substrate-ai 0.19.9 → 0.19.11

package/dist/cli/index.js

@@ -4,7 +4,7 @@ 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, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, tagRunAsBaseline, updatePipelineRun } from "../dist-adzGUKPc.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-Dg_BEJB6.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-BLxcApKZ.js";
 import "../errors-CZdr5Wqb.js";
 import "../routing-CcBOCuC9.js";
 import "../decisions-C0pz9Clx.js";
@@ -1155,7 +1155,8 @@ const SubstrateConfigSchema = z.object({
 	budget: BudgetConfigSchema.optional(),
 	token_ceilings: TokenCeilingsSchema.optional(),
 	dispatch_timeouts: DispatchTimeoutsSchema.optional(),
-	telemetry: TelemetryConfigSchema.optional()
+	telemetry: TelemetryConfigSchema.optional(),
+	default_agent: z.string().optional()
 }).strict();
 const PartialSubstrateConfigSchema = z.object({
 	config_format_version: z.enum(["1"]).optional(),
@@ -1170,7 +1171,8 @@ const PartialSubstrateConfigSchema = z.object({
 	budget: BudgetConfigSchema.partial().optional(),
 	token_ceilings: TokenCeilingsSchema.optional(),
 	dispatch_timeouts: DispatchTimeoutsSchema.optional(),
-	telemetry: TelemetryConfigSchema.partial().optional()
+	telemetry: TelemetryConfigSchema.partial().optional(),
+	default_agent: z.string().optional()
 }).strict();
 
 //#endregion
@@ -2676,7 +2678,7 @@ function mapInternalPhaseToEventPhase(internalPhase) {
 	}
 }
 async function runResumeAction(options) {
-	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName, events: eventsFlag, registry, maxReviewCycles = 2 } = options;
+	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName, events: eventsFlag, registry, maxReviewCycles = 2, agent: agentId$1 } = options;
 	if (stopAfter !== void 0 && !VALID_PHASES.includes(stopAfter)) {
 		const errorMsg = `Invalid phase: "${stopAfter}". Valid phases: ${VALID_PHASES.join(", ")}`;
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
@@ -2836,7 +2838,7 @@ async function runFullPipelineFromPhase(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, runId, {
 						phase: "analysis",
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -2856,7 +2858,7 @@ async function runFullPipelineFromPhase(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, runId, {
 						phase: "planning",
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -2876,7 +2878,7 @@ async function runFullPipelineFromPhase(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, runId, {
 						phase: "solutioning",
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -2917,6 +2919,7 @@ async function runFullPipelineFromPhase(options) {
 						enableHeartbeat: eventsFlag === true
 					},
 					projectRoot,
+					agentId,
 					...ingestionServer !== void 0 ? { ingestionServer } : {},
 					...telemetryPersistence !== void 0 ? { telemetryPersistence } : {}
 				});
@@ -3005,7 +3008,7 @@ async function runFullPipelineFromPhase(options) {
 							const costUsd = (input * 3 + output * 15) / 1e6;
 							addTokenUsage(adapter, runId, {
 								phase: payload.phase,
-								agent: "claude-code",
+								agent: agentId ?? "claude-code",
 								input_tokens: input,
 								output_tokens: output,
 								cost_usd: costUsd
@@ -3092,7 +3095,7 @@ async function runFullPipelineFromPhase(options) {
 	}
 }
 function registerResumeCommand(program, _version = "0.0.0", projectRoot = process.cwd(), registry) {
-	program.command("resume").description("Resume a previously interrupted pipeline run").option("--run-id <id>", "Pipeline run ID to resume (defaults to latest)").option("--pack <name>", "Methodology pack name", "bmad").option("--stop-after <phase>", "Stop pipeline after this phase completes (overrides saved state)").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("--max-review-cycles <n>", "Maximum review cycles per story (default: 2)", (v) => parseInt(v, 10), 2).action(async (opts) => {
+	program.command("resume").description("Resume a previously interrupted pipeline run").option("--run-id <id>", "Pipeline run ID to resume (defaults to latest)").option("--pack <name>", "Methodology pack name", "bmad").option("--stop-after <phase>", "Stop pipeline after this phase completes (overrides saved state)").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("--max-review-cycles <n>", "Maximum review cycles per story (default: 2)", (v) => parseInt(v, 10), 2).option("--agent <id>", "Agent backend: claude-code (default), codex, or gemini").action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		const exitCode = await runResumeAction({
 			runId: opts.runId,
@@ -3103,6 +3106,7 @@ function registerResumeCommand(program, _version = "0.0.0", projectRoot = proces
 			pack: opts.pack,
 			events: opts.events,
 			maxReviewCycles: opts.maxReviewCycles,
+			agent: opts.agent,
 			registry
 		});
 		process.exitCode = exitCode;
@@ -3746,7 +3750,7 @@ async function runPostPhaseSupersessionDetection(adapter, amendmentRunId, curren
 	}
 }
 async function runAmendAction(options) {
-	const { concept: conceptArg, conceptFile, runId: specifiedRunId, stopAfter, from: startPhase, projectRoot, pack: packName, registry: injectedRegistry } = options;
+	const { concept: conceptArg, conceptFile, runId: specifiedRunId, stopAfter, from: startPhase, projectRoot, pack: packName, registry: injectedRegistry, agent: agentId$1 } = options;
 	let concept;
 	if (conceptFile !== void 0 && conceptFile !== "") try {
 		concept = await readFile(conceptFile, "utf-8");
@@ -3844,7 +3848,8 @@ async function runAmendAction(options) {
 			db: adapter,
 			pack,
 			contextCompiler,
-			dispatcher
+			dispatcher,
+			agentId: agentId$1
 		};
 		const phaseOrder = [
 			"analysis",
@@ -3888,7 +3893,7 @@ async function runAmendAction(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, amendmentRunId, {
 						phase: "analysis",
-						agent: "claude-code",
+						agent: agentId$1 ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -3910,7 +3915,7 @@ async function runAmendAction(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, amendmentRunId, {
 						phase: "planning",
-						agent: "claude-code",
+						agent: agentId$1 ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -3932,7 +3937,7 @@ async function runAmendAction(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, amendmentRunId, {
 						phase: "solutioning",
-						agent: "claude-code",
+						agent: agentId$1 ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -4003,7 +4008,7 @@ async function runAmendAction(options) {
 	}
 }
 function registerAmendCommand(program, _version = "0.0.0", projectRoot = process.cwd(), registry) {
-	program.command("amend").description("Run an amendment pipeline against a completed run and an existing run").option("--concept <text>", "Amendment concept description (inline)").option("--concept-file <path>", "Path to concept file").option("--run-id <id>", "Parent run ID (defaults to latest completed run)").option("--stop-after <phase>", "Stop pipeline after this phase completes").option("--from <phase>", "Start pipeline from this phase").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").action(async (opts) => {
+	program.command("amend").description("Run an amendment pipeline against a completed run and an existing run").option("--concept <text>", "Amendment concept description (inline)").option("--concept-file <path>", "Path to concept file").option("--run-id <id>", "Parent run ID (defaults to latest completed run)").option("--stop-after <phase>", "Stop pipeline after this phase completes").option("--from <phase>", "Start pipeline from this phase").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").option("--agent <id>", "Agent backend: claude-code (default), codex, or gemini").action(async (opts) => {
 		const exitCode = await runAmendAction({
 			concept: opts.concept,
 			conceptFile: opts.conceptFile,
@@ -4012,6 +4017,7 @@ function registerAmendCommand(program, _version = "0.0.0", projectRoot = process
 			from: opts.from,
 			projectRoot: opts.projectRoot,
 			pack: opts.pack,
+			agent: opts.agent,
 			registry
 		});
 		process.exitCode = exitCode;
@@ -4547,7 +4553,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-0y5KOffG.js"
+									"../run-Ds3ucwad.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -7159,7 +7165,7 @@ function registerBrainstormCommand(program, _version = "0.0.0", projectRoot = pr
 //#region src/cli/commands/retry-escalated.ts
 const logger$3 = createLogger("retry-escalated-cmd");
 async function runRetryEscalatedAction(options) {
-	const { runId, dryRun, force, outputFormat, projectRoot, concurrency, pack: packName, registry: injectedRegistry } = options;
+	const { runId, dryRun, force, outputFormat, projectRoot, concurrency, pack: packName, registry: injectedRegistry, agent: agentId$1 } = options;
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
 	const dbPath = join(dbRoot, ".substrate", "substrate.db");
 	const doltDir = join(dbRoot, ".substrate", "state", ".dolt");
@@ -7262,7 +7268,8 @@ async function runRetryEscalatedAction(options) {
 				pipelineRunId: pipelineRun.id,
 				...Object.keys(perStoryContextCeilings).length > 0 ? { perStoryContextCeilings } : {}
 			},
-			projectRoot
+			projectRoot,
+			agentId: agentId$1
 		});
 		eventBus.on("orchestrator:story-phase-complete", (payload) => {
 			try {
@@ -7272,7 +7279,7 @@ async function runRetryEscalatedAction(options) {
 					const costUsd = (input * 3 + output * 15) / 1e6;
 					addTokenUsage(adapter, pipelineRun.id, {
 						phase: payload.phase,
-						agent: "claude-code",
+						agent: agentId$1 ?? "claude-code",
 						input_tokens: input,
 						output_tokens: output,
 						cost_usd: costUsd
@@ -7316,7 +7323,7 @@ function registerRetryEscalatedCommand(program, _version = "0.0.0", projectRoot
 		const n = parseInt(v, 10);
 		if (isNaN(n) || n < 1) throw new Error(`--concurrency must be a positive integer, got: ${v}`);
 		return n;
-	}, 3).option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").action(async (opts) => {
+	}, 3).option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").option("--agent <id>", "Agent backend: claude-code (default), codex, or gemini").action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		const exitCode = await runRetryEscalatedAction({
 			runId: opts.runId,
@@ -7326,6 +7333,7 @@ function registerRetryEscalatedCommand(program, _version = "0.0.0", projectRoot
 			projectRoot: opts.projectRoot,
 			concurrency: opts.concurrency,
 			pack: opts.pack,
+			agent: opts.agent,
 			registry
 		});
 		process.exitCode = exitCode;

package/dist/index.d.ts

@@ -94,6 +94,8 @@ interface PipelineStartEvent {
   stories: string[];
   /** Maximum parallel conflict groups */
   concurrency: number;
+  /** Execution engine: 'linear' or 'graph' */
+  engine?: string;
 }
 /**
  * Emitted as the last event when the pipeline finishes.
@@ -1526,6 +1528,7 @@ declare const SubstrateConfigSchema: z.ZodObject<{
     enabled: z.ZodDefault<z.ZodBoolean>;
     port: z.ZodDefault<z.ZodNumber>;
   }, z.core.$strict>>;
+  default_agent: z.ZodOptional<z.ZodString>;
 }, z.core.$strict>;
 type SubstrateConfig = z.infer<typeof SubstrateConfigSchema>;
 

package/dist/{run-Dg_BEJB6.js → run-BLxcApKZ.js}

@@ -5284,6 +5284,15 @@ async function runCreateStory(deps, params) {
 	const implementationDecisions = await getImplementationDecisions(deps);
 	const epicShardContent = getEpicShard(implementationDecisions, epicId, deps.projectRoot, storyKey);
 	const prevDevNotesContent = getPrevDevNotes(implementationDecisions, epicId);
+	let storyDefinitionContent = "";
+	try {
+		const storyDecisions = await getDecisionsByPhase(deps.db, "solutioning");
+		const storyDef = storyDecisions.find((d) => d.category === "stories" && d.key === storyKey);
+		if (storyDef) {
+			storyDefinitionContent = storyDef.value;
+			logger$18.debug({ storyKey }, "Injected story definition from solutioning decisions");
+		}
+	} catch {}
 	const archConstraintsContent = await getArchConstraints$3(deps);
 	const storyTemplateContent = await getStoryTemplate(deps);
 	const { prompt, tokenCount, truncated } = assemblePrompt(template, [
@@ -5297,6 +5306,11 @@ async function runCreateStory(deps, params) {
 			content: epicShardContent,
 			priority: "required"
 		},
+		{
+			name: "story_definition",
+			content: storyDefinitionContent,
+			priority: "required"
+		},
 		{
 			name: "arch_constraints",
 			content: archConstraintsContent,
@@ -5320,7 +5334,7 @@ async function runCreateStory(deps, params) {
 	}, "Prompt assembled for create-story");
 	const handle = deps.dispatcher.dispatch({
 		prompt,
-		agent: "claude-code",
+		agent: deps.agentId ?? "claude-code",
 		taskType: "create-story",
 		outputSchema: CreateStoryResultSchema,
 		maxTurns: 50,
@@ -6542,7 +6556,7 @@ async function runDevStory(deps, params) {
 	try {
 		const handle = deps.dispatcher.dispatch({
 			prompt,
-			agent: "claude-code",
+			agent: deps.agentId ?? "claude-code",
 			taskType: "dev-story",
 			timeout: DEFAULT_TIMEOUT_MS$1,
 			outputSchema: DevStoryResultSchema,
@@ -7011,7 +7025,7 @@ async function runCodeReview(deps, params) {
 	const { prompt } = assembleResult;
 	const handle = deps.dispatcher.dispatch({
 		prompt,
-		agent: "claude-code",
+		agent: deps.agentId ?? "claude-code",
 		taskType: "code-review",
 		outputSchema: CodeReviewResultSchema,
 		workingDirectory: deps.projectRoot,
@@ -7226,7 +7240,7 @@ async function runTestPlan(deps, params) {
 	try {
 		const handle = deps.dispatcher.dispatch({
 			prompt,
-			agent: "claude-code",
+			agent: deps.agentId ?? "claude-code",
 			taskType: "test-plan",
 			timeout: DEFAULT_TIMEOUT_MS,
 			outputSchema: TestPlanResultSchema,
@@ -7497,7 +7511,7 @@ async function runTestExpansion(deps, params) {
 	const { prompt } = assembleResult;
 	const handle = deps.dispatcher.dispatch({
 		prompt,
-		agent: "claude-code",
+		agent: deps.agentId ?? "claude-code",
 		taskType: "test-expansion",
 		outputSchema: TestExpansionResultSchema,
 		workingDirectory: deps.projectRoot,
@@ -11617,7 +11631,7 @@ function createImplementationOrchestrator(deps) {
 					startPhase(storyKey, "dev-story-retry");
 					const checkpointRetryHandle = dispatcher.dispatch({
 						prompt: checkpointRetryPrompt,
-						agent: "claude-code",
+						agent: deps.agentId ?? "claude-code",
 						taskType: "dev-story",
 						outputSchema: DevStoryResultSchema,
 						...checkpointRetryMaxTurns !== void 0 ? { maxTurns: checkpointRetryMaxTurns } : {},
@@ -11888,7 +11902,7 @@ function createImplementationOrchestrator(deps) {
 						incrementDispatches(storyKey);
 						const fixHandle = dispatcher.dispatch({
 							prompt: buildFixPrompt,
-							agent: "claude-code",
+							agent: deps.agentId ?? "claude-code",
 							taskType: "build-fix",
 							maxTurns: 15,
 							workingDirectory: projectRoot ?? process.cwd(),
@@ -12378,7 +12392,7 @@ function createImplementationOrchestrator(deps) {
 					}
 					const handle = dispatcher.dispatch({
 						prompt: fixPrompt,
-						agent: "claude-code",
+						agent: deps.agentId ?? "claude-code",
 						taskType: "minor-fixes",
 						workingDirectory: projectRoot,
 						...autoApproveMaxTurns !== void 0 ? { maxTurns: autoApproveMaxTurns } : {},
@@ -12537,7 +12551,7 @@ function createImplementationOrchestrator(deps) {
 				incrementDispatches(storyKey);
 				const handle = isMajorRework ? dispatcher.dispatch({
 					prompt: fixPrompt,
-					agent: "claude-code",
+					agent: deps.agentId ?? "claude-code",
 					taskType,
 					...fixModel !== void 0 ? { model: fixModel } : {},
 					outputSchema: DevStoryResultSchema,
@@ -12547,7 +12561,7 @@ function createImplementationOrchestrator(deps) {
 					..._otlpEndpoint !== void 0 ? { otlpEndpoint: _otlpEndpoint } : {}
 				}) : dispatcher.dispatch({
 					prompt: fixPrompt,
-					agent: "claude-code",
+					agent: deps.agentId ?? "claude-code",
 					taskType,
 					...fixModel !== void 0 ? { model: fixModel } : {},
 					...fixMaxTurns !== void 0 ? { maxTurns: fixMaxTurns } : {},
@@ -13757,7 +13771,7 @@ async function runCritiqueLoop(artifact, phaseId, runId, phase, deps, options =
 		try {
 			const handle = deps.dispatcher.dispatch({
 				prompt: critiquePrompt,
-				agent: "claude-code",
+				agent: deps.agentId ?? "claude-code",
 				taskType: "critique",
 				outputSchema: CritiqueOutputSchema
 			});
@@ -13868,7 +13882,7 @@ async function runCritiqueLoop(artifact, phaseId, runId, phase, deps, options =
 			try {
 				const refineHandle = deps.dispatcher.dispatch({
 					prompt: refinePrompt,
-					agent: "claude-code",
+					agent: deps.agentId ?? "claude-code",
 					taskType: "critique",
 					outputSchema: void 0
 				});
@@ -14546,7 +14560,7 @@ async function runSteps(steps, deps, runId, phase, params) {
 		}
 		const handle = deps.dispatcher.dispatch({
 			prompt,
-			agent: "claude-code",
+			agent: deps.agentId ?? "claude-code",
 			taskType: step.taskType,
 			outputSchema: step.outputSchema
 		});
@@ -14725,7 +14739,7 @@ async function runSteps(steps, deps, runId, phase, params) {
 					const elicitPrompt = elicitationTemplate.replace(/\{\{method_name\}\}/g, method.name).replace(/\{\{method_description\}\}/g, method.description).replace(/\{\{output_pattern\}\}/g, method.output_pattern).replace(/\{\{artifact_content\}\}/g, artifactContent);
 					const elicitHandle = deps.dispatcher.dispatch({
 						prompt: elicitPrompt,
-						agent: "claude-code",
+						agent: deps.agentId ?? "claude-code",
 						taskType: "elicitation",
 						outputSchema: ElicitationOutputSchema
 					});
@@ -15069,7 +15083,7 @@ async function runAnalysisPhase(deps, params) {
 		};
 		const handle = dispatcher.dispatch({
 			prompt,
-			agent: "claude-code",
+			agent: deps.agentId ?? "claude-code",
 			taskType: "analysis",
 			outputSchema: AnalysisOutputSchema
 		});
@@ -15381,7 +15395,7 @@ async function runPlanningMultiStep(deps, params) {
 				correctedPrompt = correctionPrefix + correctedPrompt;
 				const retryHandle = deps.dispatcher.dispatch({
 					prompt: correctedPrompt,
-					agent: "claude-code",
+					agent: deps.agentId ?? "claude-code",
 					taskType: "planning-nfrs",
 					outputSchema: PlanningNFRsOutputSchema
 				});
@@ -15501,7 +15515,7 @@ async function runPlanningPhase(deps, params) {
 		};
 		const handle = dispatcher.dispatch({
 			prompt,
-			agent: "claude-code",
+			agent: deps.agentId ?? "claude-code",
 			taskType: "planning",
 			outputSchema: PlanningOutputSchema
 		});
@@ -15801,7 +15815,7 @@ async function runArchitectureGeneration(deps, params) {
 	};
 	const handle = dispatcher.dispatch({
 		prompt,
-		agent: "claude-code",
+		agent: deps.agentId ?? "claude-code",
 		taskType: "architecture",
 		outputSchema: ArchitectureOutputSchema
 	});
@@ -15903,7 +15917,7 @@ async function runStoryGeneration(deps, params, gapAnalysis) {
 	};
 	const handle = dispatcher.dispatch({
 		prompt,
-		agent: "claude-code",
+		agent: deps.agentId ?? "claude-code",
 		taskType: "story-generation",
 		outputSchema: StoryGenerationOutputSchema
 	});
@@ -16081,7 +16095,7 @@ async function runReadinessCheck(deps, runId) {
 	else prompt = prompt.replace(READINESS_UX_PLACEHOLDER, "");
 	const handle = dispatcher.dispatch({
 		prompt,
-		agent: "claude-code",
+		agent: deps.agentId ?? "claude-code",
 		taskType: "readiness-check",
 		outputSchema: ReadinessOutputSchema
 	});
@@ -40360,7 +40374,7 @@ 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, epic: epicNumber, dryRun, maxReviewCycles = 2, engine, registry: injectedRegistry } = 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, epic: epicNumber, dryRun, maxReviewCycles = 2, engine, agent: agentId, registry: injectedRegistry } = options;
 	const resolvedEngine = engine ?? "linear";
 	if (!VALID_ENGINES.includes(resolvedEngine)) {
 		const errorMsg = `Invalid engine '${engine}'. Valid values: ${VALID_ENGINES.join(", ")}`;
@@ -40524,7 +40538,8 @@ async function runRunAction(options) {
 			telemetryEnabled: true,
 			telemetryPort
 		} : {},
-		maxReviewCycles
+		maxReviewCycles,
+		agentId
 	});
 	let storyKeys = [...parsedStoryKeys];
 	if (!existsSync$1(dbDir)) mkdirSync$1(dbDir, { recursive: true });
@@ -40742,7 +40757,7 @@ async function runRunAction(options) {
 					const costUsd = (input * 3 + output * 15) / 1e6;
 					addTokenUsage(adapter, pipelineRun.id, {
 						phase: payload.phase,
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: input,
 						output_tokens: output,
 						cost_usd: costUsd,
@@ -40956,7 +40971,8 @@ async function runRunAction(options) {
 				pack,
 				contextCompiler,
 				dispatcher,
-				projectRoot
+				projectRoot,
+				agentId
 			};
 			const sdlcEventBus = eventBus;
 			const handlerRegistry = buildSdlcHandlerRegistry({
@@ -40966,7 +40982,8 @@ async function runRunAction(options) {
 						db: adapter,
 						pack,
 						contextCompiler,
-						dispatcher
+						dispatcher,
+						agentId
 					},
 					phases: {
 						analysis: runAnalysisPhase,
@@ -41034,6 +41051,7 @@ async function runRunAction(options) {
 				},
 				projectRoot,
 				tokenCeilings,
+				agentId,
 				...ingestionServer !== void 0 ? { ingestionServer } : {},
 				...telemetryPersistence !== void 0 ? { telemetryPersistence } : {},
 				...repoMapInjector !== void 0 ? {
@@ -41147,7 +41165,7 @@ 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, maxReviewCycles = 2, registry: injectedRegistry, tokenCeilings, stories: explicitStories, telemetryEnabled: fullTelemetryEnabled, telemetryPort: fullTelemetryPort } = options;
+	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, projectRoot, events: eventsFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, maxReviewCycles = 2, registry: injectedRegistry, tokenCeilings, stories: explicitStories, telemetryEnabled: fullTelemetryEnabled, telemetryPort: fullTelemetryPort, agentId } = options;
 	if (!existsSync$1(dbDir)) mkdirSync$1(dbDir, { recursive: true });
 	const adapter = createDatabaseAdapter({
 		backend: "auto",
@@ -41188,7 +41206,8 @@ async function runFullPipeline(options) {
 			db: adapter,
 			pack,
 			contextCompiler,
-			dispatcher
+			dispatcher,
+			agentId
 		};
 		let effectiveResearch = pack.manifest.research === true;
 		if (researchFlag === true) effectiveResearch = true;
@@ -41280,7 +41299,7 @@ async function runFullPipeline(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, runId, {
 						phase: "analysis",
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -41305,7 +41324,7 @@ async function runFullPipeline(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, runId, {
 						phase: "planning",
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -41333,7 +41352,7 @@ async function runFullPipeline(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, runId, {
 						phase: "research",
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -41358,7 +41377,7 @@ async function runFullPipeline(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, runId, {
 						phase: "ux-design",
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -41383,7 +41402,7 @@ async function runFullPipeline(options) {
 					const costUsd = (result.tokenUsage.input * 3 + result.tokenUsage.output * 15) / 1e6;
 					await addTokenUsage(adapter, runId, {
 						phase: "solutioning",
-						agent: "claude-code",
+						agent: agentId ?? "claude-code",
 						input_tokens: result.tokenUsage.input,
 						output_tokens: result.tokenUsage.output,
 						cost_usd: costUsd
@@ -41442,6 +41461,7 @@ async function runFullPipeline(options) {
 					},
 					projectRoot,
 					tokenCeilings,
+					agentId,
 					...fpIngestionServer !== void 0 ? { ingestionServer: fpIngestionServer } : {},
 					...fpTelemetryPersistence !== void 0 ? { telemetryPersistence: fpTelemetryPersistence } : {}
 				});
@@ -41453,7 +41473,7 @@ async function runFullPipeline(options) {
 							const costUsd = (input * 3 + output * 15) / 1e6;
 							addTokenUsage(adapter, runId, {
 								phase: payload.phase,
-								agent: "claude-code",
+								agent: agentId ?? "claude-code",
 								input_tokens: input,
 								output_tokens: output,
 								cost_usd: costUsd
@@ -41574,7 +41594,7 @@ 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("--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").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("--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").action(async (opts) => {
 		if (opts.helpAgent) {
 			process.exitCode = await runHelpAgent();
 			return;
@@ -41612,6 +41632,7 @@ function registerRunCommand(program, _version = "0.0.0", projectRoot = process.c
 			maxReviewCycles: opts.maxReviewCycles,
 			dryRun: opts.dryRun,
 			engine: opts.engine,
+			agent: opts.agent,
 			registry
 		});
 		process.exitCode = exitCode;
@@ -41620,4 +41641,4 @@ 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, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runRunAction, runSolutioningPhase, validateStopAfterFromConflict };
-//# sourceMappingURL=run-Dg_BEJB6.js.map
+//# sourceMappingURL=run-BLxcApKZ.js.map

package/dist/{run-0y5KOffG.js → run-Ds3ucwad.js}

@@ -2,7 +2,7 @@ import "./health-DJgGZhW-.js";
 import "./logger-KeHncl-f.js";
 import "./helpers-CElYrONe.js";
 import "./dist-adzGUKPc.js";
-import { normalizeGraphSummaryToStatus, registerRunCommand, runRunAction } from "./run-Dg_BEJB6.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, runRunAction } from "./run-BLxcApKZ.js";
 import "./routing-CcBOCuC9.js";
 import "./decisions-C0pz9Clx.js";
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.19.9",
+  "version": "0.19.11",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",

package/packs/bmad/prompts/create-story.md

@@ -16,13 +16,22 @@
 
 ---
 
+### Story Definition (from Solutioning Phase)
+{{story_definition}}
+
+---
+
 ## Mission
 
 Using the context above, write a complete, implementation-ready story file for story **{{story_key}}**.
 
+**CRITICAL**: The Story Definition above is the authoritative specification for this story's scope.
+Use the title, description, and acceptance criteria from the Story Definition — do NOT substitute
+a different story from the epic scope. The story key, title, and core scope are non-negotiable.
+
 ## Instructions
 
-1. **Parse the epic scope** to understand what this epic is building and where this story fits
+1. **Use the Story Definition as your primary input** — it specifies exactly what this story builds. The epic scope provides surrounding context only.
 2. **Apply architecture constraints** — every constraint listed above is mandatory (file paths, import style, test framework, etc.)
 3. **Use previous dev notes** as guardrails — don't repeat mistakes, build on patterns that worked
 4. **Fill out the story template** with:

package/packs/bmad/prompts/readiness-check.md

@@ -88,7 +88,21 @@ For EVERY story with dependencies on other stories:
 3. Flag invalid references as **blocker** findings
 4. Flag potentially circular dependencies as **major** findings
 
-### Step 7: Final Verdict
+### Step 7: Cross-Epic Story Duplication Check
+
+For EVERY pair of stories from DIFFERENT epics:
+1. Do they implement the same core functionality? (e.g., both create a MatchRunner, both build a tournament CLI, both implement a logging module)
+2. Do they have overlapping acceptance criteria? (same testable condition appears in both)
+3. Does a later epic's story RE-IMPLEMENT what an earlier epic's story already built, rather than extending or depending on it?
+4. Flag duplicate stories as **major** findings with both story keys in affected_items
+5. Flag near-duplicates (>50% AC overlap) as **major** findings
+
+Common duplication patterns:
+- Infrastructure stories (logging, CLI, config) appearing in multiple epics
+- Runner/harness classes duplicated across epics
+- The same data model or service being created by stories in different epics
+
+### Step 8: Final Verdict
 
 Determine your verdict:
 - **NOT_READY**: Any of these conditions are true:
@@ -130,7 +144,7 @@ findings:
 ```
 
 Valid verdict values: READY, NEEDS_WORK, NOT_READY
-Valid category values: fr_coverage, architecture_compliance, story_quality, constraint_adherence, ux_alignment, dependency_validity
+Valid category values: fr_coverage, architecture_compliance, story_quality, constraint_adherence, ux_alignment, dependency_validity, story_duplication
 Valid severity values: blocker, major, minor
 
 If you cannot perform the review:

package/packs/bmad/prompts/story-generation.md

@@ -42,12 +42,19 @@ Break down the requirements and architecture above into **epics and stories**
    - If architecture specifies a project structure, Epic 1 Story 1 should be project scaffolding
    - Database tables, API endpoints, and infrastructure are created in the epic where they are FIRST NEEDED
 
-5. **Size stories appropriately:**
+5. **Eliminate cross-epic duplication (CRITICAL):**
+   - Before finalizing, compare EVERY story against stories in OTHER epics
+   - If two stories from different epics implement the same core functionality (e.g., both create a MatchRunner, both build a tournament CLI), consolidate into ONE story in the earliest epic that needs it
+   - The later epic should DEPEND ON the earlier epic's story, not re-implement it
+   - Common duplication patterns to watch for: logging infrastructure, CLI subcommands, runner/harness classes, configuration modules
+   - A story that "extends" functionality from an earlier epic is OK; a story that "re-implements" the same functionality is NOT
+
+6. **Size stories appropriately:**
    - Each story should be completable by one developer in 1-3 days
    - If a story feels too large, split it into multiple stories within the same epic
    - If an epic has more than 8 stories, consider splitting the epic
 
-6. **Amendment awareness**: If amendment context from a parent run is provided below, generate stories for the NEW scope introduced by the amendment. Do not regenerate stories for unchanged requirements.
+7. **Amendment awareness**: If amendment context from a parent run is provided below, generate stories for the NEW scope introduced by the amendment. Do not regenerate stories for unchanged requirements.
 
 ## Output Contract