substrate-ai 0.5.0 → 0.5.1

package/dist/cli/index.js

@@ -1,5 +1,5 @@
 #!/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, buildPipelineStatusOutput, checkDoltInstalled, createConfigSystem, createContextCompiler, createDatabaseAdapter, createDispatcher, createDoltClient, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStateStore, createStopAfterGate, 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-GqmIa5YW.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, buildPipelineStatusOutput, checkDoltInstalled, createConfigSystem, createContextCompiler, createDatabaseAdapter, createDispatcher, createDoltClient, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStateStore, createStopAfterGate, 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-BD0Ugp7F.js";
 import { createLogger } from "../logger-D2fS2ccL.js";
 import { AdapterRegistry } from "../adapter-registry-BkUvZSKJ.js";
 import { CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, PartialSubstrateConfigSchema } from "../config-migrator-DtZW1maj.js";
@@ -19,7 +19,7 @@ import yaml from "js-yaml";
 import { createRequire } from "node:module";
 import * as path$1 from "node:path";
 import { isAbsolute, join as join$1 } from "node:path";
-import { existsSync as existsSync$1, mkdirSync as mkdirSync$1, writeFileSync as writeFileSync$1 } from "node:fs";
+import { existsSync as existsSync$1, mkdirSync as mkdirSync$1, readFileSync as readFileSync$1, writeFileSync as writeFileSync$1 } from "node:fs";
 import { access as access$1, readFile as readFile$1 } from "node:fs/promises";
 import { createInterface } from "node:readline";
 import { homedir } from "os";
@@ -574,8 +574,8 @@ async function directoryExists(path$2) {
 */
 async function runInitAction(options) {
 	const { pack: packName, projectRoot, outputFormat, force = false, yes: nonInteractive = false } = options;
-	const packPath = join(projectRoot, "packs", packName);
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
+	const packPath = join(dbRoot, "packs", packName);
 	const substrateDir = join(dbRoot, ".substrate");
 	const dbPath = join(substrateDir, "substrate.db");
 	const configPath = join(substrateDir, "config.yaml");
@@ -1007,16 +1007,30 @@ function registerConfigCommand(program, _version) {
 //#endregion
 //#region src/cli/commands/resume.ts
 const logger$16 = createLogger("resume-cmd");
+/**
+* Map internal orchestrator phase names to pipeline event protocol phase names.
+*/
+function mapInternalPhaseToEventPhase(internalPhase) {
+	switch (internalPhase) {
+		case "IN_STORY_CREATION": return "create-story";
+		case "IN_DEV": return "dev-story";
+		case "IN_REVIEW": return "code-review";
+		case "IN_MINOR_FIX":
+		case "IN_MAJOR_FIX": return "fix";
+		case "IN_TEST_PLANNING": return "test-planning";
+		default: return null;
+	}
+}
 async function runResumeAction(options) {
-	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName, registry } = options;
+	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName, events: eventsFlag, registry } = options;
 	if (stopAfter !== void 0 && !VALID_PHASES.includes(stopAfter)) {
 		const errorMsg = `Invalid phase: "${stopAfter}". Valid phases: ${VALID_PHASES.join(", ")}`;
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
 		else process.stderr.write(`Error: ${errorMsg}\n`);
 		return 1;
 	}
-	const packPath = join(projectRoot, "packs", packName);
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
+	const packPath = join(dbRoot, "packs", packName);
 	const dbPath = join(dbRoot, ".substrate", "substrate.db");
 	const doltDir = join(dbRoot, ".substrate", "state", ".dolt");
 	if (!existsSync(dbPath) && !existsSync(doltDir)) {
@@ -1086,6 +1100,7 @@ async function runResumeAction(options) {
 			concept,
 			concurrency,
 			outputFormat,
+			events: eventsFlag,
 			existingRunId: runId,
 			projectRoot,
 			registry
@@ -1103,7 +1118,7 @@ async function runResumeAction(options) {
 	}
 }
 async function runFullPipelineFromPhase(options) {
-	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, existingRunId, projectRoot, registry: injectedRegistry } = options;
+	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, events: eventsFlag, existingRunId, projectRoot, registry: injectedRegistry } = options;
 	if (!existsSync(dbDir)) mkdirSync(dbDir, { recursive: true });
 	const adapter = createDatabaseAdapter({
 		backend: "auto",
@@ -1143,6 +1158,8 @@ async function runFullPipelineFromPhase(options) {
 		let runId;
 		if (existingRunId !== void 0) runId = existingRunId;
 		else runId = await phaseOrchestrator.startRun(concept, startPhase);
+		let ndjsonEmitter;
+		if (eventsFlag === true) ndjsonEmitter = createEventEmitter(process.stdout);
 		const phaseOrder = [
 			"analysis",
 			"planning",
@@ -1239,12 +1256,87 @@ async function runFullPipelineFromPhase(options) {
 					config: {
 						maxConcurrency: concurrency,
 						maxReviewCycles: 2,
-						pipelineRunId: runId
+						pipelineRunId: runId,
+						enableHeartbeat: eventsFlag === true
 					},
 					projectRoot,
 					...ingestionServer !== void 0 ? { ingestionServer } : {},
 					...telemetryPersistence !== void 0 ? { telemetryPersistence } : {}
 				});
+				if (ndjsonEmitter !== void 0) {
+					const resolvedKeys = await resolveStoryKeys(adapter, projectRoot, { pipelineRunId: runId });
+					ndjsonEmitter.emit({
+						type: "pipeline:start",
+						ts: new Date().toISOString(),
+						run_id: runId,
+						stories: resolvedKeys,
+						concurrency
+					});
+					eventBus.on("orchestrator:story-phase-start", (payload) => {
+						const phase = mapInternalPhaseToEventPhase(payload.phase);
+						if (phase !== null) ndjsonEmitter.emit({
+							type: "story:phase",
+							ts: new Date().toISOString(),
+							key: payload.storyKey,
+							phase,
+							status: "in_progress"
+						});
+					});
+					eventBus.on("orchestrator:story-phase-complete", (payload) => {
+						const phase = mapInternalPhaseToEventPhase(payload.phase);
+						if (phase !== null) {
+							const result = payload.result;
+							ndjsonEmitter.emit({
+								type: "story:phase",
+								ts: new Date().toISOString(),
+								key: payload.storyKey,
+								phase,
+								status: "complete",
+								...phase === "code-review" && result?.verdict !== void 0 ? { verdict: result.verdict } : {},
+								...phase === "create-story" && result?.story_file !== void 0 ? { file: result.story_file } : {}
+							});
+						}
+					});
+					eventBus.on("orchestrator:story-complete", (payload) => {
+						ndjsonEmitter.emit({
+							type: "story:done",
+							ts: new Date().toISOString(),
+							key: payload.storyKey,
+							result: "success",
+							review_cycles: payload.reviewCycles
+						});
+					});
+					eventBus.on("orchestrator:story-escalated", (payload) => {
+						const rawIssues = Array.isArray(payload.issues) ? payload.issues : [];
+						const issues = rawIssues.map((issue) => {
+							const iss = issue;
+							return {
+								severity: iss.severity ?? "unknown",
+								file: iss.file ?? "",
+								desc: iss.desc ?? iss.description ?? ""
+							};
+						});
+						ndjsonEmitter.emit({
+							type: "story:escalation",
+							ts: new Date().toISOString(),
+							key: payload.storyKey,
+							reason: payload.lastVerdict ?? "escalated",
+							cycles: payload.reviewCycles ?? 0,
+							issues,
+							...payload.diagnosis !== void 0 ? { diagnosis: payload.diagnosis } : {}
+						});
+					});
+					eventBus.on("orchestrator:heartbeat", (payload) => {
+						ndjsonEmitter.emit({
+							type: "pipeline:heartbeat",
+							ts: new Date().toISOString(),
+							run_id: payload.runId,
+							active_dispatches: payload.activeDispatches,
+							completed_dispatches: payload.completedDispatches,
+							queued_dispatches: payload.queuedDispatches
+						});
+					});
+				}
 				eventBus.on("orchestrator:story-phase-complete", (payload) => {
 					try {
 						const result = payload.result;
@@ -1268,6 +1360,13 @@ async function runFullPipelineFromPhase(options) {
 				const storyKeys = await resolveStoryKeys(adapter, projectRoot, { pipelineRunId: runId });
 				if (storyKeys.length === 0 && outputFormat === "human") process.stdout.write("[IMPLEMENTATION] No stories found for this run. Check solutioning phase output.\n");
 				await orchestrator.run(storyKeys);
+				if (ndjsonEmitter !== void 0) ndjsonEmitter.emit({
+					type: "pipeline:complete",
+					ts: new Date().toISOString(),
+					succeeded: storyKeys,
+					failed: [],
+					escalated: []
+				});
 				if (outputFormat === "human") process.stdout.write("[IMPLEMENTATION] Complete\n");
 			}
 			if (stopAfter !== void 0 && currentPhase === stopAfter) {
@@ -1330,7 +1429,7 @@ 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").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").action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		const exitCode = await runResumeAction({
 			runId: opts.runId,
@@ -1339,6 +1438,7 @@ function registerResumeCommand(program, _version = "0.0.0", projectRoot = proces
 			projectRoot: opts.projectRoot,
 			concurrency: opts.concurrency,
 			pack: opts.pack,
+			events: opts.events,
 			registry
 		});
 		process.exitCode = exitCode;
@@ -2031,7 +2131,7 @@ async function runAmendAction(options) {
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
 	const dbDir = join(dbRoot, ".substrate");
 	const dbPath = join(dbDir, "substrate.db");
-	const packPath = join(projectRoot, "packs", packName);
+	const packPath = join(dbRoot, "packs", packName);
 	const doltDir = join(dbRoot, ".substrate", "state", ".dolt");
 	if (!existsSync(dbPath) && !existsSync(doltDir)) {
 		process.stderr.write(`Error: Decision store not initialized. Run 'substrate init' first.\n`);
@@ -2749,7 +2849,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-C-yCMYlt.js"
+									"../run-B-TUWMCv.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -7142,7 +7242,7 @@ async function runRetryEscalatedAction(options) {
 			}
 			return 0;
 		}
-		const packPath = join(projectRoot, "packs", packName);
+		const packPath = join(dbRoot, "packs", packName);
 		const packLoader = createPackLoader();
 		let pack;
 		try {
@@ -7701,6 +7801,261 @@ function registerRoutingCommand(program) {
 	});
 }
 
+//#endregion
+//#region src/modules/work-graph/schema.ts
+/**
+* Work-graph schema DDL constants.
+*
+* Story 31-1 placeholder — defines the `stories`, `story_dependencies`, and
+* `ready_stories` DDL used by the EpicIngester and downstream consumers.
+*
+* NOTE: This file is a minimal placeholder created by story 31-2 because story
+* 31-1 (schema creation) had not yet run.  If story 31-1 produces a richer
+* schema, merge carefully and remove this note.
+*/
+const CREATE_STORIES_TABLE = `
+CREATE TABLE IF NOT EXISTS stories (
+  story_key VARCHAR(50) NOT NULL,
+  epic_num INT NOT NULL,
+  story_num INT NOT NULL,
+  title VARCHAR(500) NOT NULL,
+  priority VARCHAR(10) NOT NULL,
+  size VARCHAR(50) NOT NULL,
+  sprint INT NOT NULL,
+  status VARCHAR(50) NOT NULL DEFAULT 'planned',
+  PRIMARY KEY (story_key)
+)
+`.trim();
+const CREATE_STORY_DEPENDENCIES_TABLE = `
+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',
+  PRIMARY KEY (story_key, depends_on)
+)
+`.trim();
+const CREATE_READY_STORIES_VIEW = `
+CREATE VIEW IF NOT EXISTS ready_stories AS
+SELECT s.*
+FROM stories s
+WHERE s.status = 'planned'
+  AND NOT EXISTS (
+    SELECT 1 FROM story_dependencies sd
+    JOIN stories blocking ON sd.depends_on = blocking.story_key
+    WHERE sd.story_key = s.story_key
+      AND blocking.status != 'done'
+  )
+`.trim();
+
+//#endregion
+//#region src/modules/work-graph/epic-parser.ts
+/** Regex for sprint header lines: `**Sprint 1 —` (em dash or hyphen) */
+const SPRINT_HEADER_RE = /^\*\*Sprint\s+(\d+)\s*[—–-]/i;
+/**
+* Regex for story lines: `- 31-2: Epic doc ingestion (P0, Medium)`
+* Captures: epicNum, storyNum, title, priority, size
+*/
+const STORY_LINE_RE = /^-\s+(\d+)-(\d+):\s+(.+?)\s+\((P\d+),\s+([\w-]+)\)\s*$/;
+/** Regex to find the story map section heading */
+const STORY_MAP_HEADING_RE = /^#{1,6}\s+.*Story\s+Map/im;
+/** Regex to find the dependency chain line */
+const DEPENDENCY_CHAIN_RE = /\*\*Dependency\s+chain\*\*:\s*(.+)/i;
+/** Regex for "also gates" clauses: `31-3 also gates 31-6, 31-7` */
+const ALSO_GATES_RE = /^([\d]+-[\d]+)\s+also\s+gates\s+(.+)$/i;
+var EpicParser = class {
+	/**
+	* Parse story metadata from an epic planning document.
+	*
+	* @param content - Full text of the epic markdown document.
+	* @returns Array of `ParsedStory` objects, one per story line found.
+	* @throws {Error} If the story map section is absent or no stories can be parsed.
+	*/
+	parseStories(content) {
+		const headingMatch = STORY_MAP_HEADING_RE.exec(content);
+		if (!headingMatch) throw new Error("No story map section found in document");
+		const afterHeading = content.slice(headingMatch.index + headingMatch[0].length);
+		const stories = [];
+		let currentSprint = 0;
+		for (const rawLine of afterHeading.split("\n")) {
+			const line = rawLine.trim();
+			const sprintMatch = SPRINT_HEADER_RE.exec(line);
+			if (sprintMatch) {
+				currentSprint = parseInt(sprintMatch[1], 10);
+				continue;
+			}
+			const storyMatch = STORY_LINE_RE.exec(line);
+			if (storyMatch) {
+				const epicNum = parseInt(storyMatch[1], 10);
+				const storyNum = parseInt(storyMatch[2], 10);
+				stories.push({
+					story_key: `${epicNum}-${storyNum}`,
+					epic_num: epicNum,
+					story_num: storyNum,
+					title: storyMatch[3].trim(),
+					priority: storyMatch[4],
+					size: storyMatch[5],
+					sprint: currentSprint
+				});
+			}
+		}
+		if (stories.length === 0) throw new Error("Story map section found but contained no parseable story lines");
+		return stories;
+	}
+	/**
+	* Parse dependency relationships from an epic planning document.
+	*
+	* If the `**Dependency chain**:` line is absent, returns an empty array
+	* (not all epics declare dependencies).
+	*
+	* @param content - Full text of the epic markdown document.
+	* @returns Array of `ParsedDependency` objects.
+	*/
+	parseDependencies(content) {
+		const chainLineMatch = DEPENDENCY_CHAIN_RE.exec(content);
+		if (!chainLineMatch) return [];
+		const chainStr = chainLineMatch[1].trim();
+		const dependencies = [];
+		const clauses = chainStr.split(";").map((c) => c.trim()).filter(Boolean);
+		for (const clause of clauses) {
+			const alsoGatesMatch = ALSO_GATES_RE.exec(clause);
+			if (alsoGatesMatch) {
+				const gater = alsoGatesMatch[1].trim();
+				const gatedList = alsoGatesMatch[2].split(",").map((t) => t.trim()).filter(Boolean);
+				for (const gated of gatedList) dependencies.push({
+					story_key: gated,
+					depends_on: gater,
+					dependency_type: "blocks",
+					source: "explicit"
+				});
+				continue;
+			}
+			const parts = clause.split("→").map((p) => p.trim()).filter(Boolean);
+			for (let i = 0; i < parts.length - 1; i++) {
+				const upstream = parts[i];
+				const downstream = parts[i + 1];
+				dependencies.push({
+					story_key: downstream,
+					depends_on: upstream,
+					dependency_type: "blocks",
+					source: "explicit"
+				});
+			}
+		}
+		return dependencies;
+	}
+};
+
+//#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) {
+		return this.adapter.transaction(async (tx) => {
+			let storiesUpserted = 0;
+			for (const story of stories) {
+				const existing = await tx.query("SELECT status FROM stories WHERE story_key = ?", [story.story_key]);
+				if (existing.length > 0) await tx.query("UPDATE stories SET title = ?, priority = ?, size = ?, sprint = ? WHERE story_key = ?", [
+					story.title,
+					story.priority,
+					story.size,
+					story.sprint,
+					story.story_key
+				]);
+				else {
+					await tx.query("INSERT INTO stories (story_key, epic_num, story_num, title, priority, size, sprint, status) VALUES (?, ?, ?, ?, ?, ?, ?, ?)", [
+						story.story_key,
+						story.epic_num,
+						story.story_num,
+						story.title,
+						story.priority,
+						story.size,
+						story.sprint,
+						"planned"
+					]);
+					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) {
+	program.command("ingest-epic <epic-doc-path>").description("Parse an epic planning doc and upsert story metadata into the work-graph").action(async (epicDocPath) => {
+		if (!existsSync$1(epicDocPath)) {
+			process.stderr.write(`Error: File not found: ${epicDocPath}\n`);
+			process.exitCode = 1;
+			return;
+		}
+		let content;
+		try {
+			content = readFileSync$1(epicDocPath, "utf-8");
+		} catch (err) {
+			const msg = err instanceof Error ? err.message : String(err);
+			process.stderr.write(`Error: Cannot read file ${epicDocPath}: ${msg}\n`);
+			process.exitCode = 1;
+			return;
+		}
+		const parser = new EpicParser();
+		let stories;
+		let dependencies;
+		try {
+			stories = parser.parseStories(content);
+			dependencies = parser.parseDependencies(content);
+		} catch (err) {
+			const msg = err instanceof Error ? err.message : String(err);
+			process.stderr.write(`Error: ${msg}\n`);
+			process.exitCode = 1;
+			return;
+		}
+		const adapter = createDatabaseAdapter({
+			backend: "auto",
+			basePath: process.cwd()
+		});
+		try {
+			await adapter.exec(CREATE_STORIES_TABLE);
+			await adapter.exec(CREATE_STORY_DEPENDENCIES_TABLE);
+			const ingester = new EpicIngester(adapter);
+			const result = await ingester.ingest(stories, dependencies);
+			const epicNum = stories[0].epic_num;
+			process.stdout.write(`Ingested ${result.storiesUpserted} stories and ${result.dependenciesReplaced} dependencies from epic ${epicNum}\n`);
+		} catch (err) {
+			const msg = err instanceof Error ? err.message : String(err);
+			process.stderr.write(`Error: ${msg}\n`);
+			process.exitCode = 1;
+		} finally {
+			await adapter.close();
+		}
+	});
+}
+
 //#endregion
 //#region src/cli/index.ts
 process.setMaxListeners(20);
@@ -7761,6 +8116,7 @@ async function createProgram() {
 	registerWorktreesCommand(program, version);
 	registerBrainstormCommand(program, version);
 	registerExportCommand(program, version);
+	registerIngestEpicCommand(program);
 	registerUpgradeCommand(program);
 	return program;
 }

package/dist/{run-C-yCMYlt.js → run-B-TUWMCv.js}

@@ -1,4 +1,4 @@
-import { registerRunCommand, runRunAction } from "./run-GqmIa5YW.js";
+import { registerRunCommand, runRunAction } from "./run-BD0Ugp7F.js";
 import "./logger-D2fS2ccL.js";
 import "./config-migrator-DtZW1maj.js";
 import "./helpers-BihqWgVe.js";

package/dist/{run-GqmIa5YW.js → run-BD0Ugp7F.js}

@@ -247,7 +247,8 @@ var InMemoryDatabaseAdapter = class {
 		const upper = resolved.trimStart().toUpperCase();
 		if (/^CREATE\s+TABLE/i.test(upper)) return this._createTable(resolved);
 		if (/^DROP\s+TABLE/i.test(upper)) return this._dropTable(resolved);
-		if (/^INSERT\s+INTO/i.test(upper)) return this._insert(resolved);
+		if (/^CREATE\s+(?:OR\s+REPLACE\s+)?VIEW/i.test(upper)) return [];
+		if (/^INSERT\s+(?:IGNORE\s+)?INTO/i.test(upper)) return this._insert(resolved, /^INSERT\s+IGNORE\s+INTO/i.test(upper));
 		if (/^SELECT/i.test(upper)) return this._select(resolved);
 		if (/^UPDATE/i.test(upper)) return this._update(resolved);
 		if (/^DELETE\s+FROM/i.test(upper)) return this._delete(resolved);
@@ -539,6 +540,8 @@ var DoltClient = class {
 	_pool = null;
 	_useCliMode = false;
 	_connected = false;
+	/** Promise-chain mutex that serializes all CLI operations to prevent concurrent noms manifest access */
+	_cliMutex = Promise.resolve();
 	constructor(options) {
 		this.repoPath = options.repoPath;
 		this.socketPath = options.socketPath ?? `${options.repoPath}/.dolt/dolt.sock`;
@@ -586,6 +589,20 @@ var DoltClient = class {
 			throw new DoltQueryError(sql, detail);
 		}
 	}
+	/**
+	* Acquire an exclusive CLI lock. Dolt CLI takes an exclusive lock on the noms
+	* manifest, so concurrent `dolt sql -q` / `dolt <subcommand>` processes
+	* produce "cannot update manifest: database is read only" errors.
+	* Serialize all CLI operations through a single promise chain.
+	*/
+	_withCliLock(fn) {
+		const prev = this._cliMutex;
+		let release;
+		this._cliMutex = new Promise((resolve$2) => {
+			release = resolve$2;
+		});
+		return prev.then(fn).finally(() => release());
+	}
 	async _queryCli(sql, params, branch) {
 		let resolvedSql = sql;
 		if (params && params.length > 0) {
@@ -597,24 +614,27 @@ var DoltClient = class {
 				return `'${String(val).replace(/'/g, "''")}'`;
 			});
 		}
-		try {
-			const branchPrefix = branch ? `CALL DOLT_CHECKOUT('${branch.replace(/'/g, "''")}'); ` : "";
-			const args = [
-				"sql",
-				"-q",
-				branchPrefix + resolvedSql,
-				"--result-format",
-				"json"
-			];
-			const { stdout } = await runExecFile("dolt", args, { cwd: this.repoPath });
-			const lines = (stdout || "").trim().split("\n").filter(Boolean);
-			const lastLine = lines.length > 0 ? lines[lines.length - 1] : "{\"rows\":[]}";
-			const parsed = JSON.parse(lastLine);
-			return parsed.rows ?? [];
-		} catch (err) {
-			const detail = err instanceof Error ? err.message : String(err);
-			throw new DoltQueryError(resolvedSql, detail);
-		}
+		const finalSql = resolvedSql;
+		return this._withCliLock(async () => {
+			try {
+				const branchPrefix = branch ? `CALL DOLT_CHECKOUT('${branch.replace(/'/g, "''")}'); ` : "";
+				const args = [
+					"sql",
+					"-q",
+					branchPrefix + finalSql,
+					"--result-format",
+					"json"
+				];
+				const { stdout } = await runExecFile("dolt", args, { cwd: this.repoPath });
+				const lines = (stdout || "").trim().split("\n").filter(Boolean);
+				const lastLine = lines.length > 0 ? lines[lines.length - 1] : "{\"rows\":[]}";
+				const parsed = JSON.parse(lastLine);
+				return parsed.rows ?? [];
+			} catch (err) {
+				const detail = err instanceof Error ? err.message : String(err);
+				throw new DoltQueryError(finalSql, detail);
+			}
+		});
 	}
 	/**
 	* Execute a raw Dolt CLI command (e.g. `dolt diff main...story/26-1 --stat`)
@@ -635,13 +655,15 @@ var DoltClient = class {
 	* messages) to avoid whitespace-splitting issues.
 	*/
 	async execArgs(args) {
-		try {
-			const { stdout } = await runExecFile("dolt", args, { cwd: this.repoPath });
-			return stdout;
-		} catch (err) {
-			const detail = err instanceof Error ? err.message : String(err);
-			throw new DoltQueryError(args.join(" "), detail);
-		}
+		return this._withCliLock(async () => {
+			try {
+				const { stdout } = await runExecFile("dolt", args, { cwd: this.repoPath });
+				return stdout;
+			} catch (err) {
+				const detail = err instanceof Error ? err.message : String(err);
+				throw new DoltQueryError(args.join(" "), detail);
+			}
+		});
 	}
 	async close() {
 		if (this._pool) {
@@ -17004,7 +17026,12 @@ var PhaseOrchestratorImpl = class {
 			if (result.passed) lastCompletedPhaseIdx = i;
 			else break;
 		}
-		const resumePhaseIdx = lastCompletedPhaseIdx + 1;
+		const gateDerivedResumeIdx = lastCompletedPhaseIdx + 1;
+		let resumePhaseIdx = gateDerivedResumeIdx;
+		if (run.current_phase) {
+			const dbPhaseIdx = this._phases.findIndex((p) => p.name === run.current_phase);
+			if (dbPhaseIdx >= 0 && dbPhaseIdx > gateDerivedResumeIdx) resumePhaseIdx = dbPhaseIdx;
+		}
 		if (resumePhaseIdx >= this._phases.length) {
 			await updatePipelineRun(this._db, runId, { status: "completed" });
 			return this.getRunStatus(runId);
@@ -20588,8 +20615,8 @@ async function runRunAction(options) {
 			return 1;
 		}
 	}
-	const packPath = join(projectRoot, "packs", packName);
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
+	const packPath = join(dbRoot, "packs", packName);
 	const dbDir = join(dbRoot, ".substrate");
 	const dbPath = join(dbDir, "substrate.db");
 	mkdirSync(dbDir, { recursive: true });
@@ -21723,5 +21750,5 @@ 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, buildPipelineStatusOutput, checkDoltInstalled, createConfigSystem, createContextCompiler, createDatabaseAdapter, createDispatcher, createDoltClient, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStateStore, createStopAfterGate, 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-GqmIa5YW.js.map
+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, buildPipelineStatusOutput, checkDoltInstalled, createConfigSystem, createContextCompiler, createDatabaseAdapter, createDispatcher, createDoltClient, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStateStore, createStopAfterGate, 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-BD0Ugp7F.js.map

package/dist/schema.sql

@@ -236,3 +236,48 @@ CREATE TABLE IF NOT EXISTS repo_map_meta (
 
 INSERT IGNORE INTO _schema_version (version, description) VALUES (5, 'Add repo_map_symbols and repo_map_meta tables (Epic 28-2)');
 INSERT IGNORE INTO _schema_version (version, description) VALUES (6, 'Add dependencies JSON column to repo_map_symbols (Epic 28-3)');
+
+-- ---------------------------------------------------------------------------
+-- wg_stories (Epic 31-1) — planning-level work graph story nodes
+-- ---------------------------------------------------------------------------
+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)
+);
+
+CREATE INDEX IF NOT EXISTS idx_wg_stories_epic ON wg_stories (epic);
+
+-- ---------------------------------------------------------------------------
+-- story_dependencies (Epic 31-1) — directed dependency edges
+-- ---------------------------------------------------------------------------
+CREATE TABLE IF NOT EXISTS story_dependencies (
+  story_key  VARCHAR(20)   NOT NULL,
+  depends_on VARCHAR(20)   NOT NULL,
+  dep_type   VARCHAR(20)   NOT NULL,
+  source     VARCHAR(20)   NOT NULL,
+  created_at DATETIME,
+  PRIMARY KEY (story_key, depends_on)
+);
+
+-- ---------------------------------------------------------------------------
+-- ready_stories view (Epic 31-1)
+-- ---------------------------------------------------------------------------
+CREATE OR REPLACE VIEW ready_stories AS
+  SELECT s.* FROM wg_stories s
+  WHERE s.status IN ('planned', 'ready')
+    AND NOT EXISTS (
+      SELECT 1 FROM story_dependencies d
+      JOIN wg_stories dep ON dep.story_key = d.depends_on
+      WHERE d.story_key = s.story_key
+        AND d.dep_type = 'blocks'
+        AND dep.status <> 'complete'
+    );
+
+INSERT IGNORE INTO _schema_version (version, description) VALUES (7, 'Add wg_stories, story_dependencies tables and ready_stories view (Epic 31-1)');

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.5.0",
+  "version": "0.5.1",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",