@ahmed-g-gad/apothem 0.1.1

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 (674) hide show
  1. package/CHANGELOG.md +60 -0
  2. package/LICENSE +21 -0
  3. package/LICENSES/MIT.txt +18 -0
  4. package/LICENSES/PSF-2.0.txt +47 -0
  5. package/README.md +549 -0
  6. package/bin/README.md +37 -0
  7. package/bin/apothem.mjs +78 -0
  8. package/package.json +75 -0
  9. package/pyproject.toml +347 -0
  10. package/src/apothem/README.md +52 -0
  11. package/src/apothem/__init__.py +66 -0
  12. package/src/apothem/__main__.py +28 -0
  13. package/src/apothem/_vendor/.keep +0 -0
  14. package/src/apothem/_vendor/__init__.py +25 -0
  15. package/src/apothem/_vendor/attr/__init__.py +104 -0
  16. package/src/apothem/_vendor/attr/__init__.pyi +389 -0
  17. package/src/apothem/_vendor/attr/_cmp.py +160 -0
  18. package/src/apothem/_vendor/attr/_cmp.pyi +13 -0
  19. package/src/apothem/_vendor/attr/_compat.py +99 -0
  20. package/src/apothem/_vendor/attr/_config.py +31 -0
  21. package/src/apothem/_vendor/attr/_funcs.py +497 -0
  22. package/src/apothem/_vendor/attr/_make.py +3406 -0
  23. package/src/apothem/_vendor/attr/_next_gen.py +674 -0
  24. package/src/apothem/_vendor/attr/_typing_compat.pyi +15 -0
  25. package/src/apothem/_vendor/attr/_version_info.py +89 -0
  26. package/src/apothem/_vendor/attr/_version_info.pyi +9 -0
  27. package/src/apothem/_vendor/attr/converters.py +162 -0
  28. package/src/apothem/_vendor/attr/converters.pyi +19 -0
  29. package/src/apothem/_vendor/attr/exceptions.py +95 -0
  30. package/src/apothem/_vendor/attr/exceptions.pyi +17 -0
  31. package/src/apothem/_vendor/attr/filters.py +72 -0
  32. package/src/apothem/_vendor/attr/filters.pyi +6 -0
  33. package/src/apothem/_vendor/attr/py.typed +0 -0
  34. package/src/apothem/_vendor/attr/setters.py +79 -0
  35. package/src/apothem/_vendor/attr/setters.pyi +20 -0
  36. package/src/apothem/_vendor/attr/validators.py +750 -0
  37. package/src/apothem/_vendor/attr/validators.pyi +140 -0
  38. package/src/apothem/_vendor/attr.LICENSE +21 -0
  39. package/src/apothem/_vendor/attrs/__init__.py +72 -0
  40. package/src/apothem/_vendor/attrs/__init__.pyi +314 -0
  41. package/src/apothem/_vendor/attrs/converters.py +3 -0
  42. package/src/apothem/_vendor/attrs/exceptions.py +3 -0
  43. package/src/apothem/_vendor/attrs/filters.py +3 -0
  44. package/src/apothem/_vendor/attrs/py.typed +0 -0
  45. package/src/apothem/_vendor/attrs/setters.py +3 -0
  46. package/src/apothem/_vendor/attrs/validators.py +3 -0
  47. package/src/apothem/_vendor/attrs.LICENSE +21 -0
  48. package/src/apothem/_vendor/jsonschema/__init__.py +120 -0
  49. package/src/apothem/_vendor/jsonschema/__main__.py +6 -0
  50. package/src/apothem/_vendor/jsonschema/_format.py +546 -0
  51. package/src/apothem/_vendor/jsonschema/_keywords.py +449 -0
  52. package/src/apothem/_vendor/jsonschema/_legacy_keywords.py +449 -0
  53. package/src/apothem/_vendor/jsonschema/_types.py +204 -0
  54. package/src/apothem/_vendor/jsonschema/_typing.py +29 -0
  55. package/src/apothem/_vendor/jsonschema/_utils.py +355 -0
  56. package/src/apothem/_vendor/jsonschema/benchmarks/__init__.py +5 -0
  57. package/src/apothem/_vendor/jsonschema/benchmarks/const_vs_enum.py +30 -0
  58. package/src/apothem/_vendor/jsonschema/benchmarks/contains.py +28 -0
  59. package/src/apothem/_vendor/jsonschema/benchmarks/import_benchmark.py +31 -0
  60. package/src/apothem/_vendor/jsonschema/benchmarks/issue232/issue.json +2653 -0
  61. package/src/apothem/_vendor/jsonschema/benchmarks/issue232.py +25 -0
  62. package/src/apothem/_vendor/jsonschema/benchmarks/json_schema_test_suite.py +12 -0
  63. package/src/apothem/_vendor/jsonschema/benchmarks/nested_schemas.py +56 -0
  64. package/src/apothem/_vendor/jsonschema/benchmarks/subcomponents.py +42 -0
  65. package/src/apothem/_vendor/jsonschema/benchmarks/unused_registry.py +35 -0
  66. package/src/apothem/_vendor/jsonschema/benchmarks/useless_applicator_schemas.py +106 -0
  67. package/src/apothem/_vendor/jsonschema/benchmarks/useless_keywords.py +32 -0
  68. package/src/apothem/_vendor/jsonschema/benchmarks/validator_creation.py +14 -0
  69. package/src/apothem/_vendor/jsonschema/cli.py +292 -0
  70. package/src/apothem/_vendor/jsonschema/exceptions.py +490 -0
  71. package/src/apothem/_vendor/jsonschema/protocols.py +230 -0
  72. package/src/apothem/_vendor/jsonschema/validators.py +1410 -0
  73. package/src/apothem/_vendor/jsonschema.LICENSE +19 -0
  74. package/src/apothem/_vendor/jsonschema_specifications/__init__.py +12 -0
  75. package/src/apothem/_vendor/jsonschema_specifications/_core.py +38 -0
  76. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/metaschema.json +42 -0
  77. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/vocabularies/applicator +56 -0
  78. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/vocabularies/content +17 -0
  79. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/vocabularies/core +57 -0
  80. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/vocabularies/format +14 -0
  81. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/vocabularies/meta-data +37 -0
  82. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/vocabularies/validation +98 -0
  83. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/metaschema.json +58 -0
  84. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/applicator +48 -0
  85. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/content +17 -0
  86. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/core +51 -0
  87. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/format-annotation +14 -0
  88. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/format-assertion +14 -0
  89. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/meta-data +37 -0
  90. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/unevaluated +15 -0
  91. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/validation +98 -0
  92. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft3/metaschema.json +172 -0
  93. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft4/metaschema.json +149 -0
  94. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft6/metaschema.json +153 -0
  95. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft7/metaschema.json +166 -0
  96. package/src/apothem/_vendor/jsonschema_specifications.LICENSE +19 -0
  97. package/src/apothem/_vendor/referencing/__init__.py +7 -0
  98. package/src/apothem/_vendor/referencing/_attrs.py +31 -0
  99. package/src/apothem/_vendor/referencing/_attrs.pyi +21 -0
  100. package/src/apothem/_vendor/referencing/_core.py +739 -0
  101. package/src/apothem/_vendor/referencing/exceptions.py +165 -0
  102. package/src/apothem/_vendor/referencing/jsonschema.py +642 -0
  103. package/src/apothem/_vendor/referencing/py.typed +0 -0
  104. package/src/apothem/_vendor/referencing/retrieval.py +94 -0
  105. package/src/apothem/_vendor/referencing/typing.py +61 -0
  106. package/src/apothem/_vendor/referencing.LICENSE +19 -0
  107. package/src/apothem/_vendor/rpds/__init__.py +251 -0
  108. package/src/apothem/_vendor/typing_extensions.LICENSE +279 -0
  109. package/src/apothem/_vendor/typing_extensions.py +4317 -0
  110. package/src/apothem/_vendor/vendor.txt +22 -0
  111. package/src/apothem/_vendor/yaml/__init__.py +389 -0
  112. package/src/apothem/_vendor/yaml/composer.py +138 -0
  113. package/src/apothem/_vendor/yaml/constructor.py +748 -0
  114. package/src/apothem/_vendor/yaml/cyaml.py +100 -0
  115. package/src/apothem/_vendor/yaml/dumper.py +61 -0
  116. package/src/apothem/_vendor/yaml/emitter.py +1137 -0
  117. package/src/apothem/_vendor/yaml/error.py +74 -0
  118. package/src/apothem/_vendor/yaml/events.py +85 -0
  119. package/src/apothem/_vendor/yaml/loader.py +63 -0
  120. package/src/apothem/_vendor/yaml/nodes.py +48 -0
  121. package/src/apothem/_vendor/yaml/parser.py +588 -0
  122. package/src/apothem/_vendor/yaml/reader.py +185 -0
  123. package/src/apothem/_vendor/yaml/representer.py +388 -0
  124. package/src/apothem/_vendor/yaml/resolver.py +226 -0
  125. package/src/apothem/_vendor/yaml/scanner.py +1435 -0
  126. package/src/apothem/_vendor/yaml/serializer.py +110 -0
  127. package/src/apothem/_vendor/yaml/tokens.py +103 -0
  128. package/src/apothem/_vendor/yaml.LICENSE +20 -0
  129. package/src/apothem/agents/README.md +60 -0
  130. package/src/apothem/agents/codebase-explorer.md +91 -0
  131. package/src/apothem/agents/convention-auditor.md +93 -0
  132. package/src/apothem/agents/dependency-auditor.md +97 -0
  133. package/src/apothem/agents/fact-checker.md +84 -0
  134. package/src/apothem/agents/mcp-builder.md +86 -0
  135. package/src/apothem/agents/memory-auditor.md +93 -0
  136. package/src/apothem/agents/prompt-evaluator.md +87 -0
  137. package/src/apothem/agents/quality-gate.md +103 -0
  138. package/src/apothem/agents/refactor-surgeon.md +74 -0
  139. package/src/apothem/agents/research-scout.md +73 -0
  140. package/src/apothem/agents/security-scanner.md +83 -0
  141. package/src/apothem/agents/test-runner.md +84 -0
  142. package/src/apothem/audit/README.md +73 -0
  143. package/src/apothem/audit/_scan_lib.py +182 -0
  144. package/src/apothem/audit/analyze_graph.py +260 -0
  145. package/src/apothem/audit/build_capability_graph.py +607 -0
  146. package/src/apothem/audit/build_inventory.py +657 -0
  147. package/src/apothem/audit/build_plans_provenance.py +997 -0
  148. package/src/apothem/audit/check_links.py +389 -0
  149. package/src/apothem/audit/classify_artifacts.py +381 -0
  150. package/src/apothem/audit/deprecated-tokens.txt +10 -0
  151. package/src/apothem/audit/execute_plans_migration.py +491 -0
  152. package/src/apothem/audit/known-projects.txt +15 -0
  153. package/src/apothem/audit/render_capability_index.py +467 -0
  154. package/src/apothem/audit/render_inventory.py +405 -0
  155. package/src/apothem/audit/scan_ai_surfaces.py +1125 -0
  156. package/src/apothem/audit/scan_ai_surfaces_coarse.py +261 -0
  157. package/src/apothem/audit/scan_drift_features.py +143 -0
  158. package/src/apothem/audit/scan_frontmatter.py +293 -0
  159. package/src/apothem/audit/scan_header_coverage.py +1134 -0
  160. package/src/apothem/audit/scan_plan_leakage.py +540 -0
  161. package/src/apothem/audit/scan_plans_discipline.py +188 -0
  162. package/src/apothem/audit/scan_secrets_pii.py +245 -0
  163. package/src/apothem/audit/scan_stale_tokens.py +296 -0
  164. package/src/apothem/audit/synthesize_drift.py +205 -0
  165. package/src/apothem/benchmarks/README.md +33 -0
  166. package/src/apothem/benchmarks/__init__.py +3 -0
  167. package/src/apothem/benchmarks/bench_agents.py +63 -0
  168. package/src/apothem/benchmarks/bench_hooks.py +93 -0
  169. package/src/apothem/benchmarks/bench_install.py +58 -0
  170. package/src/apothem/benchmarks/bench_tests.py +93 -0
  171. package/src/apothem/benchmarks/bench_validate_ecosystem.py +84 -0
  172. package/src/apothem/cli/README.md +33 -0
  173. package/src/apothem/cli/__init__.py +229 -0
  174. package/src/apothem/cli/_cmd_completion.py +88 -0
  175. package/src/apothem/cli/_cmd_diff.py +181 -0
  176. package/src/apothem/cli/_cmd_doctor.py +143 -0
  177. package/src/apothem/cli/_cmd_harnesses.py +167 -0
  178. package/src/apothem/cli/_cmd_install.py +327 -0
  179. package/src/apothem/cli/_cmd_migrate_workspace.py +143 -0
  180. package/src/apothem/cli/_cmd_profile.py +341 -0
  181. package/src/apothem/cli/_cmd_status.py +180 -0
  182. package/src/apothem/cli/_cmd_uninstall.py +215 -0
  183. package/src/apothem/cli/_cmd_update.py +397 -0
  184. package/src/apothem/cli/_cmd_verify.py +194 -0
  185. package/src/apothem/cli/_common_flags.py +90 -0
  186. package/src/apothem/cli/_epilogs.py +296 -0
  187. package/src/apothem/cli/_helpers.py +857 -0
  188. package/src/apothem/cli/_json_formatter.py +21 -0
  189. package/src/apothem/cli/_materialize.py +376 -0
  190. package/src/apothem/cli/completions/apothem.bash +30 -0
  191. package/src/apothem/cli/completions/apothem.fish +19 -0
  192. package/src/apothem/cli/completions/apothem.ps1 +27 -0
  193. package/src/apothem/cli/completions/apothem.zsh +42 -0
  194. package/src/apothem/cli/reference_export.py +126 -0
  195. package/src/apothem/commands/README.md +125 -0
  196. package/src/apothem/commands/a11y-audit.md +203 -0
  197. package/src/apothem/commands/architecture-review.md +194 -0
  198. package/src/apothem/commands/audit.md +165 -0
  199. package/src/apothem/commands/code-audit.md +218 -0
  200. package/src/apothem/commands/code-review.md +193 -0
  201. package/src/apothem/commands/dependency-audit.md +209 -0
  202. package/src/apothem/commands/docs-review.md +199 -0
  203. package/src/apothem/commands/elevate.md +285 -0
  204. package/src/apothem/commands/eval.md +149 -0
  205. package/src/apothem/commands/fortress.md +172 -0
  206. package/src/apothem/commands/freshify.md +168 -0
  207. package/src/apothem/commands/github-deploy-fresh.md +178 -0
  208. package/src/apothem/commands/github-deploy-next.md +167 -0
  209. package/src/apothem/commands/perf-audit.md +198 -0
  210. package/src/apothem/commands/plan-amend.md +104 -0
  211. package/src/apothem/commands/plan-audit.md +127 -0
  212. package/src/apothem/commands/plan-design.md +257 -0
  213. package/src/apothem/commands/plan-execute.md +495 -0
  214. package/src/apothem/commands/plan-generate.md +351 -0
  215. package/src/apothem/commands/plan-review.md +555 -0
  216. package/src/apothem/commands/plan-spec.md +359 -0
  217. package/src/apothem/commands/plan-status.md +222 -0
  218. package/src/apothem/commands/plan.md +173 -0
  219. package/src/apothem/commands/projectify.md +142 -0
  220. package/src/apothem/commands/release-readiness.md +142 -0
  221. package/src/apothem/commands/research-analysis.md +241 -0
  222. package/src/apothem/commands/research-design.md +231 -0
  223. package/src/apothem/commands/research-disseminate.md +225 -0
  224. package/src/apothem/commands/research-experiment.md +232 -0
  225. package/src/apothem/commands/research-ideate.md +213 -0
  226. package/src/apothem/commands/research-paper.md +252 -0
  227. package/src/apothem/commands/research-proposal.md +220 -0
  228. package/src/apothem/commands/research-publish.md +255 -0
  229. package/src/apothem/commands/research-review.md +251 -0
  230. package/src/apothem/commands/research-sources.md +266 -0
  231. package/src/apothem/commands/research-spec.md +255 -0
  232. package/src/apothem/commands/research-synthesis.md +233 -0
  233. package/src/apothem/commands/research-theory.md +218 -0
  234. package/src/apothem/commands/research.md +181 -0
  235. package/src/apothem/commands/security-audit.md +196 -0
  236. package/src/apothem/commands/supply-chain-audit.md +192 -0
  237. package/src/apothem/commands/test-suite.md +146 -0
  238. package/src/apothem/commands/threat-model-audit.md +199 -0
  239. package/src/apothem/commands/ux-review.md +202 -0
  240. package/src/apothem/commands/workflow.md +162 -0
  241. package/src/apothem/conformity/README.md +173 -0
  242. package/src/apothem/conformity/__init__.py +1 -0
  243. package/src/apothem/conformity/_grep_base.py +93 -0
  244. package/src/apothem/conformity/agent_capability_grep.py +306 -0
  245. package/src/apothem/conformity/agents_md_coverage_grep.py +382 -0
  246. package/src/apothem/conformity/agnosticism_grep.py +311 -0
  247. package/src/apothem/conformity/always_on_budget_grep.py +318 -0
  248. package/src/apothem/conformity/bare_except_grep.py +115 -0
  249. package/src/apothem/conformity/binding_reciprocity_grep.py +151 -0
  250. package/src/apothem/conformity/brand_mark_grep.py +272 -0
  251. package/src/apothem/conformity/commented_out_code_grep.py +176 -0
  252. package/src/apothem/conformity/completion_claim_grep.py +169 -0
  253. package/src/apothem/conformity/conventional_commit_grep.py +319 -0
  254. package/src/apothem/conformity/copilot_instructions_presence_grep.py +324 -0
  255. package/src/apothem/conformity/cross_platform_matrix_grep.py +297 -0
  256. package/src/apothem/conformity/determinism_grep.py +306 -0
  257. package/src/apothem/conformity/diagram_staleness_grep.py +154 -0
  258. package/src/apothem/conformity/dynamism_grep.py +284 -0
  259. package/src/apothem/conformity/editorconfig_presence_grep.py +281 -0
  260. package/src/apothem/conformity/file_header_grep.py +502 -0
  261. package/src/apothem/conformity/freshness_token_grep.py +233 -0
  262. package/src/apothem/conformity/frontmatter_grep.py +274 -0
  263. package/src/apothem/conformity/frontmatter_value_grep.py +386 -0
  264. package/src/apothem/conformity/gate.py +1386 -0
  265. package/src/apothem/conformity/gitattributes_presence_grep.py +238 -0
  266. package/src/apothem/conformity/harden_runner_grep.py +320 -0
  267. package/src/apothem/conformity/hedging_grep.py +129 -0
  268. package/src/apothem/conformity/license_author_consistency_grep.py +204 -0
  269. package/src/apothem/conformity/link_check.py +327 -0
  270. package/src/apothem/conformity/magic_number_grep.py +182 -0
  271. package/src/apothem/conformity/multi_surface_coherence_grep.py +620 -0
  272. package/src/apothem/conformity/naming_grep.py +224 -0
  273. package/src/apothem/conformity/no_global_plans_grep.py +339 -0
  274. package/src/apothem/conformity/no_toplevel_docs_grep.py +120 -0
  275. package/src/apothem/conformity/oidc_trusted_publishing_grep.py +291 -0
  276. package/src/apothem/conformity/option_annotation_grep.py +352 -0
  277. package/src/apothem/conformity/orphan_output_grep.py +206 -0
  278. package/src/apothem/conformity/permissions_minimum_scope_grep.py +299 -0
  279. package/src/apothem/conformity/plain_language_grep.py +559 -0
  280. package/src/apothem/conformity/plan_next_step_consistency_grep.py +450 -0
  281. package/src/apothem/conformity/plan_suite_structure_grep.py +534 -0
  282. package/src/apothem/conformity/plans_discipline_language_grep.py +245 -0
  283. package/src/apothem/conformity/production_ready_pr_grep.py +200 -0
  284. package/src/apothem/conformity/recommend_next_step_grep.py +250 -0
  285. package/src/apothem/conformity/redundancy_grep.py +401 -0
  286. package/src/apothem/conformity/reference_token_grep.py +230 -0
  287. package/src/apothem/conformity/registry_capability_consistency_grep.py +368 -0
  288. package/src/apothem/conformity/secret_leak_grep.py +193 -0
  289. package/src/apothem/conformity/semver_stability_grep.py +358 -0
  290. package/src/apothem/conformity/smoke_install_grep.py +194 -0
  291. package/src/apothem/conformity/static_version_grep.py +284 -0
  292. package/src/apothem/conformity/token_efficiency_grep.py +185 -0
  293. package/src/apothem/conformity/unpinned_action_grep.py +115 -0
  294. package/src/apothem/conformity/user_confirm_grep.py +74 -0
  295. package/src/apothem/conformity/workflow_concurrency_grep.py +283 -0
  296. package/src/apothem/harnesses/README.md +63 -0
  297. package/src/apothem/harnesses/__init__.py +16 -0
  298. package/src/apothem/harnesses/_shared/README.md +36 -0
  299. package/src/apothem/harnesses/_shared/__init__.py +12 -0
  300. package/src/apothem/harnesses/_shared/install_driver.py +281 -0
  301. package/src/apothem/harnesses/_shared/install_driver_apply.py +612 -0
  302. package/src/apothem/harnesses/_shared/install_driver_backup.py +535 -0
  303. package/src/apothem/harnesses/_shared/install_driver_converters.py +310 -0
  304. package/src/apothem/harnesses/_shared/install_driver_lifecycle.py +495 -0
  305. package/src/apothem/harnesses/_shared/install_driver_materialize.py +675 -0
  306. package/src/apothem/harnesses/_shared/install_driver_merge.py +656 -0
  307. package/src/apothem/harnesses/_shared/install_driver_pathsafety.py +137 -0
  308. package/src/apothem/harnesses/_shared/install_driver_planvalidation.py +240 -0
  309. package/src/apothem/harnesses/_shared/install_driver_removal.py +366 -0
  310. package/src/apothem/harnesses/_shared/install_driver_treeops.py +248 -0
  311. package/src/apothem/harnesses/_shared/install_driver_types.py +330 -0
  312. package/src/apothem/harnesses/_shared/wrapper_factories.py +448 -0
  313. package/src/apothem/harnesses/antigravity/STANDARD-CONVENTION-PIN.md +91 -0
  314. package/src/apothem/harnesses/antigravity/__init__.py +70 -0
  315. package/src/apothem/harnesses/antigravity/capabilities.yml +40 -0
  316. package/src/apothem/harnesses/antigravity/install.py +63 -0
  317. package/src/apothem/harnesses/antigravity/templates/GEMINI.md +40 -0
  318. package/src/apothem/harnesses/antigravity/templates/plugin.json +5 -0
  319. package/src/apothem/harnesses/antigravity/uninstall.py +22 -0
  320. package/src/apothem/harnesses/antigravity/update.py +10 -0
  321. package/src/apothem/harnesses/antigravity/verify.py +11 -0
  322. package/src/apothem/harnesses/claude_code/STANDARD-CONVENTION-PIN.md +65 -0
  323. package/src/apothem/harnesses/claude_code/__init__.py +107 -0
  324. package/src/apothem/harnesses/claude_code/capabilities.yml +42 -0
  325. package/src/apothem/harnesses/claude_code/install.py +147 -0
  326. package/src/apothem/harnesses/claude_code/templates/settings.json +351 -0
  327. package/src/apothem/harnesses/claude_code/uninstall.py +23 -0
  328. package/src/apothem/harnesses/claude_code/update.py +10 -0
  329. package/src/apothem/harnesses/claude_code/verify.py +11 -0
  330. package/src/apothem/harnesses/codebuddy/STANDARD-CONVENTION-PIN.md +74 -0
  331. package/src/apothem/harnesses/codebuddy/__init__.py +49 -0
  332. package/src/apothem/harnesses/codebuddy/capabilities.yml +34 -0
  333. package/src/apothem/harnesses/codebuddy/install.py +40 -0
  334. package/src/apothem/harnesses/codebuddy/templates/apothem-rules.md +37 -0
  335. package/src/apothem/harnesses/codebuddy/uninstall.py +25 -0
  336. package/src/apothem/harnesses/codebuddy/update.py +10 -0
  337. package/src/apothem/harnesses/codebuddy/verify.py +11 -0
  338. package/src/apothem/harnesses/codex/STANDARD-CONVENTION-PIN.md +79 -0
  339. package/src/apothem/harnesses/codex/__init__.py +72 -0
  340. package/src/apothem/harnesses/codex/capabilities.yml +40 -0
  341. package/src/apothem/harnesses/codex/install.py +69 -0
  342. package/src/apothem/harnesses/codex/templates/AGENTS.md +40 -0
  343. package/src/apothem/harnesses/codex/templates/hooks.json +127 -0
  344. package/src/apothem/harnesses/codex/uninstall.py +23 -0
  345. package/src/apothem/harnesses/codex/update.py +10 -0
  346. package/src/apothem/harnesses/codex/verify.py +11 -0
  347. package/src/apothem/harnesses/cursor/STANDARD-CONVENTION-PIN.md +79 -0
  348. package/src/apothem/harnesses/cursor/__init__.py +48 -0
  349. package/src/apothem/harnesses/cursor/capabilities.yml +42 -0
  350. package/src/apothem/harnesses/cursor/install.py +38 -0
  351. package/src/apothem/harnesses/cursor/templates/apothem-rules.mdc +40 -0
  352. package/src/apothem/harnesses/cursor/uninstall.py +25 -0
  353. package/src/apothem/harnesses/cursor/update.py +10 -0
  354. package/src/apothem/harnesses/cursor/verify.py +11 -0
  355. package/src/apothem/harnesses/gemini_cli/STANDARD-CONVENTION-PIN.md +102 -0
  356. package/src/apothem/harnesses/gemini_cli/__init__.py +52 -0
  357. package/src/apothem/harnesses/gemini_cli/capabilities.yml +43 -0
  358. package/src/apothem/harnesses/gemini_cli/install.py +43 -0
  359. package/src/apothem/harnesses/gemini_cli/templates/GEMINI.md +38 -0
  360. package/src/apothem/harnesses/gemini_cli/uninstall.py +25 -0
  361. package/src/apothem/harnesses/gemini_cli/update.py +10 -0
  362. package/src/apothem/harnesses/gemini_cli/verify.py +11 -0
  363. package/src/apothem/harnesses/github_copilot/STANDARD-CONVENTION-PIN.md +84 -0
  364. package/src/apothem/harnesses/github_copilot/__init__.py +47 -0
  365. package/src/apothem/harnesses/github_copilot/capabilities.yml +42 -0
  366. package/src/apothem/harnesses/github_copilot/install.py +40 -0
  367. package/src/apothem/harnesses/github_copilot/templates/copilot-instructions.md +33 -0
  368. package/src/apothem/harnesses/github_copilot/uninstall.py +25 -0
  369. package/src/apothem/harnesses/github_copilot/update.py +10 -0
  370. package/src/apothem/harnesses/github_copilot/verify.py +11 -0
  371. package/src/apothem/harnesses/glm/STANDARD-CONVENTION-PIN.md +77 -0
  372. package/src/apothem/harnesses/glm/__init__.py +56 -0
  373. package/src/apothem/harnesses/glm/capabilities.yml +33 -0
  374. package/src/apothem/harnesses/glm/install.py +45 -0
  375. package/src/apothem/harnesses/glm/templates/glm.toml +58 -0
  376. package/src/apothem/harnesses/glm/uninstall.py +25 -0
  377. package/src/apothem/harnesses/glm/update.py +10 -0
  378. package/src/apothem/harnesses/glm/verify.py +11 -0
  379. package/src/apothem/harnesses/hermes/STANDARD-CONVENTION-PIN.md +57 -0
  380. package/src/apothem/harnesses/hermes/__init__.py +33 -0
  381. package/src/apothem/harnesses/hermes/capabilities.yml +36 -0
  382. package/src/apothem/harnesses/hermes/install.py +17 -0
  383. package/src/apothem/harnesses/hermes/materializer.py +35 -0
  384. package/src/apothem/harnesses/hermes/uninstall.py +33 -0
  385. package/src/apothem/harnesses/hermes/update.py +10 -0
  386. package/src/apothem/harnesses/hermes/verify.py +11 -0
  387. package/src/apothem/harnesses/kimi_code/STANDARD-CONVENTION-PIN.md +128 -0
  388. package/src/apothem/harnesses/kimi_code/__init__.py +59 -0
  389. package/src/apothem/harnesses/kimi_code/capabilities.yml +40 -0
  390. package/src/apothem/harnesses/kimi_code/install.py +42 -0
  391. package/src/apothem/harnesses/kimi_code/templates/AGENTS.md +43 -0
  392. package/src/apothem/harnesses/kimi_code/uninstall.py +27 -0
  393. package/src/apothem/harnesses/kimi_code/update.py +10 -0
  394. package/src/apothem/harnesses/kimi_code/verify.py +11 -0
  395. package/src/apothem/harnesses/kiro/STANDARD-CONVENTION-PIN.md +77 -0
  396. package/src/apothem/harnesses/kiro/__init__.py +49 -0
  397. package/src/apothem/harnesses/kiro/capabilities.yml +36 -0
  398. package/src/apothem/harnesses/kiro/install.py +39 -0
  399. package/src/apothem/harnesses/kiro/templates/apothem-rules.md +36 -0
  400. package/src/apothem/harnesses/kiro/uninstall.py +25 -0
  401. package/src/apothem/harnesses/kiro/update.py +10 -0
  402. package/src/apothem/harnesses/kiro/verify.py +11 -0
  403. package/src/apothem/harnesses/open_claw/STANDARD-CONVENTION-PIN.md +62 -0
  404. package/src/apothem/harnesses/open_claw/__init__.py +35 -0
  405. package/src/apothem/harnesses/open_claw/capabilities.yml +35 -0
  406. package/src/apothem/harnesses/open_claw/install.py +17 -0
  407. package/src/apothem/harnesses/open_claw/materializer.py +36 -0
  408. package/src/apothem/harnesses/open_claw/uninstall.py +32 -0
  409. package/src/apothem/harnesses/open_claw/update.py +10 -0
  410. package/src/apothem/harnesses/open_claw/verify.py +11 -0
  411. package/src/apothem/harnesses/opencode/STANDARD-CONVENTION-PIN.md +76 -0
  412. package/src/apothem/harnesses/opencode/__init__.py +35 -0
  413. package/src/apothem/harnesses/opencode/capabilities.yml +43 -0
  414. package/src/apothem/harnesses/opencode/install.py +17 -0
  415. package/src/apothem/harnesses/opencode/materializer.py +31 -0
  416. package/src/apothem/harnesses/opencode/uninstall.py +34 -0
  417. package/src/apothem/harnesses/opencode/update.py +10 -0
  418. package/src/apothem/harnesses/opencode/verify.py +11 -0
  419. package/src/apothem/harnesses/qwen_code/STANDARD-CONVENTION-PIN.md +87 -0
  420. package/src/apothem/harnesses/qwen_code/__init__.py +37 -0
  421. package/src/apothem/harnesses/qwen_code/capabilities.yml +43 -0
  422. package/src/apothem/harnesses/qwen_code/install.py +19 -0
  423. package/src/apothem/harnesses/qwen_code/materializer.py +174 -0
  424. package/src/apothem/harnesses/qwen_code/templates/QWEN.md +30 -0
  425. package/src/apothem/harnesses/qwen_code/uninstall.py +34 -0
  426. package/src/apothem/harnesses/qwen_code/update.py +10 -0
  427. package/src/apothem/harnesses/qwen_code/verify.py +11 -0
  428. package/src/apothem/harnesses/trae/STANDARD-CONVENTION-PIN.md +70 -0
  429. package/src/apothem/harnesses/trae/__init__.py +49 -0
  430. package/src/apothem/harnesses/trae/capabilities.yml +34 -0
  431. package/src/apothem/harnesses/trae/install.py +38 -0
  432. package/src/apothem/harnesses/trae/templates/apothem-rules.md +37 -0
  433. package/src/apothem/harnesses/trae/uninstall.py +25 -0
  434. package/src/apothem/harnesses/trae/update.py +10 -0
  435. package/src/apothem/harnesses/trae/verify.py +11 -0
  436. package/src/apothem/harnesses/windsurf/STANDARD-CONVENTION-PIN.md +91 -0
  437. package/src/apothem/harnesses/windsurf/__init__.py +52 -0
  438. package/src/apothem/harnesses/windsurf/capabilities.yml +40 -0
  439. package/src/apothem/harnesses/windsurf/install.py +41 -0
  440. package/src/apothem/harnesses/windsurf/templates/apothem-rules.md +37 -0
  441. package/src/apothem/harnesses/windsurf/uninstall.py +25 -0
  442. package/src/apothem/harnesses/windsurf/update.py +10 -0
  443. package/src/apothem/harnesses/windsurf/verify.py +11 -0
  444. package/src/apothem/harnesses/zed/STANDARD-CONVENTION-PIN.md +92 -0
  445. package/src/apothem/harnesses/zed/__init__.py +57 -0
  446. package/src/apothem/harnesses/zed/capabilities.yml +38 -0
  447. package/src/apothem/harnesses/zed/install.py +41 -0
  448. package/src/apothem/harnesses/zed/templates/apothem-rules.md +32 -0
  449. package/src/apothem/harnesses/zed/uninstall.py +28 -0
  450. package/src/apothem/harnesses/zed/update.py +10 -0
  451. package/src/apothem/harnesses/zed/verify.py +11 -0
  452. package/src/apothem/hooks/README.md +81 -0
  453. package/src/apothem/hooks/__init__.py +24 -0
  454. package/src/apothem/hooks/askuserquestion_validator.py +380 -0
  455. package/src/apothem/hooks/dispatch.py +296 -0
  456. package/src/apothem/hooks/emit_hook_context.py +444 -0
  457. package/src/apothem/hooks/hooks.json +318 -0
  458. package/src/apothem/hooks/lib/README.md +39 -0
  459. package/src/apothem/hooks/lib/__init__.py +18 -0
  460. package/src/apothem/hooks/lib/bootstrap.ps1 +129 -0
  461. package/src/apothem/hooks/lib/bootstrap.sh +103 -0
  462. package/src/apothem/hooks/lib/events.py +51 -0
  463. package/src/apothem/hooks/lib/find-pwsh.ps1 +78 -0
  464. package/src/apothem/hooks/lib/find-pwsh.sh +76 -0
  465. package/src/apothem/hooks/lib/find-python.ps1 +63 -0
  466. package/src/apothem/hooks/lib/find-python.sh +97 -0
  467. package/src/apothem/hooks/lib/log.py +43 -0
  468. package/src/apothem/hooks/lib/resolve_root.py +264 -0
  469. package/src/apothem/hooks/messages/postcompact.md +14 -0
  470. package/src/apothem/hooks/messages/posttooluse-proactive-compaction.md +46 -0
  471. package/src/apothem/hooks/messages/precompact.md +14 -0
  472. package/src/apothem/hooks/messages/pretooluse-askuserquestion-recommended.md +65 -0
  473. package/src/apothem/hooks/messages/pretooluse-bash-plan-guard.md +97 -0
  474. package/src/apothem/hooks/messages/pretooluse-bash.md +39 -0
  475. package/src/apothem/hooks/messages/pretooluse-conformity.md +70 -0
  476. package/src/apothem/hooks/messages/pretooluse-dependency-guard.md +21 -0
  477. package/src/apothem/hooks/messages/pretooluse-edit-header-guard.md +61 -0
  478. package/src/apothem/hooks/messages/pretooluse-edit.md +21 -0
  479. package/src/apothem/hooks/messages/pretooluse-eval-guard.md +39 -0
  480. package/src/apothem/hooks/messages/pretooluse-notebookedit.md +11 -0
  481. package/src/apothem/hooks/messages/pretooluse-write-header-guard.md +45 -0
  482. package/src/apothem/hooks/messages/pretooluse-write-plan-guard.md +72 -0
  483. package/src/apothem/hooks/messages/pretooluse-write.md +21 -0
  484. package/src/apothem/hooks/messages/sessionstart.md +15 -0
  485. package/src/apothem/hooks/messages/stop.md +27 -0
  486. package/src/apothem/hooks/proactive_compaction_tracker.py +327 -0
  487. package/src/apothem/hooks/session_start_bootstrap.py +472 -0
  488. package/src/apothem/lib/README.md +42 -0
  489. package/src/apothem/lib/__init__.py +13 -0
  490. package/src/apothem/lib/atomic_io.py +189 -0
  491. package/src/apothem/lib/auditor.py +687 -0
  492. package/src/apothem/lib/clean_slate.py +396 -0
  493. package/src/apothem/lib/contexts.py +352 -0
  494. package/src/apothem/lib/data_home.py +255 -0
  495. package/src/apothem/lib/frontmatter.py +101 -0
  496. package/src/apothem/lib/harness_materializer.py +213 -0
  497. package/src/apothem/lib/harness_protocol.py +59 -0
  498. package/src/apothem/lib/harness_registry.py +282 -0
  499. package/src/apothem/lib/harness_registry_data.py +843 -0
  500. package/src/apothem/lib/install_ledger.py +347 -0
  501. package/src/apothem/lib/learning.py +540 -0
  502. package/src/apothem/lib/memory.py +347 -0
  503. package/src/apothem/lib/parallel_sweep.py +234 -0
  504. package/src/apothem/lib/plan_tiers.py +200 -0
  505. package/src/apothem/lib/plugin_bootstrap.py +132 -0
  506. package/src/apothem/lib/plugin_tree.py +599 -0
  507. package/src/apothem/lib/profile.py +755 -0
  508. package/src/apothem/lib/profile_projection.py +198 -0
  509. package/src/apothem/lib/propagation-manifest.yaml +878 -0
  510. package/src/apothem/lib/propagation.py +220 -0
  511. package/src/apothem/lib/python_resolver.py +189 -0
  512. package/src/apothem/lib/reporter.py +62 -0
  513. package/src/apothem/lib/workspace_migration.py +323 -0
  514. package/src/apothem/output-styles/README.md +41 -0
  515. package/src/apothem/output-styles/concise-engineer.md +49 -0
  516. package/src/apothem/output-styles/default-architect.md +52 -0
  517. package/src/apothem/output-styles/default.md +113 -0
  518. package/src/apothem/output-styles/forensic-auditor.md +63 -0
  519. package/src/apothem/py.typed +0 -0
  520. package/src/apothem/rules/README.md +121 -0
  521. package/src/apothem/rules/agent-capability-discipline-matrix.md +89 -0
  522. package/src/apothem/rules/agent-capability-discipline.md +78 -0
  523. package/src/apothem/rules/agent-orchestration-patterns.md +144 -0
  524. package/src/apothem/rules/agent-orchestration.md +65 -0
  525. package/src/apothem/rules/agents-md-convention.md +86 -0
  526. package/src/apothem/rules/agile-sprints-elements.md +135 -0
  527. package/src/apothem/rules/agile-sprints.md +64 -0
  528. package/src/apothem/rules/agnostic-posture-checklist.md +47 -0
  529. package/src/apothem/rules/agnostic-posture.md +48 -0
  530. package/src/apothem/rules/authoritative-referencing-quotation.md +50 -0
  531. package/src/apothem/rules/authoritative-referencing.md +66 -0
  532. package/src/apothem/rules/authority-inquiry-categories.md +58 -0
  533. package/src/apothem/rules/authority-inquiry.md +54 -0
  534. package/src/apothem/rules/auto-memory-topic-files.md +86 -0
  535. package/src/apothem/rules/auto-memory.md +67 -0
  536. package/src/apothem/rules/bidirectional-binding.md +123 -0
  537. package/src/apothem/rules/canonical-layout-reporting-tiers.md +212 -0
  538. package/src/apothem/rules/canonical-layout.md +60 -0
  539. package/src/apothem/rules/clean-architecture-layers.md +186 -0
  540. package/src/apothem/rules/clean-room-generation-protocols.md +124 -0
  541. package/src/apothem/rules/clean-room-generation.md +59 -0
  542. package/src/apothem/rules/code-craft-conventions.md +101 -0
  543. package/src/apothem/rules/code-craft-markdown.md +138 -0
  544. package/src/apothem/rules/code-craft-python.md +154 -0
  545. package/src/apothem/rules/code-craft-shell.md +192 -0
  546. package/src/apothem/rules/cognitive-identity-techniques.md +180 -0
  547. package/src/apothem/rules/cognitive-identity.md +81 -0
  548. package/src/apothem/rules/context-management-budget.md +46 -0
  549. package/src/apothem/rules/context-management-protocol.md +161 -0
  550. package/src/apothem/rules/context-management-scratch.md +128 -0
  551. package/src/apothem/rules/context-management.md +85 -0
  552. package/src/apothem/rules/definitiveness-virtues.md +67 -0
  553. package/src/apothem/rules/definitiveness.md +58 -0
  554. package/src/apothem/rules/determinism.md +81 -0
  555. package/src/apothem/rules/disclosure-ledger-markers.md +58 -0
  556. package/src/apothem/rules/disclosure-ledger.md +52 -0
  557. package/src/apothem/rules/dynamism.md +38 -0
  558. package/src/apothem/rules/etc-extension.md +57 -0
  559. package/src/apothem/rules/expertise-posture-elements.md +68 -0
  560. package/src/apothem/rules/expertise-posture.md +54 -0
  561. package/src/apothem/rules/freshness-facade.md +64 -0
  562. package/src/apothem/rules/harness-adapter-shape-schemas.md +162 -0
  563. package/src/apothem/rules/harness-adapter-shape.md +42 -0
  564. package/src/apothem/rules/host-discovery-manifests.md +50 -0
  565. package/src/apothem/rules/host-discovery.md +56 -0
  566. package/src/apothem/rules/i18n-discipline-locale-cohorts.md +120 -0
  567. package/src/apothem/rules/i18n-discipline.md +70 -0
  568. package/src/apothem/rules/interactive-questions-canonical-shapes.md +590 -0
  569. package/src/apothem/rules/interactive-questions-detail.md +41 -0
  570. package/src/apothem/rules/interactive-questions-sweep-matchers.md +184 -0
  571. package/src/apothem/rules/interactive-questions.md +89 -0
  572. package/src/apothem/rules/large-file-generation.md +112 -0
  573. package/src/apothem/rules/large-file-reading.md +59 -0
  574. package/src/apothem/rules/living-docs.md +85 -0
  575. package/src/apothem/rules/multi-agent-workflow.md +57 -0
  576. package/src/apothem/rules/operational-mandates-expanded.md +78 -0
  577. package/src/apothem/rules/operational-mandates.md +88 -0
  578. package/src/apothem/rules/option-annotation-form.md +60 -0
  579. package/src/apothem/rules/option-annotation.md +45 -0
  580. package/src/apothem/rules/own-voice-reimplementation.md +86 -0
  581. package/src/apothem/rules/performance-discipline.md +91 -0
  582. package/src/apothem/rules/persistent-conventions-vigilance-checklist.md +54 -0
  583. package/src/apothem/rules/persistent-conventions-vigilance.md +61 -0
  584. package/src/apothem/rules/plain-language.md +56 -0
  585. package/src/apothem/rules/planning-techniques.md +130 -0
  586. package/src/apothem/rules/pre-emission-gate-bars.md +86 -0
  587. package/src/apothem/rules/pre-emission-gate.md +54 -0
  588. package/src/apothem/rules/production-ready-prs-surfaces.md +162 -0
  589. package/src/apothem/rules/production-ready-prs.md +83 -0
  590. package/src/apothem/rules/propagation.md +63 -0
  591. package/src/apothem/rules/recommend-next-step.md +106 -0
  592. package/src/apothem/rules/refactoring-discipline.md +76 -0
  593. package/src/apothem/rules/session-closure.md +44 -0
  594. package/src/apothem/rules/sota-elevation-exemplars.md +76 -0
  595. package/src/apothem/rules/sota-elevation.md +52 -0
  596. package/src/apothem/rules/source-accessibility.md +58 -0
  597. package/src/apothem/rules/surgical-manipulation.md +48 -0
  598. package/src/apothem/rules/systemic-participation-relations.md +108 -0
  599. package/src/apothem/rules/systemic-participation.md +70 -0
  600. package/src/apothem/rules/ten-dimension-check-dimensions.md +52 -0
  601. package/src/apothem/rules/ten-dimension-check.md +59 -0
  602. package/src/apothem/rules/token-budget-discipline.md +81 -0
  603. package/src/apothem/rules/token-efficiency-rewrite-protocol.md +79 -0
  604. package/src/apothem/rules/token-efficiency-rewrite.md +77 -0
  605. package/src/apothem/rules/tool-use-discipline.md +48 -0
  606. package/src/apothem/rules/visual-leverage.md +102 -0
  607. package/src/apothem/schemas/NOTICE.md +9 -0
  608. package/src/apothem/schemas/README.md +104 -0
  609. package/src/apothem/schemas/__init__.py +176 -0
  610. package/src/apothem/schemas/advisory-finding.schema.json +111 -0
  611. package/src/apothem/schemas/agent.schema.json +106 -0
  612. package/src/apothem/schemas/authorship-header.txt +1 -0
  613. package/src/apothem/schemas/cohort-manifest.yaml +248 -0
  614. package/src/apothem/schemas/cohort-metadata-vocabulary.yaml +168 -0
  615. package/src/apothem/schemas/cohort.schema.json +113 -0
  616. package/src/apothem/schemas/command.schema.json +68 -0
  617. package/src/apothem/schemas/compatibility-matrix.yaml +432 -0
  618. package/src/apothem/schemas/context-fragment.schema.json +64 -0
  619. package/src/apothem/schemas/freshness-token-denylist.txt +51 -0
  620. package/src/apothem/schemas/handoff-manifest.yaml +353 -0
  621. package/src/apothem/schemas/header-exceptions.txt +141 -0
  622. package/src/apothem/schemas/header-visibility.yaml +39 -0
  623. package/src/apothem/schemas/learning-signal.schema.json +46 -0
  624. package/src/apothem/schemas/memory-record.schema.json +61 -0
  625. package/src/apothem/schemas/output-style.schema.json +40 -0
  626. package/src/apothem/schemas/plan.schema.json +51 -0
  627. package/src/apothem/schemas/plugin.schema.json +83 -0
  628. package/src/apothem/schemas/profile.example.yaml +70 -0
  629. package/src/apothem/schemas/profile.minimal.yaml +6 -0
  630. package/src/apothem/schemas/profile.schema.json +396 -0
  631. package/src/apothem/schemas/reference-token-denylist.txt +25 -0
  632. package/src/apothem/schemas/skill.schema.json +75 -0
  633. package/src/apothem/skills/README.md +93 -0
  634. package/src/apothem/skills/dependency-upgrade/SKILL.md +105 -0
  635. package/src/apothem/skills/dev-toolkit/SKILL.md +120 -0
  636. package/src/apothem/skills/diagram-authoring/SKILL.md +113 -0
  637. package/src/apothem/skills/document-authoring/SKILL.md +118 -0
  638. package/src/apothem/skills/ecosystem-audit/SKILL.md +108 -0
  639. package/src/apothem/skills/ecosystem-audit/references/audit-fortress.md +85 -0
  640. package/src/apothem/skills/ecosystem-audit/references/procedure.md +162 -0
  641. package/src/apothem/skills/eval-harness/SKILL.md +88 -0
  642. package/src/apothem/skills/incident-runbook/SKILL.md +92 -0
  643. package/src/apothem/skills/multi-source-research/SKILL.md +90 -0
  644. package/src/apothem/skills/plan-suite/SKILL.md +118 -0
  645. package/src/apothem/skills/plan-suite/master_template.md +1324 -0
  646. package/src/apothem/skills/projectify/SKILL.md +117 -0
  647. package/src/apothem/skills/prompt-engineering/SKILL.md +122 -0
  648. package/src/apothem/skills/refactor-extract/SKILL.md +85 -0
  649. package/src/apothem/skills/research-suite/SKILL.md +170 -0
  650. package/src/apothem/skills/research-suite/references/directory-structure.md +47 -0
  651. package/src/apothem/skills/research-suite/references/lifecycle.md +67 -0
  652. package/src/apothem/skills/research-suite/references/principal-investigator-framework.md +37 -0
  653. package/src/apothem/skills/research-suite/references/rigor-mandates.md +30 -0
  654. package/src/apothem/skills/research-suite/research_template.md +476 -0
  655. package/src/apothem/skills/secret-rotation/SKILL.md +87 -0
  656. package/src/apothem/skills/source-synthesis/SKILL.md +92 -0
  657. package/src/apothem/skills/surgical-guard/SKILL.md +118 -0
  658. package/src/apothem/skills/test-authoring/SKILL.md +85 -0
  659. package/src/apothem/skills/vuln-triage/SKILL.md +91 -0
  660. package/src/apothem/skills/workflow/SKILL.md +139 -0
  661. package/src/apothem/statuslines/README.md +26 -0
  662. package/src/apothem/statuslines/__init__.py +20 -0
  663. package/src/apothem/statuslines/conformity.json +5 -0
  664. package/src/apothem/statuslines/render.py +334 -0
  665. package/src/apothem/statuslines/statusline.md +50 -0
  666. package/src/apothem/templates/README.md +43 -0
  667. package/src/apothem/templates/agents-md-template.md +80 -0
  668. package/src/apothem/templates/consideration-log.md +39 -0
  669. package/src/apothem/templates/expertise-gap-log.md +56 -0
  670. package/src/apothem/templates/master-index-template.md +93 -0
  671. package/src/apothem/templates/potency-map.md +53 -0
  672. package/src/apothem/templates/preservation-audit.md +60 -0
  673. package/src/apothem/templates/question-resolution-audit.md +52 -0
  674. package/src/apothem/templates/trace-matrix-template.md +77 -0
@@ -0,0 +1,386 @@
1
+ # SPDX-License-Identifier: MIT
2
+
3
+ """Validate frontmatter VALUES against the per-class JSON Schema enum/pattern constraints.
4
+
5
+ Why this validator exists. The sibling ``frontmatter_grep`` matcher checks
6
+ that an artifact carries the required frontmatter *keys* (and that the keys are
7
+ kebab-case); it deliberately does not parse or constrain the *values* — and it
8
+ rejects camelCase keys, so it is not run against the agent corpus whose schema
9
+ declares camelCase optional fields (``permissionMode``, ``disallowedTools``,
10
+ ``maxTurns``, …). The doc-example test ``tests/unit/docs/test_frontmatter_examples.py``
11
+ checks documented example *keys* against the shipped-agent key union, not the
12
+ values either. The result is a real gap: nothing enforced that an enum-
13
+ constrained value stayed inside its enum. Every shipped agent carried
14
+ ``permissionMode: "ask"`` for an extended period even though ``ask`` is not in
15
+ the schema's ``permissionMode`` enum
16
+ (``["default", "acceptEdits", "auto", "dontAsk", "bypassPermissions", "plan"]``,
17
+ mirroring the Claude Code vendor canon) — the drift went undetected because no
18
+ gate enforced enum values. This validator closes that gap.
19
+
20
+ What it checks. For each governed artifact class it loads the class's JSON
21
+ Schema from the ``schemas/`` sibling and, for every property that declares a
22
+ value constraint — an ``enum`` and/or a ``pattern``, directly or inside a
23
+ ``oneOf`` / ``anyOf`` branch — validates that the artifact's frontmatter value
24
+ satisfies the constraint. The governed classes and their schemas:
25
+
26
+ - ``agents`` → ``agent.schema.json`` (enums: ``permissionMode``, ``effort``,
27
+ ``isolation``, ``color``, and the ``memory`` ``oneOf`` string-enum/boolean;
28
+ patterns: ``name``, ``version``, ``updated``).
29
+ - ``commands`` → ``command.schema.json`` (patterns: ``name``, ``version``,
30
+ ``updated``). ``additionalProperties: false``, but key/required validation is
31
+ owned by ``frontmatter_grep`` and the doc-example test — this validator adds
32
+ the value-level pattern enforcement those surfaces lack.
33
+ - ``skills`` → ``skill.schema.json`` (enum: ``effort``; patterns: ``name``,
34
+ ``version``, ``updated``, ``archetype``).
35
+
36
+ Scope boundary. This validator is value-only and schema-driven: it never
37
+ hardcodes a field list (a new enum/pattern property added to a schema is picked
38
+ up automatically), and it raises no finding for a *missing* key or an *absent*
39
+ frontmatter block — presence is owned by ``frontmatter_grep``. Type / required /
40
+ ``additionalProperties`` / ``maxLength`` enforcement are deliberately out of
41
+ scope here; only ``enum`` and ``pattern`` value constraints are checked, which is
42
+ exactly the class of drift the documented gap names. A frontmatter block that
43
+ does not parse as a YAML mapping is skipped (its parse failure is a
44
+ ``frontmatter_grep`` concern), so every finding this validator emits is an
45
+ enum/pattern value violation a fix can clear.
46
+
47
+ Detection. For each class, glob the corpus under ``root`` (``src/apothem/
48
+ agents/*.md``, ``src/apothem/commands/*.md``, ``src/apothem/skills/*/SKILL.md``),
49
+ extract the leading ``---``-delimited frontmatter block (tolerating an optional
50
+ leading HTML-comment banner per the sibling-convention), parse it with PyYAML,
51
+ and validate each constraint-bearing property present in the mapping.
52
+
53
+ Exit semantics. Exits 0 when every governed artifact's constrained values
54
+ satisfy their schema, OR when no governed artifact is present under ``root``
55
+ (an installed tree with no source cohort). Exits 2 on any enum/pattern value
56
+ violation. The exit-2 convention matches the conformity-gate orchestrator's
57
+ ``EXIT_FAIL``; the gate runs this validator (blocking, like
58
+ ``agent_capability_grep``) via subprocess in ``--all`` mode.
59
+ """
60
+
61
+ from __future__ import annotations
62
+
63
+ import json
64
+ import re
65
+ import sys
66
+ from dataclasses import asdict, dataclass, field
67
+ from pathlib import Path
68
+ from typing import Any, Final
69
+
70
+ import yaml
71
+
72
+ GREP_NAME: Final[str] = "frontmatter-value-grep"
73
+ RULE_ANCHOR: Final[str] = "per-class JSON Schema enum/pattern value constraints"
74
+
75
+ EXIT_PASS: Final[int] = 0
76
+ EXIT_FAIL: Final[int] = 2
77
+
78
+ # Schema/data files ride beside the conformity package in both the repo
79
+ # checkout (``src/apothem/{conformity,schemas}``) and the installed tree
80
+ # (``<install-root>/apothem/{conformity,schemas}``). Resolve one parent hop
81
+ # above this module so the same code finds its schemas in both shapes — the
82
+ # dual-shape anchor convention shared with ``file_header_grep`` /
83
+ # ``reference_token_grep`` and asserted by
84
+ # ``tests/conformity/test_schema_anchor_resolution.py``.
85
+ SCHEMAS_DIR: Final[Path] = Path(__file__).resolve().parents[1] / "schemas"
86
+
87
+ FRONTMATTER_DELIMITER: Final[str] = "---"
88
+
89
+ # Governed artifact classes: (class, schema filename, corpus glob under root).
90
+ # Schema-driven — the constrained properties are read from each schema's
91
+ # ``properties`` block, never hardcoded here, so a new enum/pattern property
92
+ # added to a schema is enforced without editing this validator.
93
+ _COHORTS: Final[tuple[tuple[str, str, str], ...]] = (
94
+ ("agents", "agent.schema.json", "src/apothem/agents/*.md"),
95
+ ("commands", "command.schema.json", "src/apothem/commands/*.md"),
96
+ ("skills", "skill.schema.json", "src/apothem/skills/*/SKILL.md"),
97
+ )
98
+
99
+ # JSON Schema ``type`` -> the Python type(s) a conforming value carries. Only
100
+ # the types that appear in the governed schemas need exact handling; ``integer``
101
+ # and ``boolean`` need the bool/int disambiguation Python's ``isinstance``
102
+ # otherwise blurs (``bool`` is a subclass of ``int``).
103
+ _JSON_SCALAR_TYPES: Final[frozenset[str]] = frozenset(
104
+ {"string", "boolean", "integer", "number", "array", "object", "null"}
105
+ )
106
+
107
+
108
+ @dataclass(frozen=True)
109
+ class Finding:
110
+ """One frontmatter value that violates its schema enum/pattern constraint."""
111
+
112
+ surface: str
113
+ artifact_class: str
114
+ key: str
115
+ detail: str
116
+ rule: str = RULE_ANCHOR
117
+
118
+
119
+ @dataclass(frozen=True)
120
+ class GrepResult:
121
+ """Aggregated walk result for one corpus sweep."""
122
+
123
+ grep: str
124
+ root: str
125
+ files_inspected: int
126
+ passed: bool
127
+ informational: str | None = None
128
+ findings: list[Finding] = field(default_factory=list)
129
+
130
+ def to_json(self) -> str:
131
+ payload = {
132
+ "grep": self.grep,
133
+ "root": self.root,
134
+ "files_inspected": self.files_inspected,
135
+ "passed": self.passed,
136
+ "informational": self.informational,
137
+ "findings": [asdict(f) for f in self.findings],
138
+ }
139
+ return json.dumps(payload, indent=2)
140
+
141
+
142
+ def _extract_frontmatter(content: str) -> str | None:
143
+ """Return the leading ``---``-delimited YAML block, or None when absent.
144
+
145
+ Mirrors the sibling-convention extractor: tolerate a leading region of
146
+ blank lines plus one optional HTML-comment banner before the opening
147
+ ``---`` delimiter, then return the text between the opening and the next
148
+ ``---`` line. The governed cohorts place frontmatter first; the optional
149
+ leading-comment tolerance keeps the extractor robust to the
150
+ banner-then-frontmatter ordering some surfaces use.
151
+ """
152
+ lines = content.splitlines()
153
+ index = 0
154
+
155
+ while index < len(lines) and not lines[index].strip():
156
+ index += 1
157
+
158
+ if index < len(lines) and lines[index].lstrip().startswith("<!--"):
159
+ first = lines[index].strip()
160
+ if first.endswith("-->") and first != "<!--":
161
+ index += 1
162
+ else:
163
+ index += 1
164
+ while index < len(lines) and not lines[index].strip().endswith("-->"):
165
+ index += 1
166
+ if index < len(lines):
167
+ index += 1
168
+
169
+ while index < len(lines) and not lines[index].strip():
170
+ index += 1
171
+
172
+ if index >= len(lines) or lines[index].strip() != FRONTMATTER_DELIMITER:
173
+ return None
174
+
175
+ open_index = index
176
+ for close_index in range(open_index + 1, len(lines)):
177
+ if lines[close_index].strip() == FRONTMATTER_DELIMITER:
178
+ return "\n".join(lines[open_index + 1 : close_index])
179
+ return None
180
+
181
+
182
+ def _branches(prop_schema: dict[str, Any]) -> list[dict[str, Any]]:
183
+ """Return a property's alternative schemas: its ``oneOf`` / ``anyOf`` branch
184
+ list, or ``[prop_schema]`` when the property is a single un-branched schema.
185
+ A value is conforming when it satisfies at least one alternative."""
186
+ for combinator in ("oneOf", "anyOf"):
187
+ branches = prop_schema.get(combinator)
188
+ if isinstance(branches, list):
189
+ return [b for b in branches if isinstance(b, dict)]
190
+ return [prop_schema]
191
+
192
+
193
+ def _carries_value_constraint(prop_schema: dict[str, Any]) -> bool:
194
+ """True iff the property declares an ``enum`` or ``pattern`` in any branch."""
195
+ return any(
196
+ ("enum" in branch or "pattern" in branch) for branch in _branches(prop_schema)
197
+ )
198
+
199
+
200
+ def _type_matches(value: Any, json_type: str) -> bool: # noqa: ANN401 - duck-typed YAML scalar
201
+ """True iff *value* satisfies the JSON Schema scalar ``type``.
202
+
203
+ Disambiguates ``bool`` from ``int``/``number`` (a Python ``bool`` is an
204
+ ``int`` subclass, but JSON treats them as distinct types). Unknown types are
205
+ not constrained (return True) so a future schema type never fail-closes.
206
+ """
207
+ if json_type not in _JSON_SCALAR_TYPES:
208
+ return True
209
+ if json_type == "boolean":
210
+ return isinstance(value, bool)
211
+ if json_type == "integer":
212
+ return isinstance(value, int) and not isinstance(value, bool)
213
+ if json_type == "number":
214
+ return isinstance(value, (int, float)) and not isinstance(value, bool)
215
+ if json_type == "string":
216
+ return isinstance(value, str)
217
+ if json_type == "array":
218
+ return isinstance(value, list)
219
+ if json_type == "object":
220
+ return isinstance(value, dict)
221
+ return value is None # "null"
222
+
223
+
224
+ def _branch_accepts(value: Any, branch: dict[str, Any]) -> bool: # noqa: ANN401 - duck-typed YAML scalar
225
+ """True iff *value* satisfies one branch's type + enum + pattern constraints."""
226
+ json_type = branch.get("type")
227
+ if isinstance(json_type, str) and not _type_matches(value, json_type):
228
+ return False
229
+ enum = branch.get("enum")
230
+ if isinstance(enum, list) and value not in enum:
231
+ return False
232
+ pattern = branch.get("pattern")
233
+ # JSON Schema ``pattern`` is an unanchored search; the governed schemas all
234
+ # carry their own ``^...$`` anchors, so search == full match here.
235
+ if isinstance(pattern, str):
236
+ return isinstance(value, str) and re.search(pattern, value) is not None
237
+ return True
238
+
239
+
240
+ def _value_valid(value: Any, prop_schema: dict[str, Any]) -> bool: # noqa: ANN401 - duck-typed YAML scalar
241
+ """True iff *value* satisfies at least one of the property's alternatives."""
242
+ return any(_branch_accepts(value, branch) for branch in _branches(prop_schema))
243
+
244
+
245
+ def _expected_summary(prop_schema: dict[str, Any]) -> str:
246
+ """Human-readable summary of a property's accepted forms, for the finding."""
247
+ parts: list[str] = []
248
+ for branch in _branches(prop_schema):
249
+ enum = branch.get("enum")
250
+ pattern = branch.get("pattern")
251
+ if isinstance(enum, list):
252
+ parts.append("one of " + ", ".join(repr(v) for v in enum))
253
+ if isinstance(pattern, str):
254
+ parts.append(f"a string matching /{pattern}/")
255
+ if enum is None and pattern is None and isinstance(branch.get("type"), str):
256
+ parts.append(f"a {branch['type']}")
257
+ return " or ".join(parts) if parts else "a schema-conformant value"
258
+
259
+
260
+ def _load_value_constraints(schema_path: Path) -> dict[str, dict[str, Any]]:
261
+ """Return ``{property: schema}`` for every constraint-bearing property.
262
+
263
+ A missing or unparseable schema yields an empty constraint map (the cohort
264
+ is then skipped with no findings) rather than fail-closing the whole sweep.
265
+ """
266
+ try:
267
+ raw = schema_path.read_text(encoding="utf-8")
268
+ except OSError:
269
+ return {}
270
+ try:
271
+ schema = json.loads(raw)
272
+ except json.JSONDecodeError:
273
+ return {}
274
+ properties = schema.get("properties") if isinstance(schema, dict) else None
275
+ if not isinstance(properties, dict):
276
+ return {}
277
+ return {
278
+ name: prop
279
+ for name, prop in properties.items()
280
+ if isinstance(prop, dict) and _carries_value_constraint(prop)
281
+ }
282
+
283
+
284
+ def _check_file(
285
+ path: Path,
286
+ root: Path,
287
+ artifact_class: str,
288
+ constraints: dict[str, dict[str, Any]],
289
+ ) -> tuple[bool, list[Finding]]:
290
+ """Validate one artifact file's constrained frontmatter values.
291
+
292
+ Returns ``(inspected, findings)``: ``inspected`` is True when the file
293
+ carried a parseable frontmatter mapping (and was therefore value-checked).
294
+ A file with no frontmatter block, or a block that does not parse to a
295
+ mapping, is not inspected and contributes no findings — presence and parse
296
+ integrity are owned by ``frontmatter_grep``.
297
+ """
298
+ try:
299
+ content = path.read_text(encoding="utf-8")
300
+ except (OSError, UnicodeDecodeError):
301
+ return False, []
302
+ block = _extract_frontmatter(content)
303
+ if block is None:
304
+ return False, []
305
+ try:
306
+ parsed = yaml.safe_load(block)
307
+ except yaml.YAMLError:
308
+ return False, []
309
+ if not isinstance(parsed, dict):
310
+ return False, []
311
+
312
+ try:
313
+ surface = str(path.relative_to(root))
314
+ except ValueError:
315
+ surface = str(path)
316
+
317
+ findings: list[Finding] = []
318
+ for key, prop_schema in constraints.items():
319
+ if key not in parsed:
320
+ continue
321
+ value = parsed[key]
322
+ if _value_valid(value, prop_schema):
323
+ continue
324
+ findings.append(
325
+ Finding(
326
+ surface=surface,
327
+ artifact_class=artifact_class,
328
+ key=key,
329
+ detail=(
330
+ f"{key!r} value {value!r} violates the {artifact_class} schema: "
331
+ f"expected {_expected_summary(prop_schema)}"
332
+ ),
333
+ )
334
+ )
335
+ return True, findings
336
+
337
+
338
+ def check(root: Path) -> GrepResult:
339
+ """Walk every governed cohort under *root*; flag enum/pattern value violations."""
340
+ findings: list[Finding] = []
341
+ files_inspected = 0
342
+ for artifact_class, schema_filename, glob_pattern in _COHORTS:
343
+ constraints = _load_value_constraints(SCHEMAS_DIR / schema_filename)
344
+ if not constraints:
345
+ continue
346
+ for path in sorted(root.glob(glob_pattern)):
347
+ if not path.is_file():
348
+ continue
349
+ inspected, file_findings = _check_file(
350
+ path, root, artifact_class, constraints
351
+ )
352
+ if inspected:
353
+ files_inspected += 1
354
+ findings.extend(file_findings)
355
+
356
+ informational: str | None = None
357
+ if files_inspected == 0:
358
+ informational = (
359
+ "no governed artifact (agent / command / skill) carrying frontmatter "
360
+ f"found under {root}; validator is in an absence-tolerant pass"
361
+ )
362
+ return GrepResult(
363
+ grep=GREP_NAME,
364
+ root=str(root),
365
+ files_inspected=files_inspected,
366
+ passed=not findings,
367
+ informational=informational,
368
+ findings=findings,
369
+ )
370
+
371
+
372
+ def _read_input(argv: list[str]) -> Path:
373
+ if len(argv) >= 2:
374
+ return Path(argv[1])
375
+ return Path.cwd()
376
+
377
+
378
+ def _main(argv: list[str]) -> int:
379
+ root = _read_input(argv)
380
+ result = check(root)
381
+ print(result.to_json())
382
+ return EXIT_PASS if result.passed else EXIT_FAIL
383
+
384
+
385
+ if __name__ == "__main__":
386
+ sys.exit(_main(sys.argv))