@iowarp/clio-coder 0.4.6 → 0.4.8

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 (1142) hide show
  1. package/.claude-plugin/marketplace.json +283 -0
  2. package/CHANGELOG.md +79 -0
  3. package/CONTRIBUTING.md +178 -96
  4. package/NOTICE +8 -0
  5. package/README.md +100 -47
  6. package/dist/acp-JWPQZM2D.js +130 -0
  7. package/dist/agents-4GCDIRVX.js +149 -0
  8. package/dist/assets/codewiki.json +1 -1
  9. package/dist/assets/tui-notices/get-east-asian-width-LICENSE +9 -0
  10. package/dist/assets/tui-notices/marked-LICENSE +44 -0
  11. package/dist/assets/tui-notices/pi-tui-LICENSE +21 -0
  12. package/dist/assets/web-notices/@hono__node-server-LICENSE +21 -0
  13. package/dist/assets/web-notices/hono-LICENSE +21 -0
  14. package/dist/auth-SYAKTDQE.js +551 -0
  15. package/dist/background-OW67WMYR.js +37 -0
  16. package/dist/builtins-TKS63VNV.js +22 -0
  17. package/dist/chunk-2JSCCEKO.js +85 -0
  18. package/dist/chunk-2SXGG2IV.js +391 -0
  19. package/dist/chunk-2U2U5POA.js +59 -0
  20. package/dist/chunk-2ZWLMA3T.js +658 -0
  21. package/dist/chunk-36XSBPXL.js +579 -0
  22. package/dist/chunk-3IQOZRQ6.js +396 -0
  23. package/dist/chunk-3XE4NRLF.js +324 -0
  24. package/dist/chunk-44U2OUSM.js +243 -0
  25. package/dist/chunk-4P6M2TTE.js +119 -0
  26. package/dist/chunk-526ABLHD.js +1219 -0
  27. package/dist/chunk-5C2OQHLR.js +674 -0
  28. package/dist/chunk-5D2FNBMG.js +185 -0
  29. package/dist/chunk-5EQO5NWP.js +243 -0
  30. package/dist/chunk-5HULHKT2.js +32 -0
  31. package/dist/chunk-5UG6EZI3.js +66 -0
  32. package/dist/chunk-5W4FRA5Q.js +22283 -0
  33. package/dist/chunk-6R5MBXBJ.js +386 -0
  34. package/dist/chunk-6TKOFFGE.js +1058 -0
  35. package/dist/chunk-6UJ7RDI7.js +1143 -0
  36. package/dist/chunk-6X7VOCDY.js +44 -0
  37. package/dist/chunk-7QQRPB2E.js +915 -0
  38. package/dist/chunk-ARRUMZ7X.js +1377 -0
  39. package/dist/chunk-ATB3Q7YO.js +663 -0
  40. package/dist/chunk-AUHVBIDW.js +19 -0
  41. package/dist/chunk-BE4I3UJ2.js +668 -0
  42. package/dist/chunk-BFPHMSK7.js +169 -0
  43. package/dist/chunk-BHJMMCXS.js +466 -0
  44. package/dist/chunk-BIY22UUK.js +1322 -0
  45. package/dist/chunk-D55WO5J7.js +110 -0
  46. package/dist/chunk-DVJL77SO.js +162 -0
  47. package/dist/chunk-E2NSPYLC.js +814 -0
  48. package/dist/chunk-EFXMQYI6.js +4484 -0
  49. package/dist/chunk-EPYATQMG.js +2718 -0
  50. package/dist/chunk-EXKUF426.js +1801 -0
  51. package/dist/chunk-F7Y6QTPL.js +689 -0
  52. package/dist/chunk-FB3KTE2J.js +1710 -0
  53. package/dist/chunk-FNVPQQYT.js +117 -0
  54. package/dist/chunk-GEVQNST4.js +101 -0
  55. package/dist/chunk-GEYX2NZ5.js +697 -0
  56. package/dist/chunk-GJBJHJNY.js +2120 -0
  57. package/dist/chunk-GM4TY6VN.js +1233 -0
  58. package/dist/chunk-GVU4CXPJ.js +5191 -0
  59. package/dist/chunk-H5DPSUBB.js +637 -0
  60. package/dist/chunk-H77XBUBM.js +688 -0
  61. package/dist/chunk-HMGAKB7E.js +380 -0
  62. package/dist/chunk-HP7KJ5O2.js +797 -0
  63. package/dist/chunk-HVCAY2FH.js +67 -0
  64. package/dist/chunk-ICYIUNO4.js +35 -0
  65. package/dist/chunk-IILXVWJY.js +223 -0
  66. package/dist/chunk-JCVIL6TY.js +595 -0
  67. package/dist/chunk-JIMWEYWO.js +63 -0
  68. package/dist/chunk-JLBVCROW.js +562 -0
  69. package/dist/chunk-JOBN2YQQ.js +176 -0
  70. package/dist/chunk-JOL2QRLE.js +152 -0
  71. package/dist/chunk-JRA6OBHY.js +974 -0
  72. package/dist/chunk-JV25I7ID.js +1865 -0
  73. package/dist/chunk-JYKUMHCQ.js +705 -0
  74. package/dist/chunk-K3W6BF5C.js +283 -0
  75. package/dist/chunk-K45LHSCI.js +194 -0
  76. package/dist/chunk-K53E2PTW.js +1289 -0
  77. package/dist/chunk-K5UJD6MM.js +39 -0
  78. package/dist/chunk-KGP3UQGJ.js +200 -0
  79. package/dist/chunk-KKRXONXG.js +43 -0
  80. package/dist/chunk-KWJXCL2X.js +103 -0
  81. package/dist/chunk-L75H5B3B.js +446 -0
  82. package/dist/chunk-LLCGGVSW.js +108 -0
  83. package/dist/chunk-LZCCBLRC.js +57 -0
  84. package/dist/chunk-LZDLYSUN.js +197 -0
  85. package/dist/chunk-MATCRH3M.js +667 -0
  86. package/dist/chunk-MEHBW2SP.js +132 -0
  87. package/dist/chunk-MUXNDNMZ.js +659 -0
  88. package/dist/chunk-MWMW53WW.js +7346 -0
  89. package/dist/chunk-MZDPF35R.js +45 -0
  90. package/dist/chunk-MZKYVIWW.js +188 -0
  91. package/dist/chunk-O2QJDRWP.js +362 -0
  92. package/dist/chunk-O3HSB2YL.js +693 -0
  93. package/dist/chunk-OEMFEL26.js +891 -0
  94. package/dist/chunk-OH3YYA3B.js +15 -0
  95. package/dist/chunk-OPC4DQD6.js +634 -0
  96. package/dist/chunk-ORRNGQDV.js +207 -0
  97. package/dist/chunk-P4JS3MH5.js +165 -0
  98. package/dist/chunk-P7GTE4FX.js +308 -0
  99. package/dist/chunk-PAQVETLA.js +962 -0
  100. package/dist/chunk-PFZJMXIY.js +146 -0
  101. package/dist/chunk-PGEFOTJB.js +1974 -0
  102. package/dist/chunk-PJ5H5B7A.js +3151 -0
  103. package/dist/chunk-PMUUAABD.js +604 -0
  104. package/dist/chunk-Q32C6AWI.js +236 -0
  105. package/dist/chunk-QGIC5SX5.js +139 -0
  106. package/dist/chunk-QLAGXTTV.js +482 -0
  107. package/dist/chunk-QLKCCC2J.js +573 -0
  108. package/dist/chunk-QWUSS2QP.js +3630 -0
  109. package/dist/chunk-QYSAZMSH.js +47 -0
  110. package/dist/chunk-R5NRX5N4.js +123 -0
  111. package/dist/chunk-RAUOKUZV.js +1572 -0
  112. package/dist/chunk-RBES4TCZ.js +302 -0
  113. package/dist/chunk-RFCKPS2V.js +26 -0
  114. package/dist/chunk-RFULVPBX.js +318 -0
  115. package/dist/chunk-RKFNU5UA.js +404 -0
  116. package/dist/chunk-RM3XJX7P.js +1148 -0
  117. package/dist/chunk-RNLAPBJL.js +386 -0
  118. package/dist/chunk-RPMNIFRY.js +65 -0
  119. package/dist/chunk-RRZFRIJP.js +42 -0
  120. package/dist/chunk-RXI7K4J5.js +4493 -0
  121. package/dist/chunk-SER7RRAE.js +4271 -0
  122. package/dist/chunk-STC6CWUZ.js +402 -0
  123. package/dist/chunk-TEHVMHOK.js +97 -0
  124. package/dist/chunk-TOPICHGR.js +33 -0
  125. package/dist/chunk-U3TPUXOQ.js +2653 -0
  126. package/dist/chunk-UB33F3YW.js +709 -0
  127. package/dist/chunk-UDAK6GR2.js +175 -0
  128. package/dist/chunk-USBBEKHW.js +177 -0
  129. package/dist/chunk-V4ZKOKRB.js +13433 -0
  130. package/dist/chunk-W5RM7YAH.js +78 -0
  131. package/dist/chunk-W7KNI3F5.js +215 -0
  132. package/dist/chunk-WFTSK7N3.js +637 -0
  133. package/dist/chunk-WJWNZXRM.js +395 -0
  134. package/dist/chunk-WLHX3MM5.js +63 -0
  135. package/dist/chunk-WS4FOGLY.js +686 -0
  136. package/dist/chunk-WTZVSMQZ.js +52 -0
  137. package/dist/chunk-WWRV5RJI.js +165 -0
  138. package/dist/chunk-X6FLVUM5.js +141 -0
  139. package/dist/chunk-XC5POIL4.js +68 -0
  140. package/dist/chunk-XTLJDC2X.js +1013 -0
  141. package/dist/chunk-XW2UZICE.js +372 -0
  142. package/dist/chunk-Y3JU5RPK.js +8 -0
  143. package/dist/chunk-YGIV24MF.js +1018 -0
  144. package/dist/chunk-YJCCMYYT.js +125 -0
  145. package/dist/chunk-YKIIWURD.js +36 -0
  146. package/dist/chunk-YQ3GFEUY.js +341 -0
  147. package/dist/chunk-YXANQGCX.js +179 -0
  148. package/dist/chunk-YXFKLMX2.js +222 -0
  149. package/dist/chunk-ZST3FRCV.js +132 -0
  150. package/dist/cli/index.js +40 -40
  151. package/dist/clio-BPBAPZGA.js +26 -0
  152. package/dist/code-nav-KBQ3RIFK.js +686 -0
  153. package/dist/components-6DKAXWFN.js +674 -0
  154. package/dist/config-FWL5JK2H.js +270 -0
  155. package/dist/config-graph-ACDB26L2.js +156 -0
  156. package/dist/configure-ZIZ4YV62.js +85 -0
  157. package/dist/context-EZZPT2ZV.js +1074 -0
  158. package/dist/context-VIL5MFRH.js +282 -0
  159. package/dist/context-Z3GOBHDK.js +344 -0
  160. package/dist/context-clear-ZPB3L7MN.js +188 -0
  161. package/dist/context-index-W6A4V7OC.js +120 -0
  162. package/dist/context-map-DKL3QT6D.js +555 -0
  163. package/dist/context-working-set-2GLBVF7L.js +1559 -0
  164. package/dist/detail-VSBWYSGZ.js +119 -0
  165. package/dist/dispatch-runner-EEEHGKX4.js +2442 -0
  166. package/dist/docs-VMMWFVHL.js +101 -0
  167. package/dist/doctor-V5L4IQGP.js +812 -0
  168. package/dist/eval-VJYJ2BV3.js +5050 -0
  169. package/dist/eval-inventory-CX24K2JT.js +260 -0
  170. package/dist/evals-J2H5V6DD.js +104 -0
  171. package/dist/evidence-POWAEBEW.js +229 -0
  172. package/dist/evidence-XCCCLS36.js +242 -0
  173. package/dist/evidence-Y35YSXH6.js +388 -0
  174. package/dist/evolve-GPG72VB6.js +613 -0
  175. package/dist/extensions-YIZ7W3DA.js +308 -0
  176. package/dist/fleet-2MDCQ2VK.js +264 -0
  177. package/dist/fleet-W2AF3TOJ.js +919 -0
  178. package/dist/fleet-commands-WS56G26H.js +75 -0
  179. package/dist/fleet-decisions-MYGZ3JW7.js +52 -0
  180. package/dist/fleet-graph-ELTBXBAV.js +136 -0
  181. package/dist/fleet-inspect-45IK73L4.js +308 -0
  182. package/dist/fleet-preflight-T5NCZKHE.js +22 -0
  183. package/dist/fleet-validate-VG4JBLA4.js +91 -0
  184. package/dist/fleet-verify-VTSABAYO.js +206 -0
  185. package/dist/fleet-view-XC7WMKSS.js +123 -0
  186. package/dist/init-VTJNNTIP.js +329 -0
  187. package/dist/install-6PIF6F6W.js +19 -0
  188. package/dist/interop-IU6BNA7C.js +246 -0
  189. package/dist/inventory-QPQUTUUZ.js +123 -0
  190. package/dist/library-HUTAS57T.js +492 -0
  191. package/dist/library-LF7DLU6S.js +306 -0
  192. package/dist/library-Q3NWL5CM.js +75 -0
  193. package/dist/library-import-PPW4YUC5.js +183 -0
  194. package/dist/library-inventory-DIRVFRZU.js +56 -0
  195. package/dist/library-validation-XHUZ3INE.js +42 -0
  196. package/dist/memory-Z2LSKNV6.js +516 -0
  197. package/dist/models-3FTREYPY.js +302 -0
  198. package/dist/monitor-HF2MQRB3.js +781 -0
  199. package/dist/orchestrator-UYPA6W4S.js +41502 -0
  200. package/dist/panes-736XB73K.js +74 -0
  201. package/dist/panes-C4P3PIWT.js +103 -0
  202. package/dist/paths-JQ4QYIYB.js +67 -0
  203. package/dist/preload-XSLRYH3Y.js +120 -0
  204. package/dist/reset-V7QSPZYE.js +345 -0
  205. package/dist/resources-OJGDFHYT.js +181 -0
  206. package/dist/run-T354SMDW.js +892 -0
  207. package/dist/settings-MWZXO6RV.js +72 -0
  208. package/dist/share-Y5ZKJPND.js +293 -0
  209. package/dist/skills-4GLZC4LN.js +100 -0
  210. package/dist/skills-eval-L5T7GODM.js +1074 -0
  211. package/dist/skills-inventory-LASKXEZI.js +138 -0
  212. package/dist/slash-commands-OIMRU36D.js +95 -0
  213. package/dist/steer-KMAM2Y2C.js +77 -0
  214. package/dist/support-AWC3XKPX.js +38 -0
  215. package/dist/system-CD75NYBU.js +116 -0
  216. package/dist/targets-VSZX2J2S.js +1116 -0
  217. package/dist/tasks-AN567LYH.js +36 -0
  218. package/dist/terminal-lease-6KTWNHVY.js +418 -0
  219. package/dist/tools-AGRK3V5J.js +28 -0
  220. package/dist/trace-P4MQZD33.js +524 -0
  221. package/dist/tui-primitives-A6MUW32V.js +18 -0
  222. package/dist/uninstall-BRUTEPIC.js +432 -0
  223. package/dist/upgrade-SBCGHQGJ.js +307 -0
  224. package/dist/usage-BIDVTO6V.js +1061 -0
  225. package/dist/verifiers-LTGCAMXS.js +630 -0
  226. package/dist/verify-OZU4LLNP.js +30 -0
  227. package/dist/web/client/THIRD_PARTY_LICENSES.md +1809 -0
  228. package/dist/web/client/assets/abnfDiagram-VCTEODGH-C5wfoHm3.js +1 -0
  229. package/dist/web/client/assets/arc-oH91sfLl.js +1 -0
  230. package/dist/web/client/assets/architecture-7GRP2DOG-EGozsYEO.js +1 -0
  231. package/dist/web/client/assets/architectureDiagram-5GKGNRK7-z9FokbJl.js +36 -0
  232. package/dist/web/client/assets/array-BifhSqXX.js +1 -0
  233. package/dist/web/client/assets/atkinson-hyperlegible-next-latin-ext-wght-normal-C6vrW8VD.woff2 +0 -0
  234. package/dist/web/client/assets/atkinson-hyperlegible-next-latin-wght-normal-BcXVPD7q.woff2 +0 -0
  235. package/dist/web/client/assets/blockDiagram-I7D4REHJ-wi0_CYHL.js +129 -0
  236. package/dist/web/client/assets/c4Diagram-7LVT6UL2-DV7NYc2W.js +38 -0
  237. package/dist/web/client/assets/channel-CiUWbHN9.js +1 -0
  238. package/dist/web/client/assets/chunk-2Q5K7J3B-C1jixKkw.js +1 -0
  239. package/dist/web/client/assets/chunk-4HAMMTFA-Bhsegh3F.js +62 -0
  240. package/dist/web/client/assets/chunk-5VM5RSS4-ZNzvKenW.js +15 -0
  241. package/dist/web/client/assets/chunk-75Z2AOVW-RQCckcQG.js +2 -0
  242. package/dist/web/client/assets/chunk-DU6HZSFF-C5USiOAy.js +125 -0
  243. package/dist/web/client/assets/chunk-F27PBJKO-BcNqv2x1.js +1 -0
  244. package/dist/web/client/assets/chunk-FOHPRMQF-CoA4358r.js +161 -0
  245. package/dist/web/client/assets/chunk-GMAD6QVW-Bq8JWiZT.js +72 -0
  246. package/dist/web/client/assets/chunk-GVQU2GXP-DbchrAeJ.js +1 -0
  247. package/dist/web/client/assets/chunk-IMKFNOWR-DrpvjocK.js +231 -0
  248. package/dist/web/client/assets/chunk-JWPE2WC7-DVXcaiue.js +1 -0
  249. package/dist/web/client/assets/chunk-L3NEJ4N5-DHLmTnCe.js +1 -0
  250. package/dist/web/client/assets/chunk-OSK3NFVY-CsRbtN9n.js +10 -0
  251. package/dist/web/client/assets/chunk-P2QGCYS3-aqPbxoMh.js +1 -0
  252. package/dist/web/client/assets/chunk-POPQ4Y6H-Dl5vw0h0.js +1 -0
  253. package/dist/web/client/assets/chunk-PWAF6VOD-D7OBRSdO.js +1 -0
  254. package/dist/web/client/assets/chunk-SHT3W25Y-CdKCIwuB.js +168 -0
  255. package/dist/web/client/assets/chunk-SVP7TREG-B94Nu_1-.js +88 -0
  256. package/dist/web/client/assets/chunk-TICWLB2K-jjRQI_hk.js +206 -0
  257. package/dist/web/client/assets/chunk-XXDRQBXY-azkbKE37.js +1 -0
  258. package/dist/web/client/assets/chunk-Y2CYZVJY-DsF7k-Jl.js +1 -0
  259. package/dist/web/client/assets/classDiagram-ZZMXUADV-CMODalmo.js +1 -0
  260. package/dist/web/client/assets/classDiagram-v2-VYDZK3BY-CMODalmo.js +1 -0
  261. package/dist/web/client/assets/commit-mono-latin-400-normal-s0S3qwFW.woff +0 -0
  262. package/dist/web/client/assets/commit-mono-latin-400-normal-wzhe4RuD.woff2 +0 -0
  263. package/dist/web/client/assets/cose-bilkent-JH36ORCC-RbQL23qS.js +1 -0
  264. package/dist/web/client/assets/cynefin-OW5HDTMX--i9RDU5f.js +1 -0
  265. package/dist/web/client/assets/cynefinDiagram-5FMLGOSQ-cRcvyBdp.js +62 -0
  266. package/dist/web/client/assets/cytoscape.esm-c2aL46s-.js +321 -0
  267. package/dist/web/client/assets/dagre-C-rnJpZF.js +1 -0
  268. package/dist/web/client/assets/dagre-GXQ25YYZ-C9mZmAPe.js +4 -0
  269. package/dist/web/client/assets/defaultLocale-BFoDCU3G.js +1 -0
  270. package/dist/web/client/assets/diagram-S7CK7UJ4-Oj_zlLDY.js +30 -0
  271. package/dist/web/client/assets/diagram-UQ7AKVKN-BWKbbfcR.js +41 -0
  272. package/dist/web/client/assets/diagram-VSXAHHWV-C3N3f7DO.js +3 -0
  273. package/dist/web/client/assets/diagram-VX7I27RA-CtDKDAWe.js +24 -0
  274. package/dist/web/client/assets/diagram-Z3DM3KII-B8bkBRCz.js +24 -0
  275. package/dist/web/client/assets/dist-D0_q-A2b.js +1 -0
  276. package/dist/web/client/assets/ebnfDiagram-PWID7BFC-CskW-Whx.js +1 -0
  277. package/dist/web/client/assets/erDiagram-RLTQ6QDP-C-83cgCW.js +99 -0
  278. package/dist/web/client/assets/eventmodeling-NTZA5JFV-DjVq8wKU.js +1 -0
  279. package/dist/web/client/assets/flowDiagram-HODETNUW-BUiCBGXt.js +1 -0
  280. package/dist/web/client/assets/ganttDiagram-EL5Y4UJY-B2lb8lvF.js +292 -0
  281. package/dist/web/client/assets/gitGraph-4MIJSDKK-B40cQtBE.js +1 -0
  282. package/dist/web/client/assets/gitGraphDiagram-WWUBYQGX-CH-7P7Di.js +106 -0
  283. package/dist/web/client/assets/graphlib-DS17s2tU.js +1 -0
  284. package/dist/web/client/assets/index-Dsi52apB.css +1 -0
  285. package/dist/web/client/assets/index-FSIC94pi.js +83 -0
  286. package/dist/web/client/assets/info-A6RAGUB7-eCCE9D_Q.js +1 -0
  287. package/dist/web/client/assets/infoDiagram-27XIBGKW-DRnvqMjM.js +2 -0
  288. package/dist/web/client/assets/init-C-OQMol4.js +1 -0
  289. package/dist/web/client/assets/ishikawaDiagram-5VMMS53U-DBA_55wp.js +70 -0
  290. package/dist/web/client/assets/journeyDiagram-3NMN7TZE-C-ewpNl7.js +139 -0
  291. package/dist/web/client/assets/kanban-definition-UXKFOSKX-B1taGsu0.js +89 -0
  292. package/dist/web/client/assets/katex-ZlcWpGUi.js +257 -0
  293. package/dist/web/client/assets/line-lZ0kyxDI.js +1 -0
  294. package/dist/web/client/assets/linear-DIc8FgZj.js +1 -0
  295. package/dist/web/client/assets/mermaid-parser.core-SXolxpXw.js +7 -0
  296. package/dist/web/client/assets/mermaid.core-DXgQtkNg.js +44 -0
  297. package/dist/web/client/assets/mindmap-definition-YA3MSWOX-DXJas9K7.js +96 -0
  298. package/dist/web/client/assets/newsreader-latin-ext-wght-normal-C-3rgBeH.woff2 +0 -0
  299. package/dist/web/client/assets/newsreader-latin-wght-normal-CCVVNp6i.woff2 +0 -0
  300. package/dist/web/client/assets/newsreader-vietnamese-wght-normal-Czsa-EzN.woff2 +0 -0
  301. package/dist/web/client/assets/ordinal-BDEzSJ7C.js +1 -0
  302. package/dist/web/client/assets/packet-AYTQ26CC-OqVl_07o.js +1 -0
  303. package/dist/web/client/assets/path-fybaL0A-.js +1 -0
  304. package/dist/web/client/assets/pegDiagram-XKGWAZYB-CPE_zdfN.js +1 -0
  305. package/dist/web/client/assets/pie-WAS4IAKB-DAxnMBLe.js +1 -0
  306. package/dist/web/client/assets/pieDiagram-E7YTZNPT-Uwjpufxv.js +39 -0
  307. package/dist/web/client/assets/prism-bash-D6zCJ74D.js +1 -0
  308. package/dist/web/client/assets/prism-c-04YixN25.js +1 -0
  309. package/dist/web/client/assets/prism-clike-DapgWyxx.js +1 -0
  310. package/dist/web/client/assets/prism-core-BngLtbUd.js +1 -0
  311. package/dist/web/client/assets/prism-cpp-C-lJbC-6.js +1 -0
  312. package/dist/web/client/assets/prism-css-CPgOzxXp.js +1 -0
  313. package/dist/web/client/assets/prism-diff-BF8m0_mq.js +3 -0
  314. package/dist/web/client/assets/prism-docker-DkT6yOFj.js +1 -0
  315. package/dist/web/client/assets/prism-fortran-Be5x3y1V.js +1 -0
  316. package/dist/web/client/assets/prism-go-C_8qAH5n.js +1 -0
  317. package/dist/web/client/assets/prism-ini-BESK3y0r.js +1 -0
  318. package/dist/web/client/assets/prism-javascript-BnO-swvr.js +1 -0
  319. package/dist/web/client/assets/prism-json-Dp_-W-Hv.js +1 -0
  320. package/dist/web/client/assets/prism-jsx-D-D0NWtC.js +1 -0
  321. package/dist/web/client/assets/prism-julia-DIjOgiAV.js +1 -0
  322. package/dist/web/client/assets/prism-latex-DNMbqcH_.js +1 -0
  323. package/dist/web/client/assets/prism-makefile-CRKWLQ8l.js +1 -0
  324. package/dist/web/client/assets/prism-markdown-C0FPJ1Iz.js +1 -0
  325. package/dist/web/client/assets/prism-markup-Cp04rIa1.js +1 -0
  326. package/dist/web/client/assets/prism-matlab-D-nk08al.js +1 -0
  327. package/dist/web/client/assets/prism-python-CfiSVtM6.js +1 -0
  328. package/dist/web/client/assets/prism-r-QmNGR8LX.js +1 -0
  329. package/dist/web/client/assets/prism-rust-Bu9N8X3N.js +1 -0
  330. package/dist/web/client/assets/prism-shell-session-Be4UuYoM.js +1 -0
  331. package/dist/web/client/assets/prism-sql-CYhVDMEE.js +1 -0
  332. package/dist/web/client/assets/prism-toml-DKb54GAT.js +1 -0
  333. package/dist/web/client/assets/prism-tsx-p6J2Kc_4.js +1 -0
  334. package/dist/web/client/assets/prism-typescript-BMqONzxf.js +1 -0
  335. package/dist/web/client/assets/prism-yaml-C0JHu8gr.js +1 -0
  336. package/dist/web/client/assets/purify.es-ChwZkWde.js +3 -0
  337. package/dist/web/client/assets/quadrantDiagram-AXDQQJYC-Bjs4yjgs.js +7 -0
  338. package/dist/web/client/assets/radar-RG4KPBEZ-CuCKjHM3.js +1 -0
  339. package/dist/web/client/assets/railroad-74A4TZTK-CnQK-Cc1.js +1 -0
  340. package/dist/web/client/assets/railroad-abnf-HS5TGJTU-BcW01NZG.js +1 -0
  341. package/dist/web/client/assets/railroad-ebnf-LZEXJU2U-B7YCEDDd.js +1 -0
  342. package/dist/web/client/assets/railroad-peg-WCYAUIDC-DjNZbSTZ.js +1 -0
  343. package/dist/web/client/assets/railroadDiagram-O6MQD6OU-BDDIPNLL.js +1 -0
  344. package/dist/web/client/assets/requirementDiagram-BXWQKSXE-B5Ydyxc1.js +84 -0
  345. package/dist/web/client/assets/rough.esm-Dy-Kn_BL.js +1 -0
  346. package/dist/web/client/assets/sankeyDiagram-P5KCCOFB-Bw2Qym75.js +40 -0
  347. package/dist/web/client/assets/sequenceDiagram-WJ2MYXX4-BZf36nO0.js +162 -0
  348. package/dist/web/client/assets/sizeCapture-INFHLROL-B0uUizjq.js +1 -0
  349. package/dist/web/client/assets/src-yeptRXpt.js +1 -0
  350. package/dist/web/client/assets/stateDiagram-D77RDMKH-DnH6JRkp.js +1 -0
  351. package/dist/web/client/assets/stateDiagram-v2-MP3YSRHH-C7QtHeK4.js +1 -0
  352. package/dist/web/client/assets/swimlanes-42K2YHIH-D9PZmtZg.js +1 -0
  353. package/dist/web/client/assets/swimlanesDiagram-VR7AAH4N-CBZlPFky.js +8 -0
  354. package/dist/web/client/assets/timeline-definition-24CTP7MA-CrkZZBo7.js +120 -0
  355. package/dist/web/client/assets/treeView-Q6P3EWNA-C9zDShoC.js +1 -0
  356. package/dist/web/client/assets/treemap-WGGIJYW6-B-plj9yK.js +1 -0
  357. package/dist/web/client/assets/vennDiagram-4TSXK5OY-VeOdaphN.js +34 -0
  358. package/dist/web/client/assets/wardley-WFR3VGLG-Wl1P_m6L.js +1 -0
  359. package/dist/web/client/assets/wardleyDiagram-VM6X3IG4-B85-R9t2.js +78 -0
  360. package/dist/web/client/assets/xychartDiagram-S5SC5T6Z-BrD8OW8m.js +7 -0
  361. package/dist/web/client/clio-coder-logo.webp +0 -0
  362. package/dist/web/client/icon-192.png +0 -0
  363. package/dist/web/client/icon-512.png +0 -0
  364. package/dist/web/client/index.html +4 -0
  365. package/dist/web/client/manifest.webmanifest +15 -0
  366. package/dist/web/client/offline.css +55 -0
  367. package/dist/web/client/offline.html +5 -0
  368. package/dist/web/client/offline.js +27 -0
  369. package/dist/web/client/sw.js +34 -0
  370. package/dist/web/ops-worker.js +37 -0
  371. package/dist/web/reads-worker.js +1726 -0
  372. package/dist/web/server.js +8499 -0
  373. package/dist/web-EU6ATJWA.js +13 -0
  374. package/dist/web-fetch-U22Q7HV4.js +788 -0
  375. package/dist/wiki-generate-LZRLFG6I.js +623 -0
  376. package/dist/with-panes-X5CZOGML.js +628 -0
  377. package/dist/worker/entry.js +300 -93
  378. package/docs/README.md +58 -14
  379. package/docs/architecture/acp.md +5 -9
  380. package/docs/architecture/alcf-provider.md +0 -3
  381. package/docs/architecture/architecture.md +8 -10
  382. package/docs/architecture/artifact-placement.md +0 -3
  383. package/docs/architecture/artifact-versions.md +3 -6
  384. package/docs/architecture/capacity-and-scheduling.md +0 -3
  385. package/docs/architecture/context-engine.md +35 -4
  386. package/docs/architecture/context-working-set.md +0 -3
  387. package/docs/architecture/dispatch-architecture-rationale.md +0 -3
  388. package/docs/architecture/dispatch-typed-intent.md +0 -3
  389. package/docs/architecture/evidence-and-memory.md +0 -3
  390. package/docs/architecture/library.md +30 -0
  391. package/docs/architecture/middleware-and-components.md +1 -4
  392. package/docs/architecture/model-catalog.md +21 -4
  393. package/docs/architecture/observability.md +0 -3
  394. package/docs/architecture/pi-boundary.md +23 -8
  395. package/docs/architecture/prompt-envelope-and-tools.md +6 -9
  396. package/docs/architecture/provider-adapter-cookbook.md +1 -4
  397. package/docs/architecture/safety-model.md +21 -5
  398. package/docs/architecture/session-lifecycle.md +12 -4
  399. package/docs/architecture/time-conventions.md +0 -3
  400. package/docs/architecture/trace-store.md +28 -20
  401. package/docs/architecture/tui-design.md +108 -12
  402. package/docs/architecture/worker-context.md +104 -0
  403. package/docs/architecture/worker-dispatch-mechanics.md +1 -4
  404. package/docs/guide/authoring-plugins.md +158 -0
  405. package/docs/guide/built-in-agents.md +5 -8
  406. package/docs/guide/commands-and-modes.md +162 -61
  407. package/docs/guide/configuration-and-targets.md +198 -5
  408. package/docs/guide/configuration-reference.md +36 -38
  409. package/docs/guide/environment-variables.md +2 -5
  410. package/docs/guide/exit-codes-and-output.md +1 -4
  411. package/docs/guide/extensions-and-sharing.md +92 -55
  412. package/docs/guide/fleet-dispatch.md +31 -7
  413. package/docs/guide/glossary.md +1 -4
  414. package/docs/guide/harness-extensions.md +289 -0
  415. package/docs/guide/installation-and-lifecycle.md +10 -13
  416. package/docs/guide/interop.md +241 -0
  417. package/docs/guide/panes-and-files.md +3 -6
  418. package/docs/guide/plugins.md +77 -0
  419. package/docs/guide/proactive-memory.md +0 -3
  420. package/docs/guide/resource-library.md +109 -45
  421. package/docs/guide/skills-marketplace.md +34 -73
  422. package/docs/guide/tool-usage.md +19 -10
  423. package/docs/guide/troubleshooting.md +1 -4
  424. package/docs/history/config-knobs-audit.md +0 -3
  425. package/docs/history/release-cut-checklist.md +0 -3
  426. package/docs/process/development-pipeline.md +14 -17
  427. package/docs/process/documentation-coverage.md +31 -4
  428. package/docs/process/documentation-guide.md +28 -27
  429. package/docs/process/eval-runner.md +8 -6
  430. package/docs/process/evals-internal.md +0 -3
  431. package/docs/process/evolution.md +0 -3
  432. package/docs/process/fleet-demo-runbook.md +0 -3
  433. package/docs/process/git-commit-provenance.md +0 -3
  434. package/docs/process/performance-methodology.md +2 -5
  435. package/docs/process/release-cut-checklist.md +114 -217
  436. package/docs/process/scientific-validation.md +23 -3
  437. package/evals/scalar-decision-machinery.ts +1 -1
  438. package/examples/extensions/README.md +67 -0
  439. package/examples/extensions/lab-status/clio-coder-extension.json +14 -0
  440. package/examples/extensions/lab-status/extension.mjs +68 -0
  441. package/examples/extensions/lab-status/jobs.synthetic.json +9 -0
  442. package/examples/extensions/measurements/clio-coder-extension.json +28 -0
  443. package/examples/extensions/measurements/summarize.cjs +23 -0
  444. package/library/README.md +109 -0
  445. package/library/_authoring/templates/agent/README.md +28 -0
  446. package/library/_authoring/templates/agent/agents/benchmark-scout.md +30 -0
  447. package/library/_authoring/templates/agent/plugin.json +23 -0
  448. package/library/_authoring/templates/fleet/README.md +29 -0
  449. package/library/_authoring/templates/fleet/fleets/pipeline-review.md +31 -0
  450. package/library/_authoring/templates/fleet/plugin.json +23 -0
  451. package/library/_authoring/templates/plugin/README.md +37 -0
  452. package/library/_authoring/templates/plugin/agents/data-curator.md +31 -0
  453. package/library/_authoring/templates/plugin/assets/curation-guide.md +22 -0
  454. package/library/_authoring/templates/plugin/plugin.json +42 -0
  455. package/library/_authoring/templates/plugin/prompts/inspect-dataset.md +15 -0
  456. package/library/_authoring/templates/plugin/skills/dataset-curation/SKILL.md +36 -0
  457. package/library/_authoring/templates/plugin/skills/dataset-curation/evals.md +17 -0
  458. package/library/_authoring/templates/prompt/README.md +28 -0
  459. package/library/_authoring/templates/prompt/plugin.json +23 -0
  460. package/library/_authoring/templates/prompt/prompts/paper-summary.md +26 -0
  461. package/library/_authoring/templates/skill/README.md +24 -0
  462. package/library/_authoring/templates/skill/SKILL.md +39 -0
  463. package/library/_authoring/templates/skill/evals.md +30 -0
  464. package/library/_authoring/templates/skill/plugin.json +23 -0
  465. package/library/agents/README.md +7 -0
  466. package/library/fleets/README.md +7 -0
  467. package/library/plugins/materio/README.md +137 -0
  468. package/library/plugins/materio/ai.iowarp.clio/agents/materio-lab-definer.md +208 -0
  469. package/library/plugins/materio/ai.iowarp.clio/agents/materio-literature-reviewer.md +308 -0
  470. package/library/plugins/materio/ai.iowarp.clio/agents/materio-research-explorer.md +249 -0
  471. package/library/plugins/materio/ai.iowarp.clio/agents/materio-task-executor.md +416 -0
  472. package/library/plugins/materio/ai.iowarp.clio/agents/materio-task-verifier.md +60 -0
  473. package/library/plugins/materio/ai.iowarp.clio/agents/materio-workflow-planner.md +238 -0
  474. package/library/plugins/materio/ai.iowarp.clio/fleets/materio-execute-task.md +50 -0
  475. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/add-task.md +66 -0
  476. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/archive-task.md +65 -0
  477. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/checkpoint.md +26 -0
  478. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/define-research-tasks.md +230 -0
  479. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/define-virtual-lab.md +181 -0
  480. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/execute-task.md +292 -0
  481. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/help.md +129 -0
  482. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/identify-research.md +206 -0
  483. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/literature-review.md +201 -0
  484. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/pause-research.md +12 -0
  485. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/progress.md +105 -0
  486. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/remove-task.md +63 -0
  487. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/resume-research.md +64 -0
  488. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/settings.md +16 -0
  489. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/status.md +92 -0
  490. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/upload-data.md +104 -0
  491. package/library/plugins/materio/ai.iowarp.clio/prompts/materio/wtfp.md +145 -0
  492. package/library/plugins/materio/ai.iowarp.clio/references/execution.md +56 -0
  493. package/library/plugins/materio/ai.iowarp.portability/provenance.json +9 -0
  494. package/library/plugins/materio/assets/actions/add-task.md +86 -0
  495. package/library/plugins/materio/assets/actions/archive-task.md +84 -0
  496. package/library/plugins/materio/assets/actions/checkpoint.md +47 -0
  497. package/library/plugins/materio/assets/actions/define-research-tasks.md +228 -0
  498. package/library/plugins/materio/assets/actions/define-virtual-lab.md +179 -0
  499. package/library/plugins/materio/assets/actions/execute-task.md +290 -0
  500. package/library/plugins/materio/assets/actions/help.md +140 -0
  501. package/library/plugins/materio/assets/actions/identify-research.md +204 -0
  502. package/library/plugins/materio/assets/actions/literature-review.md +199 -0
  503. package/library/plugins/materio/assets/actions/pause-research.md +34 -0
  504. package/library/plugins/materio/assets/actions/progress.md +125 -0
  505. package/library/plugins/materio/assets/actions/remove-task.md +82 -0
  506. package/library/plugins/materio/assets/actions/resume-research.md +84 -0
  507. package/library/plugins/materio/assets/actions/settings.md +38 -0
  508. package/library/plugins/materio/assets/actions/status.md +112 -0
  509. package/library/plugins/materio/assets/actions/upload-data.md +123 -0
  510. package/library/plugins/materio/assets/actions/wtfp.md +179 -0
  511. package/library/plugins/materio/assets/references/research-domains.md +134 -0
  512. package/library/plugins/materio/assets/references/research-policy.md +77 -0
  513. package/library/plugins/materio/assets/references/traditional-workflows.md +146 -0
  514. package/library/plugins/materio/assets/scripts/check_physics.py +271 -0
  515. package/library/plugins/materio/assets/scripts/check_scripts.py +248 -0
  516. package/library/plugins/materio/assets/scripts/project_plugin.py +165 -0
  517. package/library/plugins/materio/assets/scripts/research_state.py +400 -0
  518. package/library/plugins/materio/assets/scripts/verify_citations.py +616 -0
  519. package/library/plugins/materio/assets/templates/RESEARCH.md +39 -0
  520. package/library/plugins/materio/assets/templates/VIRTUAL-LAB.md +120 -0
  521. package/library/plugins/materio/assets/templates/WORKFLOW.md +42 -0
  522. package/library/plugins/materio/assets/templates/config.json +5 -0
  523. package/library/plugins/materio/evals/scripts.yaml +29 -0
  524. package/library/plugins/materio/plugin.json +530 -0
  525. package/library/plugins/materio/skills/materio-lab-definer/SKILL.md +74 -0
  526. package/library/plugins/materio/skills/materio-literature-reviewer/SKILL.md +64 -0
  527. package/library/plugins/materio/skills/materio-research-explorer/SKILL.md +74 -0
  528. package/library/plugins/materio/skills/materio-task-executor/SKILL.md +214 -0
  529. package/library/plugins/materio/skills/materio-task-verifier/SKILL.md +46 -0
  530. package/library/plugins/materio/skills/materio-workflow-planner/SKILL.md +79 -0
  531. package/library/plugins/materio/tests/test_check_physics.py +139 -0
  532. package/library/plugins/materio/tests/test_check_scripts.py +140 -0
  533. package/library/plugins/materio/tests/test_research_state.py +291 -0
  534. package/library/plugins/materio/tests/test_verify_citations.py +337 -0
  535. package/library/prompts/README.md +7 -0
  536. package/library/registry.yaml +921 -0
  537. package/library/skills/README.md +120 -0
  538. package/library/skills/coding/ast-grep/SKILL.md +213 -0
  539. package/library/skills/coding/ast-grep/evals.md +82 -0
  540. package/library/skills/coding/ast-grep/plugin.json +23 -0
  541. package/library/skills/coding/coding-standards/SKILL.md +164 -0
  542. package/library/skills/coding/coding-standards/evals.md +57 -0
  543. package/library/skills/coding/coding-standards/plugin.json +23 -0
  544. package/library/skills/coding/prototype/SKILL.md +151 -0
  545. package/library/skills/coding/prototype/evals.md +61 -0
  546. package/library/skills/coding/prototype/plugin.json +23 -0
  547. package/library/skills/coding/tdd/SKILL.md +134 -0
  548. package/library/skills/coding/tdd/evals.md +61 -0
  549. package/library/skills/coding/tdd/plugin.json +23 -0
  550. package/library/skills/context/context-handoff/SKILL.md +176 -0
  551. package/library/skills/context/context-handoff/evals.md +101 -0
  552. package/library/skills/context/context-handoff/plugin.json +23 -0
  553. package/library/skills/context/context-prime/SKILL.md +131 -0
  554. package/library/skills/context/context-prime/evals.md +99 -0
  555. package/library/skills/context/context-prime/plugin.json +23 -0
  556. package/library/skills/git/branch-closeout/SKILL.md +132 -0
  557. package/library/skills/git/branch-closeout/plugin.json +23 -0
  558. package/library/skills/git/file-ticket/SKILL.md +126 -0
  559. package/library/skills/git/file-ticket/plugin.json +23 -0
  560. package/library/skills/git/fix-issue/SKILL.md +136 -0
  561. package/library/skills/git/fix-issue/plugin.json +23 -0
  562. package/library/skills/git/resolve-merge-conflicts/SKILL.md +151 -0
  563. package/library/skills/git/resolve-merge-conflicts/evals.md +85 -0
  564. package/library/skills/git/resolve-merge-conflicts/plugin.json +23 -0
  565. package/library/skills/git/ship/SKILL.md +134 -0
  566. package/library/skills/git/ship/plugin.json +23 -0
  567. package/library/skills/git/worktree-create/SKILL.md +127 -0
  568. package/library/skills/git/worktree-create/plugin.json +23 -0
  569. package/library/skills/git/worktree-merge/SKILL.md +147 -0
  570. package/library/skills/git/worktree-merge/plugin.json +23 -0
  571. package/library/skills/meta/clio-coder-dev/SKILL.md +101 -0
  572. package/library/skills/meta/clio-coder-dev/evals.md +46 -0
  573. package/library/skills/meta/clio-coder-dev/plugin.json +23 -0
  574. package/library/skills/meta/clio-coder-test/SKILL.md +156 -0
  575. package/library/skills/meta/clio-coder-test/evals.md +62 -0
  576. package/library/skills/meta/clio-coder-test/plugin.json +23 -0
  577. package/library/skills/meta/clio-coder-test/references/test-map.md +97 -0
  578. package/library/skills/meta/credentials/SKILL.md +132 -0
  579. package/library/skills/meta/credentials/evals.md +104 -0
  580. package/library/skills/meta/credentials/plugin.json +23 -0
  581. package/library/skills/meta/find-skills/SKILL.md +85 -0
  582. package/library/skills/meta/find-skills/evals.md +65 -0
  583. package/library/skills/meta/find-skills/plugin.json +23 -0
  584. package/library/skills/meta/herdr/SKILL.md +133 -0
  585. package/library/skills/meta/herdr/evals.md +38 -0
  586. package/library/skills/meta/herdr/plugin.json +23 -0
  587. package/library/skills/meta/skill-craft/SKILL.md +139 -0
  588. package/library/skills/meta/skill-craft/evals.md +49 -0
  589. package/library/skills/meta/skill-craft/plugin.json +23 -0
  590. package/library/skills/planning/archify/SKILL.md +196 -0
  591. package/library/skills/planning/archify/plugin.json +23 -0
  592. package/library/skills/planning/architecture/SKILL.md +184 -0
  593. package/library/skills/planning/architecture/evals.md +101 -0
  594. package/library/skills/planning/architecture/plugin.json +23 -0
  595. package/library/skills/planning/backlog/SKILL.md +212 -0
  596. package/library/skills/planning/backlog/evals.md +185 -0
  597. package/library/skills/planning/backlog/plugin.json +23 -0
  598. package/library/skills/planning/prd/SKILL.md +129 -0
  599. package/library/skills/planning/prd/evals.md +103 -0
  600. package/library/skills/planning/prd/plugin.json +23 -0
  601. package/library/skills/planning/product-intent/SKILL.md +173 -0
  602. package/library/skills/planning/product-intent/evals.md +106 -0
  603. package/library/skills/planning/product-intent/plugin.json +23 -0
  604. package/library/skills/planning/tech-spec/SKILL.md +172 -0
  605. package/library/skills/planning/tech-spec/evals.md +120 -0
  606. package/library/skills/planning/tech-spec/plugin.json +23 -0
  607. package/library/skills/registry.yaml +144 -0
  608. package/library/skills/remote.yaml +13 -0
  609. package/library/skills/research/arxiv-literature/SKILL.md +168 -0
  610. package/library/skills/research/arxiv-literature/evals.md +108 -0
  611. package/library/skills/research/arxiv-literature/plugin.json +23 -0
  612. package/library/skills/research/experiment-protocol/SKILL.md +148 -0
  613. package/library/skills/research/experiment-protocol/evals.md +114 -0
  614. package/library/skills/research/experiment-protocol/plugin.json +23 -0
  615. package/library/skills/research/scientific-debugging/SKILL.md +149 -0
  616. package/library/skills/research/scientific-debugging/evals.md +156 -0
  617. package/library/skills/research/scientific-debugging/plugin.json +23 -0
  618. package/library/skills/research/scientific-modernization/SKILL.md +170 -0
  619. package/library/skills/research/scientific-modernization/evals.md +111 -0
  620. package/library/skills/research/scientific-modernization/plugin.json +23 -0
  621. package/library/skills/skill-marketplace.json +507 -0
  622. package/library/skills/workflow/cut-it/SKILL.md +153 -0
  623. package/library/skills/workflow/cut-it/evals.md +143 -0
  624. package/library/skills/workflow/cut-it/plugin.json +23 -0
  625. package/library/skills/workflow/design-council/SKILL.md +233 -0
  626. package/library/skills/workflow/design-council/evals.md +258 -0
  627. package/library/skills/workflow/design-council/plugin.json +23 -0
  628. package/library/skills/workflow/grill-me/SKILL.md +267 -0
  629. package/library/skills/workflow/grill-me/evals.md +231 -0
  630. package/library/skills/workflow/grill-me/plugin.json +23 -0
  631. package/library/skills/workflow/workflow-distiller/SKILL.md +204 -0
  632. package/library/skills/workflow/workflow-distiller/evals.md +233 -0
  633. package/library/skills/workflow/workflow-distiller/plugin.json +23 -0
  634. package/package.json +23 -14
  635. package/src/cli/agents.ts +1 -1
  636. package/src/cli/config-inspect.ts +1 -1
  637. package/src/cli/configure.ts +2 -2
  638. package/src/cli/docs.ts +65 -328
  639. package/src/cli/eval.ts +40 -6
  640. package/src/cli/extensions.ts +74 -8
  641. package/src/cli/fleet-preflight.ts +2 -0
  642. package/src/cli/fleet.ts +2 -0
  643. package/src/cli/index.ts +4 -4
  644. package/src/cli/interop-inspect.ts +61 -33
  645. package/src/cli/interop.ts +79 -9
  646. package/src/cli/library-import.ts +139 -0
  647. package/src/cli/library.ts +418 -120
  648. package/src/cli/run.ts +26 -9
  649. package/src/cli/skills-eval.ts +43 -6
  650. package/src/cli/skills-inventory.ts +6 -2
  651. package/src/cli/skills.ts +44 -491
  652. package/src/cli/trace.ts +4 -65
  653. package/src/cli/uninstall.ts +26 -0
  654. package/src/cli/usage.ts +3 -0
  655. package/src/cli/web.ts +79 -0
  656. package/src/core/bus-events.ts +8 -4
  657. package/src/core/config.ts +71 -0
  658. package/src/core/defaults.ts +1 -1
  659. package/src/core/domain-loader.ts +37 -28
  660. package/src/core/recent-models.ts +2 -2
  661. package/src/core/session-routing.ts +3 -3
  662. package/src/core/state-file-lock.ts +1 -1
  663. package/src/core/termination.ts +13 -9
  664. package/src/core/tool-names.ts +5 -0
  665. package/src/domains/agents/contract.ts +1 -1
  666. package/src/domains/agents/extension.ts +53 -9
  667. package/src/domains/agents/fleet-commands.ts +92 -1
  668. package/src/domains/agents/fleet-contract.ts +87 -19
  669. package/src/domains/agents/recipe.ts +5 -4
  670. package/src/domains/agents/registry.ts +80 -24
  671. package/src/domains/config/extension.ts +5 -4
  672. package/src/domains/config/keybindings.ts +155 -95
  673. package/src/domains/context/worker/contract.ts +91 -0
  674. package/src/domains/context/worker/pressure.ts +120 -0
  675. package/src/domains/context/worker/recall.ts +62 -0
  676. package/src/domains/context/worker/select.ts +164 -0
  677. package/src/domains/context/worker/snapshot.ts +35 -0
  678. package/src/domains/context/worker/store.ts +16 -0
  679. package/src/domains/context/working-set/replay/synthetic.ts +2 -1
  680. package/src/domains/dispatch/active-route-planner.ts +2 -0
  681. package/src/domains/dispatch/backoff.ts +1 -0
  682. package/src/domains/dispatch/code-step.ts +12 -2
  683. package/src/domains/dispatch/contract.ts +3 -0
  684. package/src/domains/dispatch/execution-plan.ts +2 -0
  685. package/src/domains/dispatch/extension.ts +184 -39
  686. package/src/domains/dispatch/fleet-plan.ts +10 -0
  687. package/src/domains/dispatch/fleet-run.ts +1 -0
  688. package/src/domains/dispatch/index.ts +1 -0
  689. package/src/domains/dispatch/orphan-recovery.ts +2 -0
  690. package/src/domains/dispatch/receipt-integrity.ts +7 -0
  691. package/src/domains/dispatch/state.ts +2 -2
  692. package/src/domains/dispatch/types.ts +7 -0
  693. package/src/domains/dispatch/validation.ts +12 -0
  694. package/src/domains/dispatch/workspace-checkpoint.ts +1 -1
  695. package/src/domains/eval/metrics/tracked.ts +22 -2
  696. package/src/domains/evidence/failure-attribution.ts +1 -0
  697. package/src/domains/evidence/trust-status.ts +22 -3
  698. package/src/domains/extensions/command-schema.ts +145 -0
  699. package/src/domains/extensions/command-tools.ts +15 -0
  700. package/src/domains/extensions/compatibility.ts +7 -0
  701. package/src/domains/extensions/contract.ts +0 -4
  702. package/src/domains/extensions/discovery.ts +69 -205
  703. package/src/domains/extensions/extension.ts +0 -4
  704. package/src/domains/extensions/index.ts +1 -5
  705. package/src/domains/extensions/manager.ts +1 -6
  706. package/src/domains/extensions/operator-commands.ts +29 -0
  707. package/src/domains/extensions/operator-runtime.ts +485 -0
  708. package/src/domains/extensions/public-api.ts +53 -0
  709. package/src/domains/extensions/runtime-child.mjs +114 -0
  710. package/src/domains/extensions/runtime-process.ts +306 -0
  711. package/src/domains/extensions/runtime-schema.ts +146 -0
  712. package/src/domains/extensions/snapshot-access.ts +21 -0
  713. package/src/domains/extensions/snapshot.ts +4 -32
  714. package/src/domains/extensions/state.ts +5 -83
  715. package/src/domains/extensions/types.ts +33 -34
  716. package/src/domains/interop/adopt.ts +546 -0
  717. package/src/domains/interop/detect.ts +50 -12
  718. package/src/domains/interop/foreign.ts +554 -0
  719. package/src/domains/interop/import.ts +277 -0
  720. package/src/domains/interop/index.ts +24 -0
  721. package/src/domains/interop/install.ts +6 -0
  722. package/src/domains/interop/inventory.ts +351 -0
  723. package/src/domains/interop/projection.ts +360 -0
  724. package/src/domains/interop/registry.ts +106 -3
  725. package/src/domains/interop/types.ts +51 -0
  726. package/src/domains/lifecycle/migrations/index.ts +0 -2
  727. package/src/domains/lifecycle/naming-resources.ts +1 -1
  728. package/src/domains/middleware/hooks.ts +2 -2
  729. package/src/domains/middleware/marketplace-offer.ts +1 -1
  730. package/src/domains/mux/contract.ts +1 -1
  731. package/src/domains/observability/background-memory-usage.ts +3 -0
  732. package/src/domains/observability/compaction-usage.ts +2 -0
  733. package/src/domains/observability/cost.ts +5 -0
  734. package/src/domains/observability/extension.ts +1 -0
  735. package/src/domains/observability/out-of-turn-usage.ts +2 -0
  736. package/src/domains/observability/trace-store.ts +65 -5
  737. package/src/domains/plugins/catalog.ts +204 -0
  738. package/src/domains/plugins/contract.ts +24 -0
  739. package/src/domains/plugins/discovery.ts +316 -0
  740. package/src/domains/plugins/extension.ts +40 -0
  741. package/src/domains/plugins/index.ts +77 -0
  742. package/src/domains/plugins/integrity.ts +6 -0
  743. package/src/domains/plugins/manifest.ts +3 -0
  744. package/src/domains/plugins/resources.ts +102 -0
  745. package/src/domains/plugins/state.ts +753 -0
  746. package/src/domains/plugins/types.ts +217 -0
  747. package/src/domains/prompts/extension.ts +4 -10
  748. package/src/domains/prompts/fragments/operating/skills.md +10 -10
  749. package/src/domains/providers/cache-deployment.ts +147 -0
  750. package/src/domains/providers/catalog.ts +12 -7
  751. package/src/domains/providers/extension.ts +27 -5
  752. package/src/domains/providers/index.ts +1 -0
  753. package/src/domains/providers/plugins.ts +3 -13
  754. package/src/domains/providers/runtimes/common/local-synth.ts +4 -0
  755. package/src/domains/providers/types/target-descriptor.ts +17 -0
  756. package/src/domains/resources/common-loader.ts +9 -6
  757. package/src/domains/resources/index.ts +67 -0
  758. package/src/domains/resources/library-actions.ts +836 -0
  759. package/src/domains/resources/library-evals.ts +38 -0
  760. package/src/domains/resources/library-inventory.ts +1048 -0
  761. package/src/domains/resources/library-types.ts +50 -0
  762. package/src/domains/resources/library-validation.ts +634 -0
  763. package/src/domains/resources/library.ts +437 -156
  764. package/src/domains/resources/package-references.ts +66 -0
  765. package/src/domains/resources/prompts/loader.ts +75 -41
  766. package/src/domains/resources/skills/install.ts +2 -2
  767. package/src/domains/resources/skills/loader.ts +77 -22
  768. package/src/domains/resources/skills/marketplace.ts +48 -57
  769. package/src/domains/resources/skills/promotion.ts +2 -2
  770. package/src/domains/resources/skills/provenance-pin.ts +17 -4
  771. package/src/domains/safety/action-classifier.ts +2 -2
  772. package/src/domains/safety/default-path-policy.ts +3 -1
  773. package/src/domains/safety/policy-engine.ts +1 -1
  774. package/src/domains/safety/protected-artifacts.ts +21 -5
  775. package/src/domains/safety/skill-authority.ts +5 -2
  776. package/src/domains/session/compaction/compact.ts +4 -1
  777. package/src/domains/session/entries.ts +1 -0
  778. package/src/domains/session/usage.ts +6 -7
  779. package/src/domains/share/archive.ts +1 -1
  780. package/src/engine/acp/server.ts +11 -0
  781. package/src/engine/ai.ts +2 -0
  782. package/src/engine/apis/openai-completions.ts +61 -6
  783. package/src/engine/notices/pi-tui-LICENSE +21 -0
  784. package/src/engine/prewarm.ts +232 -0
  785. package/src/engine/provider-diagnostics.ts +6 -1
  786. package/src/engine/tui.ts +3 -0
  787. package/src/engine/worker-runtime.ts +58 -14
  788. package/src/engine/worker-tools.ts +5 -0
  789. package/src/entry/orchestrator.ts +46 -21
  790. package/src/entry/plugin-reload.ts +18 -0
  791. package/src/interactive/application-controller.ts +67 -21
  792. package/src/interactive/chat-loop-messages.ts +3 -0
  793. package/src/interactive/chat-loop.ts +32 -11
  794. package/src/interactive/chat-panel.ts +5 -1
  795. package/src/interactive/clio-editor.ts +53 -21
  796. package/src/interactive/command-output.ts +56 -1
  797. package/src/interactive/editor-submit.ts +65 -28
  798. package/src/interactive/fleet-run-preview.ts +2 -0
  799. package/src/interactive/follow-up-queue-panel.ts +3 -3
  800. package/src/interactive/footer/dashboard.ts +4 -1
  801. package/src/interactive/footer/notifications.ts +2 -2
  802. package/src/interactive/footer/widgets.ts +2 -2
  803. package/src/interactive/interactive-application.ts +209 -21
  804. package/src/interactive/interactive-input-runtime.ts +254 -7
  805. package/src/interactive/interactive-presentation.ts +41 -12
  806. package/src/interactive/interactive-slash-runtime.ts +37 -8
  807. package/src/interactive/keybinding-manager.ts +156 -79
  808. package/src/interactive/keyboard-owner.ts +37 -0
  809. package/src/interactive/leader-key.ts +49 -102
  810. package/src/interactive/leader-menu.ts +45 -0
  811. package/src/interactive/overlay-ask-user-lifecycle.ts +9 -1
  812. package/src/interactive/overlay-frame.ts +15 -0
  813. package/src/interactive/overlay-key-routing.ts +46 -47
  814. package/src/interactive/overlay-lifecycle.ts +30 -15
  815. package/src/interactive/overlay-resource-openers.ts +56 -46
  816. package/src/interactive/overlays/ask-user.ts +630 -556
  817. package/src/interactive/overlays/extension-panel.ts +70 -0
  818. package/src/interactive/overlays/extensions.ts +28 -5
  819. package/src/interactive/overlays/fleet-run-approval.ts +7 -3
  820. package/src/interactive/overlays/help-reference.ts +89 -40
  821. package/src/interactive/overlays/interop.ts +122 -3
  822. package/src/interactive/overlays/keybinding-detail.ts +2 -2
  823. package/src/interactive/overlays/library-lifecycle.ts +90 -0
  824. package/src/interactive/overlays/library-model.ts +574 -0
  825. package/src/interactive/overlays/library-review.ts +557 -0
  826. package/src/interactive/overlays/library-tabs.ts +3 -15
  827. package/src/interactive/overlays/library.ts +602 -0
  828. package/src/interactive/overlays/list-overlay.ts +218 -39
  829. package/src/interactive/overlays/model-selector.ts +28 -25
  830. package/src/interactive/overlays/session-selector.ts +9 -3
  831. package/src/interactive/overlays/settings.ts +25 -18
  832. package/src/interactive/overlays/tree-selector.ts +16 -11
  833. package/src/interactive/permission-hint.ts +13 -0
  834. package/src/interactive/permission-overlay.ts +77 -28
  835. package/src/interactive/prewarm.ts +11 -197
  836. package/src/interactive/prompt-source-label.ts +21 -0
  837. package/src/interactive/renderers/reference-card.ts +35 -0
  838. package/src/interactive/renderers/worker-entry.ts +35 -3
  839. package/src/interactive/session-usage-reseed.ts +2 -0
  840. package/src/interactive/side-question.ts +2 -0
  841. package/src/interactive/slash-autocomplete.ts +99 -1
  842. package/src/interactive/slash-commands.ts +390 -67
  843. package/src/interactive/slash-spec.ts +0 -1
  844. package/src/interactive/terminal-lease.ts +44 -12
  845. package/src/interactive/turn-context.ts +1 -0
  846. package/src/interactive/turn-persistence.ts +3 -0
  847. package/src/interactive/turn-prewarm.ts +126 -19
  848. package/src/interactive/turn-queues.ts +8 -7
  849. package/src/interactive/turn-runtime.ts +15 -1
  850. package/src/interactive/view/view-overlay.ts +19 -14
  851. package/src/interactive/welcome-dashboard.ts +525 -408
  852. package/src/tools/bootstrap.ts +8 -0
  853. package/src/tools/builtin-tool-catalog.ts +15 -6
  854. package/src/tools/context/index.ts +58 -5
  855. package/src/tools/context/library.ts +465 -0
  856. package/src/tools/context/surface.ts +20 -6
  857. package/src/tools/core-bootstrap.ts +3 -0
  858. package/src/tools/dispatch-admission.ts +24 -1
  859. package/src/tools/dispatch-arguments.ts +8 -0
  860. package/src/tools/dispatch-plan.ts +32 -0
  861. package/src/tools/dispatch-schema.ts +31 -1
  862. package/src/tools/dispatch-types.ts +3 -0
  863. package/src/tools/dispatch.ts +1 -1
  864. package/src/tools/harness-extensions.ts +169 -0
  865. package/src/tools/observation.ts +4 -0
  866. package/src/tools/policy.ts +7 -1
  867. package/src/tools/registry.ts +31 -3
  868. package/src/tools/worker-evidence.ts +5 -0
  869. package/src/worker/context-seed.ts +192 -0
  870. package/src/worker/entry.ts +1 -0
  871. package/src/worker/spec-contract.ts +35 -1
  872. package/dist/acp-UVEVWSDL.js +0 -130
  873. package/dist/agents-VWY37DTK.js +0 -148
  874. package/dist/auth-PCV2XQDV.js +0 -551
  875. package/dist/builtins-PD652MTK.js +0 -22
  876. package/dist/chunk-22PQ4TX4.js +0 -360
  877. package/dist/chunk-24T2YZ7A.js +0 -22648
  878. package/dist/chunk-2AKYFREM.js +0 -1008
  879. package/dist/chunk-2QPI3TR3.js +0 -162
  880. package/dist/chunk-3BJGMT2D.js +0 -324
  881. package/dist/chunk-3HQVBIKD.js +0 -308
  882. package/dist/chunk-3JLFK5MW.js +0 -193
  883. package/dist/chunk-3O2ZAUGQ.js +0 -283
  884. package/dist/chunk-3QKXHCGS.js +0 -59
  885. package/dist/chunk-3T4DXWP6.js +0 -668
  886. package/dist/chunk-3UW3KU4A.js +0 -21
  887. package/dist/chunk-3WBALRQH.js +0 -5076
  888. package/dist/chunk-4DU2TVI4.js +0 -108
  889. package/dist/chunk-4U4TKZFR.js +0 -5052
  890. package/dist/chunk-4VMV6OS6.js +0 -101
  891. package/dist/chunk-536HXRFE.js +0 -1257
  892. package/dist/chunk-5CMARGPF.js +0 -477
  893. package/dist/chunk-5CY4Q6QI.js +0 -141
  894. package/dist/chunk-5QRX7SLS.js +0 -1018
  895. package/dist/chunk-5VTJP36Q.js +0 -36
  896. package/dist/chunk-5ZSZEYJK.js +0 -119
  897. package/dist/chunk-6HAO6X5B.js +0 -197
  898. package/dist/chunk-6OII3LOK.js +0 -404
  899. package/dist/chunk-6RYDAVQT.js +0 -4338
  900. package/dist/chunk-6VRRJT7L.js +0 -146
  901. package/dist/chunk-6YA46L5A.js +0 -386
  902. package/dist/chunk-77CZRFTE.js +0 -634
  903. package/dist/chunk-7JSSKXG2.js +0 -1215
  904. package/dist/chunk-7WUZEB2M.js +0 -165
  905. package/dist/chunk-7YJWEF2L.js +0 -974
  906. package/dist/chunk-ACCKVSHU.js +0 -44
  907. package/dist/chunk-B3MOMLJ4.js +0 -433
  908. package/dist/chunk-BBV5TKE6.js +0 -35
  909. package/dist/chunk-BLTEAUCB.js +0 -668
  910. package/dist/chunk-BS4GAMUB.js +0 -233
  911. package/dist/chunk-BT7HGDOX.js +0 -3151
  912. package/dist/chunk-CBSKDFWL.js +0 -101
  913. package/dist/chunk-CXQ37WJH.js +0 -45
  914. package/dist/chunk-DXLUVUD4.js +0 -1490
  915. package/dist/chunk-DZK63TZJ.js +0 -1334
  916. package/dist/chunk-E7RF4KBO.js +0 -266
  917. package/dist/chunk-ECOMVOHP.js +0 -139
  918. package/dist/chunk-EHOSNVVM.js +0 -59
  919. package/dist/chunk-F5Z7EWMN.js +0 -4484
  920. package/dist/chunk-FQOOGXBH.js +0 -579
  921. package/dist/chunk-GLYBJ4RQ.js +0 -396
  922. package/dist/chunk-HHVJNVUJ.js +0 -179
  923. package/dist/chunk-HL26ADLH.js +0 -77
  924. package/dist/chunk-HPTJF6DG.js +0 -2465
  925. package/dist/chunk-HXHFDHB6.js +0 -962
  926. package/dist/chunk-HZ2T2YED.js +0 -1687
  927. package/dist/chunk-HZFBVU5X.js +0 -666
  928. package/dist/chunk-I2K2NCZQ.js +0 -659
  929. package/dist/chunk-IGLVVNEG.js +0 -402
  930. package/dist/chunk-IKRWLEDA.js +0 -1567
  931. package/dist/chunk-J2FYEQ5L.js +0 -33
  932. package/dist/chunk-JMPL7NUB.js +0 -108
  933. package/dist/chunk-K2HL3GBL.js +0 -998
  934. package/dist/chunk-KAFMW7WM.js +0 -386
  935. package/dist/chunk-KTFSFCVN.js +0 -46
  936. package/dist/chunk-LIN2K3EL.js +0 -66
  937. package/dist/chunk-LUL5Z66S.js +0 -221
  938. package/dist/chunk-LVFANMOH.js +0 -466
  939. package/dist/chunk-LY4N4TTL.js +0 -117
  940. package/dist/chunk-LZBMXNLP.js +0 -1196
  941. package/dist/chunk-M6TAYK66.js +0 -807
  942. package/dist/chunk-N2OKBREN.js +0 -243
  943. package/dist/chunk-NC4KV7EL.js +0 -39
  944. package/dist/chunk-NF3BK5WR.js +0 -42
  945. package/dist/chunk-NNWJYUNO.js +0 -573
  946. package/dist/chunk-NTK3WTHM.js +0 -141
  947. package/dist/chunk-ODUTYZIU.js +0 -688
  948. package/dist/chunk-OQM5IVJY.js +0 -1377
  949. package/dist/chunk-P5JMBPDJ.js +0 -7192
  950. package/dist/chunk-P5SC4DLJ.js +0 -47
  951. package/dist/chunk-P6M7RKMI.js +0 -97
  952. package/dist/chunk-PWWSIB2A.js +0 -52
  953. package/dist/chunk-PZN2LQY6.js +0 -674
  954. package/dist/chunk-Q7NNUHQV.js +0 -705
  955. package/dist/chunk-QCOV5DFY.js +0 -911
  956. package/dist/chunk-QNWRHOMF.js +0 -692
  957. package/dist/chunk-QRFXEO6Y.js +0 -17
  958. package/dist/chunk-QXFBABFJ.js +0 -380
  959. package/dist/chunk-RGZNQ5CT.js +0 -657
  960. package/dist/chunk-SRZOW5L2.js +0 -1865
  961. package/dist/chunk-SXQKNKRA.js +0 -223
  962. package/dist/chunk-T334FW2H.js +0 -362
  963. package/dist/chunk-T52TPHYC.js +0 -318
  964. package/dist/chunk-TJFDL26W.js +0 -658
  965. package/dist/chunk-TN5FW4XY.js +0 -172
  966. package/dist/chunk-U7H5WRG5.js +0 -123
  967. package/dist/chunk-UFYNOQK4.js +0 -302
  968. package/dist/chunk-URBGEOH3.js +0 -32
  969. package/dist/chunk-USZA7GWL.js +0 -341
  970. package/dist/chunk-UUQ5G6EZ.js +0 -697
  971. package/dist/chunk-VAHLPXPY.js +0 -399
  972. package/dist/chunk-VANN3GDP.js +0 -2488
  973. package/dist/chunk-VHMX7SXF.js +0 -1289
  974. package/dist/chunk-WJIMKGD6.js +0 -132
  975. package/dist/chunk-WKUYQBCG.js +0 -795
  976. package/dist/chunk-WNGF5AJX.js +0 -1911
  977. package/dist/chunk-WV6TDAPN.js +0 -3627
  978. package/dist/chunk-X3BI7HTV.js +0 -562
  979. package/dist/chunk-XWMSPJYN.js +0 -149
  980. package/dist/chunk-YPRSNUTC.js +0 -395
  981. package/dist/chunk-ZS43Y2FT.js +0 -438
  982. package/dist/clio-QQCMTUZE.js +0 -26
  983. package/dist/code-nav-GUPM6766.js +0 -686
  984. package/dist/components-TNIKXCBH.js +0 -674
  985. package/dist/config-IIM7YOD3.js +0 -621
  986. package/dist/configure-4ZM5HWJX.js +0 -73
  987. package/dist/context-44BZLJ3J.js +0 -344
  988. package/dist/context-AIDVQKMW.js +0 -278
  989. package/dist/context-OL5P3HEP.js +0 -1031
  990. package/dist/context-clear-OQV76MYP.js +0 -184
  991. package/dist/context-index-HP2JFUWA.js +0 -120
  992. package/dist/context-map-INTXD54D.js +0 -555
  993. package/dist/context-working-set-ZUW3EGLS.js +0 -1556
  994. package/dist/detail-UXPWRANG.js +0 -115
  995. package/dist/dispatch-runner-P3ZW6G77.js +0 -2438
  996. package/dist/docs-BL7ROUFN.js +0 -292
  997. package/dist/doctor-JJVGPZWT.js +0 -797
  998. package/dist/eval-V2RTN3UH.js +0 -4972
  999. package/dist/eval-inventory-QOYZERXJ.js +0 -315
  1000. package/dist/evidence-35PYWGSO.js +0 -225
  1001. package/dist/evidence-CIGGKI6J.js +0 -383
  1002. package/dist/evolve-33SM3NJP.js +0 -609
  1003. package/dist/extensions-YVRHX6ZI.js +0 -229
  1004. package/dist/fleet-LFO7SIPC.js +0 -908
  1005. package/dist/fleet-commands-RLK72GU3.js +0 -75
  1006. package/dist/fleet-decisions-3SBSCTCW.js +0 -159
  1007. package/dist/fleet-graph-JZIBCGMW.js +0 -134
  1008. package/dist/fleet-inspect-2L5YGGZJ.js +0 -469
  1009. package/dist/fleet-preflight-QRSHIIDE.js +0 -22
  1010. package/dist/fleet-validate-LIAVKDUU.js +0 -92
  1011. package/dist/fleet-verify-JIK3OQZR.js +0 -202
  1012. package/dist/fleet-view-IWHYGQKK.js +0 -118
  1013. package/dist/init-NJEDOTQW.js +0 -321
  1014. package/dist/interop-RVCAYECG.js +0 -115
  1015. package/dist/inventory-74UL7UHU.js +0 -118
  1016. package/dist/library-CTKZA7K3.js +0 -226
  1017. package/dist/memory-I76I5VUH.js +0 -512
  1018. package/dist/models-D4YDIQZQ.js +0 -289
  1019. package/dist/monitor-NKVD55HX.js +0 -775
  1020. package/dist/orchestrator-I6OATVPK.js +0 -39518
  1021. package/dist/panes-7BTYH3XQ.js +0 -103
  1022. package/dist/panes-WPOMEMRH.js +0 -74
  1023. package/dist/paths-J3KN7UAO.js +0 -67
  1024. package/dist/preload-EJAWJEIO.js +0 -116
  1025. package/dist/reset-4XMQKDNZ.js +0 -345
  1026. package/dist/resources-TVYVXK3Q.js +0 -125
  1027. package/dist/run-OWQNNSJU.js +0 -872
  1028. package/dist/share-NPZZMUXG.js +0 -290
  1029. package/dist/skills-OXFEAWMT.js +0 -510
  1030. package/dist/skills-eval-J5TCKSJA.js +0 -1034
  1031. package/dist/skills-inventory-7II4DM57.js +0 -133
  1032. package/dist/slash-commands-MDSDSWYF.js +0 -92
  1033. package/dist/steer-S7D7IKPU.js +0 -77
  1034. package/dist/support-5VAEC32W.js +0 -38
  1035. package/dist/targets-KILZEOCE.js +0 -1109
  1036. package/dist/tasks-R6P6OV22.js +0 -36
  1037. package/dist/terminal-lease-LZCG2KN3.js +0 -405
  1038. package/dist/tools-6OCQ6SVB.js +0 -28
  1039. package/dist/trace-JHLXWUMN.js +0 -572
  1040. package/dist/tui-primitives-RCY2HN7G.js +0 -17
  1041. package/dist/uninstall-FXYMFFRT.js +0 -407
  1042. package/dist/upgrade-D2OZH6IQ.js +0 -307
  1043. package/dist/usage-PIASNUS4.js +0 -1052
  1044. package/dist/verifiers-LTHUY2PX.js +0 -630
  1045. package/dist/verify-HYF7KBVE.js +0 -30
  1046. package/dist/web-fetch-MQN4FH3X.js +0 -788
  1047. package/dist/wiki-generate-RK7JQ5NP.js +0 -615
  1048. package/dist/with-panes-OFTNAR4Y.js +0 -628
  1049. package/skills/README.md +0 -418
  1050. package/skills/coding/ast-grep/SKILL.md +0 -213
  1051. package/skills/coding/ast-grep/evals.md +0 -82
  1052. package/skills/coding/coding-standards/SKILL.md +0 -164
  1053. package/skills/coding/coding-standards/evals.md +0 -57
  1054. package/skills/coding/prototype/SKILL.md +0 -151
  1055. package/skills/coding/prototype/evals.md +0 -61
  1056. package/skills/coding/tdd/SKILL.md +0 -134
  1057. package/skills/coding/tdd/evals.md +0 -61
  1058. package/skills/context/context-handoff/SKILL.md +0 -176
  1059. package/skills/context/context-handoff/evals.md +0 -101
  1060. package/skills/context/context-prime/SKILL.md +0 -131
  1061. package/skills/context/context-prime/evals.md +0 -99
  1062. package/skills/git/branch-closeout/SKILL.md +0 -132
  1063. package/skills/git/file-ticket/SKILL.md +0 -126
  1064. package/skills/git/fix-issue/SKILL.md +0 -136
  1065. package/skills/git/resolve-merge-conflicts/SKILL.md +0 -151
  1066. package/skills/git/resolve-merge-conflicts/evals.md +0 -85
  1067. package/skills/git/ship/SKILL.md +0 -134
  1068. package/skills/git/worktree-create/SKILL.md +0 -127
  1069. package/skills/git/worktree-merge/SKILL.md +0 -147
  1070. package/skills/meta/clio-coder-dev/SKILL.md +0 -101
  1071. package/skills/meta/clio-coder-dev/evals.md +0 -46
  1072. package/skills/meta/clio-coder-test/SKILL.md +0 -146
  1073. package/skills/meta/clio-coder-test/evals.md +0 -48
  1074. package/skills/meta/clio-coder-test/references/test-map.md +0 -96
  1075. package/skills/meta/credentials/SKILL.md +0 -132
  1076. package/skills/meta/credentials/evals.md +0 -104
  1077. package/skills/meta/find-skills/SKILL.md +0 -78
  1078. package/skills/meta/find-skills/evals.md +0 -47
  1079. package/skills/meta/herdr/SKILL.md +0 -133
  1080. package/skills/meta/herdr/evals.md +0 -38
  1081. package/skills/meta/skill-craft/SKILL.md +0 -125
  1082. package/skills/meta/skill-craft/evals.md +0 -41
  1083. package/skills/planning/archify/SKILL.md +0 -196
  1084. package/skills/planning/architecture/SKILL.md +0 -184
  1085. package/skills/planning/architecture/evals.md +0 -101
  1086. package/skills/planning/backlog/SKILL.md +0 -212
  1087. package/skills/planning/backlog/evals.md +0 -185
  1088. package/skills/planning/prd/SKILL.md +0 -129
  1089. package/skills/planning/prd/evals.md +0 -103
  1090. package/skills/planning/product-intent/SKILL.md +0 -173
  1091. package/skills/planning/product-intent/evals.md +0 -106
  1092. package/skills/planning/tech-spec/SKILL.md +0 -172
  1093. package/skills/planning/tech-spec/evals.md +0 -120
  1094. package/skills/registry.yaml +0 -144
  1095. package/skills/remote.yaml +0 -13
  1096. package/skills/research/arxiv-literature/SKILL.md +0 -168
  1097. package/skills/research/arxiv-literature/evals.md +0 -108
  1098. package/skills/research/experiment-protocol/SKILL.md +0 -148
  1099. package/skills/research/experiment-protocol/evals.md +0 -114
  1100. package/skills/research/scientific-debugging/SKILL.md +0 -149
  1101. package/skills/research/scientific-debugging/evals.md +0 -156
  1102. package/skills/research/scientific-modernization/SKILL.md +0 -170
  1103. package/skills/research/scientific-modernization/evals.md +0 -111
  1104. package/skills/skill-marketplace.json +0 -507
  1105. package/skills/workflow/cut-it/SKILL.md +0 -153
  1106. package/skills/workflow/cut-it/evals.md +0 -143
  1107. package/skills/workflow/design-council/SKILL.md +0 -233
  1108. package/skills/workflow/design-council/evals.md +0 -258
  1109. package/skills/workflow/grill-me/SKILL.md +0 -267
  1110. package/skills/workflow/grill-me/evals.md +0 -231
  1111. package/skills/workflow/workflow-distiller/SKILL.md +0 -201
  1112. package/skills/workflow/workflow-distiller/evals.md +0 -225
  1113. package/src/domains/extensions/resource-path.ts +0 -27
  1114. package/src/domains/extensions/resources.ts +0 -37
  1115. package/src/domains/lifecycle/migrations/2026-09-01-extension-install-digests.ts +0 -27
  1116. package/src/interactive/overlays/agents.ts +0 -70
  1117. package/src/interactive/overlays/library-install-confirm.ts +0 -152
  1118. package/src/interactive/overlays/prompts.ts +0 -89
  1119. package/src/interactive/overlays/skills-hub.ts +0 -615
  1120. /package/{skills → library/skills}/coding/ast-grep/references/rule_reference.md +0 -0
  1121. /package/{skills → library/skills}/coding/prototype/references/LOGIC.md +0 -0
  1122. /package/{skills → library/skills}/coding/prototype/references/UI.md +0 -0
  1123. /package/{skills → library/skills}/coding/tdd/references/mocking.md +0 -0
  1124. /package/{skills → library/skills}/coding/tdd/references/tests.md +0 -0
  1125. /package/{skills → library/skills}/context/context-handoff/scripts/new-handoff.sh +0 -0
  1126. /package/{skills → library/skills}/git/branch-closeout/evals.md +0 -0
  1127. /package/{skills → library/skills}/git/branch-closeout/references/closeout-checklist.md +0 -0
  1128. /package/{skills → library/skills}/git/file-ticket/assets/issue-template.md +0 -0
  1129. /package/{skills → library/skills}/git/file-ticket/evals.md +0 -0
  1130. /package/{skills → library/skills}/git/file-ticket/references/issue-discovery.md +0 -0
  1131. /package/{skills → library/skills}/git/fix-issue/evals.md +0 -0
  1132. /package/{skills → library/skills}/git/fix-issue/references/diagnosis-and-rca.md +0 -0
  1133. /package/{skills → library/skills}/git/resolve-merge-conflicts/references/conflict-matrix.md +0 -0
  1134. /package/{skills → library/skills}/git/ship/assets/pr-template.md +0 -0
  1135. /package/{skills → library/skills}/git/ship/evals.md +0 -0
  1136. /package/{skills → library/skills}/git/ship/references/remote-and-branch-policy.md +0 -0
  1137. /package/{skills → library/skills}/git/worktree-create/evals.md +0 -0
  1138. /package/{skills → library/skills}/git/worktree-create/references/worktree-setup.md +0 -0
  1139. /package/{skills → library/skills}/git/worktree-merge/evals.md +0 -0
  1140. /package/{skills → library/skills}/git/worktree-merge/references/merge-strategies.md +0 -0
  1141. /package/{skills → library/skills}/meta/clio-coder-test/references/harness.md +0 -0
  1142. /package/{skills → library/skills}/planning/archify/evals.md +0 -0
@@ -0,0 +1,165 @@
1
+ #!/usr/bin/env python3
2
+ """Generate a peer host package without claiming equivalent fleet enforcement."""
3
+ import argparse
4
+ import json
5
+ from pathlib import Path
6
+ import shutil
7
+ import sys
8
+
9
+
10
+ ACTION_ROLES = {
11
+ "identify-research": "research-explorer", "literature-review": "literature-reviewer",
12
+ "define-virtual-lab": "lab-definer", "define-research-tasks": "workflow-planner",
13
+ "execute-task": "task-executor",
14
+ }
15
+
16
+
17
+ def render_peer_guides(target, output, name):
18
+ """Bind logical action/skill requests to capabilities actually exported."""
19
+ actions = sorted(path.stem for path in (output / "assets/actions").glob("*.md"))
20
+ invocations = {}
21
+ for action in actions:
22
+ skill = name + "-" + ACTION_ROLES.get(action, "research-explorer")
23
+ invocations[action] = ({"kind": "skill", "name": skill, "request": action}
24
+ if target == "codex" else {"kind": "command", "name": f"/{name}:{action}"})
25
+ paths = list((output / "assets/actions").glob("*.md")) + list((output / "skills").glob("*/SKILL.md"))
26
+ for path in paths:
27
+ text = path.read_text()
28
+ if target in {"claude", "gemini"}:
29
+ for action in actions:
30
+ skill = name + "-" + ACTION_ROLES.get(action, "research-explorer")
31
+ text = text.replace(f"Run {action} using the {skill} skill", f"/{name}:{action}")
32
+ text = text.replace("this standard package registers no slash commands",
33
+ "this native package registers the command routes shown below")
34
+ text = text.replace("actual skill invocation vocabulary", "native command vocabulary")
35
+ if path.parent.name == "actions":
36
+ role = ACTION_ROLES.get(path.stem)
37
+ if target == "claude" and role:
38
+ binding = (f"\n## Native role binding\n\nThe interactive orchestrator dispatches the registered agent `{name}:{role}`\n"
39
+ f"for the `{name}-{role}` scientific skill. After a checkpoint, dispatch that\n"
40
+ "same registered agent again with the complete transcript, prior outputs and\n"
41
+ "actual researcher answer. Skill names identify instructions, not agent IDs.\n"
42
+ "A worker returns the checkpoint and does not dispatch or interview.\n")
43
+ if role == "task-executor":
44
+ binding += (f"For the separate read-only artifact review, dispatch the registered agent `{name}:task-verifier`.\n"
45
+ "Give it no write grant and preserve any host grounding limitations.\n")
46
+ elif target in {"codex", "gemini"}:
47
+ binding = ("\n## Host role execution\n\nThis export registers no named agents. Apply the role's installed skill in the\n"
48
+ "main conversation, or give that skill and complete context to a generic worker\n"
49
+ "only when the host supports delegation. The interactive assistant owns every\n"
50
+ "researcher question and resumes the role with the actual answer.\n")
51
+ else:
52
+ binding = ""
53
+ text += binding
54
+ path.write_text(text)
55
+ return invocations
56
+
57
+
58
+ def project(target, output, source=None):
59
+ source = Path(source or Path(__file__).resolve().parents[2]).resolve(strict=True)
60
+ output = Path(output).absolute()
61
+ if output.exists() or output.is_symlink():
62
+ raise ValueError("projection output must not already exist")
63
+ output = output.resolve()
64
+ if source == output or source in output.parents:
65
+ raise ValueError("projection output must be outside the canonical bundle")
66
+ manifest = json.loads((source / "plugin.json").read_text())
67
+ output.mkdir(parents=True)
68
+ try:
69
+ for directory in ("skills", "assets"):
70
+ for path in (source / directory).rglob("*"):
71
+ if path.is_symlink():
72
+ raise ValueError(f"projection refuses symbolic link: {path}")
73
+ shutil.copytree(source / directory, output / directory,
74
+ ignore=shutil.ignore_patterns("__pycache__", "*.pyc"))
75
+ metadata = {key: manifest[key] for key in ("name", "version", "description", "author", "repository", "keywords") if key in manifest}
76
+ report = {"target": target, "skills": 6, "commands": 0, "agents": 0,
77
+ "fleet": "instructions only; no native write-scope enforcement claimed",
78
+ "scripts": "local Python helpers; no automatic execution",
79
+ "validation": "generated structure; run target-native validation before publication"}
80
+ report["invocations"] = render_peer_guides(target, output, metadata["name"])
81
+ report["agent_bindings"] = {}
82
+ if target == "codex":
83
+ # Codex recognizes the current portable standard. Do not fabricate a
84
+ # separate proprietary manifest or pretend Clio recipes are native.
85
+ portable = {"$schema": manifest["$schema"], **metadata}
86
+ (output / "plugin.json").write_text(json.dumps(portable, indent=2) + "\n")
87
+ elif target == "claude":
88
+ directory = output / ".claude-plugin"
89
+ directory.mkdir()
90
+ (directory / "plugin.json").write_text(json.dumps(metadata, indent=2) + "\n")
91
+ commands = output / "commands"
92
+ agents = output / "agents"
93
+ commands.mkdir()
94
+ agents.mkdir()
95
+ roles = ACTION_ROLES
96
+ for guide in sorted((output / "assets/actions").glob("*.md")):
97
+ assignment = (f"Delegate this scientific role to the registered agent `{metadata['name']}:{roles[guide.stem]}`.\n"
98
+ if guide.stem in roles else "This action is owned by the interactive orchestrator.\n")
99
+ text = (f"---\ndescription: Materials characterization {guide.stem} workflow.\n---\n\n"
100
+ f"Read ${{CLAUDE_PLUGIN_ROOT}}/assets/actions/{guide.name} and follow that workflow.\n"
101
+ + assignment +
102
+ "Use AskUserQuestion for the interactive interview. If delegating, use the registered\n"
103
+ "materio role agent and include full context; workers return\n"
104
+ "checkpoint questions to this orchestrator. Use Bash only for approved local helper\n"
105
+ "calls; bind PACKAGE_ROOT to ${CLAUDE_PLUGIN_ROOT} in each call.\n"
106
+ "Arguments: $ARGUMENTS\n")
107
+ (commands / guide.name).write_text(text)
108
+ report["commands"] += 1
109
+ for skill in sorted((output / "skills").glob("*/SKILL.md")):
110
+ role = skill.parent.name.removeprefix("materio-")
111
+ tools = "Read, Glob, Grep" if role == "task-verifier" else "Read, Glob, Grep, Write, Edit, Bash, WebFetch"
112
+ text = (f"---\nname: {role}\ndescription: Materials characterization {role} role.\n"
113
+ f"tools: {tools}\n---\n\n"
114
+ f"Read ${{CLAUDE_PLUGIN_ROOT}}/skills/{skill.parent.name}/SKILL.md.\n"
115
+ "Apply its scientific contract within the caller's approved output paths.\n"
116
+ "Return structured complete, blocked, or needs_input with checkpoint kind\n"
117
+ "decision, human-action, or human-verify. Do not interview the researcher.\n"
118
+ "The caller owns state reconciliation, optional recording and paper gates.\n")
119
+ (agents / (role + ".md")).write_text(text)
120
+ report["agents"] += 1
121
+ report["agent_bindings"][role] = metadata["name"] + ":" + role
122
+ elif target == "gemini":
123
+ (output / "gemini-extension.json").write_text(json.dumps({
124
+ "name": metadata["name"], "version": metadata["version"],
125
+ "description": metadata["description"], "contextFileName": "GEMINI.md"
126
+ }, indent=2) + "\n")
127
+ (output / "GEMINI.md").write_text(
128
+ "# Materials characterization\n\nUse the installed materio skills and their relative action-guide links.\n"
129
+ "The interactive assistant owns researcher questions and state changes. Roles may\n"
130
+ "run inline when delegation is unavailable. No native fleet boundary is claimed.\n")
131
+ directory = output / "commands/materio"
132
+ directory.mkdir(parents=True)
133
+ for guide in sorted((output / "assets/actions").glob("*.md")):
134
+ text = (f"Use the installed materio skills to perform {guide.stem}. "
135
+ f"Read their relative link to assets/actions/{guide.name} and follow its contract. "
136
+ "Use the host conversation tool for researcher interviews. Delegate only with "
137
+ "available capabilities; otherwise perform the role inline. Arguments: {{args}}")
138
+ (directory / (guide.stem + ".toml")).write_text(
139
+ "description = " + json.dumps(f"Materials characterization {guide.stem}") + "\n"
140
+ "prompt = " + json.dumps(text) + "\n")
141
+ report["commands"] += 1
142
+ else:
143
+ raise ValueError(f"unsupported peer target: {target}")
144
+ (output / "capability-report.json").write_text(json.dumps(report, indent=2) + "\n")
145
+ return report
146
+ except Exception:
147
+ shutil.rmtree(output)
148
+ raise
149
+
150
+
151
+ def main():
152
+ parser = argparse.ArgumentParser(description=__doc__)
153
+ parser.add_argument("--target", choices=["codex", "claude", "gemini"], required=True)
154
+ parser.add_argument("--output", required=True)
155
+ args = parser.parse_args()
156
+ try:
157
+ print(json.dumps(project(args.target, args.output), indent=2))
158
+ return 0
159
+ except (OSError, ValueError) as error:
160
+ print(str(error), file=sys.stderr)
161
+ return 2
162
+
163
+
164
+ if __name__ == "__main__":
165
+ sys.exit(main())
@@ -0,0 +1,400 @@
1
+ #!/usr/bin/env python3
2
+ """Deterministic local research state operations. Python 3.10+, stdlib only.
3
+
4
+ This helper never initializes git, tags a checkpoint, or writes paper state.
5
+ It does not run experiments or generated analysis programs.
6
+ """
7
+ import argparse
8
+ import hashlib
9
+ import io
10
+ import json
11
+ import os
12
+ from pathlib import Path
13
+ import re
14
+ import shutil
15
+ import subprocess
16
+ import sys
17
+ import tarfile
18
+ import tempfile
19
+ from datetime import datetime, timezone
20
+ from uuid import uuid4
21
+
22
+ DEFAULTS = {"web_search": False, "auto_checkpoint": True, "commit_research": False}
23
+ PRESERVED = {"data", "checkpoints"}
24
+ ARCHIVE_MANIFEST = ".snapshot-manifest.json"
25
+
26
+
27
+ def unique_object(pairs):
28
+ result = {}
29
+ for key, value in pairs:
30
+ if key in result:
31
+ raise ValueError(f"duplicate JSON key: {key}")
32
+ result[key] = value
33
+ return result
34
+
35
+
36
+ def research_root(project):
37
+ project = Path(project).resolve(strict=True)
38
+ root = project / ".research"
39
+ if root.is_symlink():
40
+ raise ValueError(".research must be a real directory, not a symlink")
41
+ return root
42
+
43
+
44
+ def config(root):
45
+ path = root / "config.json"
46
+ result = dict(DEFAULTS)
47
+ if path.is_symlink():
48
+ raise ValueError("config.json must not be a symlink")
49
+ if path.exists():
50
+ value = json.loads(path.read_text(), object_pairs_hook=unique_object)
51
+ if not isinstance(value, dict):
52
+ raise ValueError("research config must be a JSON object")
53
+ for key in DEFAULTS:
54
+ if key in value and type(value[key]) is not bool:
55
+ raise ValueError(f"{key} must be a JSON boolean")
56
+ result.update(value)
57
+ return result
58
+
59
+
60
+ def contained(root, relative, allow_missing=False):
61
+ relative = Path(relative)
62
+ if relative.is_absolute() or ".." in relative.parts or not relative.parts:
63
+ raise ValueError(f"invalid relative research path: {relative}")
64
+ path = root
65
+ for part in relative.parts:
66
+ path = path / part
67
+ if path.is_symlink():
68
+ raise ValueError(f"symlink is not permitted: {path}")
69
+ if not allow_missing and not path.exists():
70
+ raise ValueError(f"missing research path: {path}")
71
+ return path
72
+
73
+
74
+ def task_number(value):
75
+ if not re.fullmatch(r"[0-9]+", str(value)) or int(value) < 1:
76
+ raise ValueError("task must be a positive decimal integer")
77
+ return f"{int(value):02d}"
78
+
79
+
80
+ def workflow(root):
81
+ path = root / "WORKFLOW.md"
82
+ if not path.exists():
83
+ return [], []
84
+ text = contained(root, "WORKFLOW.md").read_text()
85
+ active_text, _, archive_text = text.partition("## Archived Tasks")
86
+ def parse(text):
87
+ matches = list(re.finditer(r"^### Task ([0-9]+):[^\n]*", text, re.M))
88
+ return [(task_number(m.group(1)), text[m.start():matches[i + 1].start() if i + 1 < len(matches) else len(text)]) for i, m in enumerate(matches)]
89
+ active, archived = parse(active_text), parse(archive_text)
90
+ ids = [number for number, _ in active + archived]
91
+ if len(set(ids)) != len(ids):
92
+ raise ValueError("duplicate task identity in WORKFLOW.md")
93
+ return active, archived
94
+
95
+
96
+ def next_task(root):
97
+ active, archived = workflow(root)
98
+ ids = [int(number) for number, _ in active + archived]
99
+ tasks = root / "tasks"
100
+ if tasks.exists():
101
+ contained(root, "tasks")
102
+ for path in tasks.iterdir():
103
+ m = re.fullmatch(r"task-([0-9]+)", path.name)
104
+ if m:
105
+ ids.append(int(m.group(1)))
106
+ return task_number(max(ids, default=0) + 1)
107
+
108
+
109
+ def validate_workflow(root):
110
+ active, archived = workflow(root)
111
+ ids = {number for number, _ in active}
112
+ archived_ids = {number for number, _ in archived}
113
+ graph = {}
114
+ for number, block in active:
115
+ match = re.search(r"^[-*] \*\*Dependencies\*\*:\s*(.*)$", block, re.M)
116
+ refs = [task_number(value) for value in re.findall(r"Task\s+([0-9]+)", match.group(1) if match else "")]
117
+ for ref in refs:
118
+ if ref not in ids:
119
+ kind = "archived" if ref in archived_ids else "missing"
120
+ raise ValueError(f"Task {number} depends on {kind} Task {ref}")
121
+ graph[number] = refs
122
+ visiting, visited = set(), set()
123
+ def visit(number):
124
+ if number in visiting:
125
+ raise ValueError(f"dependency cycle at Task {number}")
126
+ if number in visited:
127
+ return
128
+ visiting.add(number)
129
+ for ref in graph[number]:
130
+ visit(ref)
131
+ visiting.remove(number)
132
+ visited.add(number)
133
+ for number in graph:
134
+ visit(number)
135
+ return {"active": list(graph), "archived": sorted(archived_ids), "dependencies": graph}
136
+
137
+
138
+ def next_ready_task(root):
139
+ """Choose a pending/in-progress task by workflow order and completed inputs."""
140
+ graph = validate_workflow(root)["dependencies"]
141
+ active, _ = workflow(root)
142
+ statuses = {}
143
+ for number, block in active:
144
+ match = re.search(r"^[-*] \*\*Status\*\*:\s*(.*)$", block, re.M)
145
+ status = re.sub(r"^[^a-zA-Z]+", "", match.group(1) if match else "").lower()
146
+ statuses[number] = status.split()[0] if status else "unspecified"
147
+ blocked = []
148
+ for number, _ in active:
149
+ if statuses[number] not in {"pending", "in-progress"}:
150
+ continue
151
+ unsettled = [dependency for dependency in graph[number] if statuses[dependency] != "complete"]
152
+ if not unsettled:
153
+ return {"id": number, "status": statuses[number], "blocked": blocked}
154
+ blocked.append({"id": number, "dependencies": unsettled})
155
+ return {"id": None, "reason": "no dependency-ready pending task", "blocked": blocked}
156
+
157
+
158
+ def snapshot_files(root):
159
+ files = {}
160
+ for base, directories, names in os.walk(root, followlinks=False):
161
+ base = Path(base)
162
+ if base == root:
163
+ directories[:] = [name for name in directories if name not in PRESERVED]
164
+ for name in directories:
165
+ if (base / name).is_symlink():
166
+ raise ValueError(f"snapshot refuses symlink: {base / name}")
167
+ for name in names:
168
+ path = base / name
169
+ relative = path.relative_to(root).as_posix()
170
+ if base == root and name in PRESERVED:
171
+ continue
172
+ if path == root / ARCHIVE_MANIFEST:
173
+ raise ValueError(f"reserved snapshot filename: {ARCHIVE_MANIFEST}")
174
+ if path.is_symlink() or not path.is_file():
175
+ raise ValueError(f"snapshot needs regular files: {path}")
176
+ files[relative] = path.read_bytes()
177
+ return files
178
+
179
+
180
+ def checkpoint_save(root, label):
181
+ if not re.fullmatch(r"[a-zA-Z0-9][a-zA-Z0-9._-]{0,63}", label):
182
+ raise ValueError("checkpoint label must be 1–64 path-safe characters")
183
+ if not root.is_dir():
184
+ raise ValueError("research state is not initialized")
185
+ directory = contained(root, "checkpoints", allow_missing=True)
186
+ directory.mkdir(exist_ok=True)
187
+ files = snapshot_files(root)
188
+ directories = []
189
+ for base, names, _ in os.walk(root, followlinks=False):
190
+ if Path(base) == root:
191
+ names[:] = [name for name in names if name not in PRESERVED]
192
+ directories.extend((Path(base) / name).relative_to(root).as_posix() for name in names)
193
+ modes = {name: (root / name).stat().st_mode & 0o777 for name in files}
194
+ manifest = {"version": 1, "files": {name: hashlib.sha256(data).hexdigest() for name, data in files.items()},
195
+ "directories": sorted(directories), "modes": modes}
196
+ name = datetime.now(timezone.utc).strftime("%Y%m%dT%H%M%S.%fZ") + "-" + label + "-" + uuid4().hex[:8] + ".tgz"
197
+ destination = directory / name
198
+ created = False
199
+ try:
200
+ with destination.open("xb") as output:
201
+ created = True
202
+ with tarfile.open(fileobj=output, mode="w:gz") as archive:
203
+ for relative, data in sorted({**files, ARCHIVE_MANIFEST: json.dumps(manifest).encode()}.items()):
204
+ member = tarfile.TarInfo(relative)
205
+ member.size, member.mode = len(data), 0o600
206
+ archive.addfile(member, io.BytesIO(data))
207
+ except Exception:
208
+ if created:
209
+ destination.unlink(missing_ok=True)
210
+ raise
211
+ return {"checkpoint": name, "files": len(files), "excluded": sorted(PRESERVED)}
212
+
213
+
214
+ def checkpoint_read(root, name):
215
+ if not re.fullmatch(r"[a-zA-Z0-9][a-zA-Z0-9._-]*\.tgz", name):
216
+ raise ValueError("checkpoint must be a filename listed by checkpoint list")
217
+ path = contained(root, "checkpoints/" + name)
218
+ files = {}
219
+ with tarfile.open(path, "r:gz") as archive:
220
+ for member in archive:
221
+ relative = Path(member.name)
222
+ if member.name in files or relative.is_absolute() or ".." in relative.parts or not relative.parts:
223
+ raise ValueError(f"invalid or duplicate archive member: {member.name}")
224
+ if relative.parts[0] in PRESERVED or not member.isfile():
225
+ raise ValueError(f"archive member is not permitted: {member.name}")
226
+ if relative.as_posix() != member.name:
227
+ raise ValueError(f"noncanonical archive member: {member.name}")
228
+ files[member.name] = archive.extractfile(member).read()
229
+ if ARCHIVE_MANIFEST not in files:
230
+ raise ValueError("checkpoint has no integrity manifest")
231
+ manifest = json.loads(files.pop(ARCHIVE_MANIFEST), object_pairs_hook=unique_object)
232
+ observed = {key: hashlib.sha256(value).hexdigest() for key, value in files.items()}
233
+ if not isinstance(manifest, dict) or manifest.get("version") != 1 or manifest.get("files") != observed:
234
+ raise ValueError("checkpoint content integrity mismatch")
235
+ directories = manifest.get("directories", [])
236
+ modes = manifest.get("modes", {})
237
+ if not isinstance(directories, list) or not isinstance(modes, dict):
238
+ raise ValueError("invalid snapshot directory or mode inventory")
239
+ for directory in directories:
240
+ if not isinstance(directory, str):
241
+ raise ValueError("invalid snapshot directory")
242
+ relative = Path(directory)
243
+ if relative.is_absolute() or ".." in relative.parts or not relative.parts or relative.parts[0] in PRESERVED or relative.as_posix() != directory:
244
+ raise ValueError(f"invalid snapshot directory: {directory}")
245
+ if any(name not in files or type(mode) is not int or mode < 0 or mode > 0o777 for name, mode in modes.items()):
246
+ raise ValueError("invalid snapshot mode")
247
+ return files, directories, modes
248
+
249
+
250
+ def checkpoint_restore(root, name, confirmed):
251
+ if not confirmed:
252
+ raise ValueError("restore requires --confirmed after researcher confirmation")
253
+ archive_name = name
254
+ files, directories, modes = checkpoint_read(root, name)
255
+ # Validate and stage before touching current state. Data and checkpoints are
256
+ # moved, never traversed or copied, and rollback restores the original root.
257
+ stage = Path(tempfile.mkdtemp(prefix=".research-restore-", dir=root.parent))
258
+ backup = Path(tempfile.mkdtemp(prefix=".research-previous-", dir=root.parent))
259
+ backup.rmdir()
260
+ moved = []
261
+ swapped = False
262
+ try:
263
+ for directory in directories:
264
+ (stage / directory).mkdir(parents=True, exist_ok=True)
265
+ for relative, data in files.items():
266
+ path = stage / relative
267
+ path.parent.mkdir(parents=True, exist_ok=True)
268
+ path.write_bytes(data)
269
+ path.chmod(modes.get(relative, 0o600))
270
+ root.rename(backup)
271
+ swapped = True
272
+ for name in sorted(PRESERVED):
273
+ if (backup / name).exists() or (backup / name).is_symlink():
274
+ (backup / name).rename(stage / name)
275
+ moved.append(name)
276
+ stage.rename(root)
277
+ except Exception:
278
+ if swapped:
279
+ for name in reversed(moved):
280
+ (stage / name).rename(backup / name)
281
+ backup.rename(root)
282
+ raise
283
+ finally:
284
+ if stage.exists():
285
+ shutil.rmtree(stage)
286
+ shutil.rmtree(backup)
287
+ return {"restored": archive_name, "files": len(files), "preserved": sorted(PRESERVED)}
288
+
289
+
290
+ def record(root, message, paths):
291
+ if not config(root)["commit_research"]:
292
+ return {"recorded": False, "reason": "commit_research is false"}
293
+ project = root.parent
294
+ def git(*argv, check=True):
295
+ return subprocess.run(["git", "-C", str(project), *argv], text=True, capture_output=True, check=check)
296
+ git("rev-parse", "--show-toplevel")
297
+ if git("diff", "--cached", "--name-only").stdout.strip():
298
+ raise ValueError("optional record refused: unrelated or preexisting staged changes")
299
+ selected = []
300
+ for value in paths:
301
+ relative = Path(value)
302
+ if not relative.parts or relative.parts[0] != ".research":
303
+ raise ValueError("optional record accepts only explicit .research files")
304
+ path = contained(root, Path(*relative.parts[1:]))
305
+ if not path.is_file():
306
+ raise ValueError("record needs named files, not directory staging")
307
+ selected.append(relative.as_posix())
308
+ if not selected:
309
+ return {"recorded": False, "reason": "no changed files supplied"}
310
+ git("add", "--", *selected)
311
+ if git("diff", "--cached", "--quiet", check=False).returncode == 0:
312
+ return {"recorded": False, "reason": "no staged changes"}
313
+ result = git("commit", "-m", message)
314
+ return {"recorded": True, "files": selected, "detail": result.stdout.strip()}
315
+
316
+
317
+ def register_copy(root, source):
318
+ source = Path(source).resolve(strict=True)
319
+ if not source.is_file():
320
+ raise ValueError("data registration needs an actual file")
321
+ directory = contained(root, "data", allow_missing=True)
322
+ directory.mkdir(exist_ok=True)
323
+ target = directory / source.name
324
+ data = source.read_bytes()
325
+ digest = hashlib.sha256(data).hexdigest()
326
+ if target.exists() or target.is_symlink():
327
+ if target.is_file() and not target.is_symlink() and target.read_bytes() == data:
328
+ return {"path": str(target), "source": str(source), "sha256": digest, "copied": False}
329
+ raise ValueError(f"data filename collision: {target.name}; choose a distinct name")
330
+ with target.open("xb") as output:
331
+ output.write(data)
332
+ return {"path": str(target), "source": str(source), "sha256": digest, "copied": True}
333
+
334
+
335
+ def main(argv=None):
336
+ parser = argparse.ArgumentParser(description=__doc__)
337
+ parser.add_argument("--project", default=".")
338
+ sub = parser.add_subparsers(dest="action", required=True)
339
+ sub.add_parser("init")
340
+ cfg = sub.add_parser("config")
341
+ cfg.add_argument("--key", choices=sorted(DEFAULTS))
342
+ sub.add_parser("next-task-id")
343
+ sub.add_parser("next-task")
344
+ sub.add_parser("validate-workflow")
345
+ sub.add_parser("task-dirs")
346
+ checkpoint = sub.add_parser("checkpoint")
347
+ checkpoint.add_argument("operation", choices=["save", "restore", "list"])
348
+ checkpoint.add_argument("name", nargs="?", default="manual")
349
+ checkpoint.add_argument("--confirmed", action="store_true")
350
+ rec = sub.add_parser("record")
351
+ rec.add_argument("--message", required=True)
352
+ rec.add_argument("--files", nargs="+", required=True)
353
+ copy = sub.add_parser("copy-data")
354
+ copy.add_argument("source")
355
+ args = parser.parse_args(argv)
356
+ try:
357
+ root = research_root(args.project)
358
+ if args.action == "init":
359
+ config(root)
360
+ root.mkdir(exist_ok=True)
361
+ for name in ("tasks", "data", "checkpoints"):
362
+ contained(root, name, allow_missing=True).mkdir(exist_ok=True)
363
+ if not (root / "config.json").exists():
364
+ with (root / "config.json").open("x") as output:
365
+ output.write(json.dumps(DEFAULTS, indent=2) + "\n")
366
+ result = {"initialized": True, "config": config(root)}
367
+ elif args.action == "config":
368
+ result = config(root)
369
+ if args.key:
370
+ result = result[args.key]
371
+ elif args.action == "next-task-id":
372
+ result = {"id": next_task(root)}
373
+ elif args.action == "next-task":
374
+ result = next_ready_task(root)
375
+ elif args.action in ("validate-workflow", "task-dirs"):
376
+ result = validate_workflow(root)
377
+ if args.action == "task-dirs":
378
+ for number in result["active"]:
379
+ contained(root, f"tasks/task-{number}", allow_missing=True).mkdir(parents=True, exist_ok=True)
380
+ elif args.action == "checkpoint":
381
+ if args.operation == "save":
382
+ result = checkpoint_save(root, args.name)
383
+ elif args.operation == "restore":
384
+ result = checkpoint_restore(root, args.name, args.confirmed)
385
+ else:
386
+ directory = contained(root, "checkpoints", allow_missing=True)
387
+ result = {"checkpoints": sorted(p.name for p in directory.glob("*.tgz") if p.is_file() and not p.is_symlink())}
388
+ elif args.action == "record":
389
+ result = record(root, args.message, args.files)
390
+ else:
391
+ result = register_copy(root, args.source)
392
+ print(json.dumps(result, indent=2))
393
+ return 0
394
+ except (ValueError, OSError, json.JSONDecodeError, tarfile.TarError, subprocess.CalledProcessError) as error:
395
+ print(json.dumps({"error": str(error)}), file=sys.stderr)
396
+ return 2
397
+
398
+
399
+ if __name__ == "__main__":
400
+ sys.exit(main())