substrate-ai 0.20.108 → 0.20.110

package/dist/adapter-registry-jUH7TLH4.js

@@ -0,0 +1,4 @@
+import { AdapterRegistry } from "./dist-CQ9ZuL2a.js";
+import "./adapter-registry-DIcrxjH8.js";
+
+export { AdapterRegistry };

package/dist/cli/index.js

@@ -1,20 +1,20 @@
 #!/usr/bin/env node
-import { FileKvStore, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createDatabaseAdapter, createDoltOperatorReader, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion } from "../health-D1xKwyaI.js";
+import { FileKvStore, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createDatabaseAdapter, createDoltOperatorReader, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion } from "../health-CJyzYsfu.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, InMemoryDatabaseAdapter, IngestionServer, MonitorDatabaseImpl, OPERATIONAL_FINDING, PartialGlobalSettingsSchema, PartialProviderConfigSchema, ProvidersSchema, RoutingRecommender, STORY_METRICS, TelemetryConfigSchema, addTokenUsage, aggregateTokenUsageForRun, checkDoltInstalled, compareRunMetrics, createAmendmentRun, createConfigSystem, createDecision, createPipelineRun, getActiveDecisions, getAllCostEntriesFiltered, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initWorkGraphSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, swallowDebug, tagRunAsBaseline, updatePipelineRun } from "../dist-Dm37IPMW.js";
-import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GLOBSTAR, GitClient, GrammarLoader, Minimatch, Minipass, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createGitWorktreeManager, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, escape, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runProbeAuthor, runSolutioningPhase, unescape, validateStopAfterFromConflict } from "../run-CIMNjDBH.js";
+import { AdapterRegistry, BudgetConfigSchema, CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, ConfigError, CostTrackerConfigSchema, DEFAULT_CONFIG, DoltClient, DoltNotInstalled, GlobalSettingsSchema, InMemoryDatabaseAdapter, IngestionServer, MonitorDatabaseImpl, OPERATIONAL_FINDING, PartialGlobalSettingsSchema, PartialProviderConfigSchema, ProvidersSchema, RoutingRecommender, STORY_METRICS, TelemetryConfigSchema, addTokenUsage, aggregateTokenUsageForRun, checkDoltInstalled, compareRunMetrics, createAmendmentRun, createConfigSystem, createDecision, createPipelineRun, getActiveDecisions, getAllCostEntriesFiltered, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initWorkGraphSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, swallowDebug, tagRunAsBaseline, updatePipelineRun } from "../dist-CQ9ZuL2a.js";
+import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GLOBSTAR, GitClient, GrammarLoader, Minimatch, Minipass, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createGitWorktreeManager, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, escape, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runProbeAuthor, runSolutioningPhase, unescape, validateStopAfterFromConflict } from "../run-DdTN1lge.js";
 import "../adapter-registry-DIcrxjH8.js";
-import { RunManifest, SupervisorLock, ZERO_FINDINGS_BY_AUTHOR, ZERO_FINDING_COUNTS, ZERO_PROBE_AUTHOR_METRICS, aggregateProbeAuthorMetrics, parseRuntimeProbes, readCurrentRunId, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, rollupFindingsByAuthor, rollupProbeAuthorByClass, rollupProbeAuthorMetrics, runAcTraceabilityCheck } from "../manifest-read-927qGezm.js";
-import "../errors-BaHE73L3.js";
+import { RunManifest, SupervisorLock, ZERO_FINDINGS_BY_AUTHOR, ZERO_FINDING_COUNTS, ZERO_PROBE_AUTHOR_METRICS, aggregateProbeAuthorMetrics, parseRuntimeProbes, readCurrentRunId, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, rollupFindingsByAuthor, rollupProbeAuthorByClass, rollupProbeAuthorMetrics, runAcTraceabilityCheck } from "../manifest-read-B3HU_Awn.js";
+import "../errors-Szein5Rn.js";
 import "../routing-DFxoKHDt.js";
 import { WorkGraphRepository } from "../work-graph-repository-DZyJv5pV.js";
 import "../decisions-CzSIEeGP.js";
 import "../decision-router-DblHY8se.js";
-import "../interactive-prompt-nDNiofTX.js";
+import "../interactive-prompt-CoX8AYbn.js";
 import "../recovery-engine-BKGBeBnW.js";
 import "../version-manager-impl-qFBiO4Eh.js";
-import { registerUpgradeCommand } from "../upgrade-7KujpKbf.js";
+import { registerUpgradeCommand } from "../upgrade-Bpd6pUrr.js";
 import { Command } from "commander";
 import { fileURLToPath } from "url";
 import { dirname, join, resolve } from "path";
@@ -6515,6 +6515,7 @@ async function runFullPipelineFromPhase(options) {
 			} else if (currentPhase === "implementation") {
 				let telemetryEnabled = false;
 				let telemetryPort = 4318;
+				let resumeWorktreeCopyFiles;
 				try {
 					const configSystem = createConfigSystem({ projectConfigDir: dbDir });
 					await configSystem.load();
@@ -6523,6 +6524,7 @@ async function runFullPipelineFromPhase(options) {
 						telemetryEnabled = true;
 						telemetryPort = cfg.telemetry.port ?? 4318;
 					}
+					if (Array.isArray(cfg.worktree?.copy_files) && cfg.worktree.copy_files.length > 0) resumeWorktreeCopyFiles = [...cfg.worktree.copy_files];
 				} catch {}
 				const ingestionServer = telemetryEnabled ? new IngestionServer({ port: telemetryPort }) : void 0;
 				const telemetryPersistence = telemetryEnabled ? new AdapterTelemetryPersistence(adapter) : void 0;
@@ -6536,7 +6538,8 @@ async function runFullPipelineFromPhase(options) {
 						maxConcurrency: concurrency,
 						maxReviewCycles: effectiveMaxReviewCycles,
 						pipelineRunId: runId,
-						enableHeartbeat: eventsFlag === true
+						enableHeartbeat: eventsFlag === true,
+						...resumeWorktreeCopyFiles !== void 0 ? { worktreeCopyFiles: resumeWorktreeCopyFiles } : {}
 					},
 					projectRoot,
 					agentId,
@@ -6891,7 +6894,7 @@ async function runStatusAction(options) {
 			logger$15.debug({ err }, "Work graph query failed, continuing without work graph data");
 		}
 		if (run === void 0) {
-			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-CxU-1KLv.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-BX4kfRaJ.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -7839,7 +7842,7 @@ function defaultSupervisorDeps() {
 				if (cached === null) {
 					const { AdapterRegistry: AR } = await import(
 						/* @vite-ignore */
-						"../adapter-registry-5zXxdGZq.js"
+						"../adapter-registry-jUH7TLH4.js"
 );
 					cached = new AR();
 					await cached.discoverAndRegister();
@@ -8406,11 +8409,11 @@ async function runSupervisorAction(options, deps = {}) {
 						try {
 							const { createExperimenter } = await import(
 								/* @vite-ignore */
-								"../experimenter-BW8Bab4C.js"
+								"../experimenter-COjr78xQ.js"
 );
 							const { getLatestRun: getLatest } = await import(
 								/* @vite-ignore */
-								"../decisions-BF76Y5h7.js"
+								"../decisions-BYa6S26_.js"
 );
 							const expAdapter = createDatabaseAdapter({
 								backend: "auto",
@@ -8420,7 +8423,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-CtdP1-q9.js"
+									"../run--ncQ9inj.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -8945,7 +8948,7 @@ async function runMetricsAction(options) {
 			const routingConfigPath = join(dbDir, "routing.yml");
 			let routingConfig = null;
 			if (existsSync$1(routingConfigPath)) try {
-				const { loadModelRoutingConfig } = await import("../routing-CkUTlM3M.js");
+				const { loadModelRoutingConfig } = await import("../routing-C_KbC9on.js");
 				routingConfig = loadModelRoutingConfig(routingConfigPath);
 			} catch {}
 			if (routingConfig === null) routingConfig = {
@@ -10350,6 +10353,54 @@ async function listWorktreesAction(options) {
 	}
 }
 /**
+* Cleanup action — removes one or all substrate-managed worktrees + their
+* branches. Wraps the existing GitWorktreeManager.cleanupWorktree /
+* cleanupAllWorktrees backend; v0.20.109 closes the gap where the
+* "already registered" error message advertised a `--cleanup` flag that
+* didn't exist.
+*
+* @param options - Action options
+* @returns       - Exit code (0 = success, 1 = error)
+*/
+async function cleanupWorktreesAction(options) {
+	const { taskId, projectRoot } = options;
+	try {
+		const eventBus = createEventBus();
+		const manager = createGitWorktreeManager({
+			eventBus,
+			projectRoot
+		});
+		if (taskId !== void 0) try {
+			await manager.cleanupWorktree(taskId);
+			process.stdout.write(`Cleaned up worktree for task "${taskId}"\n`);
+			return WORKTREES_EXIT_SUCCESS;
+		} catch (err) {
+			const message = err instanceof Error ? err.message : String(err);
+			process.stderr.write(`Error cleaning up worktree for task "${taskId}": ${message}\n`);
+			logger$9.error({
+				err,
+				taskId
+			}, "cleanupWorktreesAction (single) failed");
+			return WORKTREES_EXIT_ERROR;
+		}
+		try {
+			const cleaned = await manager.cleanupAllWorktrees();
+			process.stdout.write(`Cleaned up ${cleaned} worktree${cleaned === 1 ? "" : "s"}\n`);
+			return WORKTREES_EXIT_SUCCESS;
+		} catch (err) {
+			const message = err instanceof Error ? err.message : String(err);
+			process.stderr.write(`Error during bulk cleanup: ${message}\n`);
+			logger$9.error({ err }, "cleanupWorktreesAction (bulk) failed");
+			return WORKTREES_EXIT_ERROR;
+		}
+	} catch (err) {
+		const message = err instanceof Error ? err.message : String(err);
+		process.stderr.write(`Error: ${message}\n`);
+		logger$9.error({ err }, "cleanupWorktreesAction failed");
+		return WORKTREES_EXIT_ERROR;
+	}
+}
+/**
 * Register the `substrate worktrees` command with the CLI program.
 *
 * @param program     - Commander program instance
@@ -10357,7 +10408,16 @@ async function listWorktreesAction(options) {
 * @param projectRoot - Project root directory (defaults to process.cwd())
 */
 function registerWorktreesCommand(program, version = "0.0.0", projectRoot = process.cwd()) {
-	program.command("worktrees").description("List all active git worktrees and their associated tasks").option("--output-format <format>", "Output format: table (default) or json", "table").option("--json", "Output JSON (shorthand for --output-format json)", false).option("--status <status>", `Filter by task status: ${VALID_STATUSES.join(", ")}`).option("--sort <key>", `Sort by: ${VALID_SORT_KEYS.join(", ")} (default: created)`, "created").action(async (opts) => {
+	program.command("worktrees").description("List or clean up substrate git worktrees and their task branches").option("--output-format <format>", "Output format: table (default) or json", "table").option("--json", "Output JSON (shorthand for --output-format json)", false).option("--status <status>", `Filter by task status: ${VALID_STATUSES.join(", ")}`).option("--sort <key>", `Sort by: ${VALID_SORT_KEYS.join(", ")} (default: created)`, "created").option("--cleanup [task-id]", "Remove substrate worktree(s) and branches. Pass a task id to remove just one; omit the arg to remove all.").action(async (opts) => {
+		if (opts.cleanup !== void 0 && opts.cleanup !== false) {
+			const taskId = typeof opts.cleanup === "string" && opts.cleanup.trim().length > 0 ? opts.cleanup.trim() : void 0;
+			const cleanupExitCode = await cleanupWorktreesAction({
+				...taskId !== void 0 ? { taskId } : {},
+				projectRoot
+			});
+			process.exitCode = cleanupExitCode;
+			return;
+		}
 		const outputFormat = opts.json ? "json" : opts.outputFormat === "json" ? "json" : "table";
 		let statusFilter;
 		if (opts.status !== void 0) {
@@ -10953,6 +11013,13 @@ async function runRetryEscalatedAction(options) {
 		const agentAdapter = agentId != null ? injectedRegistry.get(agentId) : void 0;
 		const adapterDefaultCycles = agentAdapter?.getCapabilities?.()?.defaultMaxReviewCycles;
 		const effectiveMaxReviewCycles = adapterDefaultCycles != null ? Math.max(2, adapterDefaultCycles) : 2;
+		let retryWorktreeCopyFiles;
+		try {
+			const configSystem = createConfigSystem({ projectConfigDir: join(dbRoot, ".substrate") });
+			await configSystem.load();
+			const cfg = configSystem.getConfig();
+			if (Array.isArray(cfg.worktree?.copy_files) && cfg.worktree.copy_files.length > 0) retryWorktreeCopyFiles = [...cfg.worktree.copy_files];
+		} catch {}
 		const orchestrator = createImplementationOrchestrator({
 			db: adapter,
 			pack,
@@ -10963,7 +11030,8 @@ async function runRetryEscalatedAction(options) {
 				maxConcurrency: concurrency,
 				maxReviewCycles: effectiveMaxReviewCycles,
 				pipelineRunId: pipelineRun.id,
-				...Object.keys(perStoryContextCeilings).length > 0 ? { perStoryContextCeilings } : {}
+				...Object.keys(perStoryContextCeilings).length > 0 ? { perStoryContextCeilings } : {},
+				...retryWorktreeCopyFiles !== void 0 ? { worktreeCopyFiles: retryWorktreeCopyFiles } : {}
 			},
 			projectRoot,
 			agentId
@@ -12468,6 +12536,13 @@ function registerReconcileFromDiskCommand(program, _version = "0.0.0", projectRo
 //#region src/cli/commands/report.ts
 const logger$1 = createLogger("report");
 /**
+* v0.20.110: Minimum output_tokens for a verified/recovered story to be
+* trusted as having actually produced work. Below this, the story is flagged
+* with `low_output_warning: true` so operators don't trust misleading metrics.
+* Boardgame backlog Item 3.
+*/
+const LOW_OUTPUT_TOKEN_THRESHOLD = 100;
+/**
 * Determine whether verification ran for a story.
 *
 * Handles both real manifest format (checks array) and probe fixture format
@@ -12694,7 +12769,7 @@ function renderHuman(output, manifest) {
 		const costCell = s.cost_usd != null ? `$${s.cost_usd.toFixed(4)}` : "-";
 		const f = s.verification_findings;
 		const findingsCell = `E:${f.error} W:${f.warn} I:${f.info}`;
-		const verifiedTag = s.outcome === "verified" ? "✓" : "";
+		const verifiedTag = s.outcome === "verified" ? s.low_output_warning === true ? "⚠ low-out" : "✓" : s.low_output_warning === true ? "⚠ low-out" : "";
 		const key = s.story_key.length > 50 ? s.story_key.slice(0, 49) + "…" : s.story_key;
 		lines.push(formatRow([
 			key,
@@ -12707,6 +12782,12 @@ function renderHuman(output, manifest) {
 		], COL_WIDTHS));
 	}
 	lines.push("");
+	const lowOutputStories = stories.filter((s) => s.low_output_warning === true);
+	if (lowOutputStories.length > 0) {
+		lines.push(`⚠ ${lowOutputStories.length} story/stories produced fewer than ${LOW_OUTPUT_TOKEN_THRESHOLD} output tokens —`);
+		lines.push(`  the "verified" verdict may be misleading. Inspect dispatch artifacts before trusting.`);
+		lines.push("");
+	}
 	if (escalations.length > 0) {
 		lines.push("──── Escalation Details ────");
 		for (const esc of escalations) {
@@ -12780,7 +12861,7 @@ function renderJson(output) {
 * @param manifest - Raw manifest data.
 * @param halts - Optional operator halt notifications (Story 73-2, AC12).
 */
-function assembleReport(runId, manifest, halts) {
+function assembleReport(runId, manifest, halts, storyOutputTokens) {
 	const perStoryState = manifest.per_story_state ?? {};
 	const storyKeys = Object.keys(perStoryState);
 	const startedAt = manifest.created_at ?? "";
@@ -12821,6 +12902,9 @@ function assembleReport(runId, manifest, halts) {
 		const findings = extractVerificationFindings(state);
 		const verificationRan = didVerificationRun(state);
 		const wc = wallClockMs(state);
+		const outputTokens = storyOutputTokens?.get(key);
+		const trustworthyOutcome = outcome === "verified" || outcome === "recovered";
+		const lowOutputWarning = outputTokens !== void 0 && trustworthyOutcome && outputTokens < LOW_OUTPUT_TOKEN_THRESHOLD;
 		const storySummary = {
 			story_key: key,
 			outcome,
@@ -12828,7 +12912,9 @@ function assembleReport(runId, manifest, halts) {
 			review_cycles: state.review_cycles ?? 0,
 			cost_usd: state.cost_usd,
 			verification_findings: findings,
-			verification_ran: verificationRan
+			verification_ran: verificationRan,
+			...outputTokens !== void 0 ? { output_tokens: outputTokens } : {},
+			...lowOutputWarning ? { low_output_warning: true } : {}
 		};
 		stories.push(storySummary);
 		summary[outcome]++;
@@ -12992,7 +13078,21 @@ async function runReportAction(options) {
 		logger$1.debug({ err }, "notification read failed — continuing without halt data");
 		return [];
 	});
-	const output = assembleReport(resolvedRunId, manifest, halts);
+	const storyOutputTokens = new Map();
+	const metricsAdapter = createDatabaseAdapter({
+		backend: "auto",
+		basePath: dbRoot
+	});
+	try {
+		await initSchema(metricsAdapter);
+		const storyMetricsRows = await getStoryMetricsForRun(metricsAdapter, resolvedRunId);
+		for (const row of storyMetricsRows) if (typeof row.output_tokens === "number") storyOutputTokens.set(row.story_key, row.output_tokens);
+	} catch (err) {
+		logger$1.debug({ err }, "story_metrics read failed — low-output flagging unavailable");
+	} finally {
+		await metricsAdapter.close().catch(swallowDebug("report-metrics-close"));
+	}
+	const output = assembleReport(resolvedRunId, manifest, halts, storyOutputTokens);
 	if (verifyAc === true) {
 		const artifactsDir = join(dbRoot, "_bmad-output", "implementation-artifacts");
 		const acTraceability = {};
@@ -13130,8 +13230,8 @@ async function createProgram() {
 /** Fire-and-forget startup version check (story 8.3, AC3/AC5) */
 function checkForUpdatesInBackground(currentVersion) {
 	if (process.env.SUBSTRATE_NO_UPDATE_CHECK === "1") return;
-	import("../upgrade-fViYOn8u.js").then(async () => {
-		const { createVersionManager } = await import("../version-manager-impl-brvj1EYW.js");
+	import("../upgrade-DoWjPygF.js").then(async () => {
+		const { createVersionManager } = await import("../version-manager-impl-DyE9bMVG.js");
 		const vm = createVersionManager();
 		const result = await vm.checkForUpdates();
 		if (result.updateAvailable) {

package/dist/{decisions-BF76Y5h7.js → decisions-BYa6S26_.js}

@@ -1,4 +1,4 @@
-import { addTokenUsage, createDecision, createPipelineRun, createRequirement, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunningPipelineRuns, getTokenUsageSummary, listRequirements, registerArtifact, updateDecision, updatePipelineRun, updatePipelineRunConfig, upsertDecision } from "./dist-Dm37IPMW.js";
+import { addTokenUsage, createDecision, createPipelineRun, createRequirement, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunningPipelineRuns, getTokenUsageSummary, listRequirements, registerArtifact, updateDecision, updatePipelineRun, updatePipelineRunConfig, upsertDecision } from "./dist-CQ9ZuL2a.js";
 import "./decisions-CzSIEeGP.js";
 
 export { getLatestRun };

package/dist/{dist-Dm37IPMW.js → dist-CQ9ZuL2a.js}

@@ -2544,27 +2544,30 @@ function isDoltAvailable(basePath) {
 	console.warn("[persistence:adapter] Dolt still unavailable after retry — falling back to InMemoryDatabaseAdapter. Telemetry and cost data will NOT persist.");
 	return false;
 }
+function adapterDiag(message) {
+	process.stderr.write("[persistence:adapter] " + message + "\n");
+}
 function createDatabaseAdapter(config = { backend: "auto" }, doltClientFactory) {
 	const backend = config.backend ?? "auto";
 	const basePath = config.basePath ?? process.cwd();
 	const doltRepoPath = join$1(basePath, ".substrate", "state");
 	if (backend === "dolt") {
 		if (!doltClientFactory) {
-			console.debug("[persistence:adapter] dolt backend requested but no doltClientFactory provided; falling back to memory");
+			adapterDiag("dolt backend requested but no doltClientFactory provided; falling back to memory");
 			return new InMemoryDatabaseAdapter();
 		}
-		console.debug("[persistence:adapter] Using DoltDatabaseAdapter (explicit config)");
+		adapterDiag("Using DoltDatabaseAdapter (explicit config)");
 		return new DoltDatabaseAdapter(doltClientFactory(doltRepoPath));
 	}
 	if (backend === "memory") {
-		console.debug("[persistence:adapter] Using InMemoryDatabaseAdapter (explicit config)");
+		adapterDiag("Using InMemoryDatabaseAdapter (explicit config)");
 		return new InMemoryDatabaseAdapter();
 	}
 	if (doltClientFactory && isDoltAvailable(basePath)) {
-		console.debug("[persistence:adapter] Dolt detected, using DoltDatabaseAdapter");
+		adapterDiag("Dolt detected, using DoltDatabaseAdapter");
 		return new DoltDatabaseAdapter(doltClientFactory(doltRepoPath));
 	}
-	console.debug("[persistence:adapter] Dolt not available or no factory, using InMemoryDatabaseAdapter");
+	adapterDiag("Dolt not available or no factory, using InMemoryDatabaseAdapter");
 	return new InMemoryDatabaseAdapter();
 }
 
@@ -6109,6 +6112,7 @@ const TelemetryConfigSchema = z.object({
 	meshUrl: z.string().url().optional(),
 	projectId: z.string().optional()
 }).strict();
+const WorktreeConfigSchema = z.object({ copy_files: z.array(z.string()).default([]) }).strict();
 /** Current supported config format version */
 const CURRENT_CONFIG_FORMAT_VERSION = "1";
 /** Current supported task graph version */
@@ -6125,6 +6129,7 @@ const SubstrateConfigSchema = z.object({
 	cost_tracker: CostTrackerConfigSchema.optional(),
 	budget: BudgetConfigSchema.optional(),
 	telemetry: TelemetryConfigSchema.optional(),
+	worktree: WorktreeConfigSchema.optional(),
 	trivialOutputThreshold: z.number().int().nonnegative().optional()
 }).passthrough();
 const PartialProviderConfigSchema = ProviderConfigSchema.partial();
@@ -6141,6 +6146,7 @@ const PartialSubstrateConfigSchema = z.object({
 	cost_tracker: CostTrackerConfigSchema.partial().optional(),
 	budget: BudgetConfigSchema.partial().optional(),
 	telemetry: TelemetryConfigSchema.partial().optional(),
+	worktree: WorktreeConfigSchema.partial().optional(),
 	trivialOutputThreshold: z.number().int().nonnegative().optional()
 }).passthrough();
 
@@ -11251,4 +11257,4 @@ async function callLLM(params) {
 
 //#endregion
 export { ADVISORY_NOTES, AdapterRegistry, AdtError, BudgetConfigSchema, CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, Categorizer, ClaudeCodeAdapter, CodexCLIAdapter, ConfigError, ConfigIncompatibleFormatError, ConsumerAnalyzer, CostTrackerConfigSchema, DEFAULT_CONFIG, DEFAULT_GLOBAL_SETTINGS, DispatcherImpl, DoltClient, DoltNotInstalled, DoltQueryError, ESCALATION_DIAGNOSIS, EXPERIMENT_RESULT, EfficiencyScorer, GeminiCLIAdapter, GlobalSettingsSchema, InMemoryDatabaseAdapter, IngestionServer, LEARNING_FINDING, LogTurnAnalyzer, ModelRoutingConfigSchema, MonitorDatabaseImpl, OPERATIONAL_FINDING, PartialGlobalSettingsSchema, PartialProviderConfigSchema, ProviderPolicySchema, ProvidersSchema, Recommender, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, STORY_METRICS, STORY_OUTCOME, SubstrateConfigSchema, TASK_TYPE_PHASE_MAP, TEST_EXPANSION_FINDING, TEST_PLAN, TelemetryConfigSchema, TelemetryNormalizer, TelemetryPipeline, TurnAnalyzer, VersionManagerImpl, addTokenUsage, aggregateTokenUsageForRun, aggregateTokenUsageForStory, buildAuditLogEntry, buildBranchName, buildModificationDirective, buildPRBody, buildWorktreePath, callLLM, checkDoltInstalled, classifyVersionGap, compareRunMetrics, createAmendmentRun, createConfigSystem, createDatabaseAdapter as createDatabaseAdapter$1, createDecision, createExperimenter, createPipelineRun, createRequirement, createVersionManager, detectInterfaceChanges, determineVerdict, getActiveDecisions, getAllCostEntriesFiltered, getArtifactByTypeForRun, getArtifactsByRun, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getModelTier, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initWorkGraphSchema, initializeDolt, listRequirements, listRunMetrics, loadModelRoutingConfig, loadParentRunDecisions, registerArtifact, resolvePromptFile, supersedeDecision, swallowDebug, tagRunAsBaseline, updateDecision, updatePipelineRun, updatePipelineRunConfig, upsertDecision, writeRunMetrics, writeStoryMetrics };
-//# sourceMappingURL=dist-Dm37IPMW.js.map
+//# sourceMappingURL=dist-CQ9ZuL2a.js.map

package/dist/{errors-BaHE73L3.js → errors-Szein5Rn.js}

@@ -1,4 +1,4 @@
-import { AdtError } from "./dist-Dm37IPMW.js";
+import { AdtError } from "./dist-CQ9ZuL2a.js";
 
 //#region src/core/errors.ts
 /** Error thrown when task configuration is invalid */
@@ -71,4 +71,4 @@ var TaskGraphIncompatibleFormatError = class extends AdtError {
 
 //#endregion
 export { BudgetExceededError, GitError, RecoveryError, TaskConfigError, TaskGraphCycleError, TaskGraphError, TaskGraphIncompatibleFormatError, WorkerError, WorkerNotFoundError };
-//# sourceMappingURL=errors-BaHE73L3.js.map
+//# sourceMappingURL=errors-Szein5Rn.js.map

package/dist/{experimenter-BW8Bab4C.js → experimenter-COjr78xQ.js}

@@ -1,3 +1,3 @@
-import { buildAuditLogEntry, buildBranchName, buildModificationDirective, buildPRBody, buildWorktreePath, createExperimenter, determineVerdict, resolvePromptFile } from "./dist-Dm37IPMW.js";
+import { buildAuditLogEntry, buildBranchName, buildModificationDirective, buildPRBody, buildWorktreePath, createExperimenter, determineVerdict, resolvePromptFile } from "./dist-CQ9ZuL2a.js";
 
 export { createExperimenter };

package/dist/{health-CxU-1KLv.js → health-BX4kfRaJ.js}

@@ -1,7 +1,7 @@
-import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-D1xKwyaI.js";
+import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-CJyzYsfu.js";
 import "./logger-KeHncl-f.js";
-import "./dist-Dm37IPMW.js";
-import "./manifest-read-927qGezm.js";
+import "./dist-CQ9ZuL2a.js";
+import "./manifest-read-B3HU_Awn.js";
 import "./work-graph-repository-DZyJv5pV.js";
 import "./decisions-CzSIEeGP.js";
 

package/dist/{health-D1xKwyaI.js → health-CJyzYsfu.js}

@@ -1,6 +1,6 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { DoltClient, DoltQueryError, createDatabaseAdapter$1 as createDatabaseAdapter, getLatestRun, getPipelineRunById, initSchema } from "./dist-Dm37IPMW.js";
-import { resolveMainRepoRoot, resolveRunManifest } from "./manifest-read-927qGezm.js";
+import { DoltClient, DoltQueryError, createDatabaseAdapter$1 as createDatabaseAdapter, getLatestRun, getPipelineRunById, initSchema } from "./dist-CQ9ZuL2a.js";
+import { resolveMainRepoRoot, resolveRunManifest } from "./manifest-read-B3HU_Awn.js";
 import { createRequire } from "module";
 import { dirname, join } from "path";
 import { existsSync, readFileSync } from "node:fs";
@@ -1000,4 +1000,4 @@ function registerHealthCommand(program, _version = "0.0.0", projectRoot = proces
 
 //#endregion
 export { BMAD_BASELINE_TOKENS_FULL, DEFAULT_STALL_THRESHOLD_SECONDS, FileKvStore, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, __commonJS, __require, __toESM, buildPipelineStatusOutput, createDatabaseAdapter$1 as createDatabaseAdapter, createDoltOperatorReader, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, isOrchestratorProcessLine, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, runHealthAction, validateStoryKey };
-//# sourceMappingURL=health-D1xKwyaI.js.map
+//# sourceMappingURL=health-CJyzYsfu.js.map

package/dist/{index-C8F4ACfC.d.ts → index-DYzIw89v.d.ts}

@@ -288,6 +288,9 @@ declare const SubstrateConfigSchema: z.ZodObject<{
     meshUrl: z.ZodOptional<z.ZodString>;
     projectId: z.ZodOptional<z.ZodString>;
   }, z.core.$strict>>;
+  worktree: z.ZodOptional<z.ZodObject<{
+    copy_files: z.ZodDefault<z.ZodArray<z.ZodString>>;
+  }, z.core.$strict>>;
   trivialOutputThreshold: z.ZodOptional<z.ZodNumber>;
 }, z.core.$loose>;
 type SubstrateConfig = z.infer<typeof SubstrateConfigSchema>; //#endregion
@@ -1429,4 +1432,4 @@ interface Recommendation {
 
 //#endregion
 export { AdapterDiscoveryResult, AdapterRegistry as AdapterRegistry$1, AdtError as AdtError$1, ClaudeCodeAdapter as ClaudeCodeAdapter$1, CodexCLIAdapter as CodexCLIAdapter$1, ConfigError as ConfigError$1, ConfigIncompatibleFormatError as ConfigIncompatibleFormatError$1, CoreEvents, DatabaseAdapter, DiscoveryReport, GeminiCLIAdapter as GeminiCLIAdapter$1, Recommendation, TypedEventBus };
-//# sourceMappingURL=index-C8F4ACfC.d.ts.map
+//# sourceMappingURL=index-DYzIw89v.d.ts.map

package/dist/index.d.ts

@@ -1,4 +1,4 @@
-import { AdapterDiscoveryResult, AdapterRegistry$1 as AdapterRegistry, AdtError$1 as AdtError, ClaudeCodeAdapter$1 as ClaudeCodeAdapter, CodexCLIAdapter$1 as CodexCLIAdapter, ConfigError$1 as ConfigError, ConfigIncompatibleFormatError$1 as ConfigIncompatibleFormatError, DiscoveryReport, GeminiCLIAdapter$1 as GeminiCLIAdapter, Recommendation, TypedEventBus } from "./index-C8F4ACfC.js";
+import { AdapterDiscoveryResult, AdapterRegistry$1 as AdapterRegistry, AdtError$1 as AdtError, ClaudeCodeAdapter$1 as ClaudeCodeAdapter, CodexCLIAdapter$1 as CodexCLIAdapter, ConfigError$1 as ConfigError, ConfigIncompatibleFormatError$1 as ConfigIncompatibleFormatError, DiscoveryReport, GeminiCLIAdapter$1 as GeminiCLIAdapter, Recommendation, TypedEventBus } from "./index-DYzIw89v.js";
 import pino from "pino";
 import { z } from "zod";
 import { Readable, Writable } from "node:stream";

package/dist/index.js

@@ -1,8 +1,8 @@
 import { childLogger, createLogger, logger } from "./logger-KeHncl-f.js";
 import { assertDefined, createEventBus, createTuiApp, deepClone, formatDuration, generateId, isPlainObject, isTuiCapable, printNonTtyWarning, sleep, withRetry } from "./helpers-CElYrONe.js";
-import { AdapterRegistry, AdtError, ClaudeCodeAdapter, CodexCLIAdapter, ConfigError, ConfigIncompatibleFormatError, GeminiCLIAdapter } from "./dist-Dm37IPMW.js";
+import { AdapterRegistry, AdtError, ClaudeCodeAdapter, CodexCLIAdapter, ConfigError, ConfigIncompatibleFormatError, GeminiCLIAdapter } from "./dist-CQ9ZuL2a.js";
 import "./adapter-registry-DIcrxjH8.js";
-import { BudgetExceededError, GitError, RecoveryError, TaskConfigError, TaskGraphCycleError, TaskGraphError, TaskGraphIncompatibleFormatError, WorkerError, WorkerNotFoundError } from "./errors-BaHE73L3.js";
+import { BudgetExceededError, GitError, RecoveryError, TaskConfigError, TaskGraphCycleError, TaskGraphError, TaskGraphIncompatibleFormatError, WorkerError, WorkerNotFoundError } from "./errors-Szein5Rn.js";
 
 //#region src/core/di.ts
 /**

package/dist/{interactive-prompt-nDNiofTX.js → interactive-prompt-CoX8AYbn.js}

@@ -1,5 +1,5 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { readCurrentRunId, resolveMainRepoRoot } from "./manifest-read-927qGezm.js";
+import { readCurrentRunId, resolveMainRepoRoot } from "./manifest-read-B3HU_Awn.js";
 import { join } from "node:path";
 import { mkdir, readFile, writeFile } from "node:fs/promises";
 import * as readline from "node:readline";
@@ -180,4 +180,4 @@ async function runInteractivePrompt(decisionContext) {
 
 //#endregion
 export { runInteractivePrompt };
-//# sourceMappingURL=interactive-prompt-nDNiofTX.js.map
+//# sourceMappingURL=interactive-prompt-CoX8AYbn.js.map

package/dist/{manifest-read-927qGezm.js → manifest-read-B3HU_Awn.js}

@@ -1,5 +1,5 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { LEARNING_FINDING, createDecision, getDecisionsByCategory } from "./dist-Dm37IPMW.js";
+import { LEARNING_FINDING, createDecision, getDecisionsByCategory } from "./dist-CQ9ZuL2a.js";
 import * as path$1 from "path";
 import { join } from "path";
 import { readFile } from "fs/promises";
@@ -5845,4 +5845,4 @@ async function resolveRunManifest(dbRoot, runId) {
 
 //#endregion
 export { FindingsInjector, RunManifest, RuntimeProbeListSchema, SupervisorLock, ZERO_FINDINGS_BY_AUTHOR, ZERO_FINDING_COUNTS, ZERO_PROBE_AUTHOR_METRICS, aggregateProbeAuthorMetrics, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, parseRuntimeProbes, readCurrentRunId, renderFindings, resolveGraphPath, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, rollupFindingsByAuthor, rollupProbeAuthorByClass, rollupProbeAuthorMetrics, runAcTraceabilityCheck, runStaleVerificationRecovery };
-//# sourceMappingURL=manifest-read-927qGezm.js.map
+//# sourceMappingURL=manifest-read-B3HU_Awn.js.map

package/dist/modules/interactive-prompt/index.js

@@ -1,6 +1,6 @@
 import "../../logger-KeHncl-f.js";
-import "../../dist-Dm37IPMW.js";
-import "../../manifest-read-927qGezm.js";
-import { runInteractivePrompt } from "../../interactive-prompt-nDNiofTX.js";
+import "../../dist-CQ9ZuL2a.js";
+import "../../manifest-read-B3HU_Awn.js";
+import { runInteractivePrompt } from "../../interactive-prompt-CoX8AYbn.js";
 
 export { runInteractivePrompt };

package/dist/{routing-CkUTlM3M.js → routing-C_KbC9on.js}

@@ -1,4 +1,4 @@
-import { ModelRoutingConfigSchema, ProviderPolicySchema, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, TASK_TYPE_PHASE_MAP, getModelTier, loadModelRoutingConfig } from "./dist-Dm37IPMW.js";
+import { ModelRoutingConfigSchema, ProviderPolicySchema, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, TASK_TYPE_PHASE_MAP, getModelTier, loadModelRoutingConfig } from "./dist-CQ9ZuL2a.js";
 import "./routing-DFxoKHDt.js";
 
 export { loadModelRoutingConfig };

package/dist/{run-CtdP1-q9.js → run--ncQ9inj.js}

@@ -1,14 +1,14 @@
-import "./health-D1xKwyaI.js";
+import "./health-CJyzYsfu.js";
 import "./logger-KeHncl-f.js";
 import "./helpers-CElYrONe.js";
-import "./dist-Dm37IPMW.js";
-import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, runRunAction, wireNdjsonEmitter } from "./run-CIMNjDBH.js";
-import "./manifest-read-927qGezm.js";
+import "./dist-CQ9ZuL2a.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, runRunAction, wireNdjsonEmitter } from "./run-DdTN1lge.js";
+import "./manifest-read-B3HU_Awn.js";
 import "./routing-DFxoKHDt.js";
 import "./work-graph-repository-DZyJv5pV.js";
 import "./decisions-CzSIEeGP.js";
 import "./decision-router-DblHY8se.js";
-import "./interactive-prompt-nDNiofTX.js";
+import "./interactive-prompt-CoX8AYbn.js";
 import "./recovery-engine-BKGBeBnW.js";
 
 export { runRunAction };

package/dist/{run-CIMNjDBH.js → run-DdTN1lge.js}

@@ -1,11 +1,11 @@
-import { BMAD_BASELINE_TOKENS_FULL, FileKvStore, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, VALID_PHASES, __commonJS, __require, __toESM, buildPipelineStatusOutput, createDatabaseAdapter, formatOutput, formatPipelineSummary, formatTokenTelemetry, inspectProcessTree, parseDbTimestampAsUtc, validateStoryKey } from "./health-D1xKwyaI.js";
+import { BMAD_BASELINE_TOKENS_FULL, FileKvStore, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, VALID_PHASES, __commonJS, __require, __toESM, buildPipelineStatusOutput, createDatabaseAdapter, formatOutput, formatPipelineSummary, formatTokenTelemetry, inspectProcessTree, parseDbTimestampAsUtc, validateStoryKey } from "./health-CJyzYsfu.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, EXPERIMENT_RESULT, 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, classifyVersionGap, createConfigSystem, createDatabaseAdapter$1, createDecision, createPipelineRun, createRequirement, detectInterfaceChanges, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunMetrics, getRunningPipelineRuns, getStoryMetricsForRun, getTokenUsageSummary, initSchema, listRequirements, loadModelRoutingConfig, registerArtifact, swallowDebug, updatePipelineRun, updatePipelineRunConfig, upsertDecision, writeRunMetrics, writeStoryMetrics } from "./dist-Dm37IPMW.js";
-import { FindingsInjector, RunManifest, RuntimeProbeListSchema, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, renderFindings, resolveGraphPath, resolveMainRepoRoot, runAcTraceabilityCheck, runStaleVerificationRecovery } from "./manifest-read-927qGezm.js";
+import { ADVISORY_NOTES, Categorizer, ConsumerAnalyzer, DEFAULT_GLOBAL_SETTINGS, DispatcherImpl, DoltClient, ESCALATION_DIAGNOSIS, EXPERIMENT_RESULT, 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, classifyVersionGap, createConfigSystem, createDatabaseAdapter$1, createDecision, createPipelineRun, createRequirement, detectInterfaceChanges, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunMetrics, getRunningPipelineRuns, getStoryMetricsForRun, getTokenUsageSummary, initSchema, listRequirements, loadModelRoutingConfig, registerArtifact, swallowDebug, updatePipelineRun, updatePipelineRunConfig, upsertDecision, writeRunMetrics, writeStoryMetrics } from "./dist-CQ9ZuL2a.js";
+import { FindingsInjector, RunManifest, RuntimeProbeListSchema, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, renderFindings, resolveGraphPath, resolveMainRepoRoot, runAcTraceabilityCheck, runStaleVerificationRecovery } from "./manifest-read-B3HU_Awn.js";
 import { WorkGraphRepository, detectCycles } from "./work-graph-repository-DZyJv5pV.js";
 import { deriveExitCode, routeDecision } from "./decision-router-DblHY8se.js";
-import { runInteractivePrompt } from "./interactive-prompt-nDNiofTX.js";
+import { runInteractivePrompt } from "./interactive-prompt-CoX8AYbn.js";
 import { runRecoveryEngine } from "./recovery-engine-BKGBeBnW.js";
 import { basename, dirname, extname, join } from "path";
 import { access, readFile, readdir, stat } from "fs/promises";
@@ -21,7 +21,7 @@ import path, { basename as basename$1, dirname as dirname$1, extname as extname$
 import { tmpdir } from "node:os";
 import { createHash, randomUUID } from "node:crypto";
 import { z } from "zod";
-import { access as access$1, lstat, mkdir as mkdir$1, readFile as readFile$1, readdir as readdir$1, readlink, realpath, rename, rm, stat as stat$1, unlink as unlink$1, writeFile as writeFile$1 } from "node:fs/promises";
+import { access as access$1, copyFile, lstat, mkdir as mkdir$1, readFile as readFile$1, readdir as readdir$1, readlink, realpath, rename, rm, stat as stat$1, unlink as unlink$1, writeFile as writeFile$1 } from "node:fs/promises";
 import { existsSync as existsSync$1, lstatSync, mkdirSync as mkdirSync$1, readFileSync as readFileSync$1, readdir as readdir$2, readdirSync as readdirSync$1, readlinkSync, realpathSync as realpathSync$1, unlinkSync as unlinkSync$1, writeFileSync as writeFileSync$1 } from "fs";
 import { promisify } from "node:util";
 import { fileURLToPath } from "node:url";
@@ -144,10 +144,15 @@ async function verifyGitVersion() {
 * @param taskId      - Task identifier (used in path derivation)
 * @param branchName  - Branch name to create (e.g., "substrate/story-abc123")
 * @param baseBranch  - Branch to base the worktree on (e.g., "main")
+* @param copyFiles   - v0.20.109: Optional list of files to copy from the
+*                      project root into the new worktree after creation
+*                      (e.g., `[".env", ".env.local"]`). Missing files are
+*                      skipped silently. Useful for gitignored files that
+*                      build tooling needs but `git worktree add` won't carry.
 * @returns           - Object with the worktreePath
 * @throws            - Error if git command fails
 */
-async function createWorktree(projectRoot, taskId, branchName, baseBranch) {
+async function createWorktree(projectRoot, taskId, branchName, baseBranch, copyFiles = []) {
 	const worktreePath = path$5.join(projectRoot, ".substrate-worktrees", taskId);
 	const worktreeExists = await access$1(worktreePath).then(() => true).catch((err) => {
 		if (err.code === "ENOENT") return false;
@@ -165,7 +170,7 @@ async function createWorktree(projectRoot, taskId, branchName, baseBranch) {
 			recursive: true,
 			force: true
 		});
-		else throw new Error(`Worktree at ${worktreePath} is already registered. Run \`substrate worktrees --cleanup\` to remove it.`);
+		else throw new Error(`Worktree at ${worktreePath} is already registered (branch: ${branchName}).\nThis usually means a prior dispatch escalated and the worktree was preserved for inspection.\nIt may contain uncommitted changes that are NOT on the branch — inspect before removing.\n\nTo remove and re-dispatch:\n  substrate worktrees --cleanup ${taskId}\n\nTo remove all substrate worktrees:\n  substrate worktrees --cleanup`);
 	}
 	const addResult = await spawnGit([
 		"worktree",
@@ -176,9 +181,35 @@ async function createWorktree(projectRoot, taskId, branchName, baseBranch) {
 		baseBranch
 	], { cwd: projectRoot });
 	if (addResult.code !== 0) throw new Error(`git worktree add failed for task "${taskId}": ${addResult.stderr || addResult.stdout}`);
+	await copyFilesToWorktree(projectRoot, worktreePath, copyFiles);
 	return { worktreePath };
 }
 /**
+* Copy files from a source directory into a target worktree.
+*
+* Skips missing files silently (intentional — config like `[".env",
+* ".env.local"]` should not blow up if `.env.local` doesn't exist in the
+* parent checkout). Creates parent directories for nested paths.
+*
+* Exported for testability; not part of the public worktree API.
+*/
+async function copyFilesToWorktree(sourceRoot, worktreePath, files) {
+	if (files.length === 0) return;
+	for (const relativePath of files) {
+		if (path$5.isAbsolute(relativePath) || relativePath.split(path$5.sep).includes("..")) continue;
+		const sourcePath = path$5.join(sourceRoot, relativePath);
+		const destPath = path$5.join(worktreePath, relativePath);
+		try {
+			await access$1(sourcePath);
+		} catch {
+			continue;
+		}
+		const destDir = path$5.dirname(destPath);
+		if (destDir !== worktreePath) await mkdir$1(destDir, { recursive: true });
+		await copyFile(sourcePath, destPath);
+	}
+}
+/**
 * Remove a git worktree by path.
 *
 * Uses `git worktree remove --force` to handle unclean worktrees.
@@ -358,16 +389,19 @@ var GitWorktreeManagerImpl = class {
 	_baseDirectory;
 	_db;
 	_logger;
+	/** v0.20.109: files to copy from project root into each new worktree (e.g. `.env`). */
+	_copyFiles;
 	/** Bound listener references for cleanup in shutdown() */
 	_onTaskReady;
 	_onTaskComplete;
 	_onTaskFailed;
-	constructor(eventBus, projectRoot, baseDirectory = DEFAULT_WORKTREE_BASE, db = null, logger$27) {
+	constructor(eventBus, projectRoot, baseDirectory = DEFAULT_WORKTREE_BASE, db = null, logger$27, copyFiles = []) {
 		this._eventBus = eventBus;
 		this._projectRoot = projectRoot;
 		this._baseDirectory = baseDirectory;
 		this._db = db;
 		this._logger = logger$27 ?? console;
+		this._copyFiles = copyFiles;
 		this._onTaskReady = ({ taskId }) => {
 			this._handleTaskReady(taskId).catch((err) => {
 				this._logger.error({
@@ -431,9 +465,10 @@ var GitWorktreeManagerImpl = class {
 			taskId,
 			branchName,
 			worktreePath,
-			baseBranch
+			baseBranch,
+			copyFiles: this._copyFiles
 		}, "createWorktree");
-		await createWorktree(this._projectRoot, taskId, branchName, baseBranch);
+		await createWorktree(this._projectRoot, taskId, branchName, baseBranch, this._copyFiles);
 		const createdAt = new Date();
 		this._eventBus.emit("worktree:created", {
 			taskId,
@@ -657,7 +692,7 @@ var GitWorktreeManagerImpl = class {
 	}
 };
 function createGitWorktreeManager(options) {
-	return new GitWorktreeManagerImpl(options.eventBus, options.projectRoot, options.baseDirectory, options.db ?? null, options.logger);
+	return new GitWorktreeManagerImpl(options.eventBus, options.projectRoot, options.baseDirectory, options.db ?? null, options.logger, options.copyFiles);
 }
 
 //#endregion
@@ -13279,7 +13314,8 @@ function createImplementationOrchestrator(deps) {
 	const noWorktree = config.noWorktree ?? false;
 	const _worktreeManager = worktreeManager ?? (projectRoot !== void 0 && !noWorktree ? createGitWorktreeManager({
 		eventBus: toCoreEventBus(eventBus),
-		projectRoot
+		projectRoot,
+		...config.worktreeCopyFiles !== void 0 ? { copyFiles: config.worktreeCopyFiles } : {}
 	}) : void 0);
 	const logger$27 = createLogger("implementation-orchestrator");
 	const telemetryAdvisor = db !== void 0 ? createTelemetryAdvisor({ db }) : void 0;
@@ -45599,6 +45635,7 @@ async function runRunAction(options) {
 	let meshUrl;
 	let meshProjectId;
 	let configRetryBudget;
+	let configWorktreeCopyFiles;
 	try {
 		const configSystem = createConfigSystem({ projectConfigDir: dbDir });
 		await configSystem.load();
@@ -45617,6 +45654,10 @@ async function runRunAction(options) {
 			meshProjectId = cfg.telemetry.projectId;
 		}
 		if (typeof cfg.retry_budget === "number") configRetryBudget = cfg.retry_budget;
+		if (Array.isArray(cfg.worktree?.copy_files) && cfg.worktree.copy_files.length > 0) {
+			configWorktreeCopyFiles = [...cfg.worktree.copy_files];
+			logger.info({ copyFiles: configWorktreeCopyFiles }, "Loaded worktree.copy_files from config");
+		}
 	} catch {
 		logger.debug("Config loading skipped — using default token ceilings and telemetry settings");
 	}
@@ -45705,7 +45746,8 @@ async function runRunAction(options) {
 		maxReviewCycles: effectiveMaxReviewCycles,
 		retryBudget: configRetryBudget ?? 2,
 		agentId,
-		...noWorktree === true ? { noWorktree: true } : {}
+		...noWorktree === true ? { noWorktree: true } : {},
+		...configWorktreeCopyFiles !== void 0 ? { worktreeCopyFiles: configWorktreeCopyFiles } : {}
 	});
 	let storyKeys = [...parsedStoryKeys];
 	if (!existsSync$1(dbDir)) mkdirSync$1(dbDir, { recursive: true });
@@ -46257,7 +46299,8 @@ async function runRunAction(options) {
 					...skipVerification === true ? { skipVerification: true } : {},
 					...probeAuthor !== void 0 ? { probeAuthorMode: probeAuthor } : {},
 					probeAuthorStateIntegrating: resolvedProbeAuthorStateIntegrating,
-					...noWorktree === true ? { noWorktree: true } : {}
+					...noWorktree === true ? { noWorktree: true } : {},
+					...configWorktreeCopyFiles !== void 0 ? { worktreeCopyFiles: configWorktreeCopyFiles } : {}
 				},
 				projectRoot,
 				tokenCeilings,
@@ -46475,7 +46518,7 @@ async function runRunAction(options) {
 	}
 }
 async function runFullPipeline(options) {
-	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, projectRoot, events: eventsFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, skipVerification, maxReviewCycles = 2, retryBudget, registry: injectedRegistry, tokenCeilings, stories: explicitStories, telemetryEnabled: fullTelemetryEnabled, telemetryPort: fullTelemetryPort, agentId, meshUrl: fpMeshUrl, meshProjectId: fpMeshProjectId, engineType: fpEngineType, probeAuthor, probeAuthorStateIntegrating: fpProbeAuthorStateIntegrating, noWorktree } = options;
+	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, projectRoot, events: eventsFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, skipVerification, maxReviewCycles = 2, retryBudget, registry: injectedRegistry, tokenCeilings, stories: explicitStories, telemetryEnabled: fullTelemetryEnabled, telemetryPort: fullTelemetryPort, agentId, meshUrl: fpMeshUrl, meshProjectId: fpMeshProjectId, engineType: fpEngineType, probeAuthor, probeAuthorStateIntegrating: fpProbeAuthorStateIntegrating, noWorktree, worktreeCopyFiles: fpWorktreeCopyFiles } = options;
 	if (!existsSync$1(dbDir)) mkdirSync$1(dbDir, { recursive: true });
 	let doltServerFull = null;
 	try {
@@ -46784,7 +46827,8 @@ async function runFullPipeline(options) {
 						...skipVerification === true ? { skipVerification: true } : {},
 						...probeAuthor !== void 0 ? { probeAuthorMode: probeAuthor } : {},
 						...fpProbeAuthorStateIntegrating !== void 0 ? { probeAuthorStateIntegrating: fpProbeAuthorStateIntegrating } : {},
-						...noWorktree === true ? { noWorktree: true } : {}
+						...noWorktree === true ? { noWorktree: true } : {},
+						...fpWorktreeCopyFiles !== void 0 ? { worktreeCopyFiles: fpWorktreeCopyFiles } : {}
 					},
 					projectRoot,
 					tokenCeilings,
@@ -46954,7 +46998,7 @@ async function runFullPipeline(options) {
 */
 async function emitPreDispatchVersionAdvisory(currentVersion) {
 	if (process.env["SUBSTRATE_NO_UPDATE_CHECK"] === "1") return;
-	const { createVersionManager } = await import("./version-manager-impl-brvj1EYW.js");
+	const { createVersionManager } = await import("./version-manager-impl-DyE9bMVG.js");
 	const vm = createVersionManager();
 	const result = await vm.checkForUpdates(true);
 	const gap = classifyVersionGap(currentVersion, result.latestVersion);
@@ -47051,4 +47095,4 @@ function registerRunCommand(program, version = "0.0.0", projectRoot = process.cw
 
 //#endregion
 export { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GLOBSTAR$1 as GLOBSTAR, GitClient, GrammarLoader, Minimatch$1 as Minimatch, Minipass, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createGitWorktreeManager, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, escape$1 as escape, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, normalizeGraphSummaryToStatus, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runProbeAuthor, runRunAction, runSolutioningPhase, unescape$1 as unescape, validateStopAfterFromConflict, wireNdjsonEmitter };
-//# sourceMappingURL=run-CIMNjDBH.js.map
+//# sourceMappingURL=run-DdTN1lge.js.map

package/dist/src/modules/recovery-engine/index.d.ts

@@ -1,4 +1,4 @@
-import { CoreEvents, DatabaseAdapter, TypedEventBus } from "../../../index-C8F4ACfC.js";
+import { CoreEvents, DatabaseAdapter, TypedEventBus } from "../../../index-DYzIw89v.js";
 import { z } from "zod";
 
 //#region packages/sdlc/dist/verification/findings.d.ts

package/dist/{upgrade-7KujpKbf.js → upgrade-Bpd6pUrr.js}

@@ -1,4 +1,4 @@
-import { createVersionManager } from "./dist-Dm37IPMW.js";
+import { createVersionManager } from "./dist-CQ9ZuL2a.js";
 import { execSync, spawn } from "child_process";
 import * as readline from "readline";
 
@@ -123,4 +123,4 @@ function registerUpgradeCommand(program) {
 
 //#endregion
 export { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand };
-//# sourceMappingURL=upgrade-7KujpKbf.js.map
+//# sourceMappingURL=upgrade-Bpd6pUrr.js.map

package/dist/{upgrade-fViYOn8u.js → upgrade-DoWjPygF.js}

@@ -1,5 +1,5 @@
-import "./dist-Dm37IPMW.js";
+import "./dist-CQ9ZuL2a.js";
 import "./version-manager-impl-qFBiO4Eh.js";
-import { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand } from "./upgrade-7KujpKbf.js";
+import { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand } from "./upgrade-Bpd6pUrr.js";
 
 export { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand };

package/dist/{version-manager-impl-brvj1EYW.js → version-manager-impl-DyE9bMVG.js}

@@ -1,4 +1,4 @@
-import { VersionManagerImpl, createVersionManager } from "./dist-Dm37IPMW.js";
+import { VersionManagerImpl, createVersionManager } from "./dist-CQ9ZuL2a.js";
 import "./version-manager-impl-qFBiO4Eh.js";
 
 export { createVersionManager };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.20.108",
+  "version": "0.20.110",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",

package/dist/adapter-registry-5zXxdGZq.js

@@ -1,4 +0,0 @@
-import { AdapterRegistry } from "./dist-Dm37IPMW.js";
-import "./adapter-registry-DIcrxjH8.js";
-
-export { AdapterRegistry };