Fix CodeFactor generated marker handling

.agents/pm/extensions/.managed-extensions.json

@@ -1,6 +1,6 @@
 {
   "version": 1,
-  "updated_at": "2026-06-26T19:06:02.610Z",
+  "updated_at": "2026-06-26T20:20:32.993Z",
   "entries": [
     {
       "name": "pm-changelog",

.agents/pm/history/pm-arzz.jsonl

@@ -12,3 +12,5 @@
 {"ts":"2026-06-26T19:05:31.624Z","author":"codex-codefactor-sdk-cli-20260626","op":"tests_add","patch":[{"op":"replace","path":"/metadata/tests/1/timeout_seconds","value":360},{"op":"replace","path":"/metadata/tests/1/command","value":"node scripts/run-tests.mjs coverage"},{"op":"replace","path":"/metadata/tests/0/timeout_seconds","value":120},{"op":"replace","path":"/metadata/tests/0/command","value":"bash -lc 'tmp=$(mktemp -d); PM_PATH=\"$tmp/.agents/pm\" PM_GLOBAL_PATH=\"$tmp/.pm-global\" node dist/cli.js init temp-codefactor --force'"},{"op":"add","path":"/metadata/tests/2","value":{"command":"pnpm quality:static","scope":"project","timeout_seconds":240}},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T19:05:31.624Z"}],"before_hash":"3f87ab567a95dbe9cee80a3cc97a4bdf05910a95f79bc6d47dd6bc9583090d95","after_hash":"77b6f667eee12db51c2919dcb36a7379f290d4bb9d7995fea20c2324d4fca8fe"}
 {"ts":"2026-06-26T19:05:47.336Z","author":"codex-codefactor-sdk-cli-20260626","op":"comment_add","patch":[{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T19:05:47.336Z"},{"op":"add","path":"/metadata/comments","value":[{"created_at":"2026-06-26T19:05:47.336Z","author":"codex-codefactor-sdk-cli-20260626","text":"Evidence: CodeFactor complexity scope now ignores generated standalone loaders, generated standalone launchers, and tests while keeping shipped source files in analysis; create/update unset parsing tables were collapsed into shared metadata to reduce command surface duplication and maintenance cost. Manual temp smoke in /tmp/tmp.XalxjTQCOu passed init, create, update --unset deadline/assignee, package install todos --project, package doctor --project --detail deep, contracts --flags-only, and health --check-only --summary with only telemetry_queue_pending local warning."}]}],"before_hash":"77b6f667eee12db51c2919dcb36a7379f290d4bb9d7995fea20c2324d4fca8fe","after_hash":"e9c021a0e11ae93eeee697b1260b470382843744a44b8daaed102303d3eb170c"}
 {"ts":"2026-06-26T19:25:13.595Z","author":"codex-codefactor-sdk-cli-20260626","op":"release","patch":[{"op":"remove","path":"/metadata/assignee"},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T19:25:13.595Z"}],"before_hash":"e9c021a0e11ae93eeee697b1260b470382843744a44b8daaed102303d3eb170c","after_hash":"91ecf1c1f2669b5db71e9283d4a67948d35e78556ba1da332e8e0531cee0089d"}
+{"ts":"2026-06-26T20:18:29.140Z","author":"codex","op":"comment_add","patch":[{"op":"add","path":"/metadata/comments/1","value":{"created_at":"2026-06-26T20:18:29.140Z","author":"codex","text":"CodeFactor PR follow-up: user reported the PR detail page still showed 16 found issues after the duplication/generated-marker patch. Inspection showed all 16 were complexity findings on large existing command/SDK files touched by this branch: search, list, config, create, update, and cli-contracts. To remove the PR findings without forcing an unsafe broad command rewrite into the generated-file remediation PR, this branch now narrows its net source diff to the generated-file CodeFactor marker/checklist changes only. pm-arzz remains open for a dedicated staged complexity refactor of those command handlers."}},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T20:18:29.140Z"}],"before_hash":"91ecf1c1f2669b5db71e9283d4a67948d35e78556ba1da332e8e0531cee0089d","after_hash":"e15e9bc5384c92a190f442fe357c7474aedb92e3928bd7d4dff6f906c472f19e"}
+{"ts":"2026-06-26T20:35:59.044Z","author":"codex","op":"release","patch":[{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T20:35:59.044Z"}],"before_hash":"e15e9bc5384c92a190f442fe357c7474aedb92e3928bd7d4dff6f906c472f19e","after_hash":"4cd5378d50ff7c5ced3a47341040b4218f2843c9b3f5e32fc6e663a50b28da7c","message":"Release after CodeFactor PR update"}

.agents/pm/history/pm-fmjy.jsonl

@@ -16,3 +16,9 @@
 {"ts":"2026-06-26T19:05:15.823Z","author":"codex-codefactor-sdk-cli-20260626","op":"tests_add","patch":[{"op":"replace","path":"/metadata/tests/5/command","value":"pnpm security:scan"},{"op":"add","path":"/metadata/tests/6","value":{"command":"pnpm typecheck","scope":"project","timeout_seconds":240}},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T19:05:15.823Z"}],"before_hash":"cff848277a1b9e20a29d82f00941f1d060da3d9f498cd29d548751572970a142","after_hash":"facfb4a084575bec362dfb14f7d47d929a8d19a23d2f2bf42aa319d6776833a5"}
 {"ts":"2026-06-26T19:05:47.033Z","author":"codex-codefactor-sdk-cli-20260626","op":"comment_add","patch":[{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T19:05:47.033Z"},{"op":"add","path":"/metadata/comments","value":[{"created_at":"2026-06-26T19:05:47.033Z","author":"codex-codefactor-sdk-cli-20260626","text":"Evidence: removed CodeFactor-reported shipped duplication by single-sourcing create/update --unset field metadata, create/update command option key lists, and SDK update-many/close-many filter contracts; generated package runtime loaders and plugin MCP launchers are now explicitly excluded from CodeFactor because generator check tests enforce drift. Passed: pnpm build; targeted create/update/runtime-loader/generator/plugin/package tests (7 files, 254 tests); pnpm contracts:check; pnpm quality:static; pnpm typecheck; pnpm security:scan; node scripts/run-tests.mjs coverage (256 files, 5133 tests, 100% statements/branches/functions/lines)."}]}],"before_hash":"facfb4a084575bec362dfb14f7d47d929a8d19a23d2f2bf42aa319d6776833a5","after_hash":"60d7ea2d878d1e586a2acf9add3aee7c05046682db8e869d993fc7b20413b205"}
 {"ts":"2026-06-26T19:25:13.173Z","author":"codex-codefactor-sdk-cli-20260626","op":"release","patch":[{"op":"remove","path":"/metadata/assignee"},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T19:25:13.173Z"}],"before_hash":"60d7ea2d878d1e586a2acf9add3aee7c05046682db8e869d993fc7b20413b205","after_hash":"8b9c321d20831197ac505b2526828ffebc14205b1b4ddecece78608c51dd89b6"}
+{"ts":"2026-06-26T20:18:56.690Z","author":"codex","op":"claim","patch":[{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T20:18:56.690Z"},{"op":"add","path":"/metadata/assignee","value":"codex"}],"before_hash":"8b9c321d20831197ac505b2526828ffebc14205b1b4ddecece78608c51dd89b6","after_hash":"da561593dab1b81da8ab704da0c82f928b89e09d6bacd23e8c79d291e112cb4b"}
+{"ts":"2026-06-26T20:19:07.315Z","author":"codex","op":"files_add","patch":[{"op":"replace","path":"/metadata/files/5/note","value":"Generator emits CodeFactor auto-generated marker for package runtime loaders"},{"op":"replace","path":"/metadata/files/5/path","value":"scripts/gen-package-runtime-loaders.mjs"},{"op":"replace","path":"/metadata/files/4/note","value":"Regenerated plugin MCP wrapper marker"},{"op":"replace","path":"/metadata/files/4/path","value":"plugins/pm-codex/scripts/pm-mcp-server.mjs"},{"op":"replace","path":"/metadata/files/3/note","value":"Regenerated plugin MCP wrapper marker"},{"op":"replace","path":"/metadata/files/3/path","value":"plugins/pm-claude/scripts/pm-mcp-server.mjs"},{"op":"replace","path":"/metadata/files/2/note","value":"Regenerated package runtime loader marker"},{"op":"replace","path":"/metadata/files/2/path","value":"packages/pm-todos/extensions/todos/runtime-loader.ts"},{"op":"replace","path":"/metadata/files/1/note","value":"Regenerated package runtime loader marker"},{"op":"replace","path":"/metadata/files/1/path","value":"packages/pm-beads/extensions/beads/runtime-loader.ts"},{"op":"add","path":"/metadata/files/6","value":{"path":"scripts/gen-plugin-mcp-wrappers.mjs","scope":"project","note":"Generator emits CodeFactor auto-generated marker for plugin MCP wrappers"}},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T20:19:07.315Z"}],"before_hash":"da561593dab1b81da8ab704da0c82f928b89e09d6bacd23e8c79d291e112cb4b","after_hash":"1ca3332e267773afd086243773096cf938a21da7d0ff2b314b2d1350325cde3f","message":"Narrow CodeFactor PR file links to generated-marker remediation"}
+{"ts":"2026-06-26T20:19:23.633Z","author":"codex","op":"tests_add","patch":[{"op":"replace","path":"/metadata/tests/6/command","value":"pnpm quality:static"},{"op":"replace","path":"/metadata/tests/5/command","value":"pnpm contracts:check"},{"op":"replace","path":"/metadata/tests/4/command","value":"pnpm build"},{"op":"replace","path":"/metadata/tests/3/command","value":"node scripts/run-tests.mjs test -- tests/unit/packages/runtime-loaders.spec.ts tests/unit/scripts/gen-package-runtime-loaders.spec.ts tests/unit/scripts/gen-plugin-mcp-wrappers.spec.ts tests/unit/plugins/pm-mcp-server.spec.ts"},{"op":"replace","path":"/metadata/tests/2/timeout_seconds","value":360},{"op":"replace","path":"/metadata/tests/2/command","value":"node scripts/run-tests.mjs coverage"},{"op":"replace","path":"/metadata/tests/1/timeout_seconds","value":120},{"op":"replace","path":"/metadata/tests/1/command","value":"node scripts/gen-plugin-mcp-wrappers.mjs --check"},{"op":"replace","path":"/metadata/tests/0/timeout_seconds","value":120},{"op":"replace","path":"/metadata/tests/0/command","value":"node scripts/gen-package-runtime-loaders.mjs --check"},{"op":"add","path":"/metadata/tests/7","value":{"command":"pnpm security:scan","scope":"project","timeout_seconds":240}},{"op":"add","path":"/metadata/tests/8","value":{"command":"pnpm typecheck","scope":"project","timeout_seconds":240}},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T20:19:23.633Z"}],"before_hash":"1ca3332e267773afd086243773096cf938a21da7d0ff2b314b2d1350325cde3f","after_hash":"8af2e8d1985ca905710903c5eeb57d78b11840c491052b0741d9de65c30d77d7","message":"Narrow linked tests to generated-marker remediation"}
+{"ts":"2026-06-26T20:19:33.237Z","author":"codex","op":"comment_add","patch":[{"op":"add","path":"/metadata/comments/1","value":{"created_at":"2026-06-26T20:19:33.237Z","author":"codex","text":"CodeFactor PR follow-up: after PR #381 showed 18 fixed and 16 found, the 16 found rows were all complexity findings on command/SDK files touched by the initial dedupe refactor. This branch now keeps the generated-file remediation only: CodeFactor hosted-ignore checklist wording plus auto-generated markers emitted by the package runtime-loader and plugin MCP-wrapper generators. Source command/SDK complexity remains tracked by pm-arzz for a dedicated refactor."}},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T20:19:33.237Z"}],"before_hash":"8af2e8d1985ca905710903c5eeb57d78b11840c491052b0741d9de65c30d77d7","after_hash":"6c1e14db5c605be5f1804a3d2a1348287fb5c7901e2def0176f798910c18269d"}
+{"ts":"2026-06-26T20:25:55.857Z","author":"codex","op":"comment_add","patch":[{"op":"add","path":"/metadata/comments/2","value":{"created_at":"2026-06-26T20:25:55.857Z","author":"codex","text":"Evidence after narrowing PR #381: generator drift checks passed (node scripts/gen-package-runtime-loaders.mjs --check; node scripts/gen-plugin-mcp-wrappers.mjs --check); focused generator/runtime tests passed (4 files, 34 tests); pnpm build passed; pnpm typecheck passed; pnpm contracts:check passed; pnpm quality:static passed; pnpm security:scan passed; pnpm audit --audit-level low reported no known vulnerabilities; pnpm changelog:pm:check used pm-changelog@2026.6.20 and left CHANGELOG.md unchanged; node scripts/run-tests.mjs coverage passed 256 files, 5133 tests, 100% statements/branches/functions/lines; isolated manual temp smoke in /tmp/tmp.uTuxtFeLBr passed init/create/claim/update/files/docs/test/close/release with health ok 0 warnings and validate ok 0 warnings; repo pm health ok 0 warnings; repo validate history_drift ok with known pre-existing validate_resolution_missing_fields:258 warning; Sentry/telemetry gate ok with critical=0 high=0 total=0 and telemetry finish_error_rate_pct=0.69."}},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T20:25:55.857Z"}],"before_hash":"6c1e14db5c605be5f1804a3d2a1348287fb5c7901e2def0176f798910c18269d","after_hash":"9d57cd05481cfee37cd6cd21639722370e9d7be109906a90195cdf11827d3a0a"}
+{"ts":"2026-06-26T20:35:58.865Z","author":"codex","op":"release","patch":[{"op":"remove","path":"/metadata/assignee"},{"op":"replace","path":"/metadata/updated_at","value":"2026-06-26T20:35:58.865Z"}],"before_hash":"9d57cd05481cfee37cd6cd21639722370e9d7be109906a90195cdf11827d3a0a","after_hash":"a21883afb8a0ddcc128d0e2e64c9b921b748acf099444dd01f71ba6e1d41af9b","message":"Release after CodeFactor PR update"}

.agents/pm/tasks/pm-arzz.toon

@@ -6,12 +6,13 @@ status: in_progress
 priority: 2
 tags[4]: code-quality,codefactor,complexity,refactor
 created_at: "2026-06-26T13:33:03.901Z"
-updated_at: "2026-06-26T19:25:13.595Z"
+updated_at: "2026-06-26T20:35:59.044Z"
 author: claude-code-agent
 acceptance_criteria: "First milestone: the 3 Critical + 7 High complexity findings are eliminated. Stretch: Moderate findings trend to 0 where it does not harm readability (otherwise scoped-ignore with justification). No behavior change — full coverage suite green at 100%; pnpm typecheck, contracts:check, and quality:static pass; no directory exceeds the 120-file static-gate cap."
 parent: pm-92if
-comments[1]{created_at,author,text}:
+comments[2]{created_at,author,text}:
   "2026-06-26T19:05:47.336Z",codex-codefactor-sdk-cli-20260626,"Evidence: CodeFactor complexity scope now ignores generated standalone loaders, generated standalone launchers, and tests while keeping shipped source files in analysis; create/update unset parsing tables were collapsed into shared metadata to reduce command surface duplication and maintenance cost. Manual temp smoke in /tmp/tmp.XalxjTQCOu passed init, create, update --unset deadline/assignee, package install todos --project, package doctor --project --detail deep, contracts --flags-only, and health --check-only --summary with only telemetry_queue_pending local warning."
+  "2026-06-26T20:18:29.140Z",codex,"CodeFactor PR follow-up: user reported the PR detail page still showed 16 found issues after the duplication/generated-marker patch. Inspection showed all 16 were complexity findings on large existing command/SDK files touched by this branch: search, list, config, create, update, and cli-contracts. To remove the PR findings without forcing an unsafe broad command rewrite into the generated-file remediation PR, this branch now narrows its net source diff to the generated-file CodeFactor marker/checklist changes only. pm-arzz remains open for a dedicated staged complexity refactor of those command handlers."
 files[4]{path,scope,note}:
   .codefactor.yml,project,CodeFactor complexity signal excludes generated/test surfaces while keeping shipped source visible
   src/cli/commands/create.ts,project,Create command uses shared unset metadata without changing behavior