@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 +1,233 @@
1
+ # SPDX-License-Identifier: MIT
2
+
3
+ """Flag freshness-narrative phrases on shipped public surfaces.
4
+
5
+ Why this enforcement exists. The freshness-facade rule
6
+ (``rules/freshness-facade.md``) keeps every shipped public surface a
7
+ current-version-only facade: no AI-disclosure, no backward / legacy /
8
+ obsolete replacement narrative, no placeholder / deferral, no
9
+ fix-and-refinement story-of-becoming. This matcher is the freshness analogue
10
+ of ``plain_language_grep`` — a distinct, non-overlapping token-class on the same
11
+ shipped-surface scope. ``plain_language_grep`` forbids mechanistic vocabulary
12
+ (``AI`` / ``agent`` / harness brands); this matcher forbids the narrative
13
+ PHRASES that mark a surface telling the story of its own becoming.
14
+
15
+ High-precision PHRASES, never bare words. Bare common words — ``legacy``,
16
+ ``deprecated``, ``retired``, ``placeholder``, ``backward`` — have legitimate
17
+ uses (a Keep-a-Changelog ``Deprecated`` heading, a documented deprecation
18
+ policy, a ``placeholder identity`` product feature) and are deliberately NOT
19
+ denylisted. Only the narrative phrase forms ("replaces the legacy …",
20
+ "coming soon", "AI-generated") are flagged, so the matcher catches the
21
+ story-of-becoming without flagging the dictionary word. The forbidden phrases
22
+ live in the package-relative denylist data file, never in this module.
23
+
24
+ Scope. Corpus-level standalone validator. Walks the working tree under the
25
+ supplied root and inspects ONLY shipped public surfaces: the repository
26
+ root ``README.md`` and every ``*.md`` / ``*.mdx`` under
27
+ ``site/content/docs/``. Developer-only surfaces (rules, commands,
28
+ matchers, plans, adapter modules) are out of scope — their process
29
+ vocabulary is load-bearing, exactly as the plain-language boundary draws it.
30
+
31
+ Detection. Each denylist phrase is matched case-insensitively. Pure-alpha
32
+ phrases anchor at word boundaries; punctuation- or space-bearing phrases
33
+ match as escaped literals. Matches inside fenced code blocks (triple
34
+ backtick) are excluded — docs legitimately quote a forbidden phrase inside a
35
+ sample or tool-output fence.
36
+
37
+ Posture. The result carries an advisory flag, honoring apothem's agnostic
38
+ gate posture; CI opts into strict enforcement separately. Exits 0 when zero
39
+ findings across every in-scope file; exits 2 on any finding.
40
+ """
41
+
42
+ from __future__ import annotations
43
+
44
+ import json
45
+ import re
46
+ import sys
47
+ from dataclasses import asdict, dataclass, field
48
+ from pathlib import Path
49
+ from typing import Final
50
+
51
+ GREP_NAME: Final[str] = "freshness-token-grep"
52
+ RULE_ANCHOR: Final[str] = "rules/freshness-facade.md"
53
+
54
+ EXIT_PASS: Final[int] = 0
55
+ EXIT_FAIL: Final[int] = 2
56
+
57
+ # The denylist data file is package-relative: the conformity package ships
58
+ # beside its ``schemas/`` sibling in both the repo checkout
59
+ # (``src/apothem/{conformity,schemas}``) and the installed tree, so one parent
60
+ # hop reaches it in either shape. The data file holds the forbidden phrases so
61
+ # this module never names them.
62
+ _DENYLIST_PATH: Final[Path] = (
63
+ Path(__file__).resolve().parents[1] / "schemas" / "freshness-token-denylist.txt"
64
+ )
65
+
66
+ # Shipped-surface scope. The root README and the documentation tree are the
67
+ # user-facing release facade the freshness mandate holds to the current-version
68
+ # bar.
69
+ _README_FILENAME: Final[str] = "README.md"
70
+ _DOCS_DIR: Final[str] = "site/content/docs"
71
+ _TEXT_SUFFIXES: Final[frozenset[str]] = frozenset({".md", ".mdx"})
72
+
73
+ # Fenced code-block delimiter — a line whose first non-whitespace content is
74
+ # ```. Opening and closing fences both match; the scanner toggles state.
75
+ _CODE_FENCE_RE: Final[re.Pattern[str]] = re.compile(r"^[ \t]*```")
76
+
77
+
78
+ @dataclass(frozen=True)
79
+ class Finding:
80
+ """One freshness-narrative phrase on a shipped public surface."""
81
+
82
+ surface: str
83
+ kind: str
84
+ detail: str
85
+ rule: str = RULE_ANCHOR
86
+
87
+
88
+ @dataclass(frozen=True)
89
+ class GrepResult:
90
+ """Aggregated walk result for a single corpus sweep."""
91
+
92
+ grep: str
93
+ root: str
94
+ files_inspected: int
95
+ passed: bool
96
+ findings: list[Finding] = field(default_factory=list)
97
+
98
+ def to_json(self) -> str:
99
+ payload = {
100
+ "grep": self.grep,
101
+ "root": self.root,
102
+ "files_inspected": self.files_inspected,
103
+ "passed": self.passed,
104
+ "findings": [asdict(f) for f in self.findings],
105
+ "advisory": True,
106
+ }
107
+ return json.dumps(payload, indent=2)
108
+
109
+
110
+ def _load_tokens() -> list[str]:
111
+ """Parse the denylist data file into a list of forbidden phrases.
112
+
113
+ Pre-conditions: the package-relative denylist file exists.
114
+ Post-conditions: returns every non-empty, non-comment line, stripped.
115
+ """
116
+ try:
117
+ raw = _DENYLIST_PATH.read_text(encoding="utf-8")
118
+ except OSError:
119
+ return []
120
+ tokens: list[str] = []
121
+ for line in raw.splitlines():
122
+ stripped = line.strip()
123
+ if not stripped or stripped.startswith("#"):
124
+ continue
125
+ tokens.append(stripped)
126
+ return tokens
127
+
128
+
129
+ def _compile_tokens(tokens: list[str]) -> re.Pattern[str] | None:
130
+ """Compile the denylist into one case-insensitive alternation regex.
131
+
132
+ Pure-alphabetic phrases anchor at word boundaries (``\\bphrase\\b``) so a
133
+ larger word is not flagged. Space- or punctuation-bearing phrases are
134
+ escaped literals — word boundaries do not apply cleanly across spaces and
135
+ ``-`` characters. Returns None when the denylist is empty. Longer phrases
136
+ are ordered first so the alternation prefers the most specific match.
137
+ """
138
+ if not tokens:
139
+ return None
140
+ alternatives: list[str] = []
141
+ for token in sorted(tokens, key=len, reverse=True):
142
+ if token.isalpha():
143
+ alternatives.append(r"\b" + re.escape(token) + r"\b")
144
+ else:
145
+ alternatives.append(re.escape(token))
146
+ return re.compile(r"(?i)(?:" + "|".join(alternatives) + r")")
147
+
148
+
149
+ def _is_in_scope(rel_posix: str) -> bool:
150
+ """Return True iff a relative POSIX path is a shipped public surface.
151
+
152
+ In scope: the repository root ``README.md`` and any ``.md`` / ``.mdx``
153
+ under ``site/content/docs/``. Every other path is out of scope.
154
+ """
155
+ if rel_posix == _README_FILENAME:
156
+ return True
157
+ return rel_posix.startswith(_DOCS_DIR + "/")
158
+
159
+
160
+ def _scan_file(path: Path, rel_posix: str, pattern: re.Pattern[str]) -> list[Finding]:
161
+ """Scan one text file; return findings outside fenced code blocks."""
162
+ try:
163
+ content = path.read_text(encoding="utf-8")
164
+ except (OSError, UnicodeDecodeError):
165
+ return []
166
+ findings: list[Finding] = []
167
+ inside_fence = False
168
+ for line_index, line in enumerate(content.splitlines(), start=1):
169
+ if _CODE_FENCE_RE.match(line):
170
+ inside_fence = not inside_fence
171
+ continue
172
+ if inside_fence:
173
+ continue
174
+ for match in pattern.finditer(line):
175
+ findings.append(
176
+ Finding(
177
+ surface=rel_posix,
178
+ kind="freshness-token",
179
+ detail=f"line {line_index}: '{match.group()}'",
180
+ )
181
+ )
182
+ return findings
183
+
184
+
185
+ def check(root: Path) -> GrepResult:
186
+ """Walk the corpus under ``root``; flag freshness-narrative phrases.
187
+
188
+ Pre-conditions: ``root`` is the repository root (or an arbitrary subtree).
189
+ Post-conditions: ``result.passed`` is True iff every shipped public
190
+ surface contained zero denylisted phrases outside fenced code blocks.
191
+ """
192
+ tokens = _load_tokens()
193
+ pattern = _compile_tokens(tokens)
194
+ findings: list[Finding] = []
195
+ inspected = 0
196
+ root_resolved = root.resolve()
197
+ if pattern is not None:
198
+ for suffix in sorted(_TEXT_SUFFIXES):
199
+ for path in root.rglob(f"*{suffix}"):
200
+ if not path.is_file():
201
+ continue
202
+ try:
203
+ rel_posix = path.resolve().relative_to(root_resolved).as_posix()
204
+ except ValueError:
205
+ continue
206
+ if not _is_in_scope(rel_posix):
207
+ continue
208
+ inspected += 1
209
+ findings.extend(_scan_file(path, rel_posix, pattern))
210
+ return GrepResult(
211
+ grep=GREP_NAME,
212
+ root=str(root),
213
+ files_inspected=inspected,
214
+ passed=not findings,
215
+ findings=findings,
216
+ )
217
+
218
+
219
+ def _read_input(argv: list[str]) -> Path:
220
+ if len(argv) >= 2:
221
+ return Path(argv[1])
222
+ return Path.cwd()
223
+
224
+
225
+ def _main(argv: list[str]) -> int:
226
+ root = _read_input(argv)
227
+ result = check(root)
228
+ print(result.to_json())
229
+ return EXIT_PASS if result.passed else EXIT_FAIL
230
+
231
+
232
+ if __name__ == "__main__":
233
+ sys.exit(_main(sys.argv))
@@ -0,0 +1,274 @@
1
+ # SPDX-License-Identifier: MIT
2
+
3
+ """Validate per-artifact-class YAML frontmatter against required-key sets.
4
+
5
+ Why this enforcement exists. Spec section 4.2 ratifies that every
6
+ artifact carries YAML frontmatter delimited by ``---`` lines, with
7
+ required-key sets that vary per artifact class (rules, agents, skills,
8
+ commands, output styles each carry their own minimum schema). This
9
+ validator extends the grep family with frontmatter checks; per-class
10
+ JSON Schemas feed this validator's strict-mode.
11
+
12
+ Detection strategy. The validator reads a file, locates the leading
13
+ ``---``-delimited frontmatter block, parses the YAML, and checks the
14
+ required-key set for the inferred artifact class (inferred by the
15
+ file's path under rules/, agents/, skills/, commands/, output-styles/).
16
+ A missing required key, an unparseable YAML block, or an absent
17
+ frontmatter block on a class that requires one is a finding. Frontmatter
18
+ keys must use kebab-case per spec section 4.1; non-kebab-case keys are
19
+ flagged. Schema-presence-driven strict-mode activates when per-class
20
+ JSON Schemas exist at ``frontmatter/<class>.json`` inside the
21
+ ``schemas/`` directory shipped beside this package (one parent hop above
22
+ this module in both the repo-checkout and installed layouts); until then
23
+ the validator runs the baseline required-key check.
24
+ """
25
+
26
+ from __future__ import annotations
27
+
28
+ import json
29
+ import re
30
+ import sys
31
+ from dataclasses import asdict, dataclass, field
32
+ from pathlib import Path
33
+ from typing import Final
34
+
35
+ # Required-key sets per artifact class, derived from the canonical
36
+ # frontmatter schema declared at site/content/docs/reference/frontmatter-schema.mdx and the
37
+ # minimum schemas observed across the rules/ + agents/ + skills/ +
38
+ # commands/ + output-styles/ corpora.
39
+ REQUIRED_KEYS: Final[dict[str, frozenset[str]]] = {
40
+ "rules": frozenset({"name", "description", "alwaysApply"}),
41
+ "agents": frozenset({"name", "description"}),
42
+ "skills": frozenset({"name", "description"}),
43
+ "commands": frozenset({"name", "description"}),
44
+ "output-styles": frozenset({"name", "description"}),
45
+ "hooks-messages": frozenset({"description"}),
46
+ }
47
+
48
+ # Kebab-case key shape per spec section 4.1. Frontmatter keys are
49
+ # matched against this regex; uppercase / underscore / camelCase keys
50
+ # are findings. The harness honors an explicit allow-list for keys
51
+ # that originated in pre-ratification artifacts and are preserved by
52
+ # sibling-convergence per host-discovery.
53
+ KEBAB_KEY_RE: Final[re.Pattern[str]] = re.compile(r"^[a-z][a-z0-9]*(?:-[a-z0-9]+)*$")
54
+ KEY_ALLOW_LIST: Final[frozenset[str]] = frozenset(
55
+ {
56
+ # Path-filter keys observed across rules/ predate the
57
+ # kebab-case ratification.
58
+ "pathFilter",
59
+ "alwaysApply",
60
+ # Argument-hint and disable-model-invocation surface inside
61
+ # commands frontmatter; both predate ratification.
62
+ "argument-hint",
63
+ "disable-model-invocation",
64
+ "allowed-tools",
65
+ # User-invocability flag on skills; camelCase predates the
66
+ # kebab-case ratification and is uniform across the skill corpus
67
+ # (preserved by sibling-convergence per host-discovery).
68
+ "userInvocable",
69
+ # Tools-list key on agents.
70
+ "tools",
71
+ "model",
72
+ }
73
+ )
74
+
75
+ FRONTMATTER_DELIMITER: Final[str] = "---"
76
+ GREP_NAME: Final[str] = "frontmatter-grep"
77
+ RULE_ANCHOR: Final[str] = (
78
+ "the per-class frontmatter JSON Schemas (src/apothem/schemas/)"
79
+ )
80
+ EXIT_PASS: Final[int] = 0
81
+ EXIT_FAIL: Final[int] = 2
82
+ STDIN_FLAG: Final[str] = "--stdin"
83
+
84
+
85
+ @dataclass(frozen=True)
86
+ class Finding:
87
+ detail: str
88
+ rule: str = RULE_ANCHOR
89
+
90
+
91
+ @dataclass(frozen=True)
92
+ class GrepResult:
93
+ grep: str
94
+ path: str | None
95
+ artifact_class: str | None
96
+ passed: bool
97
+ findings: list[Finding] = field(default_factory=list)
98
+
99
+ def to_json(self) -> str:
100
+ payload = {
101
+ "grep": self.grep,
102
+ "path": self.path,
103
+ "artifact-class": self.artifact_class,
104
+ "passed": self.passed,
105
+ "findings": [asdict(f) for f in self.findings],
106
+ }
107
+ return json.dumps(payload, indent=2)
108
+
109
+
110
+ def _infer_class(path: Path) -> str | None:
111
+ """Infer the artifact class from the path's top-level directory."""
112
+ parts = path.parts
113
+ if "rules" in parts:
114
+ return "rules"
115
+ if "agents" in parts:
116
+ return "agents"
117
+ if "skills" in parts:
118
+ return "skills"
119
+ if "commands" in parts:
120
+ return "commands"
121
+ if "output-styles" in parts:
122
+ return "output-styles"
123
+ if "hooks" in parts and "messages" in parts:
124
+ return "hooks-messages"
125
+ return None
126
+
127
+
128
+ def _extract_frontmatter(content: str) -> tuple[str | None, int]:
129
+ """Return (frontmatter-yaml, body-start-line) or (None, 0).
130
+
131
+ The established sibling-convention across commands/, agents/, skills/,
132
+ rules/, and output-styles/ places the canonical authorship-header
133
+ banner (an HTML comment block opened with ``<!--`` and closed with
134
+ ``-->``) before the YAML frontmatter, separated by a blank line. The
135
+ extractor therefore tolerates a leading region of blank lines plus
136
+ one optional HTML-comment block before locating the opening ``---``
137
+ delimiter. Within the comment region, the closing ``-->`` may sit on
138
+ its own line or share a line with trailing content; the extractor
139
+ advances past the first line whose stripped contents end with
140
+ ``-->``.
141
+ """
142
+ lines = content.splitlines()
143
+ index = 0
144
+
145
+ while index < len(lines) and not lines[index].strip():
146
+ index += 1
147
+
148
+ if index < len(lines) and lines[index].lstrip().startswith("<!--"):
149
+ first_comment_line = lines[index].strip()
150
+ if first_comment_line.endswith("-->") and first_comment_line != "<!--":
151
+ index += 1
152
+ else:
153
+ index += 1
154
+ while index < len(lines) and not lines[index].strip().endswith("-->"):
155
+ index += 1
156
+ if index < len(lines):
157
+ index += 1
158
+
159
+ while index < len(lines) and not lines[index].strip():
160
+ index += 1
161
+
162
+ if index >= len(lines) or lines[index].strip() != FRONTMATTER_DELIMITER:
163
+ return None, 0
164
+
165
+ open_index = index
166
+ for close_index in range(open_index + 1, len(lines)):
167
+ if lines[close_index].strip() == FRONTMATTER_DELIMITER:
168
+ return (
169
+ "\n".join(lines[open_index + 1 : close_index]),
170
+ close_index + 1,
171
+ )
172
+ return None, 0
173
+
174
+
175
+ def _parse_keys(yaml_block: str) -> list[str]:
176
+ """Extract top-level keys from the YAML block via line-shape parsing.
177
+
178
+ The validator does not depend on PyYAML; the frontmatter's surface
179
+ is shallow (top-level scalar keys plus the occasional list value)
180
+ and the shape can be read from the first column of each line. Keys
181
+ inside nested mappings or lists are intentionally excluded — only
182
+ top-level keys count toward the required-set check.
183
+ """
184
+ keys: list[str] = []
185
+ for raw in yaml_block.splitlines():
186
+ if not raw.strip() or raw.lstrip().startswith("#"):
187
+ continue
188
+ if raw[0].isspace() or raw.startswith("-"):
189
+ continue
190
+ if ":" not in raw:
191
+ continue
192
+ key = raw.split(":", 1)[0].strip()
193
+ if key:
194
+ keys.append(key)
195
+ return keys
196
+
197
+
198
+ def check(content: str, path: Path | None = None) -> GrepResult:
199
+ """Validate frontmatter for the inferred artifact class."""
200
+ findings: list[Finding] = []
201
+ artifact_class = _infer_class(path) if path is not None else None
202
+ yaml_block, _ = _extract_frontmatter(content)
203
+
204
+ if yaml_block is None:
205
+ if artifact_class is not None:
206
+ findings.append(
207
+ Finding(
208
+ detail=(
209
+ f"frontmatter block absent on artifact-class "
210
+ f"{artifact_class!r}; required by spec section 4.2"
211
+ )
212
+ )
213
+ )
214
+ return GrepResult(
215
+ grep=GREP_NAME,
216
+ path=str(path) if path is not None else None,
217
+ artifact_class=artifact_class,
218
+ passed=not findings,
219
+ findings=findings,
220
+ )
221
+
222
+ keys = _parse_keys(yaml_block)
223
+ keyset = set(keys)
224
+
225
+ if artifact_class is not None:
226
+ required = REQUIRED_KEYS.get(artifact_class, frozenset())
227
+ missing = required - keyset
228
+ for key in sorted(missing):
229
+ findings.append(
230
+ Finding(
231
+ detail=(
232
+ f"required key {key!r} missing from "
233
+ f"{artifact_class!r} frontmatter"
234
+ )
235
+ )
236
+ )
237
+
238
+ for key in keys:
239
+ if key in KEY_ALLOW_LIST:
240
+ continue
241
+ if not KEBAB_KEY_RE.match(key):
242
+ findings.append(
243
+ Finding(
244
+ detail=(
245
+ f"frontmatter key {key!r} is not kebab-case (spec section 4.1)"
246
+ )
247
+ )
248
+ )
249
+
250
+ return GrepResult(
251
+ grep=GREP_NAME,
252
+ path=str(path) if path is not None else None,
253
+ artifact_class=artifact_class,
254
+ passed=not findings,
255
+ findings=findings,
256
+ )
257
+
258
+
259
+ def _read_input(argv: list[str]) -> tuple[str, Path | None]:
260
+ if len(argv) >= 2 and argv[1] != STDIN_FLAG:
261
+ path = Path(argv[1])
262
+ return path.read_text(encoding="utf-8"), path
263
+ return sys.stdin.read(), None
264
+
265
+
266
+ def _main(argv: list[str]) -> int:
267
+ content, path = _read_input(argv)
268
+ result = check(content, path)
269
+ print(result.to_json())
270
+ return EXIT_PASS if result.passed else EXIT_FAIL
271
+
272
+
273
+ if __name__ == "__main__":
274
+ sys.exit(_main(sys.argv))