substrate-ai 0.6.1 → 0.6.3

package/dist/cli/index.js

@@ -1,10 +1,10 @@
 #!/usr/bin/env node
-import { AdapterTelemetryPersistence, AppError, DEFAULT_CONFIG, DEFAULT_ROUTING_POLICY, DoltClient, DoltNotInstalled, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, FileStateStore, GitClient, GrammarLoader, IngestionServer, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SUBSTRATE_OWNED_SETTINGS_KEYS, SymbolParser, VALID_PHASES, WorkGraphRepository, buildPipelineStatusOutput, checkDoltInstalled, createConfigSystem, createContextCompiler, createDatabaseAdapter, createDispatcher, createDoltClient, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStateStore, createStopAfterGate, createTelemetryAdvisor, detectCycles, findPackageRoot, formatOutput, formatPhaseCompletionSummary, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, initSchema, initializeDolt, isSyncAdapter, parseDbTimestampAsUtc, registerHealthCommand, registerRunCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-IDOmPys1.js";
+import { AdapterTelemetryPersistence, AppError, DEFAULT_CONFIG, DEFAULT_ROUTING_POLICY, DoltClient, DoltNotInstalled, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, FileStateStore, GitClient, GrammarLoader, IngestionServer, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SUBSTRATE_OWNED_SETTINGS_KEYS, SymbolParser, VALID_PHASES, WorkGraphRepository, buildPipelineStatusOutput, checkDoltInstalled, createConfigSystem, createContextCompiler, createDatabaseAdapter, createDispatcher, createDoltClient, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStateStore, createStopAfterGate, createTelemetryAdvisor, detectCycles, findPackageRoot, formatOutput, formatPhaseCompletionSummary, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, initSchema, initializeDolt, isSyncAdapter, parseDbTimestampAsUtc, registerHealthCommand, registerRunCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-GwwiCYXX.js";
 import { createLogger } from "../logger-D2fS2ccL.js";
 import { AdapterRegistry } from "../adapter-registry-D2zdMwVu.js";
 import { CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, PartialSubstrateConfigSchema } from "../config-migrator-DtZW1maj.js";
 import { ConfigError, createEventBus } from "../helpers-BihqWgVe.js";
-import { RoutingRecommender } from "../routing-BUE9pIxW.js";
+import { RoutingRecommender } from "../routing-CobBiKeV.js";
 import { addTokenUsage, createDecision, createPipelineRun, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getTokenUsageSummary, listRequirements, updatePipelineRun } from "../decisions-C6MF2Cax.js";
 import { ESCALATION_DIAGNOSIS, EXPERIMENT_RESULT, OPERATIONAL_FINDING, STORY_METRICS, aggregateTokenUsageForRun, compareRunMetrics, getBaselineRunMetrics, getRunMetrics, getStoryMetricsForRun, incrementRunRestarts, listRunMetrics, tagRunAsBaseline } from "../operational-BRpT8MYF.js";
 import { abortMerge, createWorktree, getConflictingFiles, getMergedFiles, getOrphanedWorktrees, performMerge, removeBranch, removeWorktree, simulateMerge, verifyGitVersion } from "../git-utils-C-fdrHF_.js";
@@ -432,8 +432,8 @@ async function detectMonorepoProfile(rootDir) {
 	return { project: {
 		type: "monorepo",
 		tool: "turborepo",
-		buildCommand: "turbo build",
-		testCommand: "turbo test",
+		buildCommand: "npx turbo build",
+		testCommand: "npx turbo test",
 		packages
 	} };
 }
@@ -912,6 +912,22 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		const TaskToolCommandGenerator = resolveExport(taskToolMod, "TaskToolCommandGenerator");
 		const manifestMod = _require(join(installerLibPath, "core", "manifest-generator.js"));
 		const ManifestGenerator = resolveExport(manifestMod, "ManifestGenerator");
+		const pathUtilsMod = _require(join(installerLibPath, "ide", "shared", "path-utils.js"));
+		const pathUtils = { toDashPath: pathUtilsMod.toDashPath ?? pathUtilsMod.default?.toDashPath };
+		const writeDashFallback = async (baseDir, artifacts, acceptTypes) => {
+			let written = 0;
+			for (const artifact of artifacts) {
+				if (!acceptTypes.includes(artifact.type)) continue;
+				const content = artifact.content;
+				if (!content || !artifact.relativePath) continue;
+				const flatName = pathUtils.toDashPath(artifact.relativePath);
+				const dest = join(baseDir, flatName);
+				mkdirSync(dirname(dest), { recursive: true });
+				writeFileSync(dest, content, "utf-8");
+				written++;
+			}
+			return written;
+		};
 		const nonCoreModules = scanBmadModules(bmadDir);
 		const allModules = ["core", ...nonCoreModules];
 		try {
@@ -925,13 +941,13 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		clearBmadCommandFiles(commandsDir);
 		const agentGen = new AgentCommandGenerator("_bmad");
 		const { artifacts: agentArtifacts } = await agentGen.collectAgentArtifacts(bmadDir, nonCoreModules);
-		const agentCount = await agentGen.writeDashArtifacts(commandsDir, agentArtifacts);
+		const agentCount = typeof agentGen.writeDashArtifacts === "function" ? await agentGen.writeDashArtifacts(commandsDir, agentArtifacts) : await writeDashFallback(commandsDir, agentArtifacts, ["agent-launcher"]);
 		const workflowGen = new WorkflowCommandGenerator("_bmad");
 		const { artifacts: workflowArtifacts } = await workflowGen.collectWorkflowArtifacts(bmadDir);
-		const workflowCount = await workflowGen.writeDashArtifacts(commandsDir, workflowArtifacts);
+		const workflowCount = typeof workflowGen.writeDashArtifacts === "function" ? await workflowGen.writeDashArtifacts(commandsDir, workflowArtifacts) : await writeDashFallback(commandsDir, workflowArtifacts, ["workflow-command", "workflow-launcher"]);
 		const taskToolGen = new TaskToolCommandGenerator("_bmad");
 		const { artifacts: taskToolArtifacts } = await taskToolGen.collectTaskToolArtifacts(bmadDir);
-		const taskToolCount = await taskToolGen.writeDashArtifacts(commandsDir, taskToolArtifacts);
+		const taskToolCount = typeof taskToolGen.writeDashArtifacts === "function" ? await taskToolGen.writeDashArtifacts(commandsDir, taskToolArtifacts) : await writeDashFallback(commandsDir, taskToolArtifacts, ["task", "tool"]);
 		const total = agentCount + workflowCount + taskToolCount;
 		if (outputFormat !== "json") process.stdout.write(`Generated ${String(total)} Claude Code commands (${String(agentCount)} agents, ${String(workflowCount)} workflows, ${String(taskToolCount)} tasks/tools)\n`);
 		logger$18.info({
@@ -1541,7 +1557,7 @@ function mapInternalPhaseToEventPhase(internalPhase) {
 	}
 }
 async function runResumeAction(options) {
-	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName, events: eventsFlag, registry } = options;
+	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName, events: eventsFlag, registry, maxReviewCycles = 2 } = options;
 	if (stopAfter !== void 0 && !VALID_PHASES.includes(stopAfter)) {
 		const errorMsg = `Invalid phase: "${stopAfter}". Valid phases: ${VALID_PHASES.join(", ")}`;
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
@@ -1638,7 +1654,7 @@ async function runResumeAction(options) {
 	}
 }
 async function runFullPipelineFromPhase(options) {
-	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, events: eventsFlag, existingRunId, projectRoot, registry: injectedRegistry, stories: explicitStories } = options;
+	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, events: eventsFlag, existingRunId, projectRoot, registry: injectedRegistry, stories: explicitStories, maxReviewCycles = 2 } = options;
 	if (!existsSync(dbDir)) mkdirSync(dbDir, { recursive: true });
 	const adapter = createDatabaseAdapter({
 		backend: "auto",
@@ -1775,7 +1791,7 @@ async function runFullPipelineFromPhase(options) {
 					eventBus,
 					config: {
 						maxConcurrency: concurrency,
-						maxReviewCycles: 2,
+						maxReviewCycles,
 						pipelineRunId: runId,
 						enableHeartbeat: eventsFlag === true
 					},
@@ -1955,7 +1971,7 @@ 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").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).action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		const exitCode = await runResumeAction({
 			runId: opts.runId,
@@ -1965,6 +1981,7 @@ function registerResumeCommand(program, _version = "0.0.0", projectRoot = proces
 			concurrency: opts.concurrency,
 			pack: opts.pack,
 			events: opts.events,
+			maxReviewCycles: opts.maxReviewCycles,
 			registry
 		});
 		process.exitCode = exitCode;
@@ -2058,7 +2075,7 @@ async function runStatusAction(options) {
 		if (runId !== void 0 && runId !== "") run = await getPipelineRunById(adapter, runId);
 		else run = await getLatestRun(adapter);
 		if (run === void 0) {
-			const errorMsg = runId !== void 0 ? `Pipeline run '${runId}' not found.` : "No pipeline runs found. Run `substrate run` first.";
+			const errorMsg = runId !== void 0 ? `Pipeline run '${runId}' not found.` : "No pipeline runs found. Run `substrate run --events` to start a pipeline first.";
 			if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
 			else process.stderr.write(`Error: ${errorMsg}\n`);
 			return 1;
@@ -3469,7 +3486,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-DTOsG7PJ.js"
+									"../run-B5-a932y.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -3985,7 +4002,7 @@ async function runMetricsAction(options) {
 			const routingConfigPath = join(dbDir, "routing.yml");
 			let routingConfig = null;
 			if (existsSync(routingConfigPath)) try {
-				const { loadModelRoutingConfig } = await import("../routing-DbR9FPmj.js");
+				const { loadModelRoutingConfig } = await import("../routing-CpsRPjLE.js");
 				routingConfig = loadModelRoutingConfig(routingConfigPath);
 			} catch {}
 			if (routingConfig === null) routingConfig = {

package/dist/index.d.ts

@@ -514,6 +514,23 @@ interface SupervisorExperimentErrorEvent {
   /** Error message describing why the experiment failed */
   error: string;
 }
+/**
+ * Emitted after all stories complete when the `.substrate/project-profile.yaml`
+ * may be outdated relative to the actual project structure (e.g., profile says
+ * `type: single` but a `turbo.json` now exists, or new language markers appeared).
+ *
+ * Non-blocking warning — the pipeline has already finished. The user should
+ * re-run `substrate init --force` to regenerate the profile.
+ */
+interface PipelineProfileStaleEvent {
+  type: 'pipeline:profile-stale';
+  /** ISO-8601 timestamp generated at emit time */
+  ts: string;
+  /** Human-readable message describing the staleness indicators found */
+  message: string;
+  /** List of staleness indicators detected (e.g., "turbo.json exists but profile says type: single") */
+  indicators: string[];
+}
 /**
  * Emitted when post-sprint contract verification finds a mismatch between
  * declared export/import contracts (Story 25-6).
@@ -581,7 +598,7 @@ interface RoutingModelSelectedEvent {
  * }
  * ```
  */
-type PipelineEvent = PipelineStartEvent | PipelineCompleteEvent | PipelinePreFlightFailureEvent | PipelineContractMismatchEvent | PipelineContractVerificationSummaryEvent | StoryPhaseEvent | StoryDoneEvent | StoryEscalationEvent | StoryWarnEvent | StoryLogEvent | PipelineHeartbeatEvent | StoryStallEvent | StoryZeroDiffEscalationEvent | StoryBuildVerificationFailedEvent | StoryBuildVerificationPassedEvent | StoryInterfaceChangeWarningEvent | StoryMetricsEvent | SupervisorPollEvent | SupervisorKillEvent | SupervisorRestartEvent | SupervisorAbortEvent | SupervisorSummaryEvent | SupervisorAnalysisCompleteEvent | SupervisorAnalysisErrorEvent | SupervisorExperimentStartEvent | SupervisorExperimentSkipEvent | SupervisorExperimentRecommendationsEvent | SupervisorExperimentCompleteEvent | SupervisorExperimentErrorEvent | RoutingModelSelectedEvent; //#endregion
+type PipelineEvent = PipelineStartEvent | PipelineCompleteEvent | PipelinePreFlightFailureEvent | PipelineProfileStaleEvent | PipelineContractMismatchEvent | PipelineContractVerificationSummaryEvent | StoryPhaseEvent | StoryDoneEvent | StoryEscalationEvent | StoryWarnEvent | StoryLogEvent | PipelineHeartbeatEvent | StoryStallEvent | StoryZeroDiffEscalationEvent | StoryBuildVerificationFailedEvent | StoryBuildVerificationPassedEvent | StoryInterfaceChangeWarningEvent | StoryMetricsEvent | SupervisorPollEvent | SupervisorKillEvent | SupervisorRestartEvent | SupervisorAbortEvent | SupervisorSummaryEvent | SupervisorAnalysisCompleteEvent | SupervisorAnalysisErrorEvent | SupervisorExperimentStartEvent | SupervisorExperimentSkipEvent | SupervisorExperimentRecommendationsEvent | SupervisorExperimentCompleteEvent | SupervisorExperimentErrorEvent | RoutingModelSelectedEvent; //#endregion
 //#region src/core/errors.d.ts
 
 /**
@@ -1264,6 +1281,13 @@ interface OrchestratorEvents {
     /** Build output (stdout+stderr), truncated to 2000 chars */
     output: string;
   };
+  /** Project profile may be outdated relative to the actual project structure */
+  'pipeline:profile-stale': {
+    /** Human-readable message describing the staleness indicators found */
+    message: string;
+    /** List of staleness indicators detected */
+    indicators: string[];
+  };
   /** Contract verification found a mismatch between declared export/import contracts */
   'pipeline:contract-mismatch': {
     /** Story key that declared the export for this contract */

package/dist/{routing-BUE9pIxW.js → routing-CobBiKeV.js}

@@ -263,7 +263,7 @@ var RoutingResolver = class RoutingResolver {
 			return new RoutingResolver(config, logger$1);
 		} catch (err) {
 			if (err instanceof RoutingConfigError && err.code === "CONFIG_NOT_FOUND") {
-				logger$1.warn({
+				logger$1.debug({
 					configPath: filePath,
 					component: "routing",
 					reason: "config not found"
@@ -829,4 +829,4 @@ var RoutingTuner = class {
 
 //#endregion
 export { ModelRoutingConfigSchema, ProviderPolicySchema, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, TASK_TYPE_PHASE_MAP, getModelTier, loadModelRoutingConfig };
-//# sourceMappingURL=routing-BUE9pIxW.js.map
+//# sourceMappingURL=routing-CobBiKeV.js.map

package/dist/{routing-DbR9FPmj.js → routing-CpsRPjLE.js}

@@ -1,4 +1,4 @@
 import "./logger-D2fS2ccL.js";
-import { ModelRoutingConfigSchema, ProviderPolicySchema, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, TASK_TYPE_PHASE_MAP, getModelTier, loadModelRoutingConfig } from "./routing-BUE9pIxW.js";
+import { ModelRoutingConfigSchema, ProviderPolicySchema, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, TASK_TYPE_PHASE_MAP, getModelTier, loadModelRoutingConfig } from "./routing-CobBiKeV.js";
 
 export { loadModelRoutingConfig };

package/dist/{run-DTOsG7PJ.js → run-B5-a932y.js}

@@ -1,8 +1,8 @@
-import { registerRunCommand, runRunAction } from "./run-IDOmPys1.js";
+import { registerRunCommand, runRunAction } from "./run-GwwiCYXX.js";
 import "./logger-D2fS2ccL.js";
 import "./config-migrator-DtZW1maj.js";
 import "./helpers-BihqWgVe.js";
-import "./routing-BUE9pIxW.js";
+import "./routing-CobBiKeV.js";
 import "./decisions-C6MF2Cax.js";
 import "./operational-BRpT8MYF.js";
 

package/dist/{run-IDOmPys1.js → run-GwwiCYXX.js}

@@ -1,7 +1,7 @@
 import { createLogger, deepMask } from "./logger-D2fS2ccL.js";
 import { CURRENT_CONFIG_FORMAT_VERSION, PartialSubstrateConfigSchema, SUPPORTED_CONFIG_FORMAT_VERSIONS, SubstrateConfigSchema, defaultConfigMigrator } from "./config-migrator-DtZW1maj.js";
 import { ConfigError, ConfigIncompatibleFormatError, createEventBus, createTuiApp, isTuiCapable, printNonTtyWarning, sleep } from "./helpers-BihqWgVe.js";
-import { RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, loadModelRoutingConfig } from "./routing-BUE9pIxW.js";
+import { RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, loadModelRoutingConfig } from "./routing-CobBiKeV.js";
 import { addTokenUsage, createDecision, createPipelineRun, createRequirement, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunningPipelineRuns, getTokenUsageSummary, registerArtifact, updatePipelineRun, updatePipelineRunConfig, upsertDecision } from "./decisions-C6MF2Cax.js";
 import { ADVISORY_NOTES, ESCALATION_DIAGNOSIS, OPERATIONAL_FINDING, STORY_METRICS, STORY_OUTCOME, TEST_EXPANSION_FINDING, TEST_PLAN, aggregateTokenUsageForRun, aggregateTokenUsageForStory, getStoryMetricsForRun, writeRunMetrics, writeStoryMetrics } from "./operational-BRpT8MYF.js";
 import { createRequire } from "module";
@@ -325,7 +325,8 @@ var InMemoryDatabaseAdapter = class {
 			if (!m$1) return [];
 			return [this._evalSelectExprs(m$1[1].trim())];
 		}
-		const m = /SELECT\s+(.+?)\s+FROM\s+(\w+)(?:\s+WHERE\s+(.+))?$/is.exec(sql);
+		const stripped = sql.replace(/\s+ORDER\s+BY\s+.+?(?=\s+LIMIT\s|\s*$)/is, "").replace(/\s+LIMIT\s+\d+\s*$/is, "");
+		const m = /SELECT\s+(.+?)\s+FROM\s+(\w+)(?:\s+WHERE\s+(.+))?$/is.exec(stripped);
 		if (!m) return [];
 		const colsStr = m[1].trim();
 		const tableName = m[2];
@@ -334,6 +335,7 @@ var InMemoryDatabaseAdapter = class {
 		let rows = table.map((r) => ({ ...r }));
 		if (whereStr) rows = rows.filter((row) => this._matchWhere(whereStr.trim(), row));
 		if (colsStr === "*") return rows;
+		if (/\b(?:SUM|COALESCE|COUNT|AVG|MIN|MAX)\s*\(/i.test(colsStr)) return [this._evalAggregate(colsStr, rows)];
 		return rows.map((row) => this._projectCols(colsStr, row));
 	}
 	_update(sql) {
@@ -393,12 +395,22 @@ var InMemoryDatabaseAdapter = class {
 				if (row[notNullM[1]] === null || row[notNullM[1]] === void 0) return false;
 				continue;
 			}
+			const likeM = /^(\w+)\s+LIKE\s+'(.*)'$/is.exec(trimmed);
+			if (likeM) {
+				const colVal = row[likeM[1]];
+				if (colVal === null || colVal === void 0) return false;
+				const pattern = likeM[2].replace(/''/g, "'");
+				const escaped = pattern.replace(/[.*+?^${}()|[\]\\]/g, (ch) => ch === "%" || ch === "_" ? ch : "\\" + ch);
+				const regex = new RegExp("^" + escaped.replace(/%/g, ".*").replace(/_/g, ".") + "$", "s");
+				if (!regex.test(String(colVal))) return false;
+				continue;
+			}
 		}
 		return true;
 	}
 	_projectCols(colsStr, row) {
 		const result = {};
-		const cols = colsStr.split(",").map((c) => c.trim());
+		const cols = this._splitTopLevelCommas(colsStr);
 		for (const col of cols) {
 			const aliasM = /^(.+?)\s+AS\s+(\w+)$/i.exec(col);
 			if (aliasM) result[aliasM[2]] = this._evalExprAgainstRow(aliasM[1].trim(), row);
@@ -408,7 +420,7 @@ var InMemoryDatabaseAdapter = class {
 	}
 	_evalSelectExprs(exprs) {
 		const result = {};
-		const parts = exprs.split(",").map((p) => p.trim());
+		const parts = this._splitTopLevelCommas(exprs);
 		for (const part of parts) {
 			const aliasM = /^(.+?)\s+AS\s+(\w+)$/i.exec(part);
 			if (aliasM) result[aliasM[2]] = this._evalLiteral(aliasM[1].trim());
@@ -431,6 +443,87 @@ var InMemoryDatabaseAdapter = class {
 		return literal;
 	}
 	/**
+	* Split a string by commas that are NOT inside parentheses.
+	* E.g. "COALESCE(SUM(x), 0) as a, y" → ["COALESCE(SUM(x), 0) as a", "y"]
+	*/
+	_splitTopLevelCommas(str) {
+		const parts = [];
+		let current = "";
+		let depth = 0;
+		let inStr = false;
+		for (let i = 0; i < str.length; i++) {
+			const ch = str[i];
+			if (ch === "'" && !inStr) {
+				inStr = true;
+				current += ch;
+			} else if (ch === "'" && inStr) if (str[i + 1] === "'") {
+				current += "''";
+				i++;
+			} else {
+				inStr = false;
+				current += ch;
+			}
+			else if (!inStr && ch === "(") {
+				depth++;
+				current += ch;
+			} else if (!inStr && ch === ")") {
+				depth--;
+				current += ch;
+			} else if (!inStr && ch === "," && depth === 0) {
+				parts.push(current.trim());
+				current = "";
+			} else current += ch;
+		}
+		if (current.trim() !== "") parts.push(current.trim());
+		return parts;
+	}
+	/**
+	* Evaluate aggregate SELECT expressions (SUM, COALESCE, COUNT) across
+	* a set of filtered rows, returning a single result row.
+	*/
+	_evalAggregate(colsStr, rows) {
+		const result = {};
+		const cols = this._splitTopLevelCommas(colsStr);
+		for (const col of cols) {
+			const aliasM = /^(.+?)\s+AS\s+(\w+)$/i.exec(col);
+			const expr = aliasM ? aliasM[1].trim() : col.trim();
+			const alias = aliasM ? aliasM[2] : col.trim();
+			result[alias] = this._evalAggregateExpr(expr, rows);
+		}
+		return result;
+	}
+	/**
+	* Evaluate a single aggregate expression against a set of rows.
+	* Supports: SUM(col), COALESCE(expr, default), COUNT(*).
+	*/
+	_evalAggregateExpr(expr, rows) {
+		const trimmed = expr.trim();
+		const coalesceM = /^COALESCE\((.+)\)$/i.exec(trimmed);
+		if (coalesceM) {
+			const args = this._splitTopLevelCommas(coalesceM[1]);
+			for (const arg of args) {
+				const val = this._evalAggregateExpr(arg.trim(), rows);
+				if (val !== null && val !== void 0) return val;
+			}
+			return null;
+		}
+		const sumM = /^SUM\((\w+)\)$/i.exec(trimmed);
+		if (sumM) {
+			const col = sumM[1];
+			if (rows.length === 0) return null;
+			let total = 0;
+			for (const row of rows) total += Number(row[col] ?? 0);
+			return total;
+		}
+		if (/^COUNT\(\*\)$/i.test(trimmed)) return rows.length;
+		const countM = /^COUNT\((\w+)\)$/i.exec(trimmed);
+		if (countM) {
+			const col = countM[1];
+			return rows.filter((r) => r[col] !== null && r[col] !== void 0).length;
+		}
+		return this._evalLiteral(trimmed);
+	}
+	/**
 	* Parse a comma-separated list of SQL literal values.
 	* Handles: NULL, numbers, single-quoted strings.
 	* Simple split by comma (assumes no commas inside string values).
@@ -1829,8 +1922,8 @@ function resolveBmadMethodVersion(fromDir = __dirname) {
 const BMAD_BASELINE_TOKENS_FULL = 56800;
 /** BMAD baseline token total for create+dev+review comparison */
 const BMAD_BASELINE_TOKENS = 23800;
-/** Story key pattern: <epic>-<story> e.g. "10-1" */
-const STORY_KEY_PATTERN$1 = /^\d+-\d+$/;
+/** Story key pattern: <epic>-<story> e.g. "10-1", "1-1a", "NEW-26" */
+const STORY_KEY_PATTERN$1 = /^[A-Za-z0-9]+-[A-Za-z0-9]+$/;
 /**
 * Top-level keys in .claude/settings.json that substrate owns.
 * On init, these are set/updated unconditionally.
@@ -3441,6 +3534,28 @@ const PIPELINE_EVENT_METADATA = [
 				description: "Overall verification result."
 			}
 		]
+	},
+	{
+		type: "pipeline:profile-stale",
+		description: "Project profile may be outdated. Non-blocking warning — run `substrate init --force` to re-detect.",
+		when: "After all stories complete, before pipeline:complete. Emitted when staleness indicators are found.",
+		fields: [
+			{
+				name: "ts",
+				type: "string",
+				description: "Timestamp."
+			},
+			{
+				name: "message",
+				type: "string",
+				description: "Human-readable staleness warning message."
+			},
+			{
+				name: "indicators",
+				type: "string[]",
+				description: "List of staleness indicators (e.g., \"turbo.json exists but profile says type: single\")."
+			}
+		]
 	}
 ];
 /**
@@ -6338,7 +6453,8 @@ var DispatcherShuttingDownError = class extends Error {
 const YAML_ANCHOR_KEYS = [
 	"result:",
 	"verdict:",
-	"story_file:"
+	"story_file:",
+	"expansion_priority:"
 ];
 /**
 * Extract the YAML result block from sub-agent output.
@@ -7086,7 +7202,7 @@ function detectPackageManager(projectRoot) {
 	if (existsSync$1(join$1(projectRoot, "turbo.json"))) return {
 		packageManager: "none",
 		lockfile: "turbo.json",
-		command: "turbo build"
+		command: "npx turbo build"
 	};
 	const nodeCandidates = [
 		{
@@ -7188,6 +7304,16 @@ function runBuildVerification(options) {
 				output: combinedOutput,
 				reason: "build-verification-timeout"
 			};
+			const missingScriptPattern = /Missing script[:\s]|No script found|Command "build" not found/i;
+			if (missingScriptPattern.test(combinedOutput)) {
+				logger$23.warn("Build script not found — skipping pre-flight (greenfield repo)");
+				return {
+					status: "skipped",
+					exitCode,
+					output: combinedOutput,
+					reason: "build-script-not-found"
+				};
+			}
 			return {
 				status: "failed",
 				exitCode,
@@ -7665,12 +7791,12 @@ var FileStateStore = class {
 //#region src/modules/state/dolt-store.ts
 const log = createLogger("modules:state:dolt");
 /**
-* Validate that a story key matches the expected pattern (e.g. "26-7").
+* Validate that a story key matches the expected pattern (e.g. "26-7", "1-1a", "NEW-26").
 * Prevents SQL injection via string-interpolated identifiers.
 */
-const STORY_KEY_PATTERN = /^[0-9]+-[0-9]+$/;
+const STORY_KEY_PATTERN = /^[A-Za-z0-9]+-[A-Za-z0-9]+$/;
 function assertValidStoryKey(storyKey) {
-	if (!STORY_KEY_PATTERN.test(storyKey)) throw new DoltQueryError("assertValidStoryKey", `Invalid story key: '${storyKey}'. Must match pattern <number>-<number>.`);
+	if (!STORY_KEY_PATTERN.test(storyKey)) throw new DoltQueryError("assertValidStoryKey", `Invalid story key: '${storyKey}'. Must match pattern <segment>-<segment> (e.g. "10-1", "1-1a", "NEW-26").`);
 }
 /**
 * Dolt-backed implementation of the StateStore interface.
@@ -9095,9 +9221,17 @@ function readEpicShardFromFile(projectRoot, epicId) {
 		if (!epicsPath) return "";
 		const content = readFileSync$1(epicsPath, "utf-8");
 		const epicNum = epicId.replace(/^epic-/i, "");
-		const pattern = new RegExp(`^#{2,4}\\s+(?:Epic\\s+)?${epicNum}[.:\\s].*?(?=\\n#{2,4}\\s|$)`, "ms");
-		const match$1 = pattern.exec(content);
-		return match$1 ? match$1[0].trim() : "";
+		const headingPattern = new RegExp(`^(#{2,4})\\s+(?:Epic\\s+)?${epicNum}[.:\\s]`, "m");
+		const headingMatch = headingPattern.exec(content);
+		if (!headingMatch) return "";
+		const startIdx = headingMatch.index;
+		const headingLevel = headingMatch[1].length;
+		const hashes = "#".repeat(headingLevel);
+		const endPattern = new RegExp(`\\n${hashes}\\s`, "g");
+		endPattern.lastIndex = startIdx + headingMatch[0].length;
+		const endMatch = endPattern.exec(content);
+		const endIdx = endMatch ? endMatch.index : content.length;
+		return content.slice(startIdx, endIdx).trim();
 	} catch (err) {
 		logger$20.warn({
 			epicId,
@@ -9356,9 +9490,9 @@ async function getProjectFindings(db) {
 			sections.push("**Prior escalations:**");
 			for (const d of diagnoses.slice(-3)) try {
 				const val = JSON.parse(d.value);
-				sections.push(`- ${d.key.split(":")[0]}: ${val.recommendedAction} — ${val.rationale}`);
+				sections.push(`- ${(d.key ?? "").split(":")[0]}: ${val.recommendedAction} — ${val.rationale}`);
 			} catch {
-				sections.push(`- ${d.key}: escalated`);
+				sections.push(`- ${d.key ?? "unknown"}: escalated`);
 			}
 		}
 		const highCycleStories = metrics.filter((m) => {
@@ -9373,16 +9507,16 @@ async function getProjectFindings(db) {
 			sections.push("**Stories with high review cycles:**");
 			for (const m of highCycleStories) try {
 				const val = JSON.parse(m.value);
-				sections.push(`- ${m.key.split(":")[0]}: ${val.review_cycles} cycles`);
+				sections.push(`- ${(m.key ?? "").split(":")[0]}: ${val.review_cycles} cycles`);
 			} catch {}
 		}
-		const stalls = operational.filter((o) => o.key.startsWith("stall:"));
+		const stalls = operational.filter((o) => o.key?.startsWith("stall:"));
 		if (stalls.length > 0) sections.push(`**Prior stalls:** ${stalls.length} stall event(s) recorded`);
 		if (advisoryNotes.length > 0) {
 			sections.push("**Advisory notes from prior reviews (LGTM_WITH_NOTES):**");
 			for (const n of advisoryNotes.slice(-3)) try {
 				const val = JSON.parse(n.value);
-				const storyId = n.key.split(":")[0];
+				const storyId = (n.key ?? "").split(":")[0];
 				if (typeof val.notes === "string" && val.notes.length > 0) sections.push(`- ${storyId}: ${val.notes}`);
 			} catch {
 				sections.push(`- ${n.key}: advisory notes available`);
@@ -12377,7 +12511,7 @@ function detectInterfaceChanges(options) {
 		for (const name of allNames) {
 			let grepOutput = "";
 			try {
-				grepOutput = execSync(`grep -r --include="*.test.ts" --include="*.spec.ts" -l "${name}" .`, {
+				grepOutput = execSync(`grep -r --include="*.test.ts" --include="*.spec.ts" --exclude-dir=node_modules --exclude-dir=.git --exclude-dir=dist --exclude-dir=.next --exclude-dir=coverage -l "${name}" .`, {
 					cwd: projectRoot,
 					encoding: "utf-8",
 					timeout: 1e4,
@@ -15870,6 +16004,9 @@ function createTelemetryAdvisor(deps) {
 
 //#endregion
 //#region src/modules/implementation-orchestrator/orchestrator-impl.ts
+function estimateDispatchCost(input, output) {
+	return (input * 3 + output * 15) / 1e6;
+}
 function createPauseGate() {
 	let resolve$2;
 	const promise = new Promise((res) => {
@@ -15902,6 +16039,69 @@ function buildTargetedFilesContent(issueList) {
 	return lines.join("\n");
 }
 /**
+* Normalize a title string into a set of meaningful words for comparison.
+* Strips punctuation, lowercases, and filters out very short words (<=2 chars)
+* and common stop words to focus on content-bearing terms.
+*/
+function titleToWordSet(title) {
+	const stopWords = new Set([
+		"the",
+		"and",
+		"for",
+		"with",
+		"from",
+		"into",
+		"that",
+		"this",
+		"via"
+	]);
+	return new Set(title.toLowerCase().replace(/[^a-z0-9\s-]/g, " ").split(/[\s-]+/).filter((w) => w.length > 2 && !stopWords.has(w)));
+}
+/**
+* Compute the word overlap ratio between two titles.
+* Returns a value between 0 and 1, where 1 means all words in the smaller set
+* are present in the larger set.
+*
+* Uses the smaller set as the denominator so that a generated title that is a
+* reasonable subset or superset of the expected title still scores well.
+*/
+function computeTitleOverlap(titleA, titleB) {
+	const wordsA = titleToWordSet(titleA);
+	const wordsB = titleToWordSet(titleB);
+	if (wordsA.size === 0 || wordsB.size === 0) return 0;
+	let shared = 0;
+	for (const w of wordsA) if (wordsB.has(w)) shared++;
+	const denominator = Math.min(wordsA.size, wordsB.size);
+	return shared / denominator;
+}
+/**
+* Extract the expected story title from the epic shard content.
+*
+* Looks for patterns like:
+*   - "### Story 37-1: Turborepo monorepo scaffold"
+*   - "Story 37-1: Turborepo monorepo scaffold"
+*   - "**37-1**: Turborepo monorepo scaffold"
+*   - "37-1: Turborepo monorepo scaffold"
+*
+* Returns the title portion after the story key, or null if no match.
+*/
+function extractExpectedStoryTitle(shardContent, storyKey) {
+	if (!shardContent || !storyKey) return null;
+	const escaped = storyKey.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+	const patterns = [
+		new RegExp(`^#{2,4}\\s+Story\\s+${escaped}[:\\s]+\\s*(.+)$`, "mi"),
+		new RegExp(`^Story\\s+${escaped}[:\\s]+\\s*(.+)$`, "mi"),
+		new RegExp(`^\\*\\*${escaped}\\*\\*[:\\s]+\\s*(.+)$`, "mi"),
+		new RegExp(`^${escaped}[:\\s]+\\s*(.+)$`, "mi")
+	];
+	for (const pattern of patterns) {
+		const match$1 = pattern.exec(shardContent);
+		if (match$1?.[1]) return match$1[1].replace(/\*+$/, "").trim();
+	}
+	return null;
+}
+const TITLE_OVERLAP_WARNING_THRESHOLD = .3;
+/**
 * Map a StoryPhase to the corresponding WgStoryStatus for wg_stories writes.
 * Returns null for PENDING (no write needed).
 */
@@ -15918,6 +16118,55 @@ function wgStatusForPhase(phase) {
 	}
 }
 /**
+* Check whether `.substrate/project-profile.yaml` is stale relative to
+* the actual project structure.
+*
+* Returns an array of human-readable indicator strings. An empty array
+* means the profile appears current (or doesn't exist).
+*
+* Staleness indicators checked:
+* - Profile says `type: single` but `turbo.json` exists (should be monorepo)
+* - Profile has no Go language but `go.mod` exists
+* - Profile has no Python language but `pyproject.toml` exists
+* - Profile has no Rust language but `Cargo.toml` exists
+*/
+function checkProfileStaleness(projectRoot) {
+	const profilePath = join$1(projectRoot, ".substrate", "project-profile.yaml");
+	if (!existsSync$1(profilePath)) return [];
+	let profile;
+	try {
+		const raw = readFileSync$1(profilePath, "utf-8");
+		profile = yaml.load(raw) ?? {};
+	} catch {
+		return [];
+	}
+	const project = profile.project;
+	if (project === void 0) return [];
+	const indicators = [];
+	const declaredLanguages = new Set();
+	if (typeof project.language === "string") declaredLanguages.add(project.language);
+	if (Array.isArray(project.packages)) {
+		for (const pkg of project.packages) if (typeof pkg.language === "string") declaredLanguages.add(pkg.language);
+	}
+	if (project.type === "single" && existsSync$1(join$1(projectRoot, "turbo.json"))) indicators.push("turbo.json exists but profile says type: single (should be monorepo)");
+	const languageMarkers = [
+		{
+			file: "go.mod",
+			language: "go"
+		},
+		{
+			file: "pyproject.toml",
+			language: "python"
+		},
+		{
+			file: "Cargo.toml",
+			language: "rust"
+		}
+	];
+	for (const marker of languageMarkers) if (existsSync$1(join$1(projectRoot, marker.file)) && !declaredLanguages.has(marker.language)) indicators.push(`${marker.file} exists but profile does not declare ${marker.language}`);
+	return indicators;
+}
+/**
 * Factory function that creates an ImplementationOrchestrator instance.
 *
 * @param deps - Injected dependencies (db, pack, contextCompiler, dispatcher,
@@ -16274,8 +16523,7 @@ function createImplementationOrchestrator(deps) {
 			for (const s of _stories.values()) if (s.phase === "COMPLETE" || s.phase === "ESCALATED") completed++;
 			else if (s.phase === "PENDING") queued++;
 			else active++;
-			const timeSinceProgress = Date.now() - _lastProgressTs;
-			if (timeSinceProgress >= HEARTBEAT_INTERVAL_MS) eventBus.emit("orchestrator:heartbeat", {
+			eventBus.emit("orchestrator:heartbeat", {
 				runId: config.pipelineRunId ?? "",
 				activeDispatches: active,
 				completedDispatches: completed,
@@ -16474,7 +16722,7 @@ function createImplementationOrchestrator(deps) {
 					agent: "create-story",
 					input_tokens: createResult.tokenUsage.input,
 					output_tokens: createResult.tokenUsage.output,
-					cost_usd: 0,
+					cost_usd: estimateDispatchCost(createResult.tokenUsage.input, createResult.tokenUsage.output),
 					metadata: JSON.stringify({ storyKey })
 				});
 			} catch (tokenErr) {
@@ -16519,6 +16767,46 @@ function createImplementationOrchestrator(deps) {
 				return;
 			}
 			storyFilePath = createResult.story_file;
+			if (createResult.story_title) try {
+				const epicId = storyKey.split("-")[0] ?? storyKey;
+				const implDecisions = await getDecisionsByPhase(db, "implementation");
+				let shardContent;
+				const perStoryShard = implDecisions.find((d) => d.category === "epic-shard" && d.key === storyKey);
+				if (perStoryShard?.value) shardContent = perStoryShard.value;
+				else {
+					const epicShard = implDecisions.find((d) => d.category === "epic-shard" && d.key === epicId);
+					if (epicShard?.value) shardContent = extractStorySection(epicShard.value, storyKey) ?? epicShard.value;
+				}
+				if (shardContent) {
+					const expectedTitle = extractExpectedStoryTitle(shardContent, storyKey);
+					if (expectedTitle) {
+						const overlap = computeTitleOverlap(expectedTitle, createResult.story_title);
+						if (overlap < TITLE_OVERLAP_WARNING_THRESHOLD) {
+							const msg = `Story title mismatch: expected "${expectedTitle}" but got "${createResult.story_title}" (word overlap: ${Math.round(overlap * 100)}%). This may indicate the create-story agent received truncated context.`;
+							logger$27.warn({
+								storyKey,
+								expectedTitle,
+								generatedTitle: createResult.story_title,
+								overlap
+							}, msg);
+							eventBus.emit("orchestrator:story-warn", {
+								storyKey,
+								msg
+							});
+						} else logger$27.debug({
+							storyKey,
+							expectedTitle,
+							generatedTitle: createResult.story_title,
+							overlap
+						}, "Story title validation passed");
+					}
+				}
+			} catch (titleValidationErr) {
+				logger$27.debug({
+					storyKey,
+					err: titleValidationErr
+				}, "Story title validation skipped due to error");
+			}
 		} catch (err) {
 			const errMsg = err instanceof Error ? err.message : String(err);
 			endPhase(storyKey, "create-story");
@@ -16612,7 +16900,7 @@ function createImplementationOrchestrator(deps) {
 				agent: "test-plan",
 				input_tokens: testPlanTokenUsage.input,
 				output_tokens: testPlanTokenUsage.output,
-				cost_usd: 0,
+				cost_usd: estimateDispatchCost(testPlanTokenUsage.input, testPlanTokenUsage.output),
 				metadata: JSON.stringify({ storyKey })
 			});
 		} catch (tokenErr) {
@@ -16727,7 +17015,7 @@ function createImplementationOrchestrator(deps) {
 							agent: `batch-${batch.batchIndex}`,
 							input_tokens: batchResult.tokenUsage.input,
 							output_tokens: batchResult.tokenUsage.output,
-							cost_usd: 0,
+							cost_usd: estimateDispatchCost(batchResult.tokenUsage.input, batchResult.tokenUsage.output),
 							metadata: JSON.stringify({
 								storyKey,
 								batchIndex: batch.batchIndex,
@@ -16783,7 +17071,7 @@ function createImplementationOrchestrator(deps) {
 						agent: "dev-story",
 						input_tokens: devResult.tokenUsage.input,
 						output_tokens: devResult.tokenUsage.output,
-						cost_usd: 0,
+						cost_usd: estimateDispatchCost(devResult.tokenUsage.input, devResult.tokenUsage.output),
 						metadata: JSON.stringify({ storyKey })
 					});
 				} catch (tokenErr) {
@@ -17019,7 +17307,7 @@ function createImplementationOrchestrator(deps) {
 						agent: useBatchedReview ? "code-review-batched" : "code-review",
 						input_tokens: reviewResult.tokenUsage.input,
 						output_tokens: reviewResult.tokenUsage.output,
-						cost_usd: 0,
+						cost_usd: estimateDispatchCost(reviewResult.tokenUsage.input, reviewResult.tokenUsage.output),
 						metadata: JSON.stringify({
 							storyKey,
 							reviewCycle: reviewCycles
@@ -17041,6 +17329,28 @@ function createImplementationOrchestrator(deps) {
 					}, "Phantom review detected (0 issues + error) — retrying review once");
 					continue;
 				}
+				if (isPhantomReview && timeoutRetried) {
+					logger$27.warn({
+						storyKey,
+						reviewCycles,
+						error: reviewResult.error
+					}, "Consecutive review timeouts detected (original + retry both failed) — escalating immediately");
+					endPhase(storyKey, "code-review");
+					updateStory(storyKey, {
+						phase: "ESCALATED",
+						error: "consecutive-review-timeouts",
+						completedAt: new Date().toISOString()
+					});
+					await writeStoryMetricsBestEffort(storyKey, "escalated", reviewCycles + 1);
+					await emitEscalation({
+						storyKey,
+						lastVerdict: "consecutive-review-timeouts",
+						reviewCycles: reviewCycles + 1,
+						issues: ["Review dispatch failed twice consecutively (original + phantom-retry). Likely resource-constrained or diff too large for reviewer."]
+					});
+					await persistState();
+					return;
+				}
 				verdict = reviewResult.verdict;
 				issueList = reviewResult.issue_list ?? [];
 				if (verdict === "NEEDS_MAJOR_REWORK" && reviewCycles > 0 && previousIssueList.length > 0 && issueList.length < previousIssueList.length) {
@@ -17387,6 +17697,20 @@ function createImplementationOrchestrator(deps) {
 						const constraints = decisions.filter((d) => d.category === "architecture");
 						archConstraints = constraints.map((d) => `${d.key}: ${d.value}`).join("\n");
 					} catch {}
+					let gitDiffContent = "";
+					try {
+						const diffFiles = checkGitDiffFiles(projectRoot ?? process.cwd());
+						if (diffFiles.length > 0) gitDiffContent = execSync(`git diff HEAD -- ${diffFiles.map((f) => `"${f}"`).join(" ")}`, {
+							cwd: projectRoot ?? process.cwd(),
+							encoding: "utf-8",
+							timeout: 1e4,
+							stdio: [
+								"ignore",
+								"pipe",
+								"pipe"
+							]
+						}).trim();
+					} catch {}
 					const sections = isMajorRework ? [
 						{
 							name: "story_content",
@@ -17405,7 +17729,7 @@ function createImplementationOrchestrator(deps) {
 						},
 						{
 							name: "git_diff",
-							content: "",
+							content: gitDiffContent,
 							priority: "optional"
 						}
 					] : (() => {
@@ -17836,6 +18160,19 @@ function createImplementationOrchestrator(deps) {
 			} catch (err) {
 				logger$27.error({ err }, "Post-sprint contract verification threw an error — skipping");
 			}
+			if (projectRoot !== void 0) try {
+				const indicators = checkProfileStaleness(projectRoot);
+				if (indicators.length > 0) {
+					const message = "Project profile may be outdated — consider running `substrate init --force` to re-detect";
+					eventBus.emit("pipeline:profile-stale", {
+						message,
+						indicators
+					});
+					logger$27.warn({ indicators }, message);
+				}
+			} catch (err) {
+				logger$27.debug({ err }, "Profile staleness check failed (best-effort)");
+			}
 			let completed = 0;
 			let escalated = 0;
 			let failed = 0;
@@ -17966,14 +18303,14 @@ async function resolveStoryKeys(db, projectRoot, opts) {
 function parseStoryKeysFromEpics(content) {
 	if (content.length === 0) return [];
 	const keys = new Set();
-	const explicitKeyPattern = /\*\*Story key:\*\*\s*`?(\d+-\d+)(?:-[^`\s]*)?`?/g;
+	const explicitKeyPattern = /\*\*Story key:\*\*\s*`?([A-Za-z0-9]+-[A-Za-z0-9]+)(?:-[^`\s]*)?`?/g;
 	let match$1;
 	while ((match$1 = explicitKeyPattern.exec(content)) !== null) if (match$1[1] !== void 0) keys.add(match$1[1]);
-	const headingPattern = /^###\s+Story\s+(\d+)[.\-](\d+)/gm;
+	const headingPattern = /^###\s+Story\s+([A-Za-z0-9]+)[.\-]([A-Za-z0-9]+)/gm;
 	while ((match$1 = headingPattern.exec(content)) !== null) if (match$1[1] !== void 0 && match$1[2] !== void 0) keys.add(`${match$1[1]}-${match$1[2]}`);
-	const inlineStoryPattern = /Story\s+(\d+)-(\d+)[:\s]/g;
+	const inlineStoryPattern = /Story\s+([A-Za-z0-9]+)-([A-Za-z0-9]+)[:\s]/g;
 	while ((match$1 = inlineStoryPattern.exec(content)) !== null) if (match$1[1] !== void 0 && match$1[2] !== void 0) keys.add(`${match$1[1]}-${match$1[2]}`);
-	const filePathPattern = /_bmad-output\/implementation-artifacts\/(\d+-\d+)-/g;
+	const filePathPattern = /_bmad-output\/implementation-artifacts\/([A-Za-z0-9]+-[A-Za-z0-9]+)-/g;
 	while ((match$1 = filePathPattern.exec(content)) !== null) if (match$1[1] !== void 0) keys.add(match$1[1]);
 	return sortStoryKeys(Array.from(keys));
 }
@@ -18019,6 +18356,12 @@ function discoverPendingStoryKeys(projectRoot, epicNumber) {
 			allKeys = sortStoryKeys([...new Set(allKeys)]);
 		}
 	}
+	const sprintKeys = parseStoryKeysFromSprintStatus(projectRoot);
+	if (sprintKeys.length > 0) {
+		const merged = new Set(allKeys);
+		for (const k of sprintKeys) merged.add(k);
+		allKeys = sortStoryKeys([...merged]);
+	}
 	if (allKeys.length === 0) return [];
 	const existingKeys = collectExistingStoryKeys(projectRoot);
 	return allKeys.filter((k) => !existingKeys.has(k));
@@ -18069,7 +18412,7 @@ function collectExistingStoryKeys(projectRoot) {
 	} catch {
 		return existing;
 	}
-	const filePattern = /^(\d+-\d+)-/;
+	const filePattern = /^([A-Za-z0-9]+-[A-Za-z0-9]+)-/;
 	for (const entry of entries) {
 		if (!entry.endsWith(".md")) continue;
 		const m = filePattern.exec(entry);
@@ -18078,6 +18421,33 @@ function collectExistingStoryKeys(projectRoot) {
 	return existing;
 }
 /**
+* Parse story keys from sprint-status.yaml.
+* Reads the development_status map and extracts keys that match the
+* alphanumeric story key pattern (e.g., 1-1a, NEW-26, E5-accessibility).
+* Filters out epic status entries (epic-N) and retrospective entries.
+*/
+function parseStoryKeysFromSprintStatus(projectRoot) {
+	const candidates = [join$1(projectRoot, "_bmad-output", "implementation-artifacts", "sprint-status.yaml"), join$1(projectRoot, "_bmad-output", "sprint-status.yaml")];
+	const statusPath = candidates.find((p) => existsSync$1(p));
+	if (!statusPath) return [];
+	try {
+		const content = readFileSync$1(statusPath, "utf-8");
+		const keys = [];
+		const linePattern = /^\s{2}([A-Za-z0-9]+-[A-Za-z0-9]+(?:-[A-Za-z0-9-]*)?)\s*:/gm;
+		let match$1;
+		while ((match$1 = linePattern.exec(content)) !== null) {
+			const fullKey = match$1[1];
+			if (/^epic-\d+$/.test(fullKey)) continue;
+			if (fullKey.includes("retrospective")) continue;
+			const segments = fullKey.split("-");
+			if (segments.length >= 2) keys.push(`${segments[0]}-${segments[1]}`);
+		}
+		return [...new Set(keys)];
+	} catch {
+		return [];
+	}
+}
+/**
 * Collect story keys already completed in previous pipeline runs.
 * Scans pipeline_runs with status='completed' and extracts story keys
 * with phase='COMPLETE' from their token_usage_json state.
@@ -18096,16 +18466,26 @@ async function getCompletedStoryKeys(db) {
 	return completed;
 }
 /**
-* Sort story keys numerically by epic number (primary) then story number (secondary).
-* E.g. ["10-1", "1-2", "2-1"] → ["1-2", "2-1", "10-1"]
+* Sort story keys: numeric keys first (by epic then story number),
+* then alphabetic-prefix keys (NEW-*, E-*) sorted lexicographically.
+* E.g. ["10-1", "1-2a", "1-2", "NEW-26", "E5-acc"] → ["1-2", "1-2a", "10-1", "E5-acc", "NEW-26"]
 */
 function sortStoryKeys(keys) {
 	return keys.slice().sort((a, b) => {
-		const [ae, as_] = a.split("-").map(Number);
-		const [be, bs] = b.split("-").map(Number);
-		const epicDiff = (ae ?? 0) - (be ?? 0);
-		if (epicDiff !== 0) return epicDiff;
-		return (as_ ?? 0) - (bs ?? 0);
+		const aParts = a.split("-");
+		const bParts = b.split("-");
+		const aNum = Number(aParts[0]);
+		const bNum = Number(bParts[0]);
+		if (!isNaN(aNum) && !isNaN(bNum)) {
+			if (aNum !== bNum) return aNum - bNum;
+			const aStory = Number(aParts[1]);
+			const bStory = Number(bParts[1]);
+			if (!isNaN(aStory) && !isNaN(bStory) && aStory !== bStory) return aStory - bStory;
+			return (aParts[1] ?? "").localeCompare(bParts[1] ?? "");
+		}
+		if (!isNaN(aNum)) return -1;
+		if (!isNaN(bNum)) return 1;
+		return a.localeCompare(b);
 	});
 }
 
@@ -22114,7 +22494,7 @@ function mapInternalPhaseToEventPhase(internalPhase) {
 	}
 }
 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, 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, registry: injectedRegistry } = options;
 	if (startPhase !== void 0 && !VALID_PHASES.includes(startPhase)) {
 		const errorMsg = `Invalid phase '${startPhase}'. Valid phases: ${VALID_PHASES.join(", ")}`;
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
@@ -22196,7 +22576,7 @@ async function runRunAction(options) {
 	if (storiesArg !== void 0 && storiesArg !== "") {
 		parsedStoryKeys = storiesArg.split(",").map((k) => k.trim()).filter((k) => k.length > 0);
 		for (const key of parsedStoryKeys) if (!validateStoryKey(key)) {
-			const errorMsg = `Story key '${key}' is not a valid format. Expected: <epic>-<story> (e.g., 10-1)`;
+			const errorMsg = `Story key '${key}' is not a valid format. Expected: <epic>-<story> (e.g., 10-1, 1-1a, NEW-26)`;
 			if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
 			else process.stderr.write(`Error: ${errorMsg}\n`);
 			return 1;
@@ -22252,7 +22632,8 @@ async function runRunAction(options) {
 		...telemetryEnabled ? {
 			telemetryEnabled: true,
 			telemetryPort
-		} : {}
+		} : {},
+		maxReviewCycles
 	});
 	let storyKeys = [...parsedStoryKeys];
 	if (!existsSync(dbDir)) mkdirSync(dbDir, { recursive: true });
@@ -22754,7 +23135,7 @@ async function runRunAction(options) {
 					type: "pipeline:pre-flight-failure",
 					ts: new Date().toISOString(),
 					exitCode: payload.exitCode,
-					output: payload.output
+					output: payload.output + "\nTip: Use --skip-preflight to bypass, or check your build command in .substrate/project-profile.yaml"
 				});
 			});
 			eventBus.on("pipeline:contract-mismatch", (payload) => {
@@ -22777,6 +23158,14 @@ async function runRunAction(options) {
 					verdict: payload.verdict
 				});
 			});
+			eventBus.on("pipeline:profile-stale", (payload) => {
+				ndjsonEmitter.emit({
+					type: "pipeline:profile-stale",
+					ts: new Date().toISOString(),
+					message: payload.message,
+					indicators: payload.indicators
+				});
+			});
 		}
 		const ingestionServer = telemetryEnabled ? new IngestionServer({ port: telemetryPort }) : void 0;
 		if (telemetryPersistence !== void 0) {
@@ -22809,7 +23198,7 @@ async function runRunAction(options) {
 			eventBus,
 			config: {
 				maxConcurrency: concurrency,
-				maxReviewCycles: 2,
+				maxReviewCycles,
 				pipelineRunId: pipelineRun.id,
 				enableHeartbeat: eventsFlag === true,
 				skipPreflight: skipPreflight === true
@@ -22928,7 +23317,7 @@ 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, 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 } = options;
 	if (!existsSync(dbDir)) mkdirSync(dbDir, { recursive: true });
 	const adapter = createDatabaseAdapter({
 		backend: "auto",
@@ -23148,7 +23537,7 @@ async function runFullPipeline(options) {
 					eventBus,
 					config: {
 						maxConcurrency: concurrency,
-						maxReviewCycles: 2,
+						maxReviewCycles,
 						pipelineRunId: runId,
 						skipPreflight: skipPreflight === true
 					},
@@ -23257,7 +23646,7 @@ 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("--dry-run", "Preview routing and repo-map injection without dispatching (Story 28-9)").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)").action(async (opts) => {
 		if (opts.helpAgent) {
 			process.exitCode = await runHelpAgent();
 			return;
@@ -23292,6 +23681,7 @@ function registerRunCommand(program, _version = "0.0.0", projectRoot = process.c
 			research: opts.research,
 			skipResearch: opts.skipResearch,
 			skipPreflight: opts.skipPreflight,
+			maxReviewCycles: opts.maxReviewCycles,
 			dryRun: opts.dryRun,
 			registry
 		});
@@ -23301,4 +23691,4 @@ function registerRunCommand(program, _version = "0.0.0", projectRoot = process.c
 
 //#endregion
 export { AdapterTelemetryPersistence, AppError, DEFAULT_CONFIG, DEFAULT_ROUTING_POLICY, DoltClient, DoltNotInstalled, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, FileStateStore, GitClient, GrammarLoader, IngestionServer, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SUBSTRATE_OWNED_SETTINGS_KEYS, SymbolParser, VALID_PHASES, WorkGraphRepository, buildPipelineStatusOutput, checkDoltInstalled, createConfigSystem, createContextCompiler, createDatabaseAdapter, createDispatcher, createDoltClient, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStateStore, createStopAfterGate, createTelemetryAdvisor, detectCycles, findPackageRoot, formatOutput, formatPhaseCompletionSummary, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, initSchema, initializeDolt, isSyncAdapter, parseDbTimestampAsUtc, registerHealthCommand, registerRunCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runRunAction, runSolutioningPhase, validateStopAfterFromConflict };
-//# sourceMappingURL=run-IDOmPys1.js.map
+//# sourceMappingURL=run-GwwiCYXX.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.6.1",
+  "version": "0.6.3",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",