substrate-ai 0.20.36 → 0.20.39

package/dist/cli/index.js

@@ -1,26 +1,26 @@
 #!/usr/bin/env node
-import { FileStateStore, RunManifest, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, ZERO_FINDING_COUNTS, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, parseRuntimeProbes, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts } from "../health-BAcRfZ4s.js";
+import { FileStateStore, RunManifest, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, ZERO_FINDING_COUNTS, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, parseRuntimeProbes, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts } from "../health-R9GiVIiQ.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-BnMsd9hC.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, 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-VcMmfo2w.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-YBY2vrF4.js";
-import "../errors-DSGhhrgv.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, runProbeAuthor, runSolutioningPhase, validateStopAfterFromConflict } from "../run-Dm70k8bR.js";
+import "../errors-CogpxBUg.js";
 import "../routing-CcBOCuC9.js";
 import "../decisions-C0pz9Clx.js";
 import "../version-manager-impl-BmOWu8ml.js";
-import { registerUpgradeCommand } from "../upgrade-D3NuTkSL.js";
+import { registerUpgradeCommand } from "../upgrade-CF4__LCr.js";
 import { Command } from "commander";
 import { fileURLToPath } from "url";
 import { dirname, join, resolve } from "path";
 import { access, mkdir, readFile, writeFile } from "fs/promises";
 import yaml from "js-yaml";
-import { existsSync, readFileSync } from "node:fs";
+import { existsSync, readFileSync, writeFileSync } from "node:fs";
 import { execFile, spawn } from "node:child_process";
 import * as path$3 from "node:path";
 import * as path$2 from "node:path";
 import * as path$1 from "node:path";
-import { basename as basename$1, join as join$1 } from "node:path";
+import { basename as basename$1, join as join$1, resolve as resolve$1 } from "node:path";
 import { randomUUID } from "node:crypto";
 import { z } from "zod";
 import * as fs from "node:fs/promises";
@@ -333,12 +333,12 @@ var GitWorktreeManagerImpl = class {
 	_onTaskReady;
 	_onTaskComplete;
 	_onTaskFailed;
-	constructor(eventBus, projectRoot, baseDirectory = DEFAULT_WORKTREE_BASE, db = null, logger$16) {
+	constructor(eventBus, projectRoot, baseDirectory = DEFAULT_WORKTREE_BASE, db = null, logger$17) {
 		this._eventBus = eventBus;
 		this._projectRoot = projectRoot;
 		this._baseDirectory = baseDirectory;
 		this._db = db;
-		this._logger = logger$16 ?? console;
+		this._logger = logger$17 ?? console;
 		this._onTaskReady = ({ taskId }) => {
 			this._handleTaskReady(taskId).catch((err) => {
 				this._logger.error({
@@ -642,14 +642,14 @@ var RecommendationEngine = class {
 	_filters;
 	_historyDays;
 	_logger;
-	constructor(monitorDb, config = {}, logger$16) {
+	constructor(monitorDb, config = {}, logger$17) {
 		this._monitorDb = monitorDb;
 		this._filters = {
 			threshold_percentage: config.recommendation_threshold_percentage ?? 5,
 			min_sample_size: config.min_sample_size ?? 10
 		};
 		this._historyDays = config.recommendation_history_days ?? 90;
-		this._logger = logger$16 ?? console;
+		this._logger = logger$17 ?? console;
 	}
 	generateRecommendations() {
 		const sinceDate = new Date(Date.now() - this._historyDays * 24 * 60 * 60 * 1e3).toISOString();
@@ -1739,7 +1739,7 @@ function buildStackAwareDevNotes(profile) {
 
 //#endregion
 //#region src/cli/commands/init.ts
-const logger$15 = createLogger("init");
+const logger$16 = createLogger("init");
 const __dirname = dirname(new URL(import.meta.url).pathname);
 const SCAFFOLD_VERSION_REGEX = /<!-- substrate:version=([\d.]+) -->/;
 /**
@@ -1780,7 +1780,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 	const version = resolveBmadMethodVersion();
 	if (force && bmadExists) process.stderr.write(`Warning: Replacing existing _bmad/ framework with bmad-method@${version}\n`);
 	process.stdout.write(`Scaffolding BMAD framework from bmad-method@${version}\n`);
-	logger$15.info({
+	logger$16.info({
 		version,
 		dest: bmadDest
 	}, "Scaffolding BMAD framework");
@@ -1790,7 +1790,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 			const destDir = join(bmadDest, dir);
 			mkdirSync$1(destDir, { recursive: true });
 			cpSync(srcDir, destDir, { recursive: true });
-			logger$15.info({
+			logger$16.info({
 				dir,
 				dest: destDir
 			}, "Scaffolded BMAD framework directory");
@@ -1809,7 +1809,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 			"document_output_language: English"
 		].join("\n") + "\n";
 		await writeFile(configFile, configStub, "utf8");
-		logger$15.info({ configFile }, "Generated _bmad/_config/config.yaml stub");
+		logger$16.info({ configFile }, "Generated _bmad/_config/config.yaml stub");
 	}
 }
 const CLAUDE_MD_START_MARKER = "<!-- substrate:start -->";
@@ -1824,7 +1824,7 @@ async function scaffoldClaudeMd(projectRoot, profile) {
 	try {
 		sectionContent = await readFile(templatePath, "utf8");
 	} catch {
-		logger$15.warn({ templatePath }, "CLAUDE.md substrate section template not found; skipping");
+		logger$16.warn({ templatePath }, "CLAUDE.md substrate section template not found; skipping");
 		return;
 	}
 	const substrateVersion = readSubstrateVersion(pkgRoot);
@@ -1860,7 +1860,7 @@ async function scaffoldClaudeMd(projectRoot, profile) {
 		else newContent = updatedExisting;
 	}
 	await writeFile(claudeMdPath, newContent, "utf8");
-	logger$15.info({ claudeMdPath }, "Wrote substrate section to CLAUDE.md");
+	logger$16.info({ claudeMdPath }, "Wrote substrate section to CLAUDE.md");
 }
 async function scaffoldAgentsMd(projectRoot, profile) {
 	const agentsMdPath = join(projectRoot, "AGENTS.md");
@@ -1872,7 +1872,7 @@ async function scaffoldAgentsMd(projectRoot, profile) {
 	try {
 		sectionContent = await readFile(templatePath, "utf8");
 	} catch {
-		logger$15.warn({ templatePath }, "AGENTS.md substrate section template not found; skipping");
+		logger$16.warn({ templatePath }, "AGENTS.md substrate section template not found; skipping");
 		return;
 	}
 	const substrateVersion = readSubstrateVersion(pkgRoot);
@@ -1893,7 +1893,7 @@ async function scaffoldAgentsMd(projectRoot, profile) {
 		newContent = existingContent + separator + sectionContent;
 	}
 	await writeFile(agentsMdPath, newContent, "utf8");
-	logger$15.info({ agentsMdPath }, "Wrote substrate section to AGENTS.md");
+	logger$16.info({ agentsMdPath }, "Wrote substrate section to AGENTS.md");
 }
 async function scaffoldGeminiMd(projectRoot, profile) {
 	const geminiMdPath = join(projectRoot, "GEMINI.md");
@@ -1905,7 +1905,7 @@ async function scaffoldGeminiMd(projectRoot, profile) {
 	try {
 		sectionContent = await readFile(templatePath, "utf8");
 	} catch {
-		logger$15.warn({ templatePath }, "GEMINI.md substrate section template not found; skipping");
+		logger$16.warn({ templatePath }, "GEMINI.md substrate section template not found; skipping");
 		return;
 	}
 	const substrateVersion = readSubstrateVersion(pkgRoot);
@@ -1926,7 +1926,7 @@ async function scaffoldGeminiMd(projectRoot, profile) {
 		newContent = existingContent + separator + sectionContent;
 	}
 	await writeFile(geminiMdPath, newContent, "utf8");
-	logger$15.info({ geminiMdPath }, "Wrote substrate section to GEMINI.md");
+	logger$16.info({ geminiMdPath }, "Wrote substrate section to GEMINI.md");
 }
 async function scaffoldStatuslineScript(projectRoot) {
 	const pkgRoot = findPackageRoot(__dirname);
@@ -1937,7 +1937,7 @@ async function scaffoldStatuslineScript(projectRoot) {
 	try {
 		content = await readFile(templatePath, "utf8");
 	} catch {
-		logger$15.warn({ templatePath }, "statusline.sh template not found; skipping");
+		logger$16.warn({ templatePath }, "statusline.sh template not found; skipping");
 		return;
 	}
 	const claudeDir = join(projectRoot, ".claude");
@@ -1945,7 +1945,7 @@ async function scaffoldStatuslineScript(projectRoot) {
 	mkdirSync$1(claudeDir, { recursive: true });
 	await writeFile(statuslinePath, content, "utf8");
 	chmodSync(statuslinePath, 493);
-	logger$15.info({ statuslinePath }, "Wrote .claude/statusline.sh");
+	logger$16.info({ statuslinePath }, "Wrote .claude/statusline.sh");
 }
 async function scaffoldClaudeSettings(projectRoot) {
 	const claudeDir = join(projectRoot, ".claude");
@@ -1961,7 +1961,7 @@ async function scaffoldClaudeSettings(projectRoot) {
 	if (!merged["$schema"]) merged["$schema"] = "https://json.schemastore.org/claude-code-settings.json";
 	mkdirSync$1(claudeDir, { recursive: true });
 	await writeFile(settingsPath, JSON.stringify(merged, null, 2) + "\n", "utf8");
-	logger$15.info({ settingsPath }, "Wrote substrate settings to .claude/settings.json");
+	logger$16.info({ settingsPath }, "Wrote substrate settings to .claude/settings.json");
 }
 function resolveBmadMethodInstallerLibPath(fromDir = __dirname) {
 	try {
@@ -2033,7 +2033,7 @@ async function compileBmadAgents(bmadDir) {
 				writeFileSync$1(mdPath, result.xml, "utf-8");
 				compiled++;
 			} catch (compileErr) {
-				logger$15.debug({
+				logger$16.debug({
 					err: compileErr,
 					file
 				}, "Failed to compile agent YAML");
@@ -2180,9 +2180,9 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		const _require = createRequire(join(__dirname, "synthetic.js"));
 		try {
 			const compiledCount = await compileBmadAgents(bmadDir);
-			if (compiledCount > 0) logger$15.info({ compiledCount }, "Compiled agent YAML files to MD");
+			if (compiledCount > 0) logger$16.info({ compiledCount }, "Compiled agent YAML files to MD");
 		} catch (compileErr) {
-			logger$15.warn({ err: compileErr }, "Agent compilation failed; agent commands may be incomplete");
+			logger$16.warn({ err: compileErr }, "Agent compilation failed; agent commands may be incomplete");
 		}
 		const resolveExport = (mod, name) => {
 			if (typeof mod[name] === "function") return mod[name];
@@ -2196,7 +2196,7 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		const manifestGenPath = join(installerLibPath, "core", "manifest-generator.js");
 		const pathUtilsPath = join(installerLibPath, "ide", "shared", "path-utils.js");
 		if (!existsSync$1(agentGenPath)) {
-			logger$15.info("bmad-method generators not available (requires bmad-method with agent/workflow/task-tool generators)");
+			logger$16.info("bmad-method generators not available (requires bmad-method with agent/workflow/task-tool generators)");
 			return;
 		}
 		const agentMod = _require(agentGenPath);
@@ -2206,11 +2206,11 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		if (existsSync$1(workflowGenPath)) {
 			const workflowMod = _require(workflowGenPath);
 			WorkflowCommandGenerator = resolveExport(workflowMod, "WorkflowCommandGenerator");
-		} else logger$15.info("bmad-method workflow-command-generator not available; will try skill-based installation");
+		} else logger$16.info("bmad-method workflow-command-generator not available; will try skill-based installation");
 		if (existsSync$1(taskToolGenPath)) {
 			const taskToolMod = _require(taskToolGenPath);
 			TaskToolCommandGenerator = resolveExport(taskToolMod, "TaskToolCommandGenerator");
-		} else logger$15.info("bmad-method task-tool-command-generator not available; will try skill-based installation");
+		} else logger$16.info("bmad-method task-tool-command-generator not available; will try skill-based installation");
 		let ManifestGenerator = null;
 		if (existsSync$1(manifestGenPath)) {
 			const manifestMod = _require(manifestGenPath);
@@ -2242,7 +2242,7 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 			const manifestGen = new ManifestGenerator();
 			await manifestGen.generateManifests(bmadDir, allModules, [], { ides: ["claude-code"] });
 		} catch (manifestErr) {
-			logger$15.warn({ err: manifestErr }, "ManifestGenerator failed; workflow/task commands may be incomplete");
+			logger$16.warn({ err: manifestErr }, "ManifestGenerator failed; workflow/task commands may be incomplete");
 		}
 		const commandsDir = join(projectRoot, ".claude", "commands");
 		mkdirSync$1(commandsDir, { recursive: true });
@@ -2270,7 +2270,7 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		const total = agentCount + workflowCount + taskToolCount + skillCount;
 		if (outputFormat !== "json") if (skillCount > 0) process.stdout.write(`Generated ${String(total)} Claude Code commands (${String(agentCount)} agents, ${String(skillCount)} skills)\n`);
 		else process.stdout.write(`Generated ${String(total)} Claude Code commands (${String(agentCount)} agents, ${String(workflowCount)} workflows, ${String(taskToolCount)} tasks/tools)\n`);
-		logger$15.info({
+		logger$16.info({
 			agentCount,
 			workflowCount,
 			taskToolCount,
@@ -2281,7 +2281,7 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 	} catch (err) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat !== "json") process.stderr.write(`Warning: .claude/commands/ generation failed: ${msg}\n`);
-		logger$15.warn({ err }, "scaffoldClaudeCommands failed; init continues");
+		logger$16.warn({ err }, "scaffoldClaudeCommands failed; init continues");
 	}
 }
 /**
@@ -2310,7 +2310,7 @@ function syncCommandsAsPrompts(commandsDir, promptsDir, ownershipPrefixes, nameP
 			unlinkSync$1(join(promptsDir, entry.name));
 		}
 	} catch (err) {
-		logger$15.debug({
+		logger$16.debug({
 			err,
 			promptsDir
 		}, "Failed to prune stale prompts");
@@ -2352,7 +2352,7 @@ function syncSkillsToTarget(srcSkillsDir, destSkillsDir, ownershipPrefixes, name
 			});
 		}
 	} catch (err) {
-		logger$15.debug({
+		logger$16.debug({
 			err,
 			destSkillsDir
 		}, "Failed to prune stale skills");
@@ -2395,16 +2395,16 @@ function scaffoldCodexProject(projectRoot, outputFormat) {
 		const skillCount = syncSkillsToTarget(claudeSkillsDir, codexSkillsDir, PROJECT_OWNERSHIP_PREFIXES, "");
 		const total = promptCount + skillCount;
 		if (outputFormat !== "json" && total > 0) process.stdout.write(`Generated ${String(total)} Codex artifacts (${String(promptCount)} prompts, ${String(skillCount)} skills)\n`);
-		if (total > 0) logger$15.info({
+		if (total > 0) logger$16.info({
 			promptCount,
 			skillCount,
 			codexDir
 		}, "Generated .codex/");
-		else logger$15.debug({ codexDir }, "No Codex artifacts generated; source Claude content not found");
+		else logger$16.debug({ codexDir }, "No Codex artifacts generated; source Claude content not found");
 	} catch (err) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat !== "json") process.stderr.write(`Warning: .codex/ generation failed: ${msg}\n`);
-		logger$15.warn({ err }, "scaffoldCodexProject failed; init continues");
+		logger$16.warn({ err }, "scaffoldCodexProject failed; init continues");
 	}
 }
 /**
@@ -2430,16 +2430,16 @@ function scaffoldCodexUser(projectRoot, homeDir, outputFormat) {
 		const skillCount = syncSkillsToTarget(claudeSkillsDir, userSkillsDir, ["substrate-"], "substrate-");
 		const total = promptCount + skillCount;
 		if (outputFormat !== "json" && total > 0) process.stdout.write(`Installed ${String(total)} Codex artifacts to ${userCodexDir} (${String(promptCount)} prompts, ${String(skillCount)} skills)\n`);
-		if (total > 0) logger$15.info({
+		if (total > 0) logger$16.info({
 			promptCount,
 			skillCount,
 			userCodexDir
 		}, "Installed user-scope Codex content");
-		else logger$15.debug({ userCodexDir }, "No user-scope Codex content installed; source Claude content not found");
+		else logger$16.debug({ userCodexDir }, "No user-scope Codex content installed; source Claude content not found");
 	} catch (err) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat !== "json") process.stderr.write(`Warning: user-scope Codex install failed: ${msg}\n`);
-		logger$15.warn({ err }, "scaffoldCodexUser failed; init continues");
+		logger$16.warn({ err }, "scaffoldCodexUser failed; init continues");
 	}
 }
 const PROVIDER_DEFAULTS = DEFAULT_CONFIG.providers;
@@ -2559,7 +2559,7 @@ async function runInitAction(options) {
 			discoveryReport = await registry.discoverAndRegister();
 		} catch (err) {
 			const message = err instanceof Error ? err.message : String(err);
-			logger$15.error({ err }, "Adapter discovery failed");
+			logger$16.error({ err }, "Adapter discovery failed");
 			if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, `Adapter discovery failed: ${message}`) + "\n");
 			else process.stderr.write(`  Error: adapter discovery failed — ${message}\n`);
 			return INIT_EXIT_ERROR;
@@ -2602,7 +2602,7 @@ async function runInitAction(options) {
 		try {
 			detectedProfile = await detectProjectProfile(dbRoot);
 		} catch (err) {
-			logger$15.warn({ err }, "Project profile detection failed; skipping");
+			logger$16.warn({ err }, "Project profile detection failed; skipping");
 		}
 		if (detectedProfile === null) {
 			if (outputFormat !== "json") process.stdout.write("  No project stack detected. Create .substrate/project-profile.yaml manually to enable polyglot support.\n");
@@ -2636,12 +2636,12 @@ async function runInitAction(options) {
 				return INIT_EXIT_ERROR;
 			}
 			if (force && existsSync$1(localManifest)) {
-				logger$15.info({ pack: packName }, "Replacing existing pack with bundled version");
+				logger$16.info({ pack: packName }, "Replacing existing pack with bundled version");
 				process.stderr.write(`Warning: Replacing existing pack '${packName}' with bundled version\n`);
 			}
 			mkdirSync$1(dirname(packPath), { recursive: true });
 			cpSync(bundledPackPath, packPath, { recursive: true });
-			logger$15.info({
+			logger$16.info({
 				pack: packName,
 				dest: packPath
 			}, "Scaffolded methodology pack");
@@ -2693,10 +2693,10 @@ async function runInitAction(options) {
 			if (missing.length > 0) {
 				const block = "\n# Substrate runtime files\n" + missing.join("\n") + "\n";
 				appendFileSync(gitignorePath, block);
-				logger$15.info({ entries: missing }, "Added substrate runtime files to .gitignore");
+				logger$16.info({ entries: missing }, "Added substrate runtime files to .gitignore");
 			}
 		} catch (err) {
-			logger$15.debug({ err }, "Could not update .gitignore (non-fatal)");
+			logger$16.debug({ err }, "Could not update .gitignore (non-fatal)");
 		}
 		const doltMode = options.doltMode ?? "auto";
 		let doltInitialized = false;
@@ -2713,7 +2713,7 @@ async function runInitAction(options) {
 					process.stderr.write(`${err.message}\n`);
 					return INIT_EXIT_ERROR;
 				}
-				logger$15.debug("Dolt not installed, skipping auto-init");
+				logger$16.debug("Dolt not installed, skipping auto-init");
 			} else {
 				const msg = err instanceof Error ? err.message : String(err);
 				if (doltMode === "force") {
@@ -2723,7 +2723,7 @@ async function runInitAction(options) {
 				process.stderr.write(`⚠  Dolt state store initialization failed: ${msg}\n   Pipeline metrics, cost tracking, and health monitoring will not persist.\n   Fix the issue and re-run: substrate init --dolt\n`);
 			}
 		}
-		else logger$15.debug("Dolt step was skipped (--no-dolt)");
+		else logger$16.debug("Dolt step was skipped (--no-dolt)");
 		const successMsg = `Pack '${packName}' and database initialized successfully at ${dbPath}`;
 		if (outputFormat === "json") process.stdout.write(formatOutput({
 			pack: packName,
@@ -2761,7 +2761,7 @@ async function runInitAction(options) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, msg) + "\n");
 		else process.stderr.write(`Error: ${msg}\n`);
-		logger$15.error({ err }, "init failed");
+		logger$16.error({ err }, "init failed");
 		return INIT_EXIT_ERROR;
 	}
 }
@@ -2785,7 +2785,7 @@ function registerInitCommand(program, _version, registry) {
 
 //#endregion
 //#region src/cli/commands/config.ts
-const logger$14 = createLogger("config-cmd");
+const logger$15 = createLogger("config-cmd");
 const CONFIG_EXIT_SUCCESS = 0;
 const CONFIG_EXIT_ERROR = 1;
 const CONFIG_EXIT_INVALID = 2;
@@ -2811,7 +2811,7 @@ async function runConfigShow(opts = {}) {
 			return CONFIG_EXIT_INVALID;
 		}
 		const message = err instanceof Error ? err.message : String(err);
-		logger$14.error({ err }, "Failed to load configuration");
+		logger$15.error({ err }, "Failed to load configuration");
 		process.stderr.write(`  Error loading configuration: ${message}\n`);
 		return CONFIG_EXIT_ERROR;
 	}
@@ -2885,7 +2885,7 @@ async function runConfigExport(opts = {}) {
 			return CONFIG_EXIT_INVALID;
 		}
 		const message = err instanceof Error ? err.message : String(err);
-		logger$14.error({ err }, "Failed to load configuration");
+		logger$15.error({ err }, "Failed to load configuration");
 		process.stderr.write(`Error loading configuration: ${message}\n`);
 		return CONFIG_EXIT_ERROR;
 	}
@@ -3039,7 +3039,7 @@ function registerConfigCommand(program, _version) {
 
 //#endregion
 //#region src/cli/commands/resume.ts
-const logger$13 = createLogger("resume-cmd");
+const logger$14 = createLogger("resume-cmd");
 /**
 * Map internal orchestrator phase names to pipeline event protocol phase names.
 */
@@ -3131,15 +3131,15 @@ async function runResumeAction(options) {
 				const manifestStories = manifestData.cli_flags["stories"] ?? manifestData.story_scope;
 				if (Array.isArray(manifestStories) && manifestStories.length > 0) {
 					scopedStories = manifestStories;
-					logger$13.debug({
+					logger$14.debug({
 						runId,
 						stories: scopedStories
 					}, "resume scope loaded from manifest");
 				}
 			} catch {
-				logger$13.debug({ runId }, "manifest read failed in resume — using legacy config_json scope");
+				logger$14.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");
+			else logger$14.debug({ runId }, "Run manifest not found for scope preservation — using legacy config_json scope");
 		}
 		return runFullPipelineFromPhase({
 			packName,
@@ -3162,7 +3162,7 @@ async function runResumeAction(options) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, msg) + "\n");
 		else process.stderr.write(`Error: ${msg}\n`);
-		logger$13.error({ err }, "auto resume failed");
+		logger$14.error({ err }, "auto resume failed");
 		return 1;
 	} finally {
 		try {
@@ -3411,11 +3411,11 @@ async function runFullPipelineFromPhase(options) {
 								output_tokens: output,
 								cost_usd: costUsd
 							}).catch((err) => {
-								logger$13.warn({ err }, "Failed to record token usage");
+								logger$14.warn({ err }, "Failed to record token usage");
 							});
 						}
 					} catch (err) {
-						logger$13.warn({ err }, "Failed to record token usage");
+						logger$14.warn({ err }, "Failed to record token usage");
 					}
 				});
 				const storyKeys = await resolveStoryKeys(adapter, projectRoot, {
@@ -3484,7 +3484,7 @@ async function runFullPipelineFromPhase(options) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, msg) + "\n");
 		else process.stderr.write(`Error: ${msg}\n`);
-		logger$13.error({ err }, "pipeline from phase failed");
+		logger$14.error({ err }, "pipeline from phase failed");
 		return 1;
 	} finally {
 		try {
@@ -3513,7 +3513,7 @@ function registerResumeCommand(program, _version = "0.0.0", projectRoot = proces
 
 //#endregion
 //#region src/cli/commands/status.ts
-const logger$12 = createLogger("status-cmd");
+const logger$13 = createLogger("status-cmd");
 /**
 * Map a manifest per-story status string to the appropriate WorkGraphCounts bucket.
 * Unknown strings are treated as `inProgress` (safe default).
@@ -3625,9 +3625,9 @@ async function runStatusAction(options) {
 			const manifestData = await resolvedManifest.read();
 			manifestPerStoryState = manifestData.per_story_state;
 			workGraph = buildWorkGraphFromManifest(manifestData.per_story_state);
-			logger$12.debug({ runId: run?.id }, "status: workGraph built from manifest per_story_state");
+			logger$13.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");
+			logger$13.debug({ runId: run?.id }, "status: manifest read failed — falling back to wg_stories");
 		}
 		if (workGraph === void 0) try {
 			const wgRepo = new WorkGraphRepository(adapter);
@@ -3664,10 +3664,10 @@ async function runStatusAction(options) {
 				};
 			}
 		} catch (err) {
-			logger$12.debug({ err }, "Work graph query failed, continuing without work graph data");
+			logger$13.debug({ err }, "Work graph query failed, continuing without work graph data");
 		}
 		if (run === void 0) {
-			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-DvAr7miW.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-C-ZrHJwL.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -3697,7 +3697,7 @@ async function runStatusAction(options) {
 		if (stateStore) try {
 			storeStories = await stateStore.queryStories({});
 		} catch (err) {
-			logger$12.debug({ err }, "StateStore query failed, continuing without store data");
+			logger$13.debug({ err }, "StateStore query failed, continuing without store data");
 		}
 		if (outputFormat === "json") {
 			const statusOutput = buildPipelineStatusOutput(run, tokenSummary, decisionsCount, storiesCount);
@@ -3825,7 +3825,7 @@ async function runStatusAction(options) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, msg) + "\n");
 		else process.stderr.write(`Error: ${msg}\n`);
-		logger$12.error({ err }, "status action failed");
+		logger$13.error({ err }, "status action failed");
 		return 1;
 	} finally {
 		try {
@@ -4172,7 +4172,7 @@ Analyze thoroughly and return ONLY the JSON array with no additional text.`;
 
 //#endregion
 //#region src/cli/commands/amend.ts
-const logger$11 = createLogger("amend-cmd");
+const logger$12 = createLogger("amend-cmd");
 /**
 * Detect and apply supersessions after a phase completes in an amendment run.
 *
@@ -4203,7 +4203,7 @@ async function runPostPhaseSupersessionDetection(adapter, amendmentRunId, curren
 			});
 		} catch (err) {
 			const msg = err instanceof Error ? err.message : String(err);
-			logger$11.warn({
+			logger$12.warn({
 				err,
 				originalId: parentMatch.id,
 				supersedingId: newDec.id
@@ -4340,7 +4340,7 @@ async function runAmendAction(options) {
 		for (let i = startIdx; i < phaseOrder.length; i++) {
 			const currentPhase = phaseOrder[i];
 			const amendmentContext = handler.loadContextForPhase(currentPhase);
-			logger$11.info({
+			logger$12.info({
 				phase: currentPhase,
 				amendmentContextLen: amendmentContext.length
 			}, "Amendment context loaded for phase");
@@ -4461,7 +4461,7 @@ async function runAmendAction(options) {
 	} catch (err) {
 		const msg = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${msg}\n`);
-		logger$11.error({ err }, "amend failed");
+		logger$12.error({ err }, "amend failed");
 		return 1;
 	} finally {
 		try {
@@ -4617,7 +4617,7 @@ function defaultSupervisorDeps() {
 				if (cached === null) {
 					const { AdapterRegistry: AR } = await import(
 						/* @vite-ignore */
-						"../adapter-registry-Cu2eLuau.js"
+						"../adapter-registry-CcahKCG1.js"
 );
 					cached = new AR();
 					await cached.discoverAndRegister();
@@ -5184,11 +5184,11 @@ async function runSupervisorAction(options, deps = {}) {
 						try {
 							const { createExperimenter } = await import(
 								/* @vite-ignore */
-								"../experimenter-CN8PhRbv.js"
+								"../experimenter-2KGF4bLj.js"
 );
 							const { getLatestRun: getLatest } = await import(
 								/* @vite-ignore */
-								"../decisions-DlPFWRDm.js"
+								"../decisions-UFV5YFaW.js"
 );
 							const expAdapter = createDatabaseAdapter({
 								backend: "auto",
@@ -5198,7 +5198,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-__o2iU0w.js"
+									"../run-CL1C4M2f.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -5448,7 +5448,7 @@ function registerSupervisorCommand(program, _version = "0.0.0", projectRoot = pr
 
 //#endregion
 //#region src/cli/commands/metrics.ts
-const logger$10 = createLogger("metrics-cmd");
+const logger$11 = createLogger("metrics-cmd");
 async function openTelemetryAdapter(basePath) {
 	try {
 		const adapter = createDatabaseAdapter({
@@ -5730,7 +5730,7 @@ async function runMetricsAction(options) {
 			const routingConfigPath = join(dbDir, "routing.yml");
 			let routingConfig = null;
 			if (existsSync$1(routingConfigPath)) try {
-				const { loadModelRoutingConfig } = await import("../routing-sauIk945.js");
+				const { loadModelRoutingConfig } = await import("../routing-BNGNSI0w.js");
 				routingConfig = loadModelRoutingConfig(routingConfigPath);
 			} catch {}
 			if (routingConfig === null) routingConfig = {
@@ -5814,7 +5814,7 @@ async function runMetricsAction(options) {
 					}
 				}
 			} catch (err) {
-				logger$10.debug({ err }, "getScenarioResultsForRun failed");
+				logger$11.debug({ err }, "getScenarioResultsForRun failed");
 			}
 			if (rows.length === 0) {
 				const msg = `No factory run found with id: ${run}`;
@@ -5850,7 +5850,7 @@ async function runMetricsAction(options) {
 						}
 					}
 				} catch (err) {
-					logger$10.debug({ err }, "getTwinRunsForRun failed — twin_runs table may not exist yet");
+					logger$11.debug({ err }, "getTwinRunsForRun failed — twin_runs table may not exist yet");
 				}
 			}
 			return 0;
@@ -5860,7 +5860,7 @@ async function runMetricsAction(options) {
 			try {
 				factoryRuns$1 = await getFactoryRunSummaries(adapter, limit);
 			} catch (err) {
-				logger$10.debug({ err }, "getFactoryRunSummaries failed in factory-only mode");
+				logger$11.debug({ err }, "getFactoryRunSummaries failed in factory-only mode");
 			}
 			if (outputFormat === "json") process.stdout.write(formatOutput({ graph_runs: factoryRuns$1 }, "json", true) + "\n");
 			else if (factoryRuns$1.length === 0) process.stdout.write("No factory runs recorded yet.\n");
@@ -5921,7 +5921,7 @@ async function runMetricsAction(options) {
 			doltMetrics = await stateStore.queryMetrics(doltFilter);
 			await stateStore.close();
 		} catch (doltErr) {
-			logger$10.warn({ err: doltErr }, "StateStore query failed — falling back to SQLite metrics only");
+			logger$11.warn({ err: doltErr }, "StateStore query failed — falling back to SQLite metrics only");
 		}
 		const storyMetricDecisions = await getDecisionsByCategory(adapter, STORY_METRICS);
 		const storyMetrics = storyMetricDecisions.map((d) => {
@@ -5977,7 +5977,7 @@ async function runMetricsAction(options) {
 		try {
 			factoryRuns = await getFactoryRunSummaries(adapter, limit);
 		} catch (err) {
-			logger$10.debug({ err }, "getFactoryRunSummaries failed — table may not exist in older databases");
+			logger$11.debug({ err }, "getFactoryRunSummaries failed — table may not exist in older databases");
 		}
 		if (outputFormat === "json") {
 			const runsWithBreakdown = runs.map((run$1) => ({
@@ -6091,7 +6091,7 @@ async function runMetricsAction(options) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, msg) + "\n");
 		else process.stderr.write(`Error: ${msg}\n`);
-		logger$10.error({ err }, "metrics action failed");
+		logger$11.error({ err }, "metrics action failed");
 		return 1;
 	} finally {
 		try {
@@ -6291,7 +6291,7 @@ function registerMigrateCommand(program) {
 function getLatestSessionId(_adapter) {
 	return null;
 }
-const logger$9 = createLogger("cost-cmd");
+const logger$10 = createLogger("cost-cmd");
 const COST_EXIT_SUCCESS = 0;
 const COST_EXIT_ERROR = 1;
 /**
@@ -6535,7 +6535,7 @@ async function runCostAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$9.error({ err }, "runCostAction failed");
+		logger$10.error({ err }, "runCostAction failed");
 		return COST_EXIT_ERROR;
 	} finally {
 		if (adapter !== null) try {
@@ -6569,7 +6569,7 @@ function registerCostCommand(program, version = "0.0.0", projectRoot = process.c
 
 //#endregion
 //#region src/cli/commands/monitor.ts
-const logger$8 = createLogger("monitor-cmd");
+const logger$9 = createLogger("monitor-cmd");
 const MONITOR_EXIT_SUCCESS = 0;
 const MONITOR_EXIT_ERROR = 1;
 /**
@@ -6772,7 +6772,7 @@ async function runMonitorReportAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$8.error({ err }, "runMonitorReportAction failed");
+		logger$9.error({ err }, "runMonitorReportAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -6834,7 +6834,7 @@ async function runMonitorStatusAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$8.error({ err }, "runMonitorStatusAction failed");
+		logger$9.error({ err }, "runMonitorStatusAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -6869,7 +6869,7 @@ async function runMonitorResetAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$8.error({ err }, "runMonitorResetAction failed");
+		logger$9.error({ err }, "runMonitorResetAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -6917,7 +6917,7 @@ async function runMonitorRecommendationsAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$8.error({ err }, "runMonitorRecommendationsAction failed");
+		logger$9.error({ err }, "runMonitorRecommendationsAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -6995,7 +6995,7 @@ function registerMonitorCommand(program, version = "0.0.0", projectRoot = proces
 
 //#endregion
 //#region src/cli/commands/merge.ts
-const logger$7 = createLogger("merge-cmd");
+const logger$8 = createLogger("merge-cmd");
 const MERGE_EXIT_SUCCESS = 0;
 const MERGE_EXIT_CONFLICT = 1;
 const MERGE_EXIT_ERROR = 2;
@@ -7033,7 +7033,7 @@ async function mergeTask(taskId, targetBranch, projectRoot) {
 		projectRoot
 	});
 	try {
-		logger$7.info({
+		logger$8.info({
 			taskId,
 			targetBranch
 		}, "Running conflict detection...");
@@ -7055,7 +7055,7 @@ async function mergeTask(taskId, targetBranch, projectRoot) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		console.error(`Error merging task "${taskId}": ${message}`);
-		logger$7.error({
+		logger$8.error({
 			taskId,
 			err
 		}, "merge --task failed");
@@ -7109,7 +7109,7 @@ async function mergeAll(targetBranch, projectRoot, taskIds) {
 			error: message
 		});
 		console.log(`  Error for task "${taskId}": ${message}`);
-		logger$7.error({
+		logger$8.error({
 			taskId,
 			err
 		}, "merge --all: task failed");
@@ -7162,7 +7162,7 @@ function registerMergeCommand(program, projectRoot = process.cwd()) {
 
 //#endregion
 //#region src/cli/commands/worktrees.ts
-const logger$6 = createLogger("worktrees-cmd");
+const logger$7 = createLogger("worktrees-cmd");
 const WORKTREES_EXIT_SUCCESS = 0;
 const WORKTREES_EXIT_ERROR = 1;
 /** Valid task statuses for filtering */
@@ -7289,7 +7289,7 @@ async function listWorktreesAction(options) {
 		try {
 			worktreeInfos = await manager.listWorktrees();
 		} catch (err) {
-			logger$6.error({ err }, "Failed to list worktrees");
+			logger$7.error({ err }, "Failed to list worktrees");
 			const message = err instanceof Error ? err.message : String(err);
 			process.stderr.write(`Error listing worktrees: ${message}\n`);
 			return WORKTREES_EXIT_ERROR;
@@ -7316,7 +7316,7 @@ async function listWorktreesAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$6.error({ err }, "listWorktreesAction failed");
+		logger$7.error({ err }, "listWorktreesAction failed");
 		return WORKTREES_EXIT_ERROR;
 	}
 }
@@ -7357,7 +7357,7 @@ function registerWorktreesCommand(program, version = "0.0.0", projectRoot = proc
 
 //#endregion
 //#region src/cli/commands/brainstorm.ts
-const logger$5 = createLogger("brainstorm-cmd");
+const logger$6 = createLogger("brainstorm-cmd");
 /**
 * Detect whether the project has existing planning artifacts that indicate
 * this is an amendment session (vs. a brand-new project brainstorm).
@@ -7403,13 +7403,13 @@ async function loadAmendmentContextDocuments(projectRoot) {
 	try {
 		brief = await readFile(briefPath, "utf-8");
 	} catch {
-		logger$5.warn({ briefPath }, "product-brief.md not found — continuing without brief context");
+		logger$6.warn({ briefPath }, "product-brief.md not found — continuing without brief context");
 		process.stderr.write(`Warning: product-brief.md not found at ${briefPath}\n`);
 	}
 	try {
 		prd = await readFile(prdPath, "utf-8");
 	} catch {
-		logger$5.warn({ prdPath }, "requirements.md not found — continuing without PRD context");
+		logger$6.warn({ prdPath }, "requirements.md not found — continuing without PRD context");
 		process.stderr.write(`Warning: requirements.md not found at ${prdPath}\n`);
 	}
 	return {
@@ -7618,7 +7618,7 @@ async function dispatchToPersonas(userPrompt, context, llmDispatch) {
 		}
 	];
 	const defaultDispatch = async (prompt, personaName) => {
-		logger$5.debug({
+		logger$6.debug({
 			personaName,
 			promptLength: prompt.length
 		}, "Dispatching to persona (stub mode)");
@@ -7635,7 +7635,7 @@ async function dispatchToPersonas(userPrompt, context, llmDispatch) {
 			};
 		} catch (err) {
 			const msg = err instanceof Error ? err.message : String(err);
-			logger$5.error({
+			logger$6.error({
 				err,
 				personaName: persona.name
 			}, "Persona dispatch failed");
@@ -7787,7 +7787,7 @@ async function runBrainstormSession(options, llmDispatch, rlInterface) {
 			}
 		});
 		rl.on("error", (err) => {
-			logger$5.error({ err }, "readline error");
+			logger$6.error({ err }, "readline error");
 			if (!sessionEnded) endSession(false);
 		});
 	});
@@ -7828,7 +7828,7 @@ function registerBrainstormCommand(program, _version = "0.0.0", projectRoot = pr
 
 //#endregion
 //#region src/cli/commands/retry-escalated.ts
-const logger$4 = createLogger("retry-escalated-cmd");
+const logger$5 = createLogger("retry-escalated-cmd");
 async function runRetryEscalatedAction(options) {
 	const { runId, dryRun, force, outputFormat, projectRoot, concurrency, pack: packName, registry: injectedRegistry, agent: agentId, events: eventsFlag } = options;
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
@@ -7869,7 +7869,7 @@ async function runRetryEscalatedAction(options) {
 					process.stdout.write(`[INFO] ${storyKey}: Context ceiling set to ${contextCeiling} tokens due to prior context spike pattern.\n`);
 				}
 			} catch (err) {
-				logger$4.warn({
+				logger$5.warn({
 					err,
 					storyKey
 				}, "Failed to read efficiency profile — skipping gate");
@@ -8023,11 +8023,11 @@ async function runRetryEscalatedAction(options) {
 						output_tokens: output,
 						cost_usd: costUsd
 					}).catch((err) => {
-						logger$4.warn({ err }, "Failed to record token usage");
+						logger$5.warn({ err }, "Failed to record token usage");
 					});
 				}
 			} catch (err) {
-				logger$4.warn({ err }, "Failed to record token usage");
+				logger$5.warn({ err }, "Failed to record token usage");
 			}
 		});
 		if (outputFormat === "human") {
@@ -8056,7 +8056,7 @@ async function runRetryEscalatedAction(options) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, msg) + "\n");
 		else process.stderr.write(`Error: ${msg}\n`);
-		logger$4.error({ err }, "retry-escalated failed");
+		logger$5.error({ err }, "retry-escalated failed");
 		return 1;
 	} finally {
 		try {
@@ -8089,7 +8089,7 @@ function registerRetryEscalatedCommand(program, _version = "0.0.0", projectRoot
 
 //#endregion
 //#region src/cli/commands/cancel.ts
-const logger$3 = createLogger("cancel-cmd");
+const logger$4 = createLogger("cancel-cmd");
 async function runCancelAction(options) {
 	const { outputFormat, projectRoot, force } = options;
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
@@ -8128,7 +8128,7 @@ async function runCancelAction(options) {
 		}
 	} catch (err) {
 		const msg = err instanceof Error ? err.message : String(err);
-		logger$3.warn({
+		logger$4.warn({
 			pid,
 			err: msg
 		}, "Failed to kill orchestrator");
@@ -8158,7 +8158,7 @@ async function runCancelAction(options) {
 			await adapter.close();
 		}
 	} catch (err) {
-		logger$3.warn({ err }, "Could not update pipeline run status (non-fatal)");
+		logger$4.warn({ err }, "Could not update pipeline run status (non-fatal)");
 	}
 	if (outputFormat === "json") process.stdout.write(formatOutput({
 		cancelled: true,
@@ -8510,6 +8510,129 @@ function emitDiff(diff, ctx) {
 	process.stdout.write("\n");
 }
 
+//#endregion
+//#region src/cli/commands/probe-author.ts
+const logger$3 = createLogger("cli:probe-author");
+/**
+* A minimum-viable logger that routes everything to stderr. Used by the
+* subcommand to keep stdout reserved for the JSON result payload.
+* Pino's default pino()-without-destination writes to stdout; we need
+* the inverse here.
+*/
+function makeStderrLogger() {
+	const emit = (level, args) => {
+		const payload = args.map((a) => typeof a === "string" ? a : JSON.stringify(a)).join(" ");
+		process.stderr.write(`[${level}] ${payload}\n`);
+	};
+	return {
+		debug: (...args) => emit("debug", args),
+		info: (...args) => emit("info", args),
+		warn: (...args) => emit("warn", args),
+		error: (...args) => emit("error", args)
+	};
+}
+function registerProbeAuthorCommand(program, _version, projectRoot, registry) {
+	const probeAuthor = program.command("probe-author").description("probe-author phase utilities (Story 60-14)");
+	probeAuthor.command("dispatch").description("Dispatch the probe-author phase against a single story file. Reads the story artifact + epic content, calls the probe-author agent, outputs the authored probes as JSON. Powers the A/B validation harness eval (scripts/eval-probe-author.mjs) and serves as a manual operator inspection tool.").requiredOption("--story-file <path>", "Path to the story artifact (.md). Receives the appended ## Runtime Probes section.").option("--epic-file <path>", "Path to source epic content (default: same as --story-file)").option("--story-key <key>", "Story key for telemetry / event payloads", "probe-author-cli").option("--agent <id>", "Agent backend (default: claude-code)", "claude-code").option("--pack <name>", "Methodology pack name (default: bmad)", "bmad").option("--output-format <format>", "Output format: json (default; print authored probes as JSON to stdout) or append (leave story-file with appended Runtime Probes section)", "json").option("--working-dir <path>", "Working directory for the dispatcher (default: --story-file directory)").option("--bypass-gates", "Skip the event-driven AC + idempotency gates inside runProbeAuthor. Use ONLY for operator invocations / A/B eval-harness runs that need to test authoring quality across non-event-driven AC. Production pipelines should never set this — the gates are load-bearing for the orchestrator path.", false).action(async (opts) => {
+		const exitCode = await runProbeAuthorDispatch(opts, projectRoot, registry);
+		process.exitCode = exitCode;
+	});
+}
+/**
+* Core entry point for `substrate probe-author dispatch`. Returns the
+* exit code (0 on probe-author success, 1 on failure or skip).
+*/
+async function runProbeAuthorDispatch(opts, projectRoot, registry) {
+	const storyFilePath = resolve$1(opts.storyFile);
+	const epicFilePath = opts.epicFile !== void 0 ? resolve$1(opts.epicFile) : storyFilePath;
+	let epicContent;
+	try {
+		epicContent = readFileSync(epicFilePath, "utf-8");
+	} catch (err) {
+		const msg = err instanceof Error ? err.message : String(err);
+		process.stderr.write(`probe-author: failed to read epic file ${epicFilePath}: ${msg}\n`);
+		return 1;
+	}
+	let originalStoryContent;
+	try {
+		originalStoryContent = readFileSync(storyFilePath, "utf-8");
+	} catch (err) {
+		const msg = err instanceof Error ? err.message : String(err);
+		process.stderr.write(`probe-author: failed to read story file ${storyFilePath}: ${msg}\n`);
+		return 1;
+	}
+	const eventBus = createEventBus();
+	const adapter = new InMemoryDatabaseAdapter();
+	const packLoader = createPackLoader();
+	const packPath = `${projectRoot}/packs/${opts.pack}`;
+	let pack;
+	try {
+		pack = await packLoader.load(packPath);
+	} catch (err) {
+		const msg = err instanceof Error ? err.message : String(err);
+		process.stderr.write(`probe-author: failed to load methodology pack '${opts.pack}' from ${packPath}: ${msg}\n`);
+		return 1;
+	}
+	const contextCompiler = createContextCompiler({ db: adapter });
+	const stderrLogger = makeStderrLogger();
+	const dispatcher = createDispatcher({
+		eventBus,
+		adapterRegistry: registry,
+		logger: stderrLogger
+	});
+	const workingDir = opts.workingDir !== void 0 ? resolve$1(opts.workingDir) : resolve$1(storyFilePath, "..");
+	logger$3.info({
+		storyKey: opts.storyKey,
+		storyFile: storyFilePath,
+		epicFile: epicFilePath,
+		agent: opts.agent,
+		pack: opts.pack
+	}, "probe-author dispatch starting");
+	const result = await runProbeAuthor({
+		db: adapter,
+		pack,
+		contextCompiler,
+		dispatcher,
+		projectRoot: workingDir,
+		agentId: opts.agent
+	}, {
+		storyKey: opts.storyKey,
+		storyFilePath,
+		pipelineRunId: `probe-author-cli-${Date.now()}`,
+		sourceAcContent: epicContent,
+		epicContent,
+		...opts.bypassGates === true ? { bypassGates: true } : {}
+	});
+	let postDispatchContent = originalStoryContent;
+	try {
+		postDispatchContent = readFileSync(storyFilePath, "utf-8");
+	} catch {}
+	const parseResult = parseRuntimeProbes(postDispatchContent);
+	const probes = parseResult.kind === "parsed" ? parseResult.probes : [];
+	if (opts.outputFormat === "json") {
+		if (postDispatchContent !== originalStoryContent) try {
+			writeFileSync(storyFilePath, originalStoryContent, "utf-8");
+		} catch (err) {
+			const msg = err instanceof Error ? err.message : String(err);
+			process.stderr.write(`probe-author: warning — failed to restore story file: ${msg}\n`);
+		}
+		process.stdout.write(JSON.stringify({
+			success: result.result === "success",
+			result: result.result,
+			error: result.error,
+			probesAuthoredCount: result.probesAuthoredCount,
+			probes,
+			tokenUsage: result.tokenUsage,
+			durationMs: result.durationMs
+		}, null, 2) + "\n");
+	} else if (opts.outputFormat === "append") process.stderr.write(`probe-author: ${result.result} — ${result.probesAuthoredCount} probe(s) authored. Story file at ${storyFilePath}\n`);
+	else {
+		process.stderr.write(`probe-author: invalid --output-format '${opts.outputFormat}'. Valid: json | append\n`);
+		return 1;
+	}
+	return result.result === "success" ? 0 : 1;
+}
+
 //#endregion
 //#region src/cli/commands/history.ts
 function registerHistoryCommand(program) {
@@ -9114,6 +9237,7 @@ async function createProgram() {
 	registerHistoryCommand(program);
 	registerMigrateCommand(program);
 	registerProbesCommand(program);
+	registerProbeAuthorCommand(program, version, process.cwd(), registry);
 	registerRepoMapCommand(program);
 	registerRoutingCommand(program);
 	registerCostCommand(program, version);
@@ -9132,8 +9256,8 @@ 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-BXfinu5K.js").then(async () => {
-		const { createVersionManager } = await import("../version-manager-impl-ChzfLw90.js");
+	import("../upgrade-Csv0GRft.js").then(async () => {
+		const { createVersionManager } = await import("../version-manager-impl-C-mrgne3.js");
 		const vm = createVersionManager();
 		const result = await vm.checkForUpdates();
 		if (result.updateAvailable) {