substrate-ai 0.19.28 → 0.19.30

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, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot } from "../health-M0iCuP26.js";
+import { FileStateStore, RunManifest, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveRunManifest } from "../health-DKallkoo.js";
 import { createLogger } from "../logger-KeHncl-f.js";
 import { createEventBus } from "../helpers-CElYrONe.js";
 import { AdapterRegistry, BudgetConfigSchema, CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, ConfigError, CostTrackerConfigSchema, DEFAULT_CONFIG, DoltClient, DoltNotInstalled, GlobalSettingsSchema, IngestionServer, MonitorDatabaseImpl, OPERATIONAL_FINDING, PartialGlobalSettingsSchema, PartialProviderConfigSchema, ProvidersSchema, RoutingRecommender, STORY_METRICS, TelemetryConfigSchema, addTokenUsage, aggregateTokenUsageForRun, checkDoltInstalled, compareRunMetrics, createAmendmentRun, createConfigSystem, createDecision, createDoltClient, createPipelineRun, getActiveDecisions, getAllCostEntriesFiltered, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, tagRunAsBaseline, updatePipelineRun } from "../dist-R0W4ofKv.js";
 import "../adapter-registry-DXLMTmfD.js";
-import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-DabSV2xH.js";
+import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-B0Pe5kol.js";
 import "../errors-BJRMJyGb.js";
 import "../routing-CcBOCuC9.js";
 import "../decisions-C0pz9Clx.js";
@@ -21,6 +21,7 @@ import * as path$3 from "node:path";
 import * as path$2 from "node:path";
 import * as path$1 from "node:path";
 import { join as join$1 } from "node:path";
+import { randomUUID } from "node:crypto";
 import { z } from "zod";
 import * as fs from "node:fs/promises";
 import { access as access$1, readFile as readFile$1, readdir as readdir$1 } from "node:fs/promises";
@@ -29,7 +30,7 @@ import { homedir } from "os";
 import { createRequire } from "node:module";
 import { fileURLToPath as fileURLToPath$1 } from "node:url";
 import { createInterface } from "node:readline";
-import { randomUUID } from "crypto";
+import { randomUUID as randomUUID$1 } from "crypto";
 import { createInterface as createInterface$1 } from "readline";
 
 //#region packages/core/dist/git/git-utils.js
@@ -2761,6 +2762,23 @@ async function runResumeAction(options) {
 			if (Array.isArray(config.explicitStories) && config.explicitStories.length > 0) scopedStories = config.explicitStories;
 		} catch {}
 		const dbDir = dbPath.replace("/substrate.db", "");
+		if (options.stories === void 0 || options.stories.length === 0) {
+			const { manifest: resolvedManifest } = await resolveRunManifest(dbRoot, runId);
+			if (resolvedManifest !== null) try {
+				const manifestData = await resolvedManifest.read();
+				const manifestStories = manifestData.cli_flags["stories"] ?? manifestData.story_scope;
+				if (Array.isArray(manifestStories) && manifestStories.length > 0) {
+					scopedStories = manifestStories;
+					logger$13.debug({
+						runId,
+						stories: scopedStories
+					}, "resume scope loaded from manifest");
+				}
+			} catch {
+				logger$13.debug({ runId }, "manifest read failed in resume — using legacy config_json scope");
+			}
+			else logger$13.debug({ runId }, "Run manifest not found for scope preservation — using legacy config_json scope");
+		}
 		return runFullPipelineFromPhase({
 			packName,
 			packPath,
@@ -3134,6 +3152,55 @@ function registerResumeCommand(program, _version = "0.0.0", projectRoot = proces
 //#endregion
 //#region src/cli/commands/status.ts
 const logger$12 = createLogger("status-cmd");
+/**
+* Map a manifest per-story status string to the appropriate WorkGraphCounts bucket.
+* Unknown strings are treated as `inProgress` (safe default).
+*/
+function manifestStatusToWorkGraphBucket(status) {
+	switch (status) {
+		case "complete": return "complete";
+		case "escalated": return "escalated";
+		case "failed":
+		case "verification-failed": return "failed";
+		case "dispatched":
+		case "in-review":
+		case "recovered": return "inProgress";
+		case "gated":
+		case "pending": return "ready";
+		default: return "inProgress";
+	}
+}
+/**
+* Build a WorkGraphSummary from manifest `per_story_state`.
+* readyStories and blockedStories are left empty — manifest does not carry
+* dependency-graph detail (only status counts).
+*/
+function buildWorkGraphFromManifest(perStoryState) {
+	const counts = {
+		ready: 0,
+		blocked: 0,
+		inProgress: 0,
+		complete: 0,
+		escalated: 0,
+		failed: 0
+	};
+	for (const entry of Object.values(perStoryState)) {
+		const bucket = manifestStatusToWorkGraphBucket(entry.status);
+		counts[bucket]++;
+	}
+	return {
+		summary: {
+			ready: counts.ready,
+			blocked: counts.blocked,
+			inProgress: counts.inProgress,
+			complete: counts.complete,
+			escalated: counts.escalated,
+			failed: counts.failed
+		},
+		readyStories: [],
+		blockedStories: []
+	};
+}
 async function runStatusAction(options) {
 	const { outputFormat, runId, projectRoot, stateStore, history } = options;
 	if (history === true) {
@@ -3176,8 +3243,29 @@ async function runStatusAction(options) {
 	});
 	try {
 		await initSchema(adapter);
+		let run;
+		if (runId !== void 0 && runId !== "") run = await getPipelineRunById(adapter, runId);
+		else {
+			let currentRunId;
+			try {
+				const currentRunIdPath = join(dbRoot, ".substrate", "current-run-id");
+				const content = readFileSync$1(currentRunIdPath, "utf-8").trim();
+				const UUID_RE = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;
+				if (UUID_RE.test(content)) currentRunId = content;
+			} catch {}
+			if (currentRunId !== void 0) run = await getPipelineRunById(adapter, currentRunId);
+			if (run === void 0) run = await getLatestRun(adapter);
+		}
 		let workGraph;
-		try {
+		const { manifest: resolvedManifest } = await resolveRunManifest(dbRoot, run?.id);
+		if (resolvedManifest !== null) try {
+			const manifestData = await resolvedManifest.read();
+			workGraph = buildWorkGraphFromManifest(manifestData.per_story_state);
+			logger$12.debug({ runId: run?.id }, "status: workGraph built from manifest per_story_state");
+		} catch {
+			logger$12.debug({ runId: run?.id }, "status: manifest read failed — falling back to wg_stories");
+		}
+		if (workGraph === void 0) try {
 			const wgRepo = new WorkGraphRepository(adapter);
 			const allStories = await adapter.query(`SELECT story_key, title, status FROM wg_stories`);
 			if (allStories.length > 0) {
@@ -3214,21 +3302,8 @@ async function runStatusAction(options) {
 		} catch (err) {
 			logger$12.debug({ err }, "Work graph query failed, continuing without work graph data");
 		}
-		let run;
-		if (runId !== void 0 && runId !== "") run = await getPipelineRunById(adapter, runId);
-		else {
-			let currentRunId;
-			try {
-				const currentRunIdPath = join(dbRoot, ".substrate", "current-run-id");
-				const content = readFileSync$1(currentRunIdPath, "utf-8").trim();
-				const UUID_RE = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;
-				if (UUID_RE.test(content)) currentRunId = content;
-			} catch {}
-			if (currentRunId !== void 0) run = await getPipelineRunById(adapter, currentRunId);
-			if (run === void 0) run = await getLatestRun(adapter);
-		}
 		if (run === void 0) {
-			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-CVfyC7j0.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-Bb5KxPlE.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -3822,7 +3897,7 @@ async function runAmendAction(options) {
 			}
 			parentRunId = latestCompleted.id;
 		}
-		const amendmentRunId = randomUUID();
+		const amendmentRunId = randomUUID$1();
 		let methodology = packName;
 		try {
 			const packLoader$1 = createPackLoader();
@@ -4044,6 +4119,7 @@ function registerAmendCommand(program, _version = "0.0.0", projectRoot = process
 
 //#endregion
 //#region src/cli/commands/supervisor.ts
+const supervisorLogger = createLogger("supervisor-cmd");
 function defaultSupervisorDeps() {
 	return {
 		getHealth: getAutoHealthData,
@@ -4370,7 +4446,10 @@ async function handleStallRecovery(health, state, config, deps, io) {
 		};
 	}
 	const newRestartCount = state.restartCount + 1;
-	if (health.run_id !== null) await incrementRestarts(health.run_id, projectRoot);
+	if (health.run_id !== null) {
+		await incrementRestarts(health.run_id, projectRoot);
+		RunManifest.open(health.run_id, join(projectRoot, ".substrate", "runs")).update({ restart_count: newRestartCount }).catch(() => {});
+	}
 	emitEvent({
 		type: "supervisor:restart",
 		run_id: health.run_id,
@@ -4379,7 +4458,13 @@ async function handleStallRecovery(health, state, config, deps, io) {
 	log(`Supervisor: Restarting pipeline (attempt ${newRestartCount}/${maxRestarts})`);
 	try {
 		let scopedStories;
-		if (deps.getRunConfig !== void 0 && health.run_id !== null) try {
+		if (health.run_id !== null) try {
+			const manifest = RunManifest.open(health.run_id, projectRoot);
+			const data = await manifest.read();
+			const manifestStories = data?.cli_flags?.stories;
+			if (Array.isArray(manifestStories) && manifestStories.length > 0) scopedStories = manifestStories;
+		} catch {}
+		if (scopedStories === void 0 && deps.getRunConfig !== void 0 && health.run_id !== null) try {
 			const runConfig = await deps.getRunConfig(health.run_id, projectRoot);
 			if (runConfig?.explicitStories !== void 0 && runConfig.explicitStories.length > 0) scopedStories = runConfig.explicitStories;
 		} catch {}
@@ -4442,7 +4527,7 @@ async function handleStallRecovery(health, state, config, deps, io) {
 *   2 — max restarts exceeded (safety valve triggered)
 */
 async function runSupervisorAction(options, deps = {}) {
-	const { pollInterval, stallThreshold, maxRestarts, outputFormat, projectRoot, runId, pack, experiment, maxExperiments } = options;
+	const { pollInterval, stallThreshold, maxRestarts, outputFormat, projectRoot, runId, pack, experiment, maxExperiments, force } = options;
 	const resolvedDeps = {
 		...defaultSupervisorDeps(),
 		...deps
@@ -4455,6 +4540,62 @@ async function runSupervisorAction(options, deps = {}) {
 	};
 	let maxRestartsExhausted = false;
 	const startTime = Date.now();
+	const sessionId = randomUUID();
+	let supervisorLock = null;
+	/** Track whether process exit handlers have been registered for this supervisor. */
+	let exitHandlersRegistered = false;
+	/**
+	* Register process.once exit handlers to release the lock on exit.
+	* Called exactly once, after the first successful lock acquisition.
+	* Using process.once (not process.on) per Story 52-2 spec.
+	*/
+	function registerExitHandlers(lock) {
+		if (exitHandlersRegistered) return;
+		exitHandlersRegistered = true;
+		process.once("exit", () => {
+			lock.release().catch((e) => {
+				supervisorLogger.debug({ error: e }, "lock release on exit failed");
+			});
+		});
+		process.once("SIGTERM", () => {
+			lock.release().then(() => process.exit(0)).catch(() => process.exit(1));
+		});
+		process.once("SIGINT", () => {
+			lock.release().then(() => process.exit(0)).catch(() => process.exit(1));
+		});
+	}
+	/**
+	* Acquire the supervisor lock for a given run ID.
+	* Non-fatal: logs and continues on failure so the supervisor can still
+	* function in degraded mode without blocking the pipeline.
+	*/
+	async function acquireLockForRun(targetRunId) {
+		if (supervisorLock !== null) return;
+		try {
+			const runsDir = join(projectRoot, ".substrate", "runs");
+			const manifest = RunManifest.open(targetRunId, runsDir);
+			const lock = new SupervisorLock(targetRunId, manifest, supervisorLogger);
+			await lock.acquire(process.pid, sessionId, { force: force ?? false });
+			supervisorLock = lock;
+			supervisorLogger.debug({ runId: targetRunId }, "Supervisor lock acquired");
+			registerExitHandlers(lock);
+		} catch (lockErr) {
+			const msg = lockErr instanceof Error ? lockErr.message : String(lockErr);
+			supervisorLogger.warn({
+				runId: targetRunId,
+				error: msg
+			}, "Supervisor lock acquisition failed");
+			if (outputFormat === "json") process.stdout.write(JSON.stringify({
+				type: "supervisor:lock-failed",
+				run_id: targetRunId,
+				reason: msg,
+				ts: new Date().toISOString()
+			}) + "\n");
+			else process.stderr.write(`Warning: Supervisor lock acquisition failed: ${msg}\n`);
+			if (msg.includes("is already supervised by PID") && !force) throw lockErr;
+		}
+	}
+	if (runId !== void 0) await acquireLockForRun(runId);
 	function emitEvent(event) {
 		if (outputFormat === "json") {
 			const stamped = {
@@ -4479,6 +4620,7 @@ async function runSupervisorAction(options, deps = {}) {
 				runId: health.run_id
 			};
 			log(`Supervisor: auto-bound to active run ${health.run_id}`);
+			await acquireLockForRun(health.run_id);
 		}
 		if (outputFormat === "json") {
 			const tokenSnapshot = health.run_id !== null ? await getTokenSnapshot(health.run_id, projectRoot) : {
@@ -4571,7 +4713,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-CjwCYY8Q.js"
+									"../run-BIVex2-V.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -4780,7 +4922,7 @@ async function runMultiProjectSupervisor(options, deps = {}) {
 	}
 }
 function registerSupervisorCommand(program, _version = "0.0.0", projectRoot = process.cwd()) {
-	program.command("supervisor").description("Monitor a pipeline run and automatically recover from stalls").option("--poll-interval <seconds>", "Health poll interval in seconds", (v) => parseInt(v, 10), 60).option("--stall-threshold <seconds>", "Staleness in seconds before killing a stalled pipeline", (v) => parseInt(v, 10), 600).option("--max-restarts <n>", "Maximum automatic restarts before aborting", (v) => parseInt(v, 10), 3).option("--run-id <id>", "Pipeline run ID to monitor (defaults to latest)").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--projects <paths>", "Comma-separated project root directories to monitor (multi-project mode)").option("--output-format <format>", "Output format: human (default) or json", "human").option("--experiment", "After post-run analysis, enter experiment mode: create branches, apply modifications, run single-story experiments, and report verdicts (Story 17-4)", false).option("--max-experiments <n>", "Maximum number of experiments to run per analysis cycle (default: 2, Story 17-4 AC6)", (v) => parseInt(v, 10), 2).action(async (opts) => {
+	program.command("supervisor").description("Monitor a pipeline run and automatically recover from stalls").option("--poll-interval <seconds>", "Health poll interval in seconds", (v) => parseInt(v, 10), 60).option("--stall-threshold <seconds>", "Staleness in seconds before killing a stalled pipeline", (v) => parseInt(v, 10), 600).option("--max-restarts <n>", "Maximum automatic restarts before aborting", (v) => parseInt(v, 10), 3).option("--run-id <id>", "Pipeline run ID to monitor (defaults to latest)").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--projects <paths>", "Comma-separated project root directories to monitor (multi-project mode)").option("--output-format <format>", "Output format: human (default) or json", "human").option("--experiment", "After post-run analysis, enter experiment mode: create branches, apply modifications, run single-story experiments, and report verdicts (Story 17-4)", false).option("--max-experiments <n>", "Maximum number of experiments to run per analysis cycle (default: 2, Story 17-4 AC6)", (v) => parseInt(v, 10), 2).option("--force", "Forcefully evict an existing supervisor process (SIGTERM + 500ms) before attaching (Story 52-2)", false).action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		if (opts.stallThreshold < 120) console.warn(`Warning: --stall-threshold ${opts.stallThreshold}s is below 120s. Agent steps typically take 45-90s. This may cause false stall detections and wasted restarts.`);
 		if (opts.projects) {
@@ -4811,7 +4953,8 @@ function registerSupervisorCommand(program, _version = "0.0.0", projectRoot = pr
 			outputFormat,
 			projectRoot: opts.projectRoot,
 			experiment: opts.experiment,
-			maxExperiments: opts.maxExperiments
+			maxExperiments: opts.maxExperiments,
+			force: opts.force
 		});
 		process.exitCode = exitCode;
 	});
@@ -7504,6 +7647,7 @@ async function runCancelAction(options) {
 			const runningRuns = await getRunningPipelineRuns(adapter);
 			for (const run of runningRuns) {
 				await updatePipelineRun(adapter, run.id, { status: "stopped" });
+				RunManifest.open(run.id, join(dbRoot, "runs")).update({ run_status: "stopped" }).catch(() => {});
 				if (outputFormat === "human") process.stdout.write(`Marked pipeline run ${run.id} as stopped.\n`);
 			}
 		} finally {

package/dist/{health-CVfyC7j0.js → health-Bb5KxPlE.js}

@@ -1,4 +1,4 @@
-import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-M0iCuP26.js";
+import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-DKallkoo.js";
 import "./logger-KeHncl-f.js";
 import "./dist-R0W4ofKv.js";
 import "./decisions-C0pz9Clx.js";