substrate-ai 0.19.0 → 0.19.2

package/dist/cli/index.js

@@ -1,10 +1,10 @@
 #!/usr/bin/env node
-import { FileStateStore, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, WorkGraphRepository, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, detectCycles, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot } from "../health-Cx2ZhRNT.js";
+import { FileStateStore, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, WorkGraphRepository, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot } from "../health-Cx2ZhRNT.js";
 import { createLogger } from "../logger-KeHncl-f.js";
 import { createEventBus } from "../helpers-CElYrONe.js";
 import { AdapterRegistry, BudgetConfigSchema, CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, ConfigError, CostTrackerConfigSchema, DEFAULT_CONFIG, DoltClient, DoltNotInstalled, EXPERIMENT_RESULT, 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, listRequirements, listRunMetrics, loadParentRunDecisions, supersedeDecision, tagRunAsBaseline, updatePipelineRun } from "../dist-Bm0qSZer.js";
 import "../adapter-registry-DXLMTmfD.js";
-import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-C3MnOuBe.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, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-BOhSIujp.js";
 import "../errors-BSpu7pIv.js";
 import "../routing-CcBOCuC9.js";
 import "../decisions-C0pz9Clx.js";
@@ -1135,6 +1135,17 @@ const TokenCeilingsSchema = z.object({
 	"test-plan": z.number().int().positive("test-plan token ceiling must be a positive integer").optional(),
 	"test-expansion": z.number().int().positive("test-expansion token ceiling must be a positive integer").optional()
 });
+/**
+* Per-task-type dispatch timeout overrides (milliseconds).
+* Keys match task types in DEFAULT_TIMEOUTS. Values override defaults.
+*/
+const DispatchTimeoutsSchema = z.object({
+	"create-story": z.number().int().positive().optional(),
+	"dev-story": z.number().int().positive().optional(),
+	"code-review": z.number().int().positive().optional(),
+	"minor-fixes": z.number().int().positive().optional(),
+	"major-rework": z.number().int().positive().optional()
+});
 const SubstrateConfigSchema = z.object({
 	config_format_version: z.enum(["1"]),
 	task_graph_version: z.enum(["1"]).optional(),
@@ -1143,6 +1154,7 @@ const SubstrateConfigSchema = z.object({
 	cost_tracker: CostTrackerConfigSchema.optional(),
 	budget: BudgetConfigSchema.optional(),
 	token_ceilings: TokenCeilingsSchema.optional(),
+	dispatch_timeouts: DispatchTimeoutsSchema.optional(),
 	telemetry: TelemetryConfigSchema.optional()
 }).strict();
 const PartialSubstrateConfigSchema = z.object({
@@ -1157,6 +1169,7 @@ const PartialSubstrateConfigSchema = z.object({
 	cost_tracker: CostTrackerConfigSchema.partial().optional(),
 	budget: BudgetConfigSchema.partial().optional(),
 	token_ceilings: TokenCeilingsSchema.optional(),
+	dispatch_timeouts: DispatchTimeoutsSchema.optional(),
 	telemetry: TelemetryConfigSchema.partial().optional()
 }).strict();
 
@@ -2621,26 +2634,6 @@ function registerConfigCommand(program, _version) {
 	});
 }
 
-//#endregion
-//#region src/modules/work-graph/errors.ts
-/**
-* Work-graph error types.
-*
-* Story 31-7: Cycle Detection in Work Graph
-*/
-/**
-* Thrown by `EpicIngester.ingest()` when the provided dependency list
-* contains a cycle.  The `cycle` field contains the path of story keys
-* that form the cycle (first and last element are the same).
-*/
-var CyclicDependencyError = class extends Error {
-	constructor(cycle) {
-		super(`Cyclic dependency detected: ${cycle.join(" → ")}`);
-		this.cycle = cycle;
-		this.name = "CyclicDependencyError";
-	}
-};
-
 //#endregion
 //#region src/cli/commands/resume.ts
 const logger$13 = createLogger("resume-cmd");
@@ -4529,7 +4522,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-C8jeEtC6.js"
+									"../run-CCHb_JMl.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -8607,64 +8600,6 @@ var EpicParser = class {
 	}
 };
 
-//#endregion
-//#region src/modules/work-graph/epic-ingester.ts
-var EpicIngester = class {
-	adapter;
-	constructor(adapter) {
-		this.adapter = adapter;
-	}
-	/**
-	* Upsert stories and sync dependencies into the database.
-	*
-	* Both operations are wrapped in a single transaction: if either fails the
-	* entire batch is rolled back.
-	*
-	* @param stories      - Parsed story metadata from `EpicParser.parseStories()`.
-	* @param dependencies - Parsed dependency edges from `EpicParser.parseDependencies()`.
-	* @returns `IngestResult` with counts of affected rows.
-	*/
-	async ingest(stories, dependencies) {
-		const cycle = detectCycles(dependencies);
-		if (cycle !== null) throw new CyclicDependencyError(cycle);
-		return this.adapter.transaction(async (tx) => {
-			let storiesUpserted = 0;
-			for (const story of stories) {
-				const existing = await tx.query("SELECT status FROM wg_stories WHERE story_key = ?", [story.story_key]);
-				if (existing.length > 0) await tx.query("UPDATE wg_stories SET title = ?, updated_at = ? WHERE story_key = ?", [
-					story.title,
-					new Date().toISOString(),
-					story.story_key
-				]);
-				else {
-					const now = new Date().toISOString();
-					await tx.query("INSERT INTO wg_stories (story_key, epic, title, status, created_at, updated_at) VALUES (?, ?, ?, ?, ?, ?)", [
-						story.story_key,
-						String(story.epic_num),
-						story.title,
-						"planned",
-						now,
-						now
-					]);
-					storiesUpserted++;
-				}
-			}
-			const epicNum = stories.length > 0 ? stories[0].epic_num : null;
-			if (epicNum !== null) await tx.query(`DELETE FROM story_dependencies WHERE source = 'explicit' AND story_key LIKE ?`, [`${epicNum}-%`]);
-			for (const dep of dependencies) await tx.query("INSERT INTO story_dependencies (story_key, depends_on, dependency_type, source) VALUES (?, ?, ?, ?)", [
-				dep.story_key,
-				dep.depends_on,
-				dep.dependency_type,
-				dep.source
-			]);
-			return {
-				storiesUpserted,
-				dependenciesReplaced: dependencies.length
-			};
-		});
-	}
-};
-
 //#endregion
 //#region src/cli/commands/ingest-epic.ts
 function registerIngestEpicCommand(program) {

package/dist/index.d.ts

@@ -1417,6 +1417,7 @@ declare function withRetry<T>(fn: () => Promise<T>, maxRetries?: number, baseDel
 //#endregion
 //#region src/modules/config/config-schema.d.ts
 //# sourceMappingURL=helpers.d.ts.map
+
 declare const SubstrateConfigSchema: z.ZodObject<{
   config_format_version: z.ZodEnum<{
     1: "1";
@@ -1514,6 +1515,13 @@ declare const SubstrateConfigSchema: z.ZodObject<{
     'test-plan': z.ZodOptional<z.ZodNumber>;
     'test-expansion': z.ZodOptional<z.ZodNumber>;
   }, z.core.$strip>>;
+  dispatch_timeouts: z.ZodOptional<z.ZodObject<{
+    'create-story': z.ZodOptional<z.ZodNumber>;
+    'dev-story': z.ZodOptional<z.ZodNumber>;
+    'code-review': z.ZodOptional<z.ZodNumber>;
+    'minor-fixes': z.ZodOptional<z.ZodNumber>;
+    'major-rework': z.ZodOptional<z.ZodNumber>;
+  }, z.core.$strip>>;
   telemetry: z.ZodOptional<z.ZodObject<{
     enabled: z.ZodDefault<z.ZodBoolean>;
     port: z.ZodDefault<z.ZodNumber>;

package/dist/{run-C3MnOuBe.js → run-BOhSIujp.js}

@@ -1,4 +1,4 @@
-import { BMAD_BASELINE_TOKENS_FULL, DoltMergeConflict, FileStateStore, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, VALID_PHASES, WorkGraphRepository, __commonJS, __require, __toESM, buildPipelineStatusOutput, createDatabaseAdapter, formatOutput, formatPipelineSummary, formatTokenTelemetry, inspectProcessTree, parseDbTimestampAsUtc, resolveMainRepoRoot, validateStoryKey } from "./health-Cx2ZhRNT.js";
+import { BMAD_BASELINE_TOKENS_FULL, DoltMergeConflict, FileStateStore, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, VALID_PHASES, WorkGraphRepository, __commonJS, __require, __toESM, buildPipelineStatusOutput, createDatabaseAdapter, detectCycles, formatOutput, formatPipelineSummary, formatTokenTelemetry, inspectProcessTree, parseDbTimestampAsUtc, resolveMainRepoRoot, validateStoryKey } from "./health-Cx2ZhRNT.js";
 import { createLogger } from "./logger-KeHncl-f.js";
 import { TypedEventBusImpl, createEventBus, createTuiApp, isTuiCapable, printNonTtyWarning, sleep } from "./helpers-CElYrONe.js";
 import { ADVISORY_NOTES, Categorizer, ConsumerAnalyzer, DEFAULT_GLOBAL_SETTINGS, DispatcherImpl, DoltClient, ESCALATION_DIAGNOSIS, EfficiencyScorer, IngestionServer, LogTurnAnalyzer, OPERATIONAL_FINDING, Recommender, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, STORY_METRICS, STORY_OUTCOME, SubstrateConfigSchema, TEST_EXPANSION_FINDING, TEST_PLAN, TelemetryNormalizer, TelemetryPipeline, TurnAnalyzer, addTokenUsage, aggregateTokenUsageForRun, aggregateTokenUsageForStory, callLLM, createConfigSystem, createDatabaseAdapter$1, createDecision, createPipelineRun, createRequirement, detectInterfaceChanges, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getPipelineRunById, getRunningPipelineRuns, getStoryMetricsForRun, getTokenUsageSummary, initSchema, loadModelRoutingConfig, registerArtifact, updatePipelineRun, updatePipelineRunConfig, upsertDecision, writeRunMetrics, writeStoryMetrics } from "./dist-Bm0qSZer.js";
@@ -6009,6 +6009,26 @@ function countFilesInLayout(content) {
 	return count;
 }
 
+//#endregion
+//#region src/modules/work-graph/errors.ts
+/**
+* Work-graph error types.
+*
+* Story 31-7: Cycle Detection in Work Graph
+*/
+/**
+* Thrown by `EpicIngester.ingest()` when the provided dependency list
+* contains a cycle.  The `cycle` field contains the path of story keys
+* that form the cycle (first and last element are the same).
+*/
+var CyclicDependencyError = class extends Error {
+	constructor(cycle) {
+		super(`Cyclic dependency detected: ${cycle.join(" → ")}`);
+		this.cycle = cycle;
+		this.name = "CyclicDependencyError";
+	}
+};
+
 //#endregion
 //#region src/modules/work-graph/spec-migrator.ts
 /**
@@ -6671,6 +6691,43 @@ function defaultFailResult(error, tokenUsage) {
 	};
 }
 /**
+* Count test cases (`it(`, `test(`, `it.each(`, `test.each(`) in modified
+* test files. Returns a structured summary the reviewer can use as ground
+* truth instead of manually estimating test counts from code inspection.
+*/
+async function countTestMetrics(filesModified, cwd) {
+	if (!filesModified || filesModified.length === 0) return "";
+	const testFiles = filesModified.filter((f$1) => f$1.includes(".test.") || f$1.includes(".spec.") || f$1.includes("__tests__"));
+	if (testFiles.length === 0) return "";
+	const results = [];
+	let totalCount = 0;
+	for (const file of testFiles) try {
+		const out = execSync(`grep -cE "^\\s*(it|test|it\\.each|test\\.each)\\s*\\(" "${file}" 2>/dev/null || echo 0`, {
+			cwd,
+			encoding: "utf-8",
+			timeout: 5e3
+		}).trim();
+		const count = parseInt(out, 10) || 0;
+		if (count > 0) {
+			results.push({
+				file: file.split("/").pop(),
+				count
+			});
+			totalCount += count;
+		}
+	} catch {}
+	if (totalCount === 0) return "";
+	const lines = [
+		`VERIFIED TEST COUNT (automated — use as ground truth):`,
+		`Total test cases: ${totalCount} across ${results.length} test file(s)`,
+		...results.map((r) => `  ${r.file}: ${r.count} test(s)`),
+		"",
+		"IMPORTANT: Use this verified count when evaluating AC test coverage thresholds.",
+		"Do NOT manually estimate test counts — use the numbers above."
+	];
+	return lines.join("\n");
+}
+/**
 * Execute the compiled code-review workflow.
 *
 * Steps:
@@ -6808,6 +6865,8 @@ async function runCodeReview(deps, params) {
 			}, "Injecting prior findings into code-review prompt");
 		}
 	} catch {}
+	const testMetricsContent = await countTestMetrics(filesModified, cwd);
+	if (testMetricsContent) logger$12.debug({ storyKey }, "Injecting verified test-count metrics into code-review context");
 	const sections = [
 		{
 			name: "story_content",
@@ -6819,6 +6878,11 @@ async function runCodeReview(deps, params) {
 			content: gitDiffContent,
 			priority: "important"
 		},
+		{
+			name: "test_metrics",
+			content: testMetricsContent,
+			priority: "important"
+		},
 		{
 			name: "previous_findings",
 			content: previousFindingsContent,
@@ -9617,6 +9681,446 @@ function createTelemetryAdvisor(deps) {
 	return new TelemetryAdvisor(deps);
 }
 
+//#endregion
+//#region src/modules/work-graph/epic-ingester.ts
+var EpicIngester = class {
+	adapter;
+	constructor(adapter) {
+		this.adapter = adapter;
+	}
+	/**
+	* Upsert stories and sync dependencies into the database.
+	*
+	* Both operations are wrapped in a single transaction: if either fails the
+	* entire batch is rolled back.
+	*
+	* @param stories      - Parsed story metadata from `EpicParser.parseStories()`.
+	* @param dependencies - Parsed dependency edges from `EpicParser.parseDependencies()`.
+	* @returns `IngestResult` with counts of affected rows.
+	*/
+	async ingest(stories, dependencies) {
+		const cycle = detectCycles(dependencies);
+		if (cycle !== null) throw new CyclicDependencyError(cycle);
+		return this.adapter.transaction(async (tx) => {
+			let storiesUpserted = 0;
+			for (const story of stories) {
+				const existing = await tx.query("SELECT status FROM wg_stories WHERE story_key = ?", [story.story_key]);
+				if (existing.length > 0) await tx.query("UPDATE wg_stories SET title = ?, updated_at = ? WHERE story_key = ?", [
+					story.title,
+					new Date().toISOString(),
+					story.story_key
+				]);
+				else {
+					const now = new Date().toISOString();
+					await tx.query("INSERT INTO wg_stories (story_key, epic, title, status, created_at, updated_at) VALUES (?, ?, ?, ?, ?, ?)", [
+						story.story_key,
+						String(story.epic_num),
+						story.title,
+						"planned",
+						now,
+						now
+					]);
+					storiesUpserted++;
+				}
+			}
+			const epicNum = stories.length > 0 ? stories[0].epic_num : null;
+			if (epicNum !== null) await tx.query(`DELETE FROM story_dependencies WHERE source = 'explicit' AND story_key LIKE ?`, [`${epicNum}-%`]);
+			for (const dep of dependencies) await tx.query("INSERT INTO story_dependencies (story_key, depends_on, dependency_type, source) VALUES (?, ?, ?, ?)", [
+				dep.story_key,
+				dep.depends_on,
+				dep.dependency_type,
+				dep.source
+			]);
+			return {
+				storiesUpserted,
+				dependenciesReplaced: dependencies.length
+			};
+		});
+	}
+};
+
+//#endregion
+//#region src/modules/implementation-orchestrator/story-discovery.ts
+/**
+* Unified story key resolution with a 5-level fallback chain.
+*
+* 1. Explicit keys (from --stories flag) — returned as-is
+* 1.5. ready_stories SQL view — when work graph is populated (story 31-3)
+* 2. Decisions table (category='stories', phase='solutioning')
+* 3. Epic shard decisions (category='epic-shard') — parsed with parseStoryKeysFromEpics
+* 4. epics.md file on disk (via discoverPendingStoryKeys)
+*
+* Optionally filters out completed stories when filterCompleted is set.
+*
+* @returns Sorted, deduplicated array of story keys in "N-M" format
+*/
+async function resolveStoryKeys(db, projectRoot, opts) {
+	if (opts?.explicit !== void 0 && opts.explicit.length > 0) return topologicalSortByDependencies(opts.explicit, projectRoot);
+	let keys = [];
+	const readyKeys = await db.queryReadyStories();
+	if (readyKeys.length > 0) {
+		let filteredKeys = readyKeys;
+		if (opts?.epicNumber !== void 0) {
+			const prefix = `${opts.epicNumber}-`;
+			filteredKeys = filteredKeys.filter((k) => k.startsWith(prefix));
+		}
+		if (opts?.filterCompleted === true && filteredKeys.length > 0) {
+			const completedKeys = await getCompletedStoryKeys(db);
+			filteredKeys = filteredKeys.filter((k) => !completedKeys.has(k));
+		}
+		const existingArtifacts = collectExistingStoryKeys(projectRoot);
+		const alreadyDone = filteredKeys.filter((k) => existingArtifacts.has(k));
+		if (alreadyDone.length > 0) {
+			filteredKeys = filteredKeys.filter((k) => !existingArtifacts.has(k));
+			for (const key of alreadyDone) db.query(`UPDATE wg_stories SET status = 'complete', completed_at = ? WHERE story_key = ? AND status <> 'complete'`, [new Date().toISOString(), key]).catch(() => {});
+		}
+		return sortStoryKeys([...new Set(filteredKeys)]);
+	}
+	try {
+		const sql = opts?.pipelineRunId !== void 0 ? `SELECT key FROM decisions WHERE phase = 'solutioning' AND category = 'stories' AND pipeline_run_id = ? ORDER BY created_at ASC` : `SELECT key FROM decisions WHERE phase = 'solutioning' AND category = 'stories' ORDER BY created_at ASC`;
+		const params = opts?.pipelineRunId !== void 0 ? [opts.pipelineRunId] : [];
+		const rows = await db.query(sql, params);
+		for (const row of rows) if (/^\d+-\d+/.test(row.key)) {
+			const match$1 = /^(\d+-\d+)/.exec(row.key);
+			if (match$1 !== null) keys.push(match$1[1]);
+		}
+	} catch {}
+	if (keys.length === 0) try {
+		const sql = opts?.pipelineRunId !== void 0 ? `SELECT value FROM decisions WHERE category = 'epic-shard' AND pipeline_run_id = ? ORDER BY created_at ASC` : `SELECT value FROM decisions WHERE category = 'epic-shard' ORDER BY created_at ASC`;
+		const params = opts?.pipelineRunId !== void 0 ? [opts.pipelineRunId] : [];
+		const shardRows = await db.query(sql, params);
+		const allContent = shardRows.map((r) => r.value).join("\n");
+		if (allContent.length > 0) keys = parseStoryKeysFromEpics(allContent);
+	} catch {}
+	if (keys.length === 0) keys = discoverPendingStoryKeys(projectRoot, opts?.epicNumber);
+	if (opts?.epicNumber !== void 0 && keys.length > 0) {
+		const prefix = `${opts.epicNumber}-`;
+		keys = keys.filter((k) => k.startsWith(prefix));
+	}
+	if (opts?.filterCompleted === true && keys.length > 0) {
+		const completedKeys = await getCompletedStoryKeys(db);
+		keys = keys.filter((k) => !completedKeys.has(k));
+	}
+	if (keys.length > 0) {
+		const existingArtifacts = collectExistingStoryKeys(projectRoot);
+		keys = keys.filter((k) => !existingArtifacts.has(k));
+	}
+	return sortStoryKeys([...new Set(keys)]);
+}
+/**
+* Extract all story keys (N-M format) from epics.md content.
+*
+* Supports three extraction patterns found in real epics.md files:
+*   1. Explicit key lines:  **Story key:** `7-2-human-turn-loop`  → extracts "7-2"
+*   2. Story headings:      ### Story 7.2: Human Turn Loop        → extracts "7-2"
+*   3. File path refs:      _bmad-output/implementation-artifacts/7-2-human-turn-loop.md → extracts "7-2"
+*
+* Keys are deduplicated and sorted numerically (epic number primary, story number secondary).
+*
+* @param content - Raw string content of epics.md
+* @returns Sorted, deduplicated array of story key strings in "N-M" format
+*/
+function parseStoryKeysFromEpics(content) {
+	if (content.length === 0) return [];
+	const keys = new Set();
+	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+([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+([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\/([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$1[1]);
+	return sortStoryKeys(Array.from(keys));
+}
+/**
+* Discover pending story keys by diffing epics.md against existing story files.
+*
+* Algorithm:
+*   1. Read _bmad-output/planning-artifacts/epics.md (falls back to _bmad-output/epics.md)
+*   2. Extract all story keys from epics.md
+*   3. Glob _bmad-output/implementation-artifacts/ for N-M-*.md files
+*   4. Return keys from step 2 that are NOT in step 3 (pending work)
+*
+* Returns an empty array (without error) if epics.md does not exist.
+*
+* @param projectRoot - Absolute path to the project root directory
+* @returns Sorted array of pending story keys in "N-M" format
+*/
+function discoverPendingStoryKeys(projectRoot, epicNumber) {
+	let allKeys = [];
+	if (epicNumber !== void 0) {
+		const epicFiles = findEpicFiles(projectRoot);
+		const targetPattern = new RegExp(`^epic-${epicNumber}[^0-9]`);
+		const matched = epicFiles.filter((f$1) => targetPattern.test(f$1.split("/").pop()));
+		for (const epicFile of matched) try {
+			const content = readFileSync(epicFile, "utf-8");
+			const keys = parseStoryKeysFromEpics(content);
+			allKeys.push(...keys);
+		} catch {}
+		allKeys = sortStoryKeys([...new Set(allKeys)]);
+	} else {
+		const epicsPath = findEpicsFile(projectRoot);
+		if (epicsPath !== void 0) try {
+			const content = readFileSync(epicsPath, "utf-8");
+			allKeys = parseStoryKeysFromEpics(content);
+		} catch {}
+		if (allKeys.length === 0) {
+			const epicFiles = findEpicFiles(projectRoot);
+			for (const epicFile of epicFiles) try {
+				const content = readFileSync(epicFile, "utf-8");
+				const keys = parseStoryKeysFromEpics(content);
+				allKeys.push(...keys);
+			} catch {}
+			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));
+}
+/**
+* Find epic files from known candidate paths relative to projectRoot.
+*
+* Checks for:
+*   1. epics.md (consolidated epic file)
+*   2. Individual epic-*.md files in planning-artifacts/
+*
+* Returns a single path for epics.md, or undefined if not found.
+* For individual epic files, use findEpicFiles() instead.
+*/
+function findEpicsFile(projectRoot) {
+	const candidates = ["_bmad-output/planning-artifacts/epics.md", "_bmad-output/epics.md"];
+	for (const candidate of candidates) {
+		const fullPath = join$1(projectRoot, candidate);
+		if (existsSync(fullPath)) return fullPath;
+	}
+	const planningDir = join$1(projectRoot, "_bmad-output", "planning-artifacts");
+	if (existsSync(planningDir)) try {
+		const entries = readdirSync(planningDir, { encoding: "utf-8" });
+		const match$1 = entries.filter((e) => /^epics[-.].*\.md$/i.test(e) && !/^epic-\d+/.test(e)).sort();
+		if (match$1.length > 0) return join$1(planningDir, match$1[0]);
+	} catch {}
+	return void 0;
+}
+/**
+* Find individual epic-*.md files in the planning artifacts directory.
+* Returns paths sorted alphabetically.
+*/
+function findEpicFiles(projectRoot) {
+	const planningDir = join$1(projectRoot, "_bmad-output", "planning-artifacts");
+	if (!existsSync(planningDir)) return [];
+	try {
+		const entries = readdirSync(planningDir, { encoding: "utf-8" });
+		return entries.filter((e) => /^epic-\d+.*\.md$/.test(e)).sort().map((e) => join$1(planningDir, e));
+	} catch {
+		return [];
+	}
+}
+/**
+* Collect story keys that already have implementation artifact files.
+* Scans _bmad-output/implementation-artifacts/ for files matching N-M-*.md.
+*/
+function collectExistingStoryKeys(projectRoot) {
+	const existing = new Set();
+	const artifactsDir = join$1(projectRoot, "_bmad-output", "implementation-artifacts");
+	if (!existsSync(artifactsDir)) return existing;
+	let entries;
+	try {
+		entries = readdirSync(artifactsDir, { encoding: "utf-8" });
+	} catch {
+		return existing;
+	}
+	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);
+		if (m !== null && m[1] !== void 0) existing.add(m[1]);
+	}
+	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(p));
+	if (!statusPath) return [];
+	try {
+		const content = readFileSync(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.
+*/
+async function getCompletedStoryKeys(db) {
+	const completed = new Set();
+	try {
+		const rows = await db.query(`SELECT token_usage_json FROM pipeline_runs WHERE status = 'completed' AND token_usage_json IS NOT NULL`);
+		for (const row of rows) try {
+			const state = JSON.parse(row.token_usage_json);
+			if (state.stories !== void 0) {
+				for (const [key, s$1] of Object.entries(state.stories)) if (s$1.phase === "COMPLETE") completed.add(key);
+			}
+		} catch {}
+	} catch {}
+	return completed;
+}
+/**
+* Sort story keys: numeric keys first (by epic then story number),
+* then alphabetic-prefix keys (NEW-*, E-*) sorted lexicographically.
+* E.g. ["10-1", "1-2a", "1-2", "NEW-26", "E5-acc"] → ["1-2", "1-2a", "10-1", "E5-acc", "NEW-26"]
+*/
+function sortStoryKeys(keys) {
+	return keys.slice().sort((a, b) => {
+		const aParts = a.split("-");
+		const bParts = b.split("-");
+		const aNum = Number(aParts[0]);
+		const bNum = Number(bParts[0]);
+		if (!isNaN(aNum) && !isNaN(bNum)) {
+			if (aNum !== bNum) return aNum - bNum;
+			const aStory = Number(aParts[1]);
+			const bStory = Number(bParts[1]);
+			if (!isNaN(aStory) && !isNaN(bStory) && aStory !== bStory) return aStory - bStory;
+			return (aParts[1] ?? "").localeCompare(bParts[1] ?? "");
+		}
+		if (!isNaN(aNum)) return -1;
+		if (!isNaN(bNum)) return 1;
+		return a.localeCompare(b);
+	});
+}
+/**
+* Parse inter-story dependencies from the consolidated epics document.
+*
+* Scans for patterns like:
+*   ### Story 50-2: Title
+*   **Dependencies:** 50-1
+*
+* Returns a Map where key=storyKey, value=Set of dependency keys.
+* Only returns dependencies that are within the provided storyKeys set
+* (external dependencies to other epics are ignored for ordering purposes).
+*/
+function parseEpicsDependencies(projectRoot, storyKeys) {
+	const deps = new Map();
+	const epicsPath = findEpicsFile(projectRoot);
+	if (epicsPath === void 0) return deps;
+	let content;
+	try {
+		content = readFileSync(epicsPath, "utf-8");
+	} catch {
+		return deps;
+	}
+	const storyPattern = /^###\s+Story\s+(\d+)-(\d+)[:\s]/gm;
+	const depPattern = /^\*\*Dependencies:\*\*\s*(.+)$/gm;
+	const storyPositions = [];
+	let match$1;
+	while ((match$1 = storyPattern.exec(content)) !== null) storyPositions.push({
+		key: `${match$1[1]}-${match$1[2]}`,
+		pos: match$1.index
+	});
+	for (let i = 0; i < storyPositions.length; i++) {
+		const story = storyPositions[i];
+		const nextStoryPos = i + 1 < storyPositions.length ? storyPositions[i + 1].pos : content.length;
+		const section = content.slice(story.pos, nextStoryPos);
+		depPattern.lastIndex = 0;
+		const depMatch = depPattern.exec(section);
+		if (depMatch === null || /^none$/i.test(depMatch[1].trim())) continue;
+		const depText = depMatch[1];
+		const storyDeps = new Set();
+		const rangeMatch = /(\d+)-(\d+)\s+through\s+\1-(\d+)/i.exec(depText);
+		if (rangeMatch !== null) {
+			const epic = rangeMatch[1];
+			const start = Number(rangeMatch[2]);
+			const end = Number(rangeMatch[3]);
+			for (let n$1 = start; n$1 <= end; n$1++) {
+				const depKey = `${epic}-${n$1}`;
+				if (storyKeys.has(depKey)) storyDeps.add(depKey);
+			}
+		} else {
+			const keyPattern = /(\d+-\d+[a-z]?)/g;
+			let km;
+			while ((km = keyPattern.exec(depText)) !== null) {
+				const depKey = km[1];
+				if (storyKeys.has(depKey)) storyDeps.add(depKey);
+			}
+		}
+		if (storyDeps.size > 0) deps.set(story.key, storyDeps);
+	}
+	return deps;
+}
+/**
+* Topologically sort explicit story keys by inter-story dependencies.
+*
+* Parses the consolidated epics document for dependency metadata, builds
+* a DAG, and returns keys in dependency-first order using Kahn's algorithm.
+* Stories with no dependencies come first; stories that depend on others
+* are placed after their prerequisites.
+*
+* Falls back to numeric sort if no epics document exists or no
+* dependencies are found among the provided keys.
+*/
+function topologicalSortByDependencies(keys, projectRoot) {
+	if (keys.length <= 1) return keys;
+	const keySet = new Set(keys);
+	const deps = parseEpicsDependencies(projectRoot, keySet);
+	if (deps.size === 0) return sortStoryKeys(keys);
+	const inDegree = new Map();
+	const successors = new Map();
+	for (const key of keys) {
+		inDegree.set(key, 0);
+		successors.set(key, new Set());
+	}
+	for (const [dependent, depSet] of deps) {
+		if (!keySet.has(dependent)) continue;
+		for (const dep of depSet) {
+			if (!keySet.has(dep)) continue;
+			successors.get(dep).add(dependent);
+			inDegree.set(dependent, (inDegree.get(dependent) ?? 0) + 1);
+		}
+	}
+	const result = [];
+	const processed = new Set();
+	while (processed.size < keys.length) {
+		const wave = [];
+		for (const key of keys) if (!processed.has(key) && (inDegree.get(key) ?? 0) === 0) wave.push(key);
+		if (wave.length === 0) {
+			for (const key of sortStoryKeys(keys)) if (!processed.has(key)) result.push(key);
+			break;
+		}
+		for (const key of sortStoryKeys(wave)) {
+			result.push(key);
+			processed.add(key);
+			for (const succ of successors.get(key) ?? []) inDegree.set(succ, (inDegree.get(succ) ?? 0) - 1);
+		}
+	}
+	return result;
+}
+
 //#endregion
 //#region src/modules/implementation-orchestrator/orchestrator-impl.ts
 function estimateDispatchCost(input, output) {
@@ -9715,6 +10219,134 @@ function extractExpectedStoryTitle(shardContent, storyKey) {
 	}
 	return null;
 }
+/**
+* Check whether a story's expected NEW files already exist in the working tree,
+* indicating the story was implicitly implemented by adjacent stories.
+*
+* Parses the consolidated epics document for the story's "Files likely touched"
+* section and checks for files marked as "(new)". If all expected new files
+* already exist, the story is considered implicitly covered.
+*
+* Returns `true` if the story appears already covered, `false` otherwise.
+*/
+function isImplicitlyCovered(storyKey, projectRoot) {
+	const planningDir = join$1(projectRoot, "_bmad-output", "planning-artifacts");
+	if (!existsSync(planningDir)) return false;
+	let epicsPath;
+	try {
+		const entries = readdirSync(planningDir, { encoding: "utf-8" });
+		const match$1 = entries.find((e) => /^epics[-.].*\.md$/i.test(e) && !/^epic-\d+/.test(e));
+		if (match$1) epicsPath = join$1(planningDir, match$1);
+	} catch {
+		return false;
+	}
+	if (!epicsPath) return false;
+	let content;
+	try {
+		content = readFileSync(epicsPath, "utf-8");
+	} catch {
+		return false;
+	}
+	const escapedKey = storyKey.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+	const storyHeading = new RegExp(`^###\\s+Story\\s+${escapedKey}[:\\s]`, "m");
+	const headingMatch = storyHeading.exec(content);
+	if (!headingMatch) return false;
+	const sectionStart = headingMatch.index;
+	const nextHeading = content.indexOf("\n### Story ", sectionStart + 1);
+	const section = nextHeading > 0 ? content.slice(sectionStart, nextHeading) : content.slice(sectionStart);
+	const filesIdx = section.indexOf("Files likely touched:");
+	if (filesIdx < 0) return false;
+	const filesBlock = section.slice(filesIdx);
+	const newFilePattern = /^-\s*`([^`]+)`\s*\(new\)/gm;
+	const expectedNewFiles = [];
+	let fm;
+	while ((fm = newFilePattern.exec(filesBlock)) !== null) if (fm[1]) expectedNewFiles.push(fm[1]);
+	if (expectedNewFiles.length === 0) return false;
+	const existCount = expectedNewFiles.filter((f$1) => existsSync(join$1(projectRoot, f$1))).length;
+	return existCount === expectedNewFiles.length;
+}
+/**
+* Auto-ingest stories and inter-story dependencies from the consolidated
+* epics document into the work graph (`wg_stories` + `story_dependencies`).
+*
+* This bridges the gap between Level 4 discovery (file-based, no dependency
+* gating) and Level 1.5 discovery (`ready_stories` view, dependency-aware).
+*
+* Idempotent: existing stories preserve their status; dependencies are
+* replaced per-epic (EpicIngester's delete-and-reinsert pattern).
+*/
+async function autoIngestEpicsDependencies(db, projectRoot) {
+	const epicsPath = findEpicsFile(projectRoot);
+	if (!epicsPath) return {
+		storiesIngested: 0,
+		dependenciesIngested: 0
+	};
+	let content;
+	try {
+		content = readFileSync(epicsPath, "utf-8");
+	} catch {
+		return {
+			storiesIngested: 0,
+			dependenciesIngested: 0
+		};
+	}
+	const storyPattern = /^###\s+Story\s+(\d+)-(\d+):\s+(.+)$/gm;
+	const stories = [];
+	let match$1;
+	while ((match$1 = storyPattern.exec(content)) !== null) {
+		const epicNum = parseInt(match$1[1], 10);
+		const storyNum = parseInt(match$1[2], 10);
+		stories.push({
+			story_key: `${epicNum}-${storyNum}`,
+			epic_num: epicNum,
+			story_num: storyNum,
+			title: match$1[3].trim(),
+			priority: "P0",
+			size: "Medium",
+			sprint: 0
+		});
+	}
+	if (stories.length === 0) return {
+		storiesIngested: 0,
+		dependenciesIngested: 0
+	};
+	const allKeys = new Set(stories.map((s$1) => s$1.story_key));
+	const depMap = parseEpicsDependencies(projectRoot, allKeys);
+	const dependencies = [];
+	for (const [dependent, depSet] of depMap) for (const dep of depSet) dependencies.push({
+		story_key: dependent,
+		depends_on: dep,
+		dependency_type: "blocks",
+		source: "explicit"
+	});
+	try {
+		await db.query(`CREATE TABLE IF NOT EXISTS wg_stories (
+      story_key VARCHAR(20) NOT NULL,
+      epic VARCHAR(20) NOT NULL,
+      title VARCHAR(255),
+      status VARCHAR(30) NOT NULL DEFAULT 'planned',
+      spec_path VARCHAR(500),
+      created_at DATETIME,
+      updated_at DATETIME,
+      completed_at DATETIME,
+      PRIMARY KEY (story_key)
+    )`);
+		await db.query(`CREATE TABLE IF NOT EXISTS story_dependencies (
+      story_key VARCHAR(50) NOT NULL,
+      depends_on VARCHAR(50) NOT NULL,
+      dependency_type VARCHAR(50) NOT NULL DEFAULT 'blocks',
+      source VARCHAR(50) NOT NULL DEFAULT 'explicit',
+      created_at DATETIME,
+      PRIMARY KEY (story_key, depends_on)
+    )`);
+	} catch {}
+	const ingester = new EpicIngester(db);
+	const result = await ingester.ingest(stories, dependencies);
+	return {
+		storiesIngested: result.storiesUpserted,
+		dependenciesIngested: result.dependenciesReplaced
+	};
+}
 const TITLE_OVERLAP_WARNING_THRESHOLD = .3;
 /**
 * Map a StoryPhase to the corresponding WgStoryStatus for wg_stories writes.
@@ -10318,6 +10950,25 @@ function createImplementationOrchestrator(deps) {
 				}
 			}
 		} catch {}
+		if (storyFilePath === void 0 && projectRoot && isImplicitlyCovered(storyKey, projectRoot)) {
+			logger$21.info({ storyKey }, `Story ${storyKey} appears implicitly covered — all expected new files already exist. Skipping create-story.`);
+			endPhase(storyKey, "create-story");
+			eventBus.emit("orchestrator:story-phase-complete", {
+				storyKey,
+				phase: "IN_STORY_CREATION",
+				result: {
+					result: "success",
+					story_key: storyKey,
+					implicitlyCovered: true
+				}
+			});
+			updateStory(storyKey, {
+				phase: "COMPLETE",
+				completedAt: new Date().toISOString()
+			});
+			await persistState();
+			return;
+		}
 		if (storyFilePath === void 0) try {
 			incrementDispatches(storyKey);
 			const createResult = await runCreateStory({
@@ -11966,6 +12617,18 @@ function createImplementationOrchestrator(deps) {
 				durationMs: _startupTimings.seedMethodologyMs
 			}, "Methodology context seeded from planning artifacts");
 		}
+		if (projectRoot !== void 0) {
+			const ingestStart = Date.now();
+			try {
+				const ingestResult = await autoIngestEpicsDependencies(db, projectRoot);
+				if (ingestResult.storiesIngested > 0 || ingestResult.dependenciesIngested > 0) logger$21.info({
+					...ingestResult,
+					durationMs: Date.now() - ingestStart
+				}, "Auto-ingested stories and dependencies from epics document");
+			} catch (err) {
+				logger$21.debug({ err }, "Auto-ingest from epics document skipped — work graph may be unavailable");
+			}
+		}
 		try {
 			if (stateStore !== void 0) {
 				const stateStoreInitStart = Date.now();
@@ -12243,388 +12906,6 @@ function createImplementationOrchestrator(deps) {
 	};
 }
 
-//#endregion
-//#region src/modules/implementation-orchestrator/story-discovery.ts
-/**
-* Unified story key resolution with a 5-level fallback chain.
-*
-* 1. Explicit keys (from --stories flag) — returned as-is
-* 1.5. ready_stories SQL view — when work graph is populated (story 31-3)
-* 2. Decisions table (category='stories', phase='solutioning')
-* 3. Epic shard decisions (category='epic-shard') — parsed with parseStoryKeysFromEpics
-* 4. epics.md file on disk (via discoverPendingStoryKeys)
-*
-* Optionally filters out completed stories when filterCompleted is set.
-*
-* @returns Sorted, deduplicated array of story keys in "N-M" format
-*/
-async function resolveStoryKeys(db, projectRoot, opts) {
-	if (opts?.explicit !== void 0 && opts.explicit.length > 0) return topologicalSortByDependencies(opts.explicit, projectRoot);
-	let keys = [];
-	const readyKeys = await db.queryReadyStories();
-	if (readyKeys.length > 0) {
-		let filteredKeys = readyKeys;
-		if (opts?.epicNumber !== void 0) {
-			const prefix = `${opts.epicNumber}-`;
-			filteredKeys = filteredKeys.filter((k) => k.startsWith(prefix));
-		}
-		if (opts?.filterCompleted === true && filteredKeys.length > 0) {
-			const completedKeys = await getCompletedStoryKeys(db);
-			filteredKeys = filteredKeys.filter((k) => !completedKeys.has(k));
-		}
-		const existingArtifacts = collectExistingStoryKeys(projectRoot);
-		const alreadyDone = filteredKeys.filter((k) => existingArtifacts.has(k));
-		if (alreadyDone.length > 0) {
-			filteredKeys = filteredKeys.filter((k) => !existingArtifacts.has(k));
-			for (const key of alreadyDone) db.query(`UPDATE wg_stories SET status = 'complete', completed_at = ? WHERE story_key = ? AND status <> 'complete'`, [new Date().toISOString(), key]).catch(() => {});
-		}
-		return sortStoryKeys([...new Set(filteredKeys)]);
-	}
-	try {
-		const sql = opts?.pipelineRunId !== void 0 ? `SELECT key FROM decisions WHERE phase = 'solutioning' AND category = 'stories' AND pipeline_run_id = ? ORDER BY created_at ASC` : `SELECT key FROM decisions WHERE phase = 'solutioning' AND category = 'stories' ORDER BY created_at ASC`;
-		const params = opts?.pipelineRunId !== void 0 ? [opts.pipelineRunId] : [];
-		const rows = await db.query(sql, params);
-		for (const row of rows) if (/^\d+-\d+/.test(row.key)) {
-			const match$1 = /^(\d+-\d+)/.exec(row.key);
-			if (match$1 !== null) keys.push(match$1[1]);
-		}
-	} catch {}
-	if (keys.length === 0) try {
-		const sql = opts?.pipelineRunId !== void 0 ? `SELECT value FROM decisions WHERE category = 'epic-shard' AND pipeline_run_id = ? ORDER BY created_at ASC` : `SELECT value FROM decisions WHERE category = 'epic-shard' ORDER BY created_at ASC`;
-		const params = opts?.pipelineRunId !== void 0 ? [opts.pipelineRunId] : [];
-		const shardRows = await db.query(sql, params);
-		const allContent = shardRows.map((r) => r.value).join("\n");
-		if (allContent.length > 0) keys = parseStoryKeysFromEpics(allContent);
-	} catch {}
-	if (keys.length === 0) keys = discoverPendingStoryKeys(projectRoot, opts?.epicNumber);
-	if (opts?.epicNumber !== void 0 && keys.length > 0) {
-		const prefix = `${opts.epicNumber}-`;
-		keys = keys.filter((k) => k.startsWith(prefix));
-	}
-	if (opts?.filterCompleted === true && keys.length > 0) {
-		const completedKeys = await getCompletedStoryKeys(db);
-		keys = keys.filter((k) => !completedKeys.has(k));
-	}
-	if (keys.length > 0) {
-		const existingArtifacts = collectExistingStoryKeys(projectRoot);
-		keys = keys.filter((k) => !existingArtifacts.has(k));
-	}
-	return sortStoryKeys([...new Set(keys)]);
-}
-/**
-* Extract all story keys (N-M format) from epics.md content.
-*
-* Supports three extraction patterns found in real epics.md files:
-*   1. Explicit key lines:  **Story key:** `7-2-human-turn-loop`  → extracts "7-2"
-*   2. Story headings:      ### Story 7.2: Human Turn Loop        → extracts "7-2"
-*   3. File path refs:      _bmad-output/implementation-artifacts/7-2-human-turn-loop.md → extracts "7-2"
-*
-* Keys are deduplicated and sorted numerically (epic number primary, story number secondary).
-*
-* @param content - Raw string content of epics.md
-* @returns Sorted, deduplicated array of story key strings in "N-M" format
-*/
-function parseStoryKeysFromEpics(content) {
-	if (content.length === 0) return [];
-	const keys = new Set();
-	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+([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+([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\/([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$1[1]);
-	return sortStoryKeys(Array.from(keys));
-}
-/**
-* Discover pending story keys by diffing epics.md against existing story files.
-*
-* Algorithm:
-*   1. Read _bmad-output/planning-artifacts/epics.md (falls back to _bmad-output/epics.md)
-*   2. Extract all story keys from epics.md
-*   3. Glob _bmad-output/implementation-artifacts/ for N-M-*.md files
-*   4. Return keys from step 2 that are NOT in step 3 (pending work)
-*
-* Returns an empty array (without error) if epics.md does not exist.
-*
-* @param projectRoot - Absolute path to the project root directory
-* @returns Sorted array of pending story keys in "N-M" format
-*/
-function discoverPendingStoryKeys(projectRoot, epicNumber) {
-	let allKeys = [];
-	if (epicNumber !== void 0) {
-		const epicFiles = findEpicFiles(projectRoot);
-		const targetPattern = new RegExp(`^epic-${epicNumber}[^0-9]`);
-		const matched = epicFiles.filter((f$1) => targetPattern.test(f$1.split("/").pop()));
-		for (const epicFile of matched) try {
-			const content = readFileSync(epicFile, "utf-8");
-			const keys = parseStoryKeysFromEpics(content);
-			allKeys.push(...keys);
-		} catch {}
-		allKeys = sortStoryKeys([...new Set(allKeys)]);
-	} else {
-		const epicsPath = findEpicsFile(projectRoot);
-		if (epicsPath !== void 0) try {
-			const content = readFileSync(epicsPath, "utf-8");
-			allKeys = parseStoryKeysFromEpics(content);
-		} catch {}
-		if (allKeys.length === 0) {
-			const epicFiles = findEpicFiles(projectRoot);
-			for (const epicFile of epicFiles) try {
-				const content = readFileSync(epicFile, "utf-8");
-				const keys = parseStoryKeysFromEpics(content);
-				allKeys.push(...keys);
-			} catch {}
-			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));
-}
-/**
-* Find epic files from known candidate paths relative to projectRoot.
-*
-* Checks for:
-*   1. epics.md (consolidated epic file)
-*   2. Individual epic-*.md files in planning-artifacts/
-*
-* Returns a single path for epics.md, or undefined if not found.
-* For individual epic files, use findEpicFiles() instead.
-*/
-function findEpicsFile(projectRoot) {
-	const candidates = ["_bmad-output/planning-artifacts/epics.md", "_bmad-output/epics.md"];
-	for (const candidate of candidates) {
-		const fullPath = join$1(projectRoot, candidate);
-		if (existsSync(fullPath)) return fullPath;
-	}
-	const planningDir = join$1(projectRoot, "_bmad-output", "planning-artifacts");
-	if (existsSync(planningDir)) try {
-		const entries = readdirSync(planningDir, { encoding: "utf-8" });
-		const match$1 = entries.filter((e) => /^epics[-.].*\.md$/i.test(e) && !/^epic-\d+/.test(e)).sort();
-		if (match$1.length > 0) return join$1(planningDir, match$1[0]);
-	} catch {}
-	return void 0;
-}
-/**
-* Find individual epic-*.md files in the planning artifacts directory.
-* Returns paths sorted alphabetically.
-*/
-function findEpicFiles(projectRoot) {
-	const planningDir = join$1(projectRoot, "_bmad-output", "planning-artifacts");
-	if (!existsSync(planningDir)) return [];
-	try {
-		const entries = readdirSync(planningDir, { encoding: "utf-8" });
-		return entries.filter((e) => /^epic-\d+.*\.md$/.test(e)).sort().map((e) => join$1(planningDir, e));
-	} catch {
-		return [];
-	}
-}
-/**
-* Collect story keys that already have implementation artifact files.
-* Scans _bmad-output/implementation-artifacts/ for files matching N-M-*.md.
-*/
-function collectExistingStoryKeys(projectRoot) {
-	const existing = new Set();
-	const artifactsDir = join$1(projectRoot, "_bmad-output", "implementation-artifacts");
-	if (!existsSync(artifactsDir)) return existing;
-	let entries;
-	try {
-		entries = readdirSync(artifactsDir, { encoding: "utf-8" });
-	} catch {
-		return existing;
-	}
-	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);
-		if (m !== null && m[1] !== void 0) existing.add(m[1]);
-	}
-	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(p));
-	if (!statusPath) return [];
-	try {
-		const content = readFileSync(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.
-*/
-async function getCompletedStoryKeys(db) {
-	const completed = new Set();
-	try {
-		const rows = await db.query(`SELECT token_usage_json FROM pipeline_runs WHERE status = 'completed' AND token_usage_json IS NOT NULL`);
-		for (const row of rows) try {
-			const state = JSON.parse(row.token_usage_json);
-			if (state.stories !== void 0) {
-				for (const [key, s$1] of Object.entries(state.stories)) if (s$1.phase === "COMPLETE") completed.add(key);
-			}
-		} catch {}
-	} catch {}
-	return completed;
-}
-/**
-* Sort story keys: numeric keys first (by epic then story number),
-* then alphabetic-prefix keys (NEW-*, E-*) sorted lexicographically.
-* E.g. ["10-1", "1-2a", "1-2", "NEW-26", "E5-acc"] → ["1-2", "1-2a", "10-1", "E5-acc", "NEW-26"]
-*/
-function sortStoryKeys(keys) {
-	return keys.slice().sort((a, b) => {
-		const aParts = a.split("-");
-		const bParts = b.split("-");
-		const aNum = Number(aParts[0]);
-		const bNum = Number(bParts[0]);
-		if (!isNaN(aNum) && !isNaN(bNum)) {
-			if (aNum !== bNum) return aNum - bNum;
-			const aStory = Number(aParts[1]);
-			const bStory = Number(bParts[1]);
-			if (!isNaN(aStory) && !isNaN(bStory) && aStory !== bStory) return aStory - bStory;
-			return (aParts[1] ?? "").localeCompare(bParts[1] ?? "");
-		}
-		if (!isNaN(aNum)) return -1;
-		if (!isNaN(bNum)) return 1;
-		return a.localeCompare(b);
-	});
-}
-/**
-* Parse inter-story dependencies from the consolidated epics document.
-*
-* Scans for patterns like:
-*   ### Story 50-2: Title
-*   **Dependencies:** 50-1
-*
-* Returns a Map where key=storyKey, value=Set of dependency keys.
-* Only returns dependencies that are within the provided storyKeys set
-* (external dependencies to other epics are ignored for ordering purposes).
-*/
-function parseEpicsDependencies(projectRoot, storyKeys) {
-	const deps = new Map();
-	const epicsPath = findEpicsFile(projectRoot);
-	if (epicsPath === void 0) return deps;
-	let content;
-	try {
-		content = readFileSync(epicsPath, "utf-8");
-	} catch {
-		return deps;
-	}
-	const storyPattern = /^###\s+Story\s+(\d+)-(\d+)[:\s]/gm;
-	const depPattern = /^\*\*Dependencies:\*\*\s*(.+)$/gm;
-	const storyPositions = [];
-	let match$1;
-	while ((match$1 = storyPattern.exec(content)) !== null) storyPositions.push({
-		key: `${match$1[1]}-${match$1[2]}`,
-		pos: match$1.index
-	});
-	for (let i = 0; i < storyPositions.length; i++) {
-		const story = storyPositions[i];
-		const nextStoryPos = i + 1 < storyPositions.length ? storyPositions[i + 1].pos : content.length;
-		const section = content.slice(story.pos, nextStoryPos);
-		depPattern.lastIndex = 0;
-		const depMatch = depPattern.exec(section);
-		if (depMatch === null || /^none$/i.test(depMatch[1].trim())) continue;
-		const depText = depMatch[1];
-		const storyDeps = new Set();
-		const rangeMatch = /(\d+)-(\d+)\s+through\s+\1-(\d+)/i.exec(depText);
-		if (rangeMatch !== null) {
-			const epic = rangeMatch[1];
-			const start = Number(rangeMatch[2]);
-			const end = Number(rangeMatch[3]);
-			for (let n$1 = start; n$1 <= end; n$1++) {
-				const depKey = `${epic}-${n$1}`;
-				if (storyKeys.has(depKey)) storyDeps.add(depKey);
-			}
-		} else {
-			const keyPattern = /(\d+-\d+[a-z]?)/g;
-			let km;
-			while ((km = keyPattern.exec(depText)) !== null) {
-				const depKey = km[1];
-				if (storyKeys.has(depKey)) storyDeps.add(depKey);
-			}
-		}
-		if (storyDeps.size > 0) deps.set(story.key, storyDeps);
-	}
-	return deps;
-}
-/**
-* Topologically sort explicit story keys by inter-story dependencies.
-*
-* Parses the consolidated epics document for dependency metadata, builds
-* a DAG, and returns keys in dependency-first order using Kahn's algorithm.
-* Stories with no dependencies come first; stories that depend on others
-* are placed after their prerequisites.
-*
-* Falls back to numeric sort if no epics document exists or no
-* dependencies are found among the provided keys.
-*/
-function topologicalSortByDependencies(keys, projectRoot) {
-	if (keys.length <= 1) return keys;
-	const keySet = new Set(keys);
-	const deps = parseEpicsDependencies(projectRoot, keySet);
-	if (deps.size === 0) return sortStoryKeys(keys);
-	const inDegree = new Map();
-	const successors = new Map();
-	for (const key of keys) {
-		inDegree.set(key, 0);
-		successors.set(key, new Set());
-	}
-	for (const [dependent, depSet] of deps) {
-		if (!keySet.has(dependent)) continue;
-		for (const dep of depSet) {
-			if (!keySet.has(dep)) continue;
-			successors.get(dep).add(dependent);
-			inDegree.set(dependent, (inDegree.get(dependent) ?? 0) + 1);
-		}
-	}
-	const result = [];
-	const processed = new Set();
-	while (processed.size < keys.length) {
-		const wave = [];
-		for (const key of keys) if (!processed.has(key) && (inDegree.get(key) ?? 0) === 0) wave.push(key);
-		if (wave.length === 0) {
-			for (const key of sortStoryKeys(keys)) if (!processed.has(key)) result.push(key);
-			break;
-		}
-		for (const key of sortStoryKeys(wave)) {
-			result.push(key);
-			processed.add(key);
-			for (const succ of successors.get(key) ?? []) inDegree.set(succ, (inDegree.get(succ) ?? 0) - 1);
-		}
-	}
-	return result;
-}
-
 //#endregion
 //#region src/modules/phase-orchestrator/phase-detection.ts
 const PHASE_ARTIFACTS = [
@@ -39338,6 +39619,7 @@ async function runRunAction(options) {
 		});
 	} catch {}
 	let tokenCeilings;
+	let dispatchTimeouts;
 	let telemetryEnabled = false;
 	let telemetryPort = 4318;
 	try {
@@ -39345,6 +39627,10 @@ async function runRunAction(options) {
 		await configSystem.load();
 		const cfg = configSystem.getConfig();
 		tokenCeilings = cfg.token_ceilings;
+		if (cfg.dispatch_timeouts) {
+			dispatchTimeouts = Object.fromEntries(Object.entries(cfg.dispatch_timeouts).filter(([, v]) => v !== void 0));
+			logger.info({ dispatchTimeouts }, "Loaded dispatch timeout overrides from config");
+		}
 		if (cfg.telemetry?.enabled === true) {
 			telemetryEnabled = true;
 			telemetryPort = cfg.telemetry.port ?? 4318;
@@ -39631,7 +39917,10 @@ async function runRunAction(options) {
 		const dispatcher = createDispatcher({
 			eventBus,
 			adapterRegistry: injectedRegistry,
-			config: { routingResolver }
+			config: {
+				routingResolver,
+				...dispatchTimeouts ? { defaultTimeouts: dispatchTimeouts } : {}
+			}
 		});
 		eventBus.on("orchestrator:story-phase-complete", (payload) => {
 			try {
@@ -40497,5 +40786,5 @@ function registerRunCommand(program, _version = "0.0.0", projectRoot = process.c
 }
 
 //#endregion
-export { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, normalizeGraphSummaryToStatus, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runRunAction, runSolutioningPhase, validateStopAfterFromConflict };
-//# sourceMappingURL=run-C3MnOuBe.js.map
+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, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runRunAction, runSolutioningPhase, validateStopAfterFromConflict };
+//# sourceMappingURL=run-BOhSIujp.js.map

package/dist/{run-C8jeEtC6.js → run-CCHb_JMl.js}

@@ -2,7 +2,7 @@ import "./health-Cx2ZhRNT.js";
 import "./logger-KeHncl-f.js";
 import "./helpers-CElYrONe.js";
 import "./dist-Bm0qSZer.js";
-import { normalizeGraphSummaryToStatus, registerRunCommand, runRunAction } from "./run-C3MnOuBe.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, runRunAction } from "./run-BOhSIujp.js";
 import "./routing-CcBOCuC9.js";
 import "./decisions-C0pz9Clx.js";
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.19.0",
+  "version": "0.19.2",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",