted = redacted || result.redacted;
112
+ output[childKey] = result.value;
113
+ }
114
+ return { value: output, redacted };
115
+ }
116
+ return { value, redacted: false };
117
+ }
118
+ function redactText(text) {
119
+ let output = text;
120
+ output = output.replace(/(authorization\s*:\s*bearer\s+)[^\s,;]+/gi, `$1${REDACTED}`);
121
+ output = output.replace(/(--(?:password|token|secret|authorization|cookie|credential|api-key|apikey|private-key)\s+)[^\s]+/gi, `$1${REDACTED}`);
122
+ output = output.replace(/\b(password|passwd|pwd|token|secret|authorization|cookie|credential|api[_-]?key|private[_-]?key)\s*=\s*[^\s,;]+/gi, `$1=${REDACTED}`);
123
+ output = output.replace(/("(?:password|passwd|pwd|token|secret|authorization|cookie|credential|api[_-]?key|private[_-]?key)"\s*:\s*")[^"]+(")/gi, `$1${REDACTED}$2`);
124
+ return { value: output, redacted: output !== text };
125
+ }
126
+ function safePathSegment(value) {
127
+ return value.replace(/[^a-zA-Z0-9._-]/g, '-').slice(0, 120) || 'unknown-task';
128
+ }
129
+ //# sourceMappingURL=ToolEvidenceStore.js.map
@@ -0,0 +1 @@
1
+ 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@@ -0,0 +1,67 @@
1
+ import type { SkillPlan } from '../skills/routing/index.js';
2
+ import { type ToolCapabilityEntry, type ToolCapabilityReport } from './ToolCapabilityRegistry.js';
3
+ import { ToolEvidenceStore, type ToolEvidenceAdapter, type ToolEvidenceStatus, type ToolRunEvidence } from './ToolEvidenceStore.js';
4
+ import { type ResolvedToolPolicy } from './ToolPolicy.js';
5
+ export type ToolStepStatus = 'ready' | 'missing' | 'skipped';
6
+ export interface ToolExecutionStep {
7
+ id: string;
8
+ toolId: string;
9
+ domain: string;
10
+ adapter: ToolEvidenceAdapter;
11
+ required: boolean;
12
+ status: ToolStepStatus;
13
+ reason: string;
14
+ capability?: ToolCapabilityEntry;
15
+ }
16
+ export interface ToolExecutionPlan {
17
+ taskId: string;
18
+ taskName: string;
19
+ mode: ResolvedToolPolicy['mode'];
20
+ steps: ToolExecutionStep[];
21
+ blockers: string[];
22
+ warnings: string[];
23
+ }
24
+ export interface ToolPlanInput {
25
+ skillPlan: SkillPlan;
26
+ }
27
+ export interface ToolRunOptions {
28
+ dryRun?: boolean;
29
+ inputs?: Record<string, Record<string, unknown>>;
30
+ }
31
+ export interface ToolStepExecutionResult {
32
+ status: ToolEvidenceStatus;
33
+ outputSummary: string;
34
+ outputPaths: string[];
35
+ exitCode?: number;
36
+ version?: string;
37
+ }
38
+ export interface ToolRunReport {
39
+ taskId: string;
40
+ ok: boolean;
41
+ dryRun: boolean;
42
+ evidence: ToolRunEvidence[];
43
+ blockers: string[];
44
+ warnings: string[];
45
+ }
46
+ export interface ToolOrchestratorOptions {
47
+ projectDir?: string;
48
+ policy?: ResolvedToolPolicy;
49
+ capabilityReport?: ToolCapabilityReport;
50
+ evidenceStore?: ToolEvidenceStore;
51
+ executeStep?: (step: ToolExecutionStep, input: Record<string, unknown>) => Promise<ToolStepExecutionResult>;
52
+ }
53
+ export declare class ToolOrchestrator {
54
+ private projectDir;
55
+ private policy;
56
+ private capabilityReport?;
57
+ private evidenceStore;
58
+ private executeStepImpl?;
59
+ constructor(options?: ToolOrchestratorOptions);
60
+ plan(input: ToolPlanInput): ToolExecutionPlan;
61
+ run(plan: ToolExecutionPlan, options?: ToolRunOptions): Promise<ToolRunReport>;
62
+ private resolveToolIds;
63
+ private isRequired;
64
+ private resolveDomain;
65
+ private executeStep;
66
+ private safetyPolicyForStep;
67
+ }
@@ -0,0 +1,252 @@
1
+ import { execa } from 'execa';
2
+ import { inspectToolCapabilities, TOOL_CAPABILITY_CATALOG } from './ToolCapabilityRegistry.js';
3
+ import { ToolEvidenceStore } from './ToolEvidenceStore.js';
4
+ import { requiredToolsForDomains, resolveToolPolicy } from './ToolPolicy.js';
5
+ import { wrapCliCommandWithRtk } from './RtkRuntime.js';
6
+ export class ToolOrchestrator {
7
+ constructor(options = {}) {
8
+ this.projectDir = options.projectDir ?? process.cwd();
9
+ this.policy = options.policy ?? resolveToolPolicy(null);
10
+ this.capabilityReport = options.capabilityReport;
11
+ this.evidenceStore = options.evidenceStore ?? new ToolEvidenceStore({ projectDir: this.projectDir });
12
+ this.executeStepImpl = options.executeStep;
13
+ }
14
+ plan(input) {
15
+ if (this.policy.mode === 'off') {
16
+ return {
17
+ taskId: input.skillPlan.taskId,
18
+ taskName: input.skillPlan.taskName,
19
+ mode: this.policy.mode,
20
+ steps: [],
21
+ blockers: [],
22
+ warnings: ['Tool orchestration is disabled.'],
23
+ };
24
+ }
25
+ const toolIds = this.resolveToolIds(input.skillPlan);
26
+ const capabilityReport = this.capabilityReport ?? inspectToolCapabilities({
27
+ projectDir: this.projectDir,
28
+ toolIds,
29
+ });
30
+ const capabilityById = new Map(capabilityReport.tools.map(tool => [tool.id, tool]));
31
+ const blockers = [];
32
+ const warnings = [...this.policy.warnings];
33
+ const steps = [];
34
+ for (const toolId of toolIds) {
35
+ const capability = capabilityById.get(toolId);
36
+ const required = this.isRequired(toolId, input.skillPlan);
37
+ const status = capability?.installed ? 'ready' : 'missing';
38
+ const step = {
39
+ id: `tool-${steps.length + 1}-${toolId}`,
40
+ toolId,
41
+ domain: this.resolveDomain(toolId, input.skillPlan),
42
+ adapter: adapterForCategory(capability?.category ?? catalogCategory(toolId)),
43
+ required,
44
+ status,
45
+ capability,
46
+ reason: status === 'ready'
47
+ ? 'Tool is available.'
48
+ : capability?.missingReason ?? 'Tool capability is missing or not configured.',
49
+ };
50
+ steps.push(step);
51
+ if (status === 'missing' && required) {
52
+ const message = `Required tool ${toolId} is missing for task ${input.skillPlan.taskId}.`;
53
+ if (this.policy.mode === 'block')
54
+ blockers.push(message);
55
+ else
56
+ warnings.push(message);
57
+ }
58
+ }
59
+ return {
60
+ taskId: input.skillPlan.taskId,
61
+ taskName: input.skillPlan.taskName,
62
+ mode: this.policy.mode,
63
+ steps,
64
+ blockers,
65
+ warnings,
66
+ };
67
+ }
68
+ async run(plan, options = {}) {
69
+ const blockers = [...plan.blockers];
70
+ const warnings = [...plan.warnings];
71
+ const evidence = [];
72
+ if (blockers.length > 0) {
73
+ return {
74
+ taskId: plan.taskId,
75
+ ok: false,
76
+ dryRun: Boolean(options.dryRun),
77
+ evidence,
78
+ blockers,
79
+ warnings,
80
+ };
81
+ }
82
+ for (const step of plan.steps) {
83
+ if (step.status !== 'ready')
84
+ continue;
85
+ const result = options.dryRun
86
+ ? dryRunResult(step)
87
+ : await this.executeStep(step, options.inputs?.[step.toolId] ?? {});
88
+ const record = this.evidenceStore.save({
89
+ taskId: plan.taskId,
90
+ domain: step.domain,
91
+ tool: step.toolId,
92
+ adapter: step.adapter,
93
+ version: result.version ?? step.capability?.version,
94
+ command: step.capability?.command,
95
+ mcpToolName: step.capability?.category === 'mcp' ? step.capability.id : undefined,
96
+ status: result.status,
97
+ exitCode: result.exitCode,
98
+ sanitizedInput: options.inputs?.[step.toolId] ?? {},
99
+ outputSummary: result.outputSummary,
100
+ outputPaths: result.outputPaths,
101
+ safetyPolicy: this.safetyPolicyForStep(step, Boolean(options.dryRun)),
102
+ });
103
+ evidence.push(record);
104
+ if (record.status === 'failed') {
105
+ const message = `Tool ${step.toolId} failed for task ${plan.taskId}.`;
106
+ if (step.required)
107
+ blockers.push(message);
108
+ else
109
+ warnings.push(message);
110
+ }
111
+ }
112
+ return {
113
+ taskId: plan.taskId,
114
+ ok: blockers.length === 0,
115
+ dryRun: Boolean(options.dryRun),
116
+ evidence,
117
+ blockers,
118
+ warnings,
119
+ };
120
+ }
121
+ resolveToolIds(skillPlan) {
122
+ const requiredByDomain = requiredToolsForDomains(this.policy, skillPlan.intents.map(intent => intent.domain))
123
+ .map(tool => tool.id);
124
+ return unique([
125
+ ...skillPlan.requiredSkills,
126
+ ...requiredByDomain,
127
+ ...skillPlan.recommendedSkills.filter(skill => this.policy.tools[skill]?.enabled),
128
+ ]);
129
+ }
130
+ isRequired(toolId, skillPlan) {
131
+ if (skillPlan.requiredSkills.includes(toolId))
132
+ return true;
133
+ const config = this.policy.tools[toolId];
134
+ if (!config)
135
+ return false;
136
+ const domains = new Set(skillPlan.intents.map(intent => intent.domain));
137
+ return config.requiredFor.some(domain => domains.has(domain));
138
+ }
139
+ resolveDomain(toolId, skillPlan) {
140
+ const config = this.policy.tools[toolId];
141
+ const intentDomains = skillPlan.intents.map(intent => intent.domain);
142
+ const requiredDomain = config?.requiredFor.find(domain => intentDomains.includes(domain));
143
+ if (requiredDomain)
144
+ return requiredDomain;
145
+ const recommendedDomain = config?.recommendedFor?.find(domain => intentDomains.includes(domain));
146
+ if (recommendedDomain)
147
+ return recommendedDomain;
148
+ return intentDomains[0] ?? 'general';
149
+ }
150
+ async executeStep(step, input) {
151
+ if (this.executeStepImpl)
152
+ return this.executeStepImpl(step, input);
153
+ if (step.adapter === 'cli' || step.adapter === 'browser' || step.adapter === 'desktop')
154
+ return executeCliCapabilityCheck(step);
155
+ return {
156
+ status: 'skipped',
157
+ outputSummary: `No executor configured for ${step.toolId}; evidence recorded as skipped.`,
158
+ outputPaths: [],
159
+ };
160
+ }
161
+ safetyPolicyForStep(step, dryRun) {
162
+ const policies = ['redact-secrets'];
163
+ if (dryRun)
164
+ policies.push('dry-run');
165
+ if (step.adapter === 'browser')
166
+ policies.push('browser-side-effect-boundary');
167
+ if (step.adapter === 'desktop')
168
+ policies.push('desktop-side-effect-boundary');
169
+ if (step.adapter === 'cli')
170
+ policies.push('cli-version-and-exit-code');
171
+ if (step.adapter === 'mcp')
172
+ policies.push('mcp-tool-policy');
173
+ return policies;
174
+ }
175
+ }
176
+ function dryRunResult(step) {
177
+ return {
178
+ status: 'skipped',
179
+ outputSummary: `Dry-run: ${step.toolId} was planned but not executed.`,
180
+ outputPaths: [],
181
+ version: step.capability?.version,
182
+ };
183
+ }
184
+ async function executeCliCapabilityCheck(step) {
185
+ const command = step.capability?.command;
186
+ const args = step.capability?.versionArgs ?? ['--version'];
187
+ if (!command) {
188
+ return {
189
+ status: 'skipped',
190
+ outputSummary: `No safe CLI command configured for ${step.toolId}; evidence recorded as skipped.`,
191
+ outputPaths: [],
192
+ };
193
+ }
194
+ try {
195
+ const invocation = wrapCliCommandWithRtk(command, args);
196
+ const result = await execa(invocation.command, invocation.args, {
197
+ reject: false,
198
+ timeout: 10_000,
199
+ cwd: process.cwd(),
200
+ env: process.env,
201
+ stdin: 'ignore',
202
+ });
203
+ const stdout = result.stdout.trim();
204
+ const stderr = result.stderr.trim();
205
+ const exitCode = result.exitCode ?? 1;
206
+ const outputSummary = summarizeCliOutput(step.toolId, stdout, stderr, exitCode, invocation.wrapped);
207
+ return {
208
+ status: exitCode === 0 ? 'passed' : 'failed',
209
+ outputSummary,
210
+ outputPaths: [],
211
+ exitCode,
212
+ version: stdout.split(/\r?\n/).find(Boolean) ?? step.capability?.version,
213
+ };
214
+ }
215
+ catch (error) {
216
+ return {
217
+ status: 'failed',
218
+ outputSummary: `CLI check failed for ${step.toolId}: ${error instanceof Error ? error.message : String(error)}`,
219
+ outputPaths: [],
220
+ exitCode: 1,
221
+ };
222
+ }
223
+ }
224
+ function summarizeCliOutput(toolId, stdout, stderr, exitCode, wrappedByRtk = false) {
225
+ const lines = [`CLI version check for ${toolId} exited with ${exitCode}.${wrappedByRtk ? ' Wrapped with RTK.' : ''}`];
226
+ if (stdout)
227
+ lines.push(`stdout: ${tail(stdout)}`);
228
+ if (stderr)
229
+ lines.push(`stderr: ${tail(stderr)}`);
230
+ return lines.join(' ');
231
+ }
232
+ function tail(value) {
233
+ return value.split(/\r?\n/).slice(-5).join('\n').slice(0, 1000);
234
+ }
235
+ function adapterForCategory(category) {
236
+ if (category === 'browser')
237
+ return 'browser';
238
+ if (category === 'desktop')
239
+ return 'desktop';
240
+ if (category === 'cli')
241
+ return 'cli';
242
+ if (category === 'mcp')
243
+ return 'mcp';
244
+ return 'skill';
245
+ }
246
+ function catalogCategory(toolId) {
247
+ return TOOL_CAPABILITY_CATALOG.find(tool => tool.id === toolId)?.category ?? 'skill';
248
+ }
249
+ function unique(items) {
250
+ return [...new Set(items)];
251
+ }
252
+ //# sourceMappingURL=ToolOrchestrator.js.map
@@ -0,0 +1 @@
1
+ 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@@ -0,0 +1,33 @@
1
+ export type ToolOrchestrationMode = 'off' | 'advisory' | 'evidence-required' | 'block';
2
+ export type ToolDestructiveActionPolicy = 'allow' | 'confirm' | 'block';
3
+ export interface ToolPolicyToolConfig {
4
+ enabled: boolean;
5
+ requiredFor: string[];
6
+ recommendedFor?: string[];
7
+ allowedDomains?: string[];
8
+ destructiveActions?: ToolDestructiveActionPolicy;
9
+ command?: string;
10
+ mcpToolName?: string;
11
+ evidenceRequired?: boolean;
12
+ }
13
+ export interface ToolPolicyFile {
14
+ version?: number;
15
+ mode?: ToolOrchestrationMode;
16
+ tools?: Record<string, Partial<ToolPolicyToolConfig>>;
17
+ }
18
+ export interface ResolvedToolPolicy {
19
+ version: number;
20
+ mode: ToolOrchestrationMode;
21
+ tools: Record<string, ToolPolicyToolConfig>;
22
+ warnings: string[];
23
+ }
24
+ export interface RequiredTool {
25
+ id: string;
26
+ config: ToolPolicyToolConfig;
27
+ }
28
+ export declare const DEFAULT_TOOL_POLICY: ResolvedToolPolicy;
29
+ export declare function toolPolicyPath(projectDir?: string, scaleDir?: string): string;
30
+ export declare function loadToolPolicy(projectDir?: string, scaleDir?: string): ResolvedToolPolicy;
31
+ export declare function resolveToolPolicy(input: ToolPolicyFile | null | undefined): ResolvedToolPolicy;
32
+ export declare function requiredToolsForDomains(policy: ResolvedToolPolicy, domains: string[]): RequiredTool[];
33
+ export declare function toolPolicyTemplate(mode?: ToolOrchestrationMode): string;