@mutagent/helix 0.1.0-alpha.14

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Files changed (357) hide show
  1. package/.claude/skills/mutagent-helix/SKILL.md +113 -0
  2. package/.claude/skills/mutagent-helix/scripts/cli/codex-transcode.ts +143 -0
  3. package/.claude/skills/mutagent-helix/scripts/cli/doctor.ts +111 -0
  4. package/.claude/skills/mutagent-helix/scripts/cli/init.ts +382 -0
  5. package/.claude/skills/mutagent-helix/scripts/cli/run.sh +61 -0
  6. package/CLAUDE.md +193 -0
  7. package/LICENSE +201 -0
  8. package/NOTICE +22 -0
  9. package/README.md +209 -0
  10. package/assets/adl-loop.svg +162 -0
  11. package/assets/system-status.svg +422 -0
  12. package/bin/mutagent-cli.mjs +9950 -0
  13. package/bin/mutagent-helix.mjs +78 -0
  14. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/CLAUDE.md +28 -0
  15. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/SKILL.md +138 -0
  16. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/assets/templates/agentspec.yaml.tpl +247 -0
  17. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/references/frameworks/doc-pins.md +53 -0
  18. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/references/principles.md +91 -0
  19. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/references/requirements.yaml +295 -0
  20. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/references/workflows/orchestrator-protocol.md +302 -0
  21. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/scripts/cli/doctor.ts +116 -0
  22. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/scripts/cli/init.ts +230 -0
  23. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/scripts/cli/run.sh +60 -0
  24. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/scripts/config/resolve-spec-dir.ts +199 -0
  25. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/scripts/contract/agentspec.schema.ts +455 -0
  26. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/scripts/setup/detect.ts +67 -0
  27. package/mutagent-agentspec/.claude/skills/mutagent-agentspec/scripts/validate/validate-spec.ts +93 -0
  28. package/mutagent-agentspec/LICENSE +201 -0
  29. package/mutagent-agentspec/NOTICE +19 -0
  30. package/mutagent-agentspec/README.md +44 -0
  31. package/mutagent-builder/.claude/skills/mutagent-builder/SKILL.md +100 -0
  32. package/mutagent-builder/.claude/skills/mutagent-builder/assets/agents/ai-architect.md +312 -0
  33. package/mutagent-builder/.claude/skills/mutagent-builder/assets/agents/ai-engineer.md +357 -0
  34. package/mutagent-builder/.claude/skills/mutagent-builder/assets/templates/build-report.md.tpl +39 -0
  35. package/mutagent-builder/.claude/skills/mutagent-builder/references/principles.md +31 -0
  36. package/mutagent-builder/.claude/skills/mutagent-builder/references/workflows/build-protocol.md +61 -0
  37. package/mutagent-builder/.claude/skills/mutagent-builder/references/workflows/improve-handoff.md +23 -0
  38. package/mutagent-builder/.claude/skills/mutagent-builder/scripts/cli/run.sh +60 -0
  39. package/mutagent-builder/.claude/skills/mutagent-builder/scripts/handoff/validate-build-input.ts +72 -0
  40. package/mutagent-builder/.claude/skills/mutagent-builder/scripts/sync-spec/check-sync-spec.ts +499 -0
  41. package/mutagent-builder/.claude/skills/mutagent-builder/scripts/verify/spec-impl-coverage.ts +182 -0
  42. package/mutagent-builder/CLAUDE.md +25 -0
  43. package/mutagent-builder/README.md +26 -0
  44. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/README.md +192 -0
  45. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/SKILL.md +352 -0
  46. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/agents/ai-architect.md +256 -0
  47. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/agents/ai-engineer.md +344 -0
  48. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/agents/diagnostics-analyzer.md +576 -0
  49. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/agents/discovery.md +425 -0
  50. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/audit.json.tpl +24 -0
  51. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/audit.md.tpl +49 -0
  52. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/config.yaml.tpl +100 -0
  53. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/pr-body.md.tpl +56 -0
  54. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/report.html.tpl +327 -0
  55. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/shared/README.md +27 -0
  56. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/shared/iter-N-handover.md.tpl +125 -0
  57. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/shared/self-diagnosis-contract.v0.1.0.yaml.tpl +234 -0
  58. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/shared/spec.yaml.tpl +152 -0
  59. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/shared/team.yaml.tpl +127 -0
  60. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/templates/shared/wave-N-dashboard.html.tpl +1712 -0
  61. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/diagnostics/WF-2.1-nl-query.md +59 -0
  62. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/diagnostics/WF-2.2-tier0-progress.md +58 -0
  63. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/diagnostics/WF-2.3-analysis-progress.md +44 -0
  64. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/diagnostics/WF-2.4-html-report.md +61 -0
  65. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/diagnostics/WF-2.5-rca-detail.md +69 -0
  66. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/diagnostics/WF-2.6-stale-warning.md +53 -0
  67. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/onboarding/WF-1.1-welcome.md +60 -0
  68. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/onboarding/WF-1.2-source-platform-picker.md +41 -0
  69. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/onboarding/WF-1.3-source-auth.md +75 -0
  70. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/onboarding/WF-1.4-target-picker.md +48 -0
  71. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/onboarding/WF-1.5-ask-tool.md +43 -0
  72. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/onboarding/WF-1.6-config-review.md +57 -0
  73. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/onboarding/WF-1.7-filter-defaults.md +52 -0
  74. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/assets/wireframes/onboarding/WF-1.8-first-run.md +59 -0
  75. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/examples/sample-findings.json +92 -0
  76. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/examples/sample-meta.json +47 -0
  77. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/adapter-strategy.md +75 -0
  78. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/config-migration.md +84 -0
  79. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/config.md +159 -0
  80. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/filter-search-matrix.md +66 -0
  81. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/harness-knowledge.md +22 -0
  82. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/memory-format.md +78 -0
  83. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/onboarding-decisions.yaml +187 -0
  84. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/operation-inventory.md +59 -0
  85. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/overview.md +167 -0
  86. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/reference.md +119 -0
  87. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/script-index.md +101 -0
  88. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-adapter-contract.md +93 -0
  89. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-platforms/claude-code-transcripts.md +66 -0
  90. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-platforms/codex-transcripts.md +78 -0
  91. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-platforms/codex.md +145 -0
  92. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-platforms/install-paths.md +57 -0
  93. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-platforms/langfuse.md +178 -0
  94. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-platforms/local-jsonl.md +55 -0
  95. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-platforms/openobserve.md +102 -0
  96. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/source-platforms/otel.md +63 -0
  97. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/target-platforms/cloud-rest.md +84 -0
  98. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/target-platforms/local-claude.md +65 -0
  99. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/target-platforms/local-cloud-agent-sdk.md +92 -0
  100. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/target-platforms/local-codex.md +72 -0
  101. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/target-platforms/local-cursor.md +108 -0
  102. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/target-platforms/local-mastra.md +77 -0
  103. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/target-platforms/local-opencode.md +70 -0
  104. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/apply-pr-comment-format.md +82 -0
  105. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/diagnostics.md +35 -0
  106. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/handover-contract.md +247 -0
  107. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/onboarding.md +300 -0
  108. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/orchestrator-protocol.md +1861 -0
  109. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/rca.md +331 -0
  110. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/rendering-anatomy.md +314 -0
  111. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/schedule-prep.md +100 -0
  112. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/scope-model.md +128 -0
  113. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/references/workflows/verification-methodology.md +174 -0
  114. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/aggregate/sort-findings.ts +0 -0
  115. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/awareness/blind-spots.ts +167 -0
  116. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/awareness/llm-sample.ts +681 -0
  117. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/cli/doctor.ts +215 -0
  118. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/cli/init.ts +1013 -0
  119. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/cli/install-agents.ts +350 -0
  120. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/cli/run.sh +61 -0
  121. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/cli/shared-templates.ts +79 -0
  122. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/config/load.ts +392 -0
  123. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/config/resolve-credential.ts +120 -0
  124. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/config/schema.ts +641 -0
  125. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/config/validate.ts +134 -0
  126. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/context/build-diagnosis-context.ts +417 -0
  127. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/context/load-context.ts +105 -0
  128. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/contract/types.ts +166 -0
  129. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/enrich/build-render-input.ts +1964 -0
  130. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/enrich/corpus-severity.ts +172 -0
  131. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/enrich/dismissal-match.ts +270 -0
  132. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/enrich/rank-remedies.ts +75 -0
  133. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/hooks/install-hooks.sh +46 -0
  134. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/hooks/pre-push.sh +78 -0
  135. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/invocation/parse-brief.ts +188 -0
  136. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/library/match.ts +114 -0
  137. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/library/paths.ts +95 -0
  138. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/library/store.ts +535 -0
  139. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/library/types.ts +181 -0
  140. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/lint/template-inline-js.ts +267 -0
  141. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/memory/append.ts +188 -0
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  143. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/normalize/platforms/entity-context.ts +686 -0
  144. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/normalize/read-unitf.ts +267 -0
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  164. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/source/adapters/claude-code.ts +17 -0
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  166. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/source/adapters/langfuse.ts +17 -0
  167. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/source/adapters/local-jsonl.ts +12 -0
  168. package/mutagent-diagnostics/.claude/skills/mutagent-diagnostics/scripts/source/adapters/otel.ts +12 -0
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@@ -0,0 +1,326 @@
1
+ /**
2
+ * scripts/validate/wave6-checklist.ts
3
+ * PRD-SO-06 — Wave-6 methodology checklist validator + stamp emitter.
4
+ * Type A — Pure Script (file-system reads; no LLM; deterministic).
5
+ *
6
+ * The Wave-6 methodology (R2.1–R2.6 + D1/D2) requires each diagnostic run to emit
7
+ * six stamp files under `<report-dir>/wave6/<step>.json` before the render gate
8
+ * (orchestrator-protocol.md Step 8.9). This validator checks those stamps exist and
9
+ * are well-formed, then emits a gate result.
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+ *
11
+ * Steps validated:
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+ * parse-brief parse-brief.ts produced a ParsedInvocation
13
+ * awareness-sample llm-sample.ts produced a 5-trace awareness sample
14
+ * blind-spots blind-spots.ts produced the blind-spots taxonomy
15
+ * library-match library/match.ts ran the entity library check
16
+ * caps-result caps.ts produced a CapsResult
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+ * deep-read-gate deep-read-gate.ts produced a DeepReadGateResult
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+ * awareness-witness W11-05: stamped by the orchestrator at Step 3.5 to record
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+ * whether this was a fresh run AND whether awareness ran.
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+ * HARD-FAIL (regardless of isClientReport) when isFreshRun=true
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+ * AND awarenessRan=false AND no explicit exemption declared.
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+ *
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+ * Gate severity (PRD §6 Q7):
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+ * Internal reports (isClientReport = false): WARN-only on most missing stamps.
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+ * Client reports (isClientReport = true): HARD-FAIL (non-zero exit).
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+ *
27
+ * W11-05 ADDITIONAL RULE (awareness-witness):
28
+ * If awareness-witness stamp declares isFreshRun=true AND awarenessRan=false
29
+ * with no exemption → ALWAYS HARD-FAIL (overrides isClientReport=false leniency).
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+ * The operator must never silently skip awareness on a fresh run.
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+ *
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+ * Usage (CLI):
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+ * bun scripts/cli/run.sh scripts/validate/wave6-checklist.ts \
34
+ * --report-dir <dir> [--accept-exemptions <id>...] [--client]
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+ *
36
+ * Exported function:
37
+ * runWave6Checklist(opts: Wave6ChecklistOpts): Wave6ChecklistResult
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+ *
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+ * Step 8.9 integration (orchestrator-protocol.md):
40
+ * The orchestrator calls this validator after all Wave-6 scripts have run (Step 8.9).
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+ * On WARN: log to runMeta.exemptions[]; continue rendering.
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+ * On FAIL: halt; do not render; report the missing stamps to the operator.
43
+ */
44
+
45
+ import { existsSync, readFileSync, mkdirSync, writeFileSync } from "node:fs";
46
+ import { join, resolve } from "node:path";
47
+
48
+ // ── Types ────────────────────────────────────────────────────────────────────
49
+
50
+ export type Wave6StepId =
51
+ | "parse-brief"
52
+ | "awareness-sample"
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+ | "blind-spots"
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+ | "library-match"
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+ | "caps-result"
56
+ | "deep-read-gate"
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+ | "awareness-witness";
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+
59
+ export const WAVE6_STEPS: readonly Wave6StepId[] = [
60
+ "parse-brief",
61
+ "awareness-sample",
62
+ "blind-spots",
63
+ "library-match",
64
+ "caps-result",
65
+ "deep-read-gate",
66
+ "awareness-witness",
67
+ ] as const;
68
+
69
+ /**
70
+ * W11-05: Payload written to `wave6/awareness-witness.json` by the orchestrator
71
+ * at Step 3.5. Records whether this was a fresh run (no confirmed priors) and
72
+ * whether awareness actually ran.
73
+ *
74
+ * Rules enforced by the checklist:
75
+ * - isFreshRun=true + awarenessRan=true → pass
76
+ * - isFreshRun=true + awarenessRan=false → HARD-FAIL (no leniency)
77
+ * - isFreshRun=false + awarenessRan=false → pass (priors authorized the skip)
78
+ * - isFreshRun=false + awarenessRan=true → pass
79
+ */
80
+ export interface AwarenessWitnessPayload {
81
+ /**
82
+ * True when no confirmed library prior existed for this entity before the run
83
+ * (i.e. library-match returned no matches). A fresh run MUST run awareness.
84
+ */
85
+ isFreshRun: boolean;
86
+ /** True when llm-sample.ts + blind-spots.ts both ran for this run. */
87
+ awarenessRan: boolean;
88
+ /**
89
+ * When awarenessRan=false on a fresh run, this field MUST be set to a valid
90
+ * exemption reason from the Gate Exemption Taxonomy (references/workflows/rca.md).
91
+ * Absent when awarenessRan=true.
92
+ */
93
+ exemptionReason?: string;
94
+ }
95
+
96
+ export interface Wave6StepResult {
97
+ stepId: Wave6StepId;
98
+ present: boolean;
99
+ /** True when the stamp file was present but could not be parsed as JSON. */
100
+ malformed: boolean;
101
+ /** Path that was checked. */
102
+ stampPath: string;
103
+ /** Parsed content when present and well-formed. */
104
+ content?: unknown;
105
+ /** Exemption reason when this step was accepted despite being missing. */
106
+ exemptionReason?: string;
107
+ }
108
+
109
+ export interface Wave6ChecklistResult {
110
+ ok: boolean;
111
+ /** True when any missing stamps were accepted via exemptions (result is ok despite gaps). */
112
+ exempted: boolean;
113
+ /** Steps with missing or malformed stamps (after exemptions applied). */
114
+ missing: Wave6StepResult[];
115
+ /** All step results (present + absent). */
116
+ steps: Wave6StepResult[];
117
+ /** Formatted banner string for display in reports or logs. */
118
+ banner: string;
119
+ /**
120
+ * W11-05: Set when the awareness-witness gate detected a fresh-run violation.
121
+ * A fresh-run violation is when isFreshRun=true + awarenessRan=false + no exemption.
122
+ * This ALWAYS causes ok=false regardless of isClientReport.
123
+ */
124
+ awarenessViolation?: string;
125
+ }
126
+
127
+ export interface Wave6ChecklistOpts {
128
+ /** Absolute or relative path to the report directory. */
129
+ reportDir: string;
130
+ /** Step IDs that are accepted despite being missing (e.g. library-match when no library priors exist). */
131
+ acceptExemptions?: Wave6StepId[];
132
+ /** When true, missing non-exempted steps cause hard failure. When false, WARN-only. */
133
+ isClientReport?: boolean;
134
+ }
135
+
136
+ // ── Stamp helpers ─────────────────────────────────────────────────────────────
137
+
138
+ function stampPath(reportDir: string, stepId: Wave6StepId): string {
139
+ return join(reportDir, "wave6", `${stepId}.json`);
140
+ }
141
+
142
+ function readStamp(path: string): { present: boolean; malformed: boolean; content?: unknown } {
143
+ if (!existsSync(path)) return { present: false, malformed: false };
144
+ try {
145
+ const content = JSON.parse(readFileSync(path, "utf-8")) as unknown;
146
+ return { present: true, malformed: false, content };
147
+ } catch {
148
+ return { present: true, malformed: true };
149
+ }
150
+ }
151
+
152
+ // ── Core validator ────────────────────────────────────────────────────────────
153
+
154
+ /**
155
+ * PRD-SO-06 — Run the Wave-6 methodology checklist.
156
+ * Returns a structured result; the CLI entrypoint handles exit codes.
157
+ *
158
+ * W11-05: Also enforces the awareness-witness gate — hard-fails if the
159
+ * awareness-witness stamp declares isFreshRun=true + awarenessRan=false
160
+ * with no exemption, regardless of isClientReport setting.
161
+ */
162
+ export function runWave6Checklist(opts: Wave6ChecklistOpts): Wave6ChecklistResult {
163
+ const { reportDir, acceptExemptions = [], isClientReport = false } = opts;
164
+ const abs = resolve(reportDir);
165
+ const exemptSet = new Set<string>(acceptExemptions);
166
+
167
+ const steps: Wave6StepResult[] = WAVE6_STEPS.map((stepId) => {
168
+ const path = stampPath(abs, stepId);
169
+ const { present, malformed, content } = readStamp(path);
170
+ const result: Wave6StepResult = {
171
+ stepId,
172
+ present,
173
+ malformed,
174
+ stampPath: path,
175
+ content,
176
+ };
177
+ if (!present && exemptSet.has(stepId)) {
178
+ result.exemptionReason = `accepted via --accept-exemptions`;
179
+ }
180
+ return result;
181
+ });
182
+
183
+ const missing = steps.filter((s) => {
184
+ if (s.present && !s.malformed) return false; // stamp present + valid
185
+ if (s.exemptionReason) return false; // accepted exemption
186
+ return true;
187
+ });
188
+
189
+ const exempted = steps.some((s) => !s.present && !!s.exemptionReason);
190
+
191
+ // ── W11-05: Awareness witness gate ──────────────────────────────────────────
192
+ // Check the awareness-witness stamp for fresh-run violations.
193
+ // A fresh-run violation (isFreshRun=true + awarenessRan=false + no exemptionReason)
194
+ // is ALWAYS a hard-fail, overriding the isClientReport=false leniency.
195
+ let awarenessViolation: string | undefined;
196
+ const witnessStep = steps.find((s) => s.stepId === "awareness-witness");
197
+ if (witnessStep?.present && !witnessStep.malformed && witnessStep.content) {
198
+ // Stamp files are written as { stepId, timestamp, result: <payload> }
199
+ const stamped = witnessStep.content as { result?: Partial<AwarenessWitnessPayload> };
200
+ const payload = stamped.result ?? (witnessStep.content as Partial<AwarenessWitnessPayload>);
201
+ if (
202
+ payload.isFreshRun === true &&
203
+ payload.awarenessRan === false &&
204
+ !payload.exemptionReason
205
+ ) {
206
+ awarenessViolation =
207
+ "awareness-witness: isFreshRun=true + awarenessRan=false with no exemptionReason. " +
208
+ "Fresh runs MUST run the awareness layer (W11-05). " +
209
+ "Pass an exemptionReason in the witness stamp if skipping is authorized.";
210
+ }
211
+ }
212
+
213
+ const ok = missing.length === 0 && !awarenessViolation;
214
+
215
+ const lines: string[] = [];
216
+ if (awarenessViolation) {
217
+ lines.push(`Wave-6 checklist HARD-FAIL (W11-05 awareness-witness gate):`);
218
+ lines.push(` ${awarenessViolation}`);
219
+ lines.push(`\nFix: re-run the awareness layer (scripts/awareness/llm-sample.ts + blind-spots.ts)`);
220
+ lines.push(` OR write the awareness-witness stamp with a valid exemptionReason.`);
221
+ } else if (ok && !exempted) {
222
+ lines.push(`Wave-6 checklist PASSED — all ${WAVE6_STEPS.length} stamps present.`);
223
+ } else if (ok && exempted) {
224
+ const exemptedIds = steps
225
+ .filter((s) => s.exemptionReason)
226
+ .map((s) => s.stepId)
227
+ .join(", ");
228
+ lines.push(`Wave-6 checklist PASSED (with exemptions: ${exemptedIds}).`);
229
+ } else {
230
+ const severity = isClientReport ? "FAIL" : "WARN";
231
+ lines.push(`Wave-6 checklist ${severity} — ${missing.length} missing stamp(s):`);
232
+ for (const s of missing) {
233
+ const label = s.malformed ? "(malformed JSON)" : "(not found)";
234
+ lines.push(` - ${s.stepId} ${label}: ${s.stampPath}`);
235
+ }
236
+ if (isClientReport) {
237
+ lines.push(`\nHard-fail: client report requires all Wave-6 stamps (PRD-SO-06 / Q7).`);
238
+ lines.push(`Run the missing Wave-6 scripts and re-invoke the render gate.`);
239
+ } else {
240
+ lines.push(`\nWarn-only: record missing stamps in runMeta.exemptions[] and continue.`);
241
+ }
242
+ }
243
+
244
+ return { ok, exempted, missing, steps, banner: lines.join("\n"), awarenessViolation };
245
+ }
246
+
247
+ // ── Stamp writer helpers (for Wave-6 scripts to call) ─────────────────────────
248
+
249
+ /**
250
+ * Write a Wave-6 stamp file. Called by each Wave-6 script to signal completion.
251
+ * Creates the `wave6/` subdirectory if it does not exist.
252
+ *
253
+ * @param reportDir Report directory path.
254
+ * @param stepId The Wave-6 step being stamped.
255
+ * @param payload Any JSON-serializable result from the step.
256
+ */
257
+ export function writeWave6Stamp(reportDir: string, stepId: Wave6StepId, payload: unknown): void {
258
+ const dir = join(resolve(reportDir), "wave6");
259
+ mkdirSync(dir, { recursive: true });
260
+ const path = join(dir, `${stepId}.json`);
261
+ writeFileSync(path, JSON.stringify({ stepId, timestamp: new Date().toISOString(), result: payload }, null, 2), "utf-8");
262
+ }
263
+
264
+ /**
265
+ * W11-05: Write the awareness-witness stamp at Step 3.5.
266
+ * Called by the orchestrator after resolving whether priors exist for the entity:
267
+ *
268
+ * - isFreshRun: true when no confirmed library prior exists (no skip authorized)
269
+ * - isFreshRun: false when a confirmed library prior exists (skip authorized)
270
+ * - awarenessRan: true when llm-sample.ts + blind-spots.ts both ran
271
+ * - awarenessRan: false when the awareness layer was intentionally skipped
272
+ * - exemptionReason: required when awarenessRan=false on a fresh run
273
+ *
274
+ * Example (fresh run, awareness ran):
275
+ * writeAwarenessWitnessStamp("/tmp/report", { isFreshRun: true, awarenessRan: true })
276
+ *
277
+ * Example (prior-based skip):
278
+ * writeAwarenessWitnessStamp("/tmp/report", {
279
+ * isFreshRun: false, awarenessRan: false,
280
+ * exemptionReason: "library prior exists for this entity (Step 4.5 match)"
281
+ * })
282
+ */
283
+ export function writeAwarenessWitnessStamp(
284
+ reportDir: string,
285
+ payload: AwarenessWitnessPayload
286
+ ): void {
287
+ writeWave6Stamp(reportDir, "awareness-witness", payload);
288
+ }
289
+
290
+ // ── CLI entrypoint ────────────────────────────────────────────────────────────
291
+
292
+ if (import.meta.main) {
293
+ const args = process.argv.slice(2);
294
+
295
+ const reportDirIdx = args.indexOf("--report-dir");
296
+ if (reportDirIdx < 0 || !args[reportDirIdx + 1]) {
297
+ console.error("Usage: wave6-checklist.ts --report-dir <dir> [--accept-exemptions <id>...] [--client]");
298
+ process.exit(2);
299
+ }
300
+
301
+ const reportDir = args[reportDirIdx + 1];
302
+ const isClientReport = args.includes("--client");
303
+
304
+ // Collect exemption IDs: all args after --accept-exemptions until the next flag.
305
+ const exemptions: Wave6StepId[] = [];
306
+ const exemptIdx = args.indexOf("--accept-exemptions");
307
+ if (exemptIdx >= 0) {
308
+ for (let i = exemptIdx + 1; i < args.length; i++) {
309
+ if (args[i].startsWith("--")) break;
310
+ if (WAVE6_STEPS.includes(args[i] as Wave6StepId)) {
311
+ exemptions.push(args[i] as Wave6StepId);
312
+ } else {
313
+ console.warn(`Unknown step ID in --accept-exemptions: ${args[i]}`);
314
+ }
315
+ }
316
+ }
317
+
318
+ const result = runWave6Checklist({ reportDir, acceptExemptions: exemptions, isClientReport });
319
+
320
+ console.info(`\n${result.banner}\n`);
321
+
322
+ if (!result.ok && isClientReport) {
323
+ process.exit(1);
324
+ }
325
+ process.exit(0);
326
+ }
@@ -0,0 +1,41 @@
1
+ # mutagent-diagnostics/ — skill navigation map
2
+
3
+ > Lean map of THIS skill's internals. Repo-wide conventions (wave model, dispatch
4
+ > discipline, cross-skill rules) live in `../CLAUDE.md`; don't repeat them here.
5
+
6
+ **What it is:** RCA + remedy + apply workflow for AI agents — pulls evidence from traces,
7
+ surfaces ranked remedies, applies via PR/REST. Published: `pnpx @mutagent/diagnostics init`.
8
+
9
+ ## Where things live (`.claude/skills/mutagent-diagnostics/`)
10
+
11
+ | Path | What |
12
+ |---|---|
13
+ | `SKILL.md` | Canonical contract — frontmatter + §0 setup + §1 triggers + §N sections. **Read first.** |
14
+ | `references/workflows/orchestrator-protocol.md` | The run FSM (Step 3a → 9.9). The orchestrator's script. |
15
+ | `references/script-index.md` | **Data-flow map** — every script's consumes/produces/runMeta-field/gate. Read before adding a step. |
16
+ | `.meta/design-principles.md` | PR-001..PR-055 design principles — the Constitution (block-organized audit surface). **Operator-LOCKED** — propose, don't self-edit. `references/principles.md` is a thin redirect to it. |
17
+ | `.meta/{requirements.yaml,design-rationale.md,open-questions.md,oq-answers.md,operator-feedback-log.md}` | The Design/Build log — intent registry + rationale + open-questions/answers + operator feedback. **INTERNAL** — moved here from `references/`; stripped on publish. |
18
+ | `references/workflows/rca.md` · `handover-contract.md` | RCA pattern library · analyzer↔orchestrator schema. |
19
+ | `references/source-platforms/*` · `target-platforms/*` | Trace sources (Langfuse/OTel/JSONL/Claude/Codex) · write targets. |
20
+ | `assets/agents/diagnostics-analyzer.md` | Sub-agent contract (tiered RCA executor). |
21
+ | `assets/templates/report.html.tpl` | Runtime report template (Tier-2). |
22
+ | `scripts/normalize/` | UniTF intake: `read-unitf.ts` (reads the handed-over UniTF JSONL+manifest) → `unitf-adapter.ts` → `trace.ts` (canonical types); `platforms/entity-context.ts` kept. Per-platform fetch/normalize moved to `@mutagent/tools` (`mutagent-cli trace fetch`). |
23
+ | `scripts/enrich/build-render-input.ts` | Findings → RenderInput (the render contract). |
24
+ | `scripts/report/render.ts` | RenderInput → `report.html`. |
25
+ | `scripts/validate/` | The gates (below). |
26
+ | `scripts/cli/{init,doctor,run}.ts` | Onboarding · runtime probe · dispatch wrapper. |
27
+
28
+ ## The run sequence (one line)
29
+ `parse-brief → awareness-sample → read-unitf(metadata+entity) → tier0 → library-match → slice/sample → analyzer dispatch → aggregate/sort → enrich(build-render-input) → gates → render`. Full table: `references/script-index.md`.
30
+
31
+ ## The gates (fail-loud enforcement — never bypass)
32
+ 1. `validate/findings-contract.ts` (Step 7.1) — required Finding/Remedy fields or RESEND.
33
+ 2. `validate/completeness-check.ts` (Step 8.9, D-6) — exact render-contract derefs present.
34
+ 3. `validate/render-js-syntax.ts` (PR-050) — every emitted `<script>` parses.
35
+ 4. `validate/wave6-checklist.ts` — methodology widgets threaded.
36
+ 5. `validate/finalize-gate.ts` (Step 9.9, W14) — OUTPUT-side per-section completeness + bounded self-heal.
37
+
38
+ ## Invariants
39
+ - NDA: synthetic data only in source/tests/fixtures. · Audience: default **client** (leak-safe); `--audience internal` opt-in.
40
+ - Three sources of truth in agreement: `trace.ts` ↔ producer contract ↔ gate. A field in only 2 of 3 is the bug class the gates kill.
41
+ - Authored Design/Build artifacts live in the internal `.meta/` log (stripped on publish): `eval-suite-design.{html,gen.mjs,data.json}` · `wave-dashboard.gen.mjs` · `PROPOSED/**` (alongside `design-principles.md` + the moved requirements/design refs). Generated dashboards (skill-map / skill-overview / wave-dashboard / requirements / unmet HTML) are EPHEMERAL renders → gitignored under `../.memory/features/mutagent-diagnostics/` (+ `.gen-scratch/`); regenerate, never commit.
@@ -0,0 +1,201 @@
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@@ -0,0 +1,18 @@
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+ @mutagent/diagnostics
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+ Copyright 2026 MutagenT
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+
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+ This product is licensed under the Apache License, Version 2.0 (the "License");
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+ you may not use this product except in compliance with the License. You may
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+ obtain a copy of the License in the accompanying LICENSE file or at:
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+ http://www.apache.org/licenses/LICENSE-2.0
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+ Unless required by applicable law or agreed to in writing, software distributed
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+ CONDITIONS OF ANY KIND, either express or implied. See the License for the
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+ specific language governing permissions and limitations under the License.
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+
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+ ----------------------------------------------------------------------------
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+
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+ This package bundles install-time templates (assets/templates/shared/) that are
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+ authored by MutagenT and distributed under the same Apache-2.0 License.