substrate-ai 0.20.34 → 0.20.36

package/dist/cli/index.js

@@ -1,10 +1,10 @@
 #!/usr/bin/env node
-import { FileStateStore, RunManifest, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, ZERO_FINDING_COUNTS, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts } from "../health-CnV6ndAb.js";
+import { FileStateStore, RunManifest, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, ZERO_FINDING_COUNTS, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, parseRuntimeProbes, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts } from "../health-BAcRfZ4s.js";
 import { createLogger } from "../logger-KeHncl-f.js";
 import { createEventBus } from "../helpers-CElYrONe.js";
 import { AdapterRegistry, BudgetConfigSchema, CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, ConfigError, CostTrackerConfigSchema, DEFAULT_CONFIG, DoltClient, DoltNotInstalled, GlobalSettingsSchema, IngestionServer, MonitorDatabaseImpl, OPERATIONAL_FINDING, PartialGlobalSettingsSchema, PartialProviderConfigSchema, ProvidersSchema, RoutingRecommender, STORY_METRICS, TelemetryConfigSchema, addTokenUsage, aggregateTokenUsageForRun, checkDoltInstalled, compareRunMetrics, createAmendmentRun, createConfigSystem, createDecision, createDoltClient, createPipelineRun, getActiveDecisions, getAllCostEntriesFiltered, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, tagRunAsBaseline, updatePipelineRun } from "../dist-BnMsd9hC.js";
 import "../adapter-registry-DXLMTmfD.js";
-import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-BQxm1Qix.js";
+import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-YBY2vrF4.js";
 import "../errors-DSGhhrgv.js";
 import "../routing-CcBOCuC9.js";
 import "../decisions-C0pz9Clx.js";
@@ -20,7 +20,7 @@ import { execFile, spawn } from "node:child_process";
 import * as path$3 from "node:path";
 import * as path$2 from "node:path";
 import * as path$1 from "node:path";
-import { join as join$1 } from "node:path";
+import { basename as basename$1, join as join$1 } from "node:path";
 import { randomUUID } from "node:crypto";
 import { z } from "zod";
 import * as fs from "node:fs/promises";
@@ -3667,7 +3667,7 @@ async function runStatusAction(options) {
 			logger$12.debug({ err }, "Work graph query failed, continuing without work graph data");
 		}
 		if (run === void 0) {
-			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-Bqzqu6zC.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-DvAr7miW.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -5198,7 +5198,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-B7jP4apv.js"
+									"../run-__o2iU0w.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -8382,6 +8382,134 @@ function registerDiffCommand(program) {
 	});
 }
 
+//#endregion
+//#region src/cli/commands/probes-diff.ts
+/**
+* Diff two probe sets by `name` (the canonical identity of a probe per
+* `RuntimeProbeListSchema`). Differences in command/timeout/assertion
+* shape between same-named probes appear in `inBoth` for downstream
+* shape-comparison; this function does NOT diff probe internals.
+*/
+function computeProbesDiff(probesA, probesB) {
+	const byNameA = new Map(probesA.map((p) => [p.name, p]));
+	const byNameB = new Map(probesB.map((p) => [p.name, p]));
+	const onlyInA = [];
+	const onlyInB = [];
+	const inBoth = [];
+	for (const [name, a] of byNameA) {
+		const b = byNameB.get(name);
+		if (b === void 0) onlyInA.push(a);
+		else inBoth.push({
+			name,
+			a,
+			b
+		});
+	}
+	for (const [name, b] of byNameB) if (!byNameA.has(name)) onlyInB.push(b);
+	return {
+		onlyInA,
+		onlyInB,
+		inBoth
+	};
+}
+/**
+* Read an artifact file and extract its `## Runtime Probes` probe set.
+* Returns an empty array (not error) when the file has no probes section —
+* an artifact without probes is a valid input to the diff (e.g., the
+* disabled-arm output when probe-author was off).
+*
+* Throws when the file is unreadable OR when the probes block is present
+* but malformed (parse errors). Callers who want to tolerate parse errors
+* should catch.
+*/
+function extractProbesFromArtifact(artifactPath) {
+	if (!existsSync(artifactPath)) throw new Error(`probes-diff: artifact file not found: ${artifactPath}`);
+	const content = readFileSync(artifactPath, "utf-8");
+	const result = parseRuntimeProbes(content);
+	if (result.kind === "absent") return [];
+	if (result.kind === "invalid") throw new Error(`probes-diff: artifact has malformed ## Runtime Probes section: ${artifactPath}\n${result.error}`);
+	return result.probes;
+}
+function registerProbesCommand(program) {
+	const probes = program.command("probes").description("Inspect runtime-probe sections across story artifacts (Story 60-14)");
+	probes.command("diff <artifactA> <artifactB>").description("Diff `## Runtime Probes` sections across two story-artifact files").option("--output-format <format>", "Output format: human (default) or json", "human").option("--story-key <key>", "Optional story key for output context (informational)").action(async (artifactA, artifactB, options) => {
+		const format = options.outputFormat === "json" ? "json" : "human";
+		let probesA;
+		let probesB;
+		try {
+			probesA = extractProbesFromArtifact(artifactA);
+		} catch (err) {
+			const msg = err instanceof Error ? err.message : String(err);
+			emitError(format, `failed to read artifact A: ${msg}`);
+			process.exitCode = 1;
+			return;
+		}
+		try {
+			probesB = extractProbesFromArtifact(artifactB);
+		} catch (err) {
+			const msg = err instanceof Error ? err.message : String(err);
+			emitError(format, `failed to read artifact B: ${msg}`);
+			process.exitCode = 1;
+			return;
+		}
+		const diff = computeProbesDiff(probesA, probesB);
+		emitDiff(diff, {
+			artifactA,
+			artifactB,
+			storyKey: options.storyKey,
+			format,
+			countsA: probesA.length,
+			countsB: probesB.length
+		});
+	});
+}
+function emitError(format, message) {
+	if (format === "json") process.stdout.write(JSON.stringify({
+		success: false,
+		error: message
+	}) + "\n");
+	else process.stderr.write(`probes diff error: ${message}\n`);
+}
+function emitDiff(diff, ctx) {
+	if (ctx.format === "json") {
+		process.stdout.write(JSON.stringify({
+			success: true,
+			storyKey: ctx.storyKey,
+			artifactA: ctx.artifactA,
+			artifactB: ctx.artifactB,
+			counts: {
+				a: ctx.countsA,
+				b: ctx.countsB,
+				inBoth: diff.inBoth.length
+			},
+			onlyInA: diff.onlyInA.map((p) => ({
+				name: p.name,
+				sandbox: p.sandbox,
+				command: p.command
+			})),
+			onlyInB: diff.onlyInB.map((p) => ({
+				name: p.name,
+				sandbox: p.sandbox,
+				command: p.command
+			})),
+			inBoth: diff.inBoth.map((m) => ({ name: m.name }))
+		}, null, 2) + "\n");
+		return;
+	}
+	const aLabel = basename$1(ctx.artifactA);
+	const bLabel = basename$1(ctx.artifactB);
+	process.stdout.write(`\nprobes diff${ctx.storyKey ? ` (story ${ctx.storyKey})` : ""}\n`);
+	process.stdout.write(`  A: ${ctx.artifactA} — ${ctx.countsA} probe(s)\n`);
+	process.stdout.write(`  B: ${ctx.artifactB} — ${ctx.countsB} probe(s)\n\n`);
+	process.stdout.write(`Probes only in A (${aLabel}): ${diff.onlyInA.length}\n`);
+	for (const p of diff.onlyInA) process.stdout.write(`  - ${p.name} [${p.sandbox}]\n`);
+	process.stdout.write(`\nProbes only in B (${bLabel}): ${diff.onlyInB.length}\n`);
+	for (const p of diff.onlyInB) process.stdout.write(`  - ${p.name} [${p.sandbox}]\n`);
+	process.stdout.write(`\nProbes in both: ${diff.inBoth.length}\n`);
+	for (const m of diff.inBoth) process.stdout.write(`  - ${m.name}\n`);
+	process.stdout.write("\n");
+}
+
 //#endregion
 //#region src/cli/commands/history.ts
 function registerHistoryCommand(program) {
@@ -8985,6 +9113,7 @@ async function createProgram() {
 	registerDiffCommand(program);
 	registerHistoryCommand(program);
 	registerMigrateCommand(program);
+	registerProbesCommand(program);
 	registerRepoMapCommand(program);
 	registerRoutingCommand(program);
 	registerCostCommand(program, version);

package/dist/{health-CnV6ndAb.js → health-BAcRfZ4s.js}

@@ -6343,5 +6343,5 @@ function registerHealthCommand(program, _version = "0.0.0", projectRoot = proces
 }
 
 //#endregion
-export { BMAD_BASELINE_TOKENS_FULL, DEFAULT_STALL_THRESHOLD_SECONDS, DoltMergeConflict, FileStateStore, FindingsInjector, RunManifest, RuntimeProbeListSchema, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN$1 as STORY_KEY_PATTERN, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, ZERO_FINDING_COUNTS, __commonJS, __require, __toESM, applyConfigToGraph, buildPipelineStatusOutput, createDatabaseAdapter$1 as createDatabaseAdapter, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, createStateStore, detectCycles, detectsEventDrivenAC, extractTargetFilesFromStoryContent, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, isOrchestratorProcessLine, parseDbTimestampAsUtc, registerHealthCommand, renderFindings, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveGraphPath, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, runHealthAction, validateStoryKey };
-//# sourceMappingURL=health-CnV6ndAb.js.map
+export { BMAD_BASELINE_TOKENS_FULL, DEFAULT_STALL_THRESHOLD_SECONDS, DoltMergeConflict, FileStateStore, FindingsInjector, RunManifest, RuntimeProbeListSchema, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN$1 as STORY_KEY_PATTERN, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, ZERO_FINDING_COUNTS, __commonJS, __require, __toESM, applyConfigToGraph, buildPipelineStatusOutput, createDatabaseAdapter$1 as createDatabaseAdapter, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, createStateStore, detectCycles, detectsEventDrivenAC, extractTargetFilesFromStoryContent, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, isOrchestratorProcessLine, parseDbTimestampAsUtc, parseRuntimeProbes, registerHealthCommand, renderFindings, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveGraphPath, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, runHealthAction, validateStoryKey };
+//# sourceMappingURL=health-BAcRfZ4s.js.map

package/dist/{health-Bqzqu6zC.js → health-DvAr7miW.js}

@@ -1,4 +1,4 @@
-import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-CnV6ndAb.js";
+import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-BAcRfZ4s.js";
 import "./logger-KeHncl-f.js";
 import "./dist-BnMsd9hC.js";
 import "./decisions-C0pz9Clx.js";

package/dist/index.d.ts

@@ -2106,6 +2106,17 @@ interface OrchestratorEvents {
     storyKey: string;
     reason: string;
   };
+  /**
+   * Story 60-14: probe-author phase mode resolved at orchestrator start.
+   * Emitted once per run with the effective mode and where it came from
+   * (CLI flag, env var, or default). Powers the A/B validation harness
+   * by recording which arm of the experiment a given run belongs to.
+   */
+  'probe-author:enabled': {
+    runId: string;
+    mode: 'enabled' | 'disabled';
+    source: 'cli' | 'env' | 'default';
+  };
   /**
    * Story 62-3: code-review agent emitted YAML output that failed schema
    * validation (typically a parse error from unquoted-colon-in-value or

package/dist/{run-BQxm1Qix.js → run-YBY2vrF4.js}

@@ -1,4 +1,4 @@
-import { BMAD_BASELINE_TOKENS_FULL, DoltMergeConflict, FileStateStore, FindingsInjector, RunManifest, RuntimeProbeListSchema, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, VALID_PHASES, WorkGraphRepository, __commonJS, __require, __toESM, applyConfigToGraph, buildPipelineStatusOutput, createDatabaseAdapter, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectCycles, detectsEventDrivenAC, extractTargetFilesFromStoryContent, formatOutput, formatPipelineSummary, formatTokenTelemetry, inspectProcessTree, parseDbTimestampAsUtc, renderFindings, resolveGraphPath, resolveMainRepoRoot, validateStoryKey } from "./health-CnV6ndAb.js";
+import { BMAD_BASELINE_TOKENS_FULL, DoltMergeConflict, FileStateStore, FindingsInjector, RunManifest, RuntimeProbeListSchema, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, VALID_PHASES, WorkGraphRepository, __commonJS, __require, __toESM, applyConfigToGraph, buildPipelineStatusOutput, createDatabaseAdapter, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectCycles, detectsEventDrivenAC, extractTargetFilesFromStoryContent, formatOutput, formatPipelineSummary, formatTokenTelemetry, inspectProcessTree, parseDbTimestampAsUtc, renderFindings, resolveGraphPath, resolveMainRepoRoot, validateStoryKey } from "./health-BAcRfZ4s.js";
 import { createLogger } from "./logger-KeHncl-f.js";
 import { TypedEventBusImpl, createEventBus, createTuiApp, isTuiCapable, printNonTtyWarning, sleep } from "./helpers-CElYrONe.js";
 import { ADVISORY_NOTES, Categorizer, ConsumerAnalyzer, DEFAULT_GLOBAL_SETTINGS, DispatcherImpl, DoltClient, ESCALATION_DIAGNOSIS, EXPERIMENT_RESULT, EfficiencyScorer, IngestionServer, LogTurnAnalyzer, OPERATIONAL_FINDING, Recommender, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, STORY_METRICS, STORY_OUTCOME, SubstrateConfigSchema, TEST_EXPANSION_FINDING, TEST_PLAN, TelemetryNormalizer, TelemetryPipeline, TurnAnalyzer, addTokenUsage, aggregateTokenUsageForRun, aggregateTokenUsageForStory, callLLM, createConfigSystem, createDatabaseAdapter$1, createDecision, createPipelineRun, createRequirement, detectInterfaceChanges, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunMetrics, getRunningPipelineRuns, getStoryMetricsForRun, getTokenUsageSummary, initSchema, listRequirements, loadModelRoutingConfig, registerArtifact, updatePipelineRun, updatePipelineRunConfig, upsertDecision, writeRunMetrics, writeStoryMetrics } from "./dist-BnMsd9hC.js";
@@ -12176,6 +12176,7 @@ function createImplementationOrchestrator(deps) {
 		_drainResolve = resolve$6;
 	});
 	let _otlpEndpoint;
+	let _probeAuthorEffectiveMode = "enabled";
 	const verificationStore = new VerificationStore();
 	const verificationPipeline = createDefaultVerificationPipeline(toSdlcEventBus(eventBus));
 	const _stateStoreCache = new Map();
@@ -13321,7 +13322,7 @@ function createImplementationOrchestrator(deps) {
 				error: err instanceof Error ? err.message : String(err)
 			}, "Failed to parse interface contracts — continuing without contract declarations");
 		}
-		if (storyFilePath) try {
+		if (storyFilePath && _probeAuthorEffectiveMode === "enabled") try {
 			let probeAuthorEpicContent = "";
 			const probeAuthorEpicsPath = findEpicFileForStory(projectRoot ?? process.cwd(), storyKey);
 			if (probeAuthorEpicsPath) try {
@@ -14171,6 +14172,79 @@ function createImplementationOrchestrator(deps) {
 		let schemaValidationRetries = 0;
 		let previousIterationWasMalformed = false;
 		const MAX_SCHEMA_VALIDATION_RETRIES = 3;
+		async function runVerificationAndComplete(args) {
+			const { recordedVerdict, finalReviewCycles, reviewResult, autoApprove } = args;
+			endPhase(storyKey, "code-review");
+			if (config.skipVerification !== true) {
+				const latestReviewSignals = reviewResult != null ? {
+					dispatchFailed: reviewResult.dispatchFailed,
+					error: reviewResult.error,
+					rawOutput: reviewResult.rawOutput
+				} : void 0;
+				let sourceEpicContent;
+				const epicsPath = findEpicFileForStory(projectRoot ?? process.cwd(), storyKey);
+				if (epicsPath) try {
+					const epicFull = readFileSync(epicsPath, "utf-8");
+					const section = extractStorySection(epicFull, storyKey);
+					if (section) sourceEpicContent = section;
+				} catch {}
+				await persistDevStorySignals(storyKey, devStorySignals, runManifest);
+				const verifContext = assembleVerificationContext({
+					storyKey,
+					workingDir: projectRoot ?? process.cwd(),
+					reviewResult: latestReviewSignals,
+					storyContent: storyContentForVerification,
+					devStoryResult: devStorySignals,
+					outputTokenCount: devOutputTokenCount,
+					sourceEpicContent
+				});
+				const verifSummary = await verificationPipeline.run(verifContext, "A");
+				verificationStore.set(storyKey, verifSummary);
+				await persistVerificationResult(storyKey, verifSummary, runManifest);
+				if (verifSummary.status === "fail") {
+					updateStory(storyKey, {
+						phase: "VERIFICATION_FAILED",
+						completedAt: new Date().toISOString()
+					});
+					persistStoryState(storyKey, _stories.get(storyKey)).catch((err) => logger$26.warn({
+						err,
+						storyKey
+					}, "StateStore write failed after verification-failed"));
+					await writeStoryMetricsBestEffort(storyKey, "verification-failed", finalReviewCycles);
+					await persistState();
+					return "verification-failed";
+				}
+			}
+			if (autoApprove !== void 0) eventBus.emit("story:auto-approved", {
+				storyKey,
+				verdict: recordedVerdict,
+				reviewCycles: finalReviewCycles,
+				maxReviewCycles: config.maxReviewCycles,
+				issueCount: autoApprove.issueCount,
+				reason: autoApprove.reason
+			});
+			const completeUpdate = {
+				phase: "COMPLETE",
+				completedAt: new Date().toISOString()
+			};
+			if (autoApprove !== void 0) completeUpdate.reviewCycles = finalReviewCycles;
+			if (autoApprove?.downgradeLastVerdict !== void 0) completeUpdate.lastVerdict = autoApprove.downgradeLastVerdict;
+			updateStory(storyKey, completeUpdate);
+			if (config.skipVerification !== true && runManifest != null) Promise.resolve().then(() => runManifest.read()).then((manifest) => {
+				if (manifest?.per_story_state?.[storyKey]?.verification_result == null) logger$26.warn({
+					storyKey,
+					category: "verification-result-missing"
+				}, "post-COMPLETE invariant: verification_result absent in manifest");
+			}).catch(() => {});
+			await writeStoryMetricsBestEffort(storyKey, recordedVerdict, finalReviewCycles);
+			await writeStoryOutcomeBestEffort(storyKey, "complete", finalReviewCycles);
+			eventBus.emit("orchestrator:story-complete", {
+				storyKey,
+				reviewCycles: finalReviewCycles
+			});
+			await persistState();
+			return "completed";
+		}
 		while (keepReviewing) {
 			await waitIfPaused();
 			if (_state !== "RUNNING") return;
@@ -14457,65 +14531,13 @@ function createImplementationOrchestrator(deps) {
 				return;
 			}
 			if (verdict === "SHIP_IT" || verdict === "LGTM_WITH_NOTES") {
-				endPhase(storyKey, "code-review");
-				if (config.skipVerification !== true) {
-					const latestReviewSignals = reviewResult != null ? {
-						dispatchFailed: reviewResult.dispatchFailed,
-						error: reviewResult.error,
-						rawOutput: reviewResult.rawOutput
-					} : void 0;
-					let sourceEpicContent;
-					const epicsPath1 = findEpicFileForStory(projectRoot ?? process.cwd(), storyKey);
-					if (epicsPath1) try {
-						const epicFull = readFileSync(epicsPath1, "utf-8");
-						const section = extractStorySection(epicFull, storyKey);
-						if (section) sourceEpicContent = section;
-					} catch {}
-					await persistDevStorySignals(storyKey, devStorySignals, runManifest);
-					const verifContext = assembleVerificationContext({
-						storyKey,
-						workingDir: projectRoot ?? process.cwd(),
-						reviewResult: latestReviewSignals,
-						storyContent: storyContentForVerification,
-						devStoryResult: devStorySignals,
-						outputTokenCount: devOutputTokenCount,
-						sourceEpicContent
-					});
-					const verifSummary = await verificationPipeline.run(verifContext, "A");
-					verificationStore.set(storyKey, verifSummary);
-					await persistVerificationResult(storyKey, verifSummary, runManifest);
-					if (verifSummary.status === "fail") {
-						updateStory(storyKey, {
-							phase: "VERIFICATION_FAILED",
-							completedAt: new Date().toISOString()
-						});
-						persistStoryState(storyKey, _stories.get(storyKey)).catch((err) => logger$26.warn({
-							err,
-							storyKey
-						}, "StateStore write failed after verification-failed"));
-						await writeStoryMetricsBestEffort(storyKey, "verification-failed", reviewCycles);
-						await persistState();
-						return;
-					}
-				}
-				updateStory(storyKey, {
-					phase: "COMPLETE",
-					completedAt: new Date().toISOString()
-				});
-				if (config.skipVerification !== true && runManifest != null) Promise.resolve().then(() => runManifest.read()).then((manifest) => {
-					if (manifest?.per_story_state?.[storyKey]?.verification_result == null) logger$26.warn({
-						storyKey,
-						category: "verification-result-missing"
-					}, "post-COMPLETE invariant: verification_result absent in manifest");
-				}).catch(() => {});
 				const completedReviewCycles = reviewCycles + 1;
-				await writeStoryMetricsBestEffort(storyKey, verdict, completedReviewCycles);
-				await writeStoryOutcomeBestEffort(storyKey, "complete", completedReviewCycles);
-				eventBus.emit("orchestrator:story-complete", {
-					storyKey,
-					reviewCycles: completedReviewCycles
+				const outcome = await runVerificationAndComplete({
+					recordedVerdict: verdict,
+					finalReviewCycles: completedReviewCycles,
+					reviewResult
 				});
-				await persistState();
+				if (outcome === "verification-failed") return;
 				if (verdict === "LGTM_WITH_NOTES" && reviewResult.notes && config.pipelineRunId) try {
 					await createDecision(db, {
 						pipeline_run_id: config.pipelineRunId,
@@ -14730,73 +14752,16 @@ function createImplementationOrchestrator(deps) {
 						err
 					}, "Auto-approve fix dispatch failed — approving anyway (issues were minor)");
 				}
-				endPhase(storyKey, "code-review");
-				if (config.skipVerification !== true) {
-					const latestReviewSignals = reviewResult != null ? {
-						dispatchFailed: reviewResult.dispatchFailed,
-						error: reviewResult.error,
-						rawOutput: reviewResult.rawOutput
-					} : void 0;
-					let sourceEpicContent2;
-					const epicsPath2 = findEpicFileForStory(projectRoot ?? process.cwd(), storyKey);
-					if (epicsPath2) try {
-						const epicFull2 = readFileSync(epicsPath2, "utf-8");
-						const section2 = extractStorySection(epicFull2, storyKey);
-						if (section2) sourceEpicContent2 = section2;
-					} catch {}
-					await persistDevStorySignals(storyKey, devStorySignals, runManifest);
-					const verifContext = assembleVerificationContext({
-						storyKey,
-						workingDir: projectRoot ?? process.cwd(),
-						reviewResult: latestReviewSignals,
-						storyContent: storyContentForVerification,
-						devStoryResult: devStorySignals,
-						outputTokenCount: devOutputTokenCount,
-						sourceEpicContent: sourceEpicContent2
-					});
-					const verifSummary = await verificationPipeline.run(verifContext, "A");
-					verificationStore.set(storyKey, verifSummary);
-					await persistVerificationResult(storyKey, verifSummary, runManifest);
-					if (verifSummary.status === "fail") {
-						updateStory(storyKey, {
-							phase: "VERIFICATION_FAILED",
-							completedAt: new Date().toISOString()
-						});
-						persistStoryState(storyKey, _stories.get(storyKey)).catch((err) => logger$26.warn({
-							err,
-							storyKey
-						}, "StateStore write failed after verification-failed"));
-						await writeStoryMetricsBestEffort(storyKey, "verification-failed", finalReviewCycles);
-						await persistState();
-						return;
+				const outcome = await runVerificationAndComplete({
+					recordedVerdict: verdict,
+					finalReviewCycles,
+					reviewResult,
+					autoApprove: {
+						issueCount: issueList.length,
+						reason: `Review cycles exhausted (${finalReviewCycles}/${config.maxReviewCycles}) with only minor issues — auto-approving`
 					}
-				}
-				eventBus.emit("story:auto-approved", {
-					storyKey,
-					verdict,
-					reviewCycles: finalReviewCycles,
-					maxReviewCycles: config.maxReviewCycles,
-					issueCount: issueList.length,
-					reason: `Review cycles exhausted (${finalReviewCycles}/${config.maxReviewCycles}) with only minor issues — auto-approving`
-				});
-				updateStory(storyKey, {
-					phase: "COMPLETE",
-					reviewCycles: finalReviewCycles,
-					completedAt: new Date().toISOString()
 				});
-				if (config.skipVerification !== true && runManifest != null) Promise.resolve().then(() => runManifest.read()).then((manifest) => {
-					if (manifest?.per_story_state?.[storyKey]?.verification_result == null) logger$26.warn({
-						storyKey,
-						category: "verification-result-missing"
-					}, "post-COMPLETE invariant: verification_result absent in manifest");
-				}).catch(() => {});
-				await writeStoryMetricsBestEffort(storyKey, verdict, finalReviewCycles);
-				await writeStoryOutcomeBestEffort(storyKey, "complete", finalReviewCycles);
-				eventBus.emit("orchestrator:story-complete", {
-					storyKey,
-					reviewCycles: finalReviewCycles
-				});
-				await persistState();
+				if (outcome === "verification-failed") return;
 				keepReviewing = false;
 				return;
 			}
@@ -14995,74 +14960,17 @@ function createImplementationOrchestrator(deps) {
 							reviewCycles: finalReviewCycles,
 							issueCount: issueList.length
 						}, "Minor-fixes dispatch timed out — auto-approving as LGTM_WITH_NOTES (original findings retained as warnings)");
-						endPhase(storyKey, "code-review");
-						if (config.skipVerification !== true) {
-							const latestReviewSignals = reviewResult != null ? {
-								dispatchFailed: reviewResult.dispatchFailed,
-								error: reviewResult.error,
-								rawOutput: reviewResult.rawOutput
-							} : void 0;
-							let sourceEpicContent3;
-							const epicsPath3 = findEpicFileForStory(projectRoot ?? process.cwd(), storyKey);
-							if (epicsPath3) try {
-								const epicFull3 = readFileSync(epicsPath3, "utf-8");
-								const section3 = extractStorySection(epicFull3, storyKey);
-								if (section3) sourceEpicContent3 = section3;
-							} catch {}
-							await persistDevStorySignals(storyKey, devStorySignals, runManifest);
-							const verifContext = assembleVerificationContext({
-								storyKey,
-								workingDir: projectRoot ?? process.cwd(),
-								reviewResult: latestReviewSignals,
-								storyContent: storyContentForVerification,
-								devStoryResult: devStorySignals,
-								outputTokenCount: devOutputTokenCount,
-								sourceEpicContent: sourceEpicContent3
-							});
-							const verifSummary = await verificationPipeline.run(verifContext, "A");
-							verificationStore.set(storyKey, verifSummary);
-							await persistVerificationResult(storyKey, verifSummary, runManifest);
-							if (verifSummary.status === "fail") {
-								updateStory(storyKey, {
-									phase: "VERIFICATION_FAILED",
-									completedAt: new Date().toISOString()
-								});
-								persistStoryState(storyKey, _stories.get(storyKey)).catch((err) => logger$26.warn({
-									err,
-									storyKey
-								}, "StateStore write failed after verification-failed"));
-								await writeStoryMetricsBestEffort(storyKey, "verification-failed", finalReviewCycles);
-								await persistState();
-								return;
+						const outcome = await runVerificationAndComplete({
+							recordedVerdict: downgradedVerdict,
+							finalReviewCycles,
+							reviewResult,
+							autoApprove: {
+								issueCount: issueList.length,
+								reason: `Minor-fixes dispatch timed out (cycle ${finalReviewCycles}) — auto-approving as LGTM_WITH_NOTES with original findings retained as warnings`,
+								downgradeLastVerdict: downgradedVerdict
 							}
-						}
-						eventBus.emit("story:auto-approved", {
-							storyKey,
-							verdict: downgradedVerdict,
-							reviewCycles: finalReviewCycles,
-							maxReviewCycles: config.maxReviewCycles,
-							issueCount: issueList.length,
-							reason: `Minor-fixes dispatch timed out (cycle ${finalReviewCycles}) — auto-approving as LGTM_WITH_NOTES with original findings retained as warnings`
-						});
-						updateStory(storyKey, {
-							phase: "COMPLETE",
-							reviewCycles: finalReviewCycles,
-							lastVerdict: downgradedVerdict,
-							completedAt: new Date().toISOString()
 						});
-						if (config.skipVerification !== true && runManifest != null) Promise.resolve().then(() => runManifest.read()).then((manifest) => {
-							if (manifest?.per_story_state?.[storyKey]?.verification_result == null) logger$26.warn({
-								storyKey,
-								category: "verification-result-missing"
-							}, "post-COMPLETE invariant: verification_result absent in manifest");
-						}).catch(() => {});
-						await writeStoryMetricsBestEffort(storyKey, downgradedVerdict, finalReviewCycles);
-						await writeStoryOutcomeBestEffort(storyKey, "complete", finalReviewCycles);
-						eventBus.emit("orchestrator:story-complete", {
-							storyKey,
-							reviewCycles: finalReviewCycles
-						});
-						await persistState();
+						if (outcome === "verification-failed") return;
 						keepReviewing = false;
 						return;
 					}
@@ -15327,6 +15235,33 @@ function createImplementationOrchestrator(deps) {
 			storyKeys,
 			pipelineRunId: config.pipelineRunId
 		});
+		{
+			const cliMode = config.probeAuthorMode;
+			let effectiveMode;
+			let source;
+			if (cliMode === "enabled" || cliMode === "disabled") {
+				effectiveMode = cliMode;
+				source = "cli";
+			} else {
+				const envValue = process.env.SUBSTRATE_PROBE_AUTHOR_ENABLED;
+				if (envValue === "false" || envValue === "0") {
+					effectiveMode = "disabled";
+					source = "env";
+				} else if (envValue === "true" || envValue === "1") {
+					effectiveMode = "enabled";
+					source = "env";
+				} else {
+					effectiveMode = "enabled";
+					source = "default";
+				}
+			}
+			_probeAuthorEffectiveMode = effectiveMode;
+			eventBus.emit("probe-author:enabled", {
+				runId: config.pipelineRunId ?? "",
+				mode: effectiveMode,
+				source
+			});
+		}
 		await persistState();
 		recordProgress();
 		if (config.enableHeartbeat) startHeartbeat();
@@ -43831,7 +43766,18 @@ function wireNdjsonEmitter(eventBus, ndjsonEmitter) {
 	});
 }
 async function runRunAction(options) {
-	const { pack: packName, from: startPhase, stopAfter, concept: conceptArg, conceptFile, stories: storiesArg, concurrency, outputFormat, projectRoot, events: eventsFlag, verbose: verboseFlag, tui: tuiFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, skipVerification, epic: epicNumber, dryRun, maxReviewCycles = 2, engine, agent: agentId, registry: injectedRegistry, haltOn, costCeiling } = options;
+	const { pack: packName, from: startPhase, stopAfter, concept: conceptArg, conceptFile, stories: storiesArg, concurrency, outputFormat, projectRoot, events: eventsFlag, verbose: verboseFlag, tui: tuiFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, skipVerification, epic: epicNumber, dryRun, maxReviewCycles = 2, engine, agent: agentId, registry: injectedRegistry, haltOn, costCeiling, probeAuthor } = options;
+	const VALID_PROBE_AUTHOR_MODES = [
+		"enabled",
+		"disabled",
+		"auto"
+	];
+	if (probeAuthor !== void 0 && !VALID_PROBE_AUTHOR_MODES.includes(probeAuthor)) {
+		const errorMsg = `Invalid --probe-author value '${probeAuthor}'. Valid values: enabled | disabled | auto`;
+		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
+		else process.stderr.write(`Error: ${errorMsg}\n`);
+		return 1;
+	}
 	const VALID_HALT_ON = [
 		"all",
 		"critical",
@@ -44026,6 +43972,7 @@ async function runRunAction(options) {
 			meshUrl,
 			meshProjectId
 		} : {},
+		...probeAuthor !== void 0 ? { probeAuthor } : {},
 		engineType: resolvedEngine,
 		maxReviewCycles: effectiveMaxReviewCycles,
 		retryBudget: configRetryBudget ?? 2,
@@ -44563,7 +44510,8 @@ async function runRunAction(options) {
 					pipelineRunId: pipelineRun.id,
 					enableHeartbeat: eventsFlag === true,
 					skipPreflight: skipPreflight === true,
-					...skipVerification === true ? { skipVerification: true } : {}
+					...skipVerification === true ? { skipVerification: true } : {},
+					...probeAuthor !== void 0 ? { probeAuthorMode: probeAuthor } : {}
 				},
 				projectRoot,
 				tokenCeilings,
@@ -44694,7 +44642,7 @@ async function runRunAction(options) {
 	}
 }
 async function runFullPipeline(options) {
-	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, projectRoot, events: eventsFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, skipVerification, maxReviewCycles = 2, retryBudget, registry: injectedRegistry, tokenCeilings, stories: explicitStories, telemetryEnabled: fullTelemetryEnabled, telemetryPort: fullTelemetryPort, agentId, meshUrl: fpMeshUrl, meshProjectId: fpMeshProjectId, engineType: fpEngineType } = options;
+	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, projectRoot, events: eventsFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, skipVerification, maxReviewCycles = 2, retryBudget, registry: injectedRegistry, tokenCeilings, stories: explicitStories, telemetryEnabled: fullTelemetryEnabled, telemetryPort: fullTelemetryPort, agentId, meshUrl: fpMeshUrl, meshProjectId: fpMeshProjectId, engineType: fpEngineType, probeAuthor } = options;
 	if (!existsSync$1(dbDir)) mkdirSync$1(dbDir, { recursive: true });
 	let doltServerFull = null;
 	try {
@@ -44995,7 +44943,8 @@ async function runFullPipeline(options) {
 						retryBudget: retryBudget ?? 2,
 						pipelineRunId: runId,
 						skipPreflight: skipPreflight === true,
-						...skipVerification === true ? { skipVerification: true } : {}
+						...skipVerification === true ? { skipVerification: true } : {},
+						...probeAuthor !== void 0 ? { probeAuthorMode: probeAuthor } : {}
 					},
 					projectRoot,
 					tokenCeilings,
@@ -45151,7 +45100,7 @@ async function runFullPipeline(options) {
 	}
 }
 function registerRunCommand(program, _version = "0.0.0", projectRoot = process.cwd(), registry) {
-	program.command("run").description("Run the autonomous pipeline (use --from to start from a specific phase)").option("--pack <name>", "Methodology pack name", "bmad").option("--from <phase>", "Start from this phase: analysis, planning, solutioning, implementation").option("--stop-after <phase>", "Stop pipeline after this phase completes").option("--concept <text>", "Inline concept text (required when --from analysis)").option("--concept-file <path>", "Path to a file containing the concept text").option("--stories <keys>", "Comma-separated story keys (e.g., 10-1,10-2)").option("--epic <n>", "Scope story discovery to a single epic number (e.g., 27)", (v) => parseInt(v, 10)).option("--concurrency <n>", "Maximum parallel conflict groups", (v) => parseInt(v, 10), 3).option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").option("--events", "Emit structured NDJSON events on stdout for programmatic consumption").option("--verbose", "Show detailed pino log output").option("--help-agent", "Print a machine-optimized prompt fragment for AI agents and exit").option("--tui", "Show TUI dashboard").option("--skip-ux", "Skip the UX design phase even if enabled in the pack manifest").option("--research", "Enable the research phase even if not set in the pack manifest").option("--skip-research", "Skip the research phase even if enabled in the pack manifest").option("--skip-preflight", "Skip the pre-flight build check (escape hatch for known-broken projects)").option("--skip-verification", "Skip the post-dispatch verification pipeline (Story 51-5)").option("--max-review-cycles <n>", "Maximum review cycles per story (default: 2)", (v) => parseInt(v, 10), 2).option("--dry-run", "Preview routing and repo-map injection without dispatching (Story 28-9)").option("--engine <type>", "Execution engine: linear (default) or graph").option("--agent <id>", "Agent backend: claude-code (default), codex, or gemini").option("--halt-on <severity>", "Halt pipeline on escalation severity: all | critical | none (default: none)", "none").option("--cost-ceiling <amount>", "Maximum cost ceiling in USD (positive number); halts pipeline when exceeded", parseFloat).action(async (opts) => {
+	program.command("run").description("Run the autonomous pipeline (use --from to start from a specific phase)").option("--pack <name>", "Methodology pack name", "bmad").option("--from <phase>", "Start from this phase: analysis, planning, solutioning, implementation").option("--stop-after <phase>", "Stop pipeline after this phase completes").option("--concept <text>", "Inline concept text (required when --from analysis)").option("--concept-file <path>", "Path to a file containing the concept text").option("--stories <keys>", "Comma-separated story keys (e.g., 10-1,10-2)").option("--epic <n>", "Scope story discovery to a single epic number (e.g., 27)", (v) => parseInt(v, 10)).option("--concurrency <n>", "Maximum parallel conflict groups", (v) => parseInt(v, 10), 3).option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").option("--events", "Emit structured NDJSON events on stdout for programmatic consumption").option("--verbose", "Show detailed pino log output").option("--help-agent", "Print a machine-optimized prompt fragment for AI agents and exit").option("--tui", "Show TUI dashboard").option("--skip-ux", "Skip the UX design phase even if enabled in the pack manifest").option("--research", "Enable the research phase even if not set in the pack manifest").option("--skip-research", "Skip the research phase even if enabled in the pack manifest").option("--skip-preflight", "Skip the pre-flight build check (escape hatch for known-broken projects)").option("--skip-verification", "Skip the post-dispatch verification pipeline (Story 51-5)").option("--max-review-cycles <n>", "Maximum review cycles per story (default: 2)", (v) => parseInt(v, 10), 2).option("--dry-run", "Preview routing and repo-map injection without dispatching (Story 28-9)").option("--engine <type>", "Execution engine: linear (default) or graph").option("--agent <id>", "Agent backend: claude-code (default), codex, or gemini").option("--halt-on <severity>", "Halt pipeline on escalation severity: all | critical | none (default: none)", "none").option("--cost-ceiling <amount>", "Maximum cost ceiling in USD (positive number); halts pipeline when exceeded", parseFloat).option("--probe-author <mode>", "probe-author phase mode: enabled | disabled | auto (default: auto = SUBSTRATE_PROBE_AUTHOR_ENABLED env, default true) (Story 60-14)", "auto").action(async (opts) => {
 		if (opts.helpAgent) {
 			process.exitCode = await runHelpAgent();
 			return;
@@ -45193,7 +45142,8 @@ function registerRunCommand(program, _version = "0.0.0", projectRoot = process.c
 			agent: opts.agent,
 			registry,
 			haltOn: opts.haltOn,
-			costCeiling: opts.costCeiling
+			costCeiling: opts.costCeiling,
+			probeAuthor: opts.probeAuthor
 		});
 		process.exitCode = exitCode;
 	});
@@ -45201,4 +45151,4 @@ function registerRunCommand(program, _version = "0.0.0", projectRoot = process.c
 
 //#endregion
 export { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, normalizeGraphSummaryToStatus, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveMaxReviewCycles, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runRunAction, runSolutioningPhase, validateStopAfterFromConflict, wireNdjsonEmitter };
-//# sourceMappingURL=run-BQxm1Qix.js.map
+//# sourceMappingURL=run-YBY2vrF4.js.map

package/dist/{run-B7jP4apv.js → run-__o2iU0w.js}

@@ -1,8 +1,8 @@
-import "./health-CnV6ndAb.js";
+import "./health-BAcRfZ4s.js";
 import "./logger-KeHncl-f.js";
 import "./helpers-CElYrONe.js";
 import "./dist-BnMsd9hC.js";
-import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, runRunAction, wireNdjsonEmitter } from "./run-BQxm1Qix.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, runRunAction, wireNdjsonEmitter } from "./run-YBY2vrF4.js";
 import "./routing-CcBOCuC9.js";
 import "./decisions-C0pz9Clx.js";
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.20.34",
+  "version": "0.20.36",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",