substrate-ai 0.20.58 → 0.20.60

package/dist/cli/index.js

@@ -1,10 +1,10 @@
 #!/usr/bin/env node
-import { FileStateStore, RunManifest, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, ZERO_FINDINGS_BY_AUTHOR, ZERO_FINDING_COUNTS, ZERO_PROBE_AUTHOR_METRICS, aggregateProbeAuthorMetrics, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, parseRuntimeProbes, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, rollupFindingsByAuthor, rollupProbeAuthorByClass, rollupProbeAuthorMetrics } from "../health-CNqQFdaT.js";
+import { FileStateStore, RunManifest, SUBSTRATE_OWNED_SETTINGS_KEYS, SupervisorLock, VALID_PHASES, WorkGraphRepository, ZERO_FINDINGS_BY_AUTHOR, ZERO_FINDING_COUNTS, ZERO_PROBE_AUTHOR_METRICS, aggregateProbeAuthorMetrics, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, parseRuntimeProbes, readCurrentRunId, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, rollupFindingsByAuthor, rollupProbeAuthorByClass, rollupProbeAuthorMetrics } from "../health-BoXxsFSF.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, 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-W2emvN3F.js";
 import "../adapter-registry-DXLMTmfD.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, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, escape, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runProbeAuthor, runSolutioningPhase, unescape, validateStopAfterFromConflict } from "../run-DE5xoB9U.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, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, escape, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runProbeAuthor, runSolutioningPhase, unescape, validateStopAfterFromConflict } from "../run-CRz08RrU.js";
 import "../errors-CKFu8YI9.js";
 import "../routing-CcBOCuC9.js";
 import "../decisions-C0pz9Clx.js";
@@ -14,10 +14,11 @@ import { Command } from "commander";
 import { fileURLToPath } from "url";
 import { dirname, join, resolve } from "path";
 import { access, mkdir, readFile, writeFile } from "fs/promises";
+import { EventEmitter } from "node:events";
 import yaml from "js-yaml";
 import * as actualFS from "node:fs";
 import { existsSync, promises, readFileSync, writeFileSync } from "node:fs";
-import { execFile, spawn } from "node:child_process";
+import { execFile, spawn, spawnSync } 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";
@@ -30,6 +31,7 @@ import { appendFileSync, chmodSync, cpSync, existsSync as existsSync$1, lstatSyn
 import { homedir } from "os";
 import { createRequire } from "node:module";
 import { fileURLToPath as fileURLToPath$1 } from "node:url";
+import * as readline from "node:readline";
 import { createInterface } from "node:readline";
 import { randomUUID as randomUUID$1 } from "crypto";
 import { createInterface as createInterface$1 } from "readline";
@@ -334,12 +336,12 @@ var GitWorktreeManagerImpl = class {
 	_onTaskReady;
 	_onTaskComplete;
 	_onTaskFailed;
-	constructor(eventBus, projectRoot, baseDirectory = DEFAULT_WORKTREE_BASE, db = null, logger$17) {
+	constructor(eventBus, projectRoot, baseDirectory = DEFAULT_WORKTREE_BASE, db = null, logger$18) {
 		this._eventBus = eventBus;
 		this._projectRoot = projectRoot;
 		this._baseDirectory = baseDirectory;
 		this._db = db;
-		this._logger = logger$17 ?? console;
+		this._logger = logger$18 ?? console;
 		this._onTaskReady = ({ taskId }) => {
 			this._handleTaskReady(taskId).catch((err) => {
 				this._logger.error({
@@ -643,14 +645,14 @@ var RecommendationEngine = class {
 	_filters;
 	_historyDays;
 	_logger;
-	constructor(monitorDb, config = {}, logger$17) {
+	constructor(monitorDb, config = {}, logger$18) {
 		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$17 ?? console;
+		this._logger = logger$18 ?? console;
 	}
 	generateRecommendations() {
 		const sinceDate = new Date(Date.now() - this._historyDays * 24 * 60 * 60 * 1e3).toISOString();
@@ -1740,7 +1742,7 @@ function buildStackAwareDevNotes(profile) {
 
 //#endregion
 //#region src/cli/commands/init.ts
-const logger$16 = createLogger("init");
+const logger$17 = createLogger("init");
 const __dirname = dirname(new URL(import.meta.url).pathname);
 const SCAFFOLD_VERSION_REGEX = /<!-- substrate:version=([\d.]+) -->/;
 /**
@@ -1781,7 +1783,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 	const version = resolveBmadMethodVersion();
 	if (force && bmadExists) process.stderr.write(`Warning: Replacing existing _bmad/ framework with bmad-method@${version}\n`);
 	process.stdout.write(`Scaffolding BMAD framework from bmad-method@${version}\n`);
-	logger$16.info({
+	logger$17.info({
 		version,
 		dest: bmadDest
 	}, "Scaffolding BMAD framework");
@@ -1791,7 +1793,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 			const destDir = join(bmadDest, dir);
 			mkdirSync$1(destDir, { recursive: true });
 			cpSync(srcDir, destDir, { recursive: true });
-			logger$16.info({
+			logger$17.info({
 				dir,
 				dest: destDir
 			}, "Scaffolded BMAD framework directory");
@@ -1810,7 +1812,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 			"document_output_language: English"
 		].join("\n") + "\n";
 		await writeFile(configFile, configStub, "utf8");
-		logger$16.info({ configFile }, "Generated _bmad/_config/config.yaml stub");
+		logger$17.info({ configFile }, "Generated _bmad/_config/config.yaml stub");
 	}
 }
 const CLAUDE_MD_START_MARKER = "<!-- substrate:start -->";
@@ -1825,7 +1827,7 @@ async function scaffoldClaudeMd(projectRoot, profile) {
 	try {
 		sectionContent = await readFile(templatePath, "utf8");
 	} catch {
-		logger$16.warn({ templatePath }, "CLAUDE.md substrate section template not found; skipping");
+		logger$17.warn({ templatePath }, "CLAUDE.md substrate section template not found; skipping");
 		return;
 	}
 	const substrateVersion = readSubstrateVersion(pkgRoot);
@@ -1861,7 +1863,7 @@ async function scaffoldClaudeMd(projectRoot, profile) {
 		else newContent = updatedExisting;
 	}
 	await writeFile(claudeMdPath, newContent, "utf8");
-	logger$16.info({ claudeMdPath }, "Wrote substrate section to CLAUDE.md");
+	logger$17.info({ claudeMdPath }, "Wrote substrate section to CLAUDE.md");
 }
 async function scaffoldAgentsMd(projectRoot, profile) {
 	const agentsMdPath = join(projectRoot, "AGENTS.md");
@@ -1873,7 +1875,7 @@ async function scaffoldAgentsMd(projectRoot, profile) {
 	try {
 		sectionContent = await readFile(templatePath, "utf8");
 	} catch {
-		logger$16.warn({ templatePath }, "AGENTS.md substrate section template not found; skipping");
+		logger$17.warn({ templatePath }, "AGENTS.md substrate section template not found; skipping");
 		return;
 	}
 	const substrateVersion = readSubstrateVersion(pkgRoot);
@@ -1894,7 +1896,7 @@ async function scaffoldAgentsMd(projectRoot, profile) {
 		newContent = existingContent + separator + sectionContent;
 	}
 	await writeFile(agentsMdPath, newContent, "utf8");
-	logger$16.info({ agentsMdPath }, "Wrote substrate section to AGENTS.md");
+	logger$17.info({ agentsMdPath }, "Wrote substrate section to AGENTS.md");
 }
 async function scaffoldGeminiMd(projectRoot, profile) {
 	const geminiMdPath = join(projectRoot, "GEMINI.md");
@@ -1906,7 +1908,7 @@ async function scaffoldGeminiMd(projectRoot, profile) {
 	try {
 		sectionContent = await readFile(templatePath, "utf8");
 	} catch {
-		logger$16.warn({ templatePath }, "GEMINI.md substrate section template not found; skipping");
+		logger$17.warn({ templatePath }, "GEMINI.md substrate section template not found; skipping");
 		return;
 	}
 	const substrateVersion = readSubstrateVersion(pkgRoot);
@@ -1927,7 +1929,7 @@ async function scaffoldGeminiMd(projectRoot, profile) {
 		newContent = existingContent + separator + sectionContent;
 	}
 	await writeFile(geminiMdPath, newContent, "utf8");
-	logger$16.info({ geminiMdPath }, "Wrote substrate section to GEMINI.md");
+	logger$17.info({ geminiMdPath }, "Wrote substrate section to GEMINI.md");
 }
 async function scaffoldStatuslineScript(projectRoot) {
 	const pkgRoot = findPackageRoot(__dirname);
@@ -1938,7 +1940,7 @@ async function scaffoldStatuslineScript(projectRoot) {
 	try {
 		content = await readFile(templatePath, "utf8");
 	} catch {
-		logger$16.warn({ templatePath }, "statusline.sh template not found; skipping");
+		logger$17.warn({ templatePath }, "statusline.sh template not found; skipping");
 		return;
 	}
 	const claudeDir = join(projectRoot, ".claude");
@@ -1946,7 +1948,7 @@ async function scaffoldStatuslineScript(projectRoot) {
 	mkdirSync$1(claudeDir, { recursive: true });
 	await writeFile(statuslinePath, content, "utf8");
 	chmodSync(statuslinePath, 493);
-	logger$16.info({ statuslinePath }, "Wrote .claude/statusline.sh");
+	logger$17.info({ statuslinePath }, "Wrote .claude/statusline.sh");
 }
 async function scaffoldClaudeSettings(projectRoot) {
 	const claudeDir = join(projectRoot, ".claude");
@@ -1962,7 +1964,7 @@ async function scaffoldClaudeSettings(projectRoot) {
 	if (!merged["$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$16.info({ settingsPath }, "Wrote substrate settings to .claude/settings.json");
+	logger$17.info({ settingsPath }, "Wrote substrate settings to .claude/settings.json");
 }
 function resolveBmadMethodInstallerLibPath(fromDir = __dirname) {
 	try {
@@ -2034,7 +2036,7 @@ async function compileBmadAgents(bmadDir) {
 				writeFileSync$1(mdPath, result.xml, "utf-8");
 				compiled++;
 			} catch (compileErr) {
-				logger$16.debug({
+				logger$17.debug({
 					err: compileErr,
 					file
 				}, "Failed to compile agent YAML");
@@ -2181,9 +2183,9 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		const _require = createRequire(join(__dirname, "synthetic.js"));
 		try {
 			const compiledCount = await compileBmadAgents(bmadDir);
-			if (compiledCount > 0) logger$16.info({ compiledCount }, "Compiled agent YAML files to MD");
+			if (compiledCount > 0) logger$17.info({ compiledCount }, "Compiled agent YAML files to MD");
 		} catch (compileErr) {
-			logger$16.warn({ err: compileErr }, "Agent compilation failed; agent commands may be incomplete");
+			logger$17.warn({ err: compileErr }, "Agent compilation failed; agent commands may be incomplete");
 		}
 		const resolveExport = (mod, name) => {
 			if (typeof mod[name] === "function") return mod[name];
@@ -2197,7 +2199,7 @@ 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$16.info("bmad-method generators not available (requires bmad-method with agent/workflow/task-tool generators)");
+			logger$17.info("bmad-method generators not available (requires bmad-method with agent/workflow/task-tool generators)");
 			return;
 		}
 		const agentMod = _require(agentGenPath);
@@ -2207,11 +2209,11 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		if (existsSync$1(workflowGenPath)) {
 			const workflowMod = _require(workflowGenPath);
 			WorkflowCommandGenerator = resolveExport(workflowMod, "WorkflowCommandGenerator");
-		} else logger$16.info("bmad-method workflow-command-generator not available; will try skill-based installation");
+		} else logger$17.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$16.info("bmad-method task-tool-command-generator not available; will try skill-based installation");
+		} else logger$17.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);
@@ -2243,7 +2245,7 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 			const manifestGen = new ManifestGenerator();
 			await manifestGen.generateManifests(bmadDir, allModules, [], { ides: ["claude-code"] });
 		} catch (manifestErr) {
-			logger$16.warn({ err: manifestErr }, "ManifestGenerator failed; workflow/task commands may be incomplete");
+			logger$17.warn({ err: manifestErr }, "ManifestGenerator failed; workflow/task commands may be incomplete");
 		}
 		const commandsDir = join(projectRoot, ".claude", "commands");
 		mkdirSync$1(commandsDir, { recursive: true });
@@ -2271,7 +2273,7 @@ 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$16.info({
+		logger$17.info({
 			agentCount,
 			workflowCount,
 			taskToolCount,
@@ -2282,7 +2284,7 @@ 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$16.warn({ err }, "scaffoldClaudeCommands failed; init continues");
+		logger$17.warn({ err }, "scaffoldClaudeCommands failed; init continues");
 	}
 }
 /**
@@ -2311,7 +2313,7 @@ function syncCommandsAsPrompts(commandsDir, promptsDir, ownershipPrefixes, nameP
 			unlinkSync$1(join(promptsDir, entry.name));
 		}
 	} catch (err) {
-		logger$16.debug({
+		logger$17.debug({
 			err,
 			promptsDir
 		}, "Failed to prune stale prompts");
@@ -2353,7 +2355,7 @@ function syncSkillsToTarget(srcSkillsDir, destSkillsDir, ownershipPrefixes, name
 			});
 		}
 	} catch (err) {
-		logger$16.debug({
+		logger$17.debug({
 			err,
 			destSkillsDir
 		}, "Failed to prune stale skills");
@@ -2396,16 +2398,16 @@ 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$16.info({
+		if (total > 0) logger$17.info({
 			promptCount,
 			skillCount,
 			codexDir
 		}, "Generated .codex/");
-		else logger$16.debug({ codexDir }, "No Codex artifacts generated; source Claude content not found");
+		else logger$17.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$16.warn({ err }, "scaffoldCodexProject failed; init continues");
+		logger$17.warn({ err }, "scaffoldCodexProject failed; init continues");
 	}
 }
 /**
@@ -2431,16 +2433,16 @@ 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$16.info({
+		if (total > 0) logger$17.info({
 			promptCount,
 			skillCount,
 			userCodexDir
 		}, "Installed user-scope Codex content");
-		else logger$16.debug({ userCodexDir }, "No user-scope Codex content installed; source Claude content not found");
+		else logger$17.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$16.warn({ err }, "scaffoldCodexUser failed; init continues");
+		logger$17.warn({ err }, "scaffoldCodexUser failed; init continues");
 	}
 }
 const PROVIDER_DEFAULTS = DEFAULT_CONFIG.providers;
@@ -2496,8 +2498,8 @@ function formatProjectProfile(profile) {
 */
 async function promptProfileConfirmation(nonInteractive) {
 	if (nonInteractive) return true;
-	const readline = await import("readline");
-	const rl = readline.createInterface({
+	const readline$1 = await import("readline");
+	const rl = readline$1.createInterface({
 		input: process.stdin,
 		output: process.stdout
 	});
@@ -2512,8 +2514,8 @@ async function promptProfileConfirmation(nonInteractive) {
 }
 async function promptSubscriptionRouting(providerName, nonInteractive) {
 	if (nonInteractive) return "auto";
-	const readline = await import("readline");
-	const rl = readline.createInterface({
+	const readline$1 = await import("readline");
+	const rl = readline$1.createInterface({
 		input: process.stdin,
 		output: process.stdout
 	});
@@ -2560,7 +2562,7 @@ async function runInitAction(options) {
 			discoveryReport = await registry.discoverAndRegister();
 		} catch (err) {
 			const message = err instanceof Error ? err.message : String(err);
-			logger$16.error({ err }, "Adapter discovery failed");
+			logger$17.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;
@@ -2603,7 +2605,7 @@ async function runInitAction(options) {
 		try {
 			detectedProfile = await detectProjectProfile(dbRoot);
 		} catch (err) {
-			logger$16.warn({ err }, "Project profile detection failed; skipping");
+			logger$17.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");
@@ -2637,12 +2639,12 @@ async function runInitAction(options) {
 				return INIT_EXIT_ERROR;
 			}
 			if (force && existsSync$1(localManifest)) {
-				logger$16.info({ pack: packName }, "Replacing existing pack with bundled version");
+				logger$17.info({ pack: packName }, "Replacing existing pack with bundled version");
 				process.stderr.write(`Warning: Replacing existing pack '${packName}' with bundled version\n`);
 			}
 			mkdirSync$1(dirname(packPath), { recursive: true });
 			cpSync(bundledPackPath, packPath, { recursive: true });
-			logger$16.info({
+			logger$17.info({
 				pack: packName,
 				dest: packPath
 			}, "Scaffolded methodology pack");
@@ -2694,10 +2696,10 @@ async function runInitAction(options) {
 			if (missing.length > 0) {
 				const block = "\n# Substrate runtime files\n" + missing.join("\n") + "\n";
 				appendFileSync(gitignorePath, block);
-				logger$16.info({ entries: missing }, "Added substrate runtime files to .gitignore");
+				logger$17.info({ entries: missing }, "Added substrate runtime files to .gitignore");
 			}
 		} catch (err) {
-			logger$16.debug({ err }, "Could not update .gitignore (non-fatal)");
+			logger$17.debug({ err }, "Could not update .gitignore (non-fatal)");
 		}
 		const doltMode = options.doltMode ?? "auto";
 		let doltInitialized = false;
@@ -2714,7 +2716,7 @@ async function runInitAction(options) {
 					process.stderr.write(`${err.message}\n`);
 					return INIT_EXIT_ERROR;
 				}
-				logger$16.debug("Dolt not installed, skipping auto-init");
+				logger$17.debug("Dolt not installed, skipping auto-init");
 			} else {
 				const msg = err instanceof Error ? err.message : String(err);
 				if (doltMode === "force") {
@@ -2724,7 +2726,7 @@ 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$16.debug("Dolt step was skipped (--no-dolt)");
+		else logger$17.debug("Dolt step was skipped (--no-dolt)");
 		const successMsg = `Pack '${packName}' and database initialized successfully at ${dbPath}`;
 		if (outputFormat === "json") process.stdout.write(formatOutput({
 			pack: packName,
@@ -2762,7 +2764,7 @@ 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$16.error({ err }, "init failed");
+		logger$17.error({ err }, "init failed");
 		return INIT_EXIT_ERROR;
 	}
 }
@@ -2786,7 +2788,7 @@ function registerInitCommand(program, _version, registry) {
 
 //#endregion
 //#region src/cli/commands/config.ts
-const logger$15 = createLogger("config-cmd");
+const logger$16 = createLogger("config-cmd");
 const CONFIG_EXIT_SUCCESS = 0;
 const CONFIG_EXIT_ERROR = 1;
 const CONFIG_EXIT_INVALID = 2;
@@ -2812,7 +2814,7 @@ async function runConfigShow(opts = {}) {
 			return CONFIG_EXIT_INVALID;
 		}
 		const message = err instanceof Error ? err.message : String(err);
-		logger$15.error({ err }, "Failed to load configuration");
+		logger$16.error({ err }, "Failed to load configuration");
 		process.stderr.write(`  Error loading configuration: ${message}\n`);
 		return CONFIG_EXIT_ERROR;
 	}
@@ -2886,7 +2888,7 @@ async function runConfigExport(opts = {}) {
 			return CONFIG_EXIT_INVALID;
 		}
 		const message = err instanceof Error ? err.message : String(err);
-		logger$15.error({ err }, "Failed to load configuration");
+		logger$16.error({ err }, "Failed to load configuration");
 		process.stderr.write(`Error loading configuration: ${message}\n`);
 		return CONFIG_EXIT_ERROR;
 	}
@@ -6806,7 +6808,7 @@ async function detectManifestDriftAgainstWorkingTree(manifest, projectRoot) {
 
 //#endregion
 //#region src/cli/commands/resume.ts
-const logger$14 = createLogger("resume-cmd");
+const logger$15 = createLogger("resume-cmd");
 /**
 * Format a human-readable duration from an ISO-8601 timestamp to "now".
 */
@@ -6876,7 +6878,7 @@ async function runResumeAction(options) {
 				return 1;
 			}
 		} catch (driftErr) {
-			logger$14.debug({ err: driftErr }, "manifest drift check failed — proceeding with resume");
+			logger$15.debug({ err: driftErr }, "manifest drift check failed — proceeding with resume");
 		}
 	}
 	const doltDir = join(dbRoot, ".substrate", "state", ".dolt");
@@ -6946,15 +6948,15 @@ async function runResumeAction(options) {
 				const manifestStories = manifestData.cli_flags["stories"] ?? manifestData.story_scope;
 				if (Array.isArray(manifestStories) && manifestStories.length > 0) {
 					scopedStories = manifestStories;
-					logger$14.debug({
+					logger$15.debug({
 						runId,
 						stories: scopedStories
 					}, "resume scope loaded from manifest");
 				}
 			} catch {
-				logger$14.debug({ runId }, "manifest read failed in resume — using legacy config_json scope");
+				logger$15.debug({ runId }, "manifest read failed in resume — using legacy config_json scope");
 			}
-			else logger$14.debug({ runId }, "Run manifest not found for scope preservation — using legacy config_json scope");
+			else logger$15.debug({ runId }, "Run manifest not found for scope preservation — using legacy config_json scope");
 		}
 		return runFullPipelineFromPhase({
 			packName,
@@ -6977,7 +6979,7 @@ 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$14.error({ err }, "auto resume failed");
+		logger$15.error({ err }, "auto resume failed");
 		return 1;
 	} finally {
 		try {
@@ -7227,11 +7229,11 @@ async function runFullPipelineFromPhase(options) {
 								output_tokens: output,
 								cost_usd: costUsd
 							}).catch((err) => {
-								logger$14.warn({ err }, "Failed to record token usage");
+								logger$15.warn({ err }, "Failed to record token usage");
 							});
 						}
 					} catch (err) {
-						logger$14.warn({ err }, "Failed to record token usage");
+						logger$15.warn({ err }, "Failed to record token usage");
 					}
 				});
 				const storyKeys = await resolveStoryKeys(adapter, projectRoot, {
@@ -7300,7 +7302,7 @@ 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$14.error({ err }, "pipeline from phase failed");
+		logger$15.error({ err }, "pipeline from phase failed");
 		return 1;
 	} finally {
 		try {
@@ -7330,7 +7332,7 @@ function registerResumeCommand(program, _version = "0.0.0", projectRoot = proces
 
 //#endregion
 //#region src/cli/commands/status.ts
-const logger$13 = createLogger("status-cmd");
+const logger$14 = createLogger("status-cmd");
 /**
 * Map a manifest per-story status string to the appropriate WorkGraphCounts bucket.
 * Unknown strings are treated as `inProgress` (safe default).
@@ -7442,9 +7444,9 @@ async function runStatusAction(options) {
 			const manifestData = await resolvedManifest.read();
 			manifestPerStoryState = manifestData.per_story_state;
 			workGraph = buildWorkGraphFromManifest(manifestData.per_story_state);
-			logger$13.debug({ runId: run?.id }, "status: workGraph built from manifest per_story_state");
+			logger$14.debug({ runId: run?.id }, "status: workGraph built from manifest per_story_state");
 		} catch {
-			logger$13.debug({ runId: run?.id }, "status: manifest read failed — falling back to wg_stories");
+			logger$14.debug({ runId: run?.id }, "status: manifest read failed — falling back to wg_stories");
 		}
 		if (workGraph === void 0) try {
 			const wgRepo = new WorkGraphRepository(adapter);
@@ -7481,10 +7483,10 @@ async function runStatusAction(options) {
 				};
 			}
 		} catch (err) {
-			logger$13.debug({ err }, "Work graph query failed, continuing without work graph data");
+			logger$14.debug({ err }, "Work graph query failed, continuing without work graph data");
 		}
 		if (run === void 0) {
-			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-BX84L5Qe.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-FZVOBYND.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -7514,7 +7516,7 @@ async function runStatusAction(options) {
 		if (stateStore) try {
 			storeStories = await stateStore.queryStories({});
 		} catch (err) {
-			logger$13.debug({ err }, "StateStore query failed, continuing without store data");
+			logger$14.debug({ err }, "StateStore query failed, continuing without store data");
 		}
 		if (outputFormat === "json") {
 			const statusOutput = buildPipelineStatusOutput(run, tokenSummary, decisionsCount, storiesCount);
@@ -7657,7 +7659,7 @@ 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$13.error({ err }, "status action failed");
+		logger$14.error({ err }, "status action failed");
 		return 1;
 	} finally {
 		try {
@@ -8004,7 +8006,7 @@ Analyze thoroughly and return ONLY the JSON array with no additional text.`;
 
 //#endregion
 //#region src/cli/commands/amend.ts
-const logger$12 = createLogger("amend-cmd");
+const logger$13 = createLogger("amend-cmd");
 /**
 * Detect and apply supersessions after a phase completes in an amendment run.
 *
@@ -8035,7 +8037,7 @@ async function runPostPhaseSupersessionDetection(adapter, amendmentRunId, curren
 			});
 		} catch (err) {
 			const msg = err instanceof Error ? err.message : String(err);
-			logger$12.warn({
+			logger$13.warn({
 				err,
 				originalId: parentMatch.id,
 				supersedingId: newDec.id
@@ -8172,7 +8174,7 @@ async function runAmendAction(options) {
 		for (let i = startIdx; i < phaseOrder.length; i++) {
 			const currentPhase = phaseOrder[i];
 			const amendmentContext = handler.loadContextForPhase(currentPhase);
-			logger$12.info({
+			logger$13.info({
 				phase: currentPhase,
 				amendmentContextLen: amendmentContext.length
 			}, "Amendment context loaded for phase");
@@ -8293,7 +8295,7 @@ async function runAmendAction(options) {
 	} catch (err) {
 		const msg = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${msg}\n`);
-		logger$12.error({ err }, "amend failed");
+		logger$13.error({ err }, "amend failed");
 		return 1;
 	} finally {
 		try {
@@ -9030,7 +9032,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-ChqBlPYZ.js"
+									"../run-BxfeSz6G.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -9280,7 +9282,7 @@ function registerSupervisorCommand(program, _version = "0.0.0", projectRoot = pr
 
 //#endregion
 //#region src/cli/commands/metrics.ts
-const logger$11 = createLogger("metrics-cmd");
+const logger$12 = createLogger("metrics-cmd");
 async function openTelemetryAdapter(basePath) {
 	try {
 		const adapter = createDatabaseAdapter({
@@ -9646,7 +9648,7 @@ async function runMetricsAction(options) {
 					}
 				}
 			} catch (err) {
-				logger$11.debug({ err }, "getScenarioResultsForRun failed");
+				logger$12.debug({ err }, "getScenarioResultsForRun failed");
 			}
 			if (rows.length === 0) {
 				const msg = `No factory run found with id: ${run}`;
@@ -9682,7 +9684,7 @@ async function runMetricsAction(options) {
 						}
 					}
 				} catch (err) {
-					logger$11.debug({ err }, "getTwinRunsForRun failed — twin_runs table may not exist yet");
+					logger$12.debug({ err }, "getTwinRunsForRun failed — twin_runs table may not exist yet");
 				}
 			}
 			return 0;
@@ -9692,7 +9694,7 @@ async function runMetricsAction(options) {
 			try {
 				factoryRuns$1 = await getFactoryRunSummaries(adapter, limit);
 			} catch (err) {
-				logger$11.debug({ err }, "getFactoryRunSummaries failed in factory-only mode");
+				logger$12.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");
@@ -9753,7 +9755,7 @@ async function runMetricsAction(options) {
 			doltMetrics = await stateStore.queryMetrics(doltFilter);
 			await stateStore.close();
 		} catch (doltErr) {
-			logger$11.warn({ err: doltErr }, "StateStore query failed — falling back to SQLite metrics only");
+			logger$12.warn({ err: doltErr }, "StateStore query failed — falling back to SQLite metrics only");
 		}
 		const storyMetricDecisions = await getDecisionsByCategory(adapter, STORY_METRICS);
 		const storyMetrics = storyMetricDecisions.map((d) => {
@@ -9815,7 +9817,7 @@ async function runMetricsAction(options) {
 		try {
 			factoryRuns = await getFactoryRunSummaries(adapter, limit);
 		} catch (err) {
-			logger$11.debug({ err }, "getFactoryRunSummaries failed — table may not exist in older databases");
+			logger$12.debug({ err }, "getFactoryRunSummaries failed — table may not exist in older databases");
 		}
 		if (outputFormat === "json") {
 			const runsWithBreakdown = runs.map((run$1) => ({
@@ -9953,7 +9955,7 @@ 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$11.error({ err }, "metrics action failed");
+		logger$12.error({ err }, "metrics action failed");
 		return 1;
 	} finally {
 		try {
@@ -10155,7 +10157,7 @@ function registerMigrateCommand(program) {
 function getLatestSessionId(_adapter) {
 	return null;
 }
-const logger$10 = createLogger("cost-cmd");
+const logger$11 = createLogger("cost-cmd");
 const COST_EXIT_SUCCESS = 0;
 const COST_EXIT_ERROR = 1;
 /**
@@ -10399,7 +10401,7 @@ async function runCostAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$10.error({ err }, "runCostAction failed");
+		logger$11.error({ err }, "runCostAction failed");
 		return COST_EXIT_ERROR;
 	} finally {
 		if (adapter !== null) try {
@@ -10433,7 +10435,7 @@ function registerCostCommand(program, version = "0.0.0", projectRoot = process.c
 
 //#endregion
 //#region src/cli/commands/monitor.ts
-const logger$9 = createLogger("monitor-cmd");
+const logger$10 = createLogger("monitor-cmd");
 const MONITOR_EXIT_SUCCESS = 0;
 const MONITOR_EXIT_ERROR = 1;
 /**
@@ -10636,7 +10638,7 @@ async function runMonitorReportAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$9.error({ err }, "runMonitorReportAction failed");
+		logger$10.error({ err }, "runMonitorReportAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -10698,7 +10700,7 @@ async function runMonitorStatusAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$9.error({ err }, "runMonitorStatusAction failed");
+		logger$10.error({ err }, "runMonitorStatusAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -10733,7 +10735,7 @@ async function runMonitorResetAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$9.error({ err }, "runMonitorResetAction failed");
+		logger$10.error({ err }, "runMonitorResetAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -10781,7 +10783,7 @@ async function runMonitorRecommendationsAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$9.error({ err }, "runMonitorRecommendationsAction failed");
+		logger$10.error({ err }, "runMonitorRecommendationsAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -10859,7 +10861,7 @@ function registerMonitorCommand(program, version = "0.0.0", projectRoot = proces
 
 //#endregion
 //#region src/cli/commands/merge.ts
-const logger$8 = createLogger("merge-cmd");
+const logger$9 = createLogger("merge-cmd");
 const MERGE_EXIT_SUCCESS = 0;
 const MERGE_EXIT_CONFLICT = 1;
 const MERGE_EXIT_ERROR = 2;
@@ -10897,7 +10899,7 @@ async function mergeTask(taskId, targetBranch, projectRoot) {
 		projectRoot
 	});
 	try {
-		logger$8.info({
+		logger$9.info({
 			taskId,
 			targetBranch
 		}, "Running conflict detection...");
@@ -10919,7 +10921,7 @@ async function mergeTask(taskId, targetBranch, projectRoot) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		console.error(`Error merging task "${taskId}": ${message}`);
-		logger$8.error({
+		logger$9.error({
 			taskId,
 			err
 		}, "merge --task failed");
@@ -10973,7 +10975,7 @@ async function mergeAll(targetBranch, projectRoot, taskIds) {
 			error: message
 		});
 		console.log(`  Error for task "${taskId}": ${message}`);
-		logger$8.error({
+		logger$9.error({
 			taskId,
 			err
 		}, "merge --all: task failed");
@@ -11026,7 +11028,7 @@ function registerMergeCommand(program, projectRoot = process.cwd()) {
 
 //#endregion
 //#region src/cli/commands/worktrees.ts
-const logger$7 = createLogger("worktrees-cmd");
+const logger$8 = createLogger("worktrees-cmd");
 const WORKTREES_EXIT_SUCCESS = 0;
 const WORKTREES_EXIT_ERROR = 1;
 /** Valid task statuses for filtering */
@@ -11153,7 +11155,7 @@ async function listWorktreesAction(options) {
 		try {
 			worktreeInfos = await manager.listWorktrees();
 		} catch (err) {
-			logger$7.error({ err }, "Failed to list worktrees");
+			logger$8.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;
@@ -11180,7 +11182,7 @@ async function listWorktreesAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$7.error({ err }, "listWorktreesAction failed");
+		logger$8.error({ err }, "listWorktreesAction failed");
 		return WORKTREES_EXIT_ERROR;
 	}
 }
@@ -11221,7 +11223,7 @@ function registerWorktreesCommand(program, version = "0.0.0", projectRoot = proc
 
 //#endregion
 //#region src/cli/commands/brainstorm.ts
-const logger$6 = createLogger("brainstorm-cmd");
+const logger$7 = createLogger("brainstorm-cmd");
 /**
 * Detect whether the project has existing planning artifacts that indicate
 * this is an amendment session (vs. a brand-new project brainstorm).
@@ -11267,13 +11269,13 @@ async function loadAmendmentContextDocuments(projectRoot) {
 	try {
 		brief = await readFile(briefPath, "utf-8");
 	} catch {
-		logger$6.warn({ briefPath }, "product-brief.md not found — continuing without brief context");
+		logger$7.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$6.warn({ prdPath }, "requirements.md not found — continuing without PRD context");
+		logger$7.warn({ prdPath }, "requirements.md not found — continuing without PRD context");
 		process.stderr.write(`Warning: requirements.md not found at ${prdPath}\n`);
 	}
 	return {
@@ -11482,7 +11484,7 @@ async function dispatchToPersonas(userPrompt, context, llmDispatch) {
 		}
 	];
 	const defaultDispatch = async (prompt, personaName) => {
-		logger$6.debug({
+		logger$7.debug({
 			personaName,
 			promptLength: prompt.length
 		}, "Dispatching to persona (stub mode)");
@@ -11499,7 +11501,7 @@ async function dispatchToPersonas(userPrompt, context, llmDispatch) {
 			};
 		} catch (err) {
 			const msg = err instanceof Error ? err.message : String(err);
-			logger$6.error({
+			logger$7.error({
 				err,
 				personaName: persona.name
 			}, "Persona dispatch failed");
@@ -11651,7 +11653,7 @@ async function runBrainstormSession(options, llmDispatch, rlInterface) {
 			}
 		});
 		rl.on("error", (err) => {
-			logger$6.error({ err }, "readline error");
+			logger$7.error({ err }, "readline error");
 			if (!sessionEnded) endSession(false);
 		});
 	});
@@ -11692,7 +11694,7 @@ function registerBrainstormCommand(program, _version = "0.0.0", projectRoot = pr
 
 //#endregion
 //#region src/cli/commands/retry-escalated.ts
-const logger$5 = createLogger("retry-escalated-cmd");
+const logger$6 = 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);
@@ -11733,7 +11735,7 @@ 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$5.warn({
+				logger$6.warn({
 					err,
 					storyKey
 				}, "Failed to read efficiency profile — skipping gate");
@@ -11887,11 +11889,11 @@ async function runRetryEscalatedAction(options) {
 						output_tokens: output,
 						cost_usd: costUsd
 					}).catch((err) => {
-						logger$5.warn({ err }, "Failed to record token usage");
+						logger$6.warn({ err }, "Failed to record token usage");
 					});
 				}
 			} catch (err) {
-				logger$5.warn({ err }, "Failed to record token usage");
+				logger$6.warn({ err }, "Failed to record token usage");
 			}
 		});
 		if (outputFormat === "human") {
@@ -11920,7 +11922,7 @@ 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$5.error({ err }, "retry-escalated failed");
+		logger$6.error({ err }, "retry-escalated failed");
 		return 1;
 	} finally {
 		try {
@@ -11953,7 +11955,7 @@ function registerRetryEscalatedCommand(program, _version = "0.0.0", projectRoot
 
 //#endregion
 //#region src/cli/commands/cancel.ts
-const logger$4 = createLogger("cancel-cmd");
+const logger$5 = createLogger("cancel-cmd");
 async function runCancelAction(options) {
 	const { outputFormat, projectRoot, force } = options;
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
@@ -11992,7 +11994,7 @@ async function runCancelAction(options) {
 		}
 	} catch (err) {
 		const msg = err instanceof Error ? err.message : String(err);
-		logger$4.warn({
+		logger$5.warn({
 			pid,
 			err: msg
 		}, "Failed to kill orchestrator");
@@ -12022,7 +12024,7 @@ async function runCancelAction(options) {
 			await adapter.close();
 		}
 	} catch (err) {
-		logger$4.warn({ err }, "Could not update pipeline run status (non-fatal)");
+		logger$5.warn({ err }, "Could not update pipeline run status (non-fatal)");
 	}
 	if (outputFormat === "json") process.stdout.write(formatOutput({
 		cancelled: true,
@@ -12376,7 +12378,7 @@ function emitDiff(diff, ctx) {
 
 //#endregion
 //#region src/cli/commands/probe-author.ts
-const logger$3 = createLogger("cli:probe-author");
+const logger$4 = 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.
@@ -12445,7 +12447,7 @@ async function runProbeAuthorDispatch(opts, projectRoot, registry) {
 		logger: stderrLogger
 	});
 	const workingDir = opts.workingDir !== void 0 ? resolve$1(opts.workingDir) : resolve$1(storyFilePath, "..");
-	logger$3.info({
+	logger$4.info({
 		storyKey: opts.storyKey,
 		storyFile: storyFilePath,
 		epicFile: epicFilePath,
@@ -12626,7 +12628,7 @@ function registerHistoryCommand(program) {
 
 //#endregion
 //#region src/cli/commands/repo-map.ts
-const logger$2 = createLogger("cli:repo-map");
+const logger$3 = createLogger("cli:repo-map");
 /** Validate that a symbol name contains only safe identifier characters. */
 function isValidSymbolName(name) {
 	return /^[a-zA-Z0-9_]+$/.test(name);
@@ -12661,15 +12663,15 @@ function registerRepoMapCommand(program) {
 			const colRows = await doltClient.query(`SHOW COLUMNS FROM repo_map_symbols LIKE 'dependencies'`);
 			if (colRows.length === 0) {
 				await doltClient.query(`ALTER TABLE repo_map_symbols ADD COLUMN dependencies JSON`);
-				logger$2.info("Applied migration: added dependencies column to repo_map_symbols");
+				logger$3.info("Applied migration: added dependencies column to repo_map_symbols");
 			}
 		} catch {
-			logger$2.debug("Skipping repo_map_symbols migration: table not yet created");
+			logger$3.debug("Skipping repo_map_symbols migration: table not yet created");
 		}
-		const symbolRepo = new DoltSymbolRepository(doltClient, logger$2);
+		const symbolRepo = new DoltSymbolRepository(doltClient, logger$3);
 		const metaRepo = new DoltRepoMapMetaRepository(doltClient);
-		const repoMapModule = new RepoMapModule(metaRepo, logger$2);
-		const queryEngine = new RepoMapQueryEngine(symbolRepo, logger$2);
+		const repoMapModule = new RepoMapModule(metaRepo, logger$3);
+		const queryEngine = new RepoMapQueryEngine(symbolRepo, logger$3);
 		if (options.show === true || !options.update && !options.query && !options.dryRun) {
 			const meta = await metaRepo.getMeta();
 			const staleResult = await repoMapModule.checkStaleness();
@@ -12695,9 +12697,9 @@ function registerRepoMapCommand(program) {
 			return;
 		}
 		if (options.update === true) {
-			logger$2.info("repo-map --update: triggering incremental update");
-			const gitClient = new GitClient(logger$2);
-			const grammarLoader = new GrammarLoader(logger$2);
+			logger$3.info("repo-map --update: triggering incremental update");
+			const gitClient = new GitClient(logger$3);
+			const grammarLoader = new GrammarLoader(logger$3);
 			if (grammarLoader.getGrammar(".ts") === null) {
 				const msg = "tree-sitter grammars not installed. Run `npm install tree-sitter tree-sitter-typescript tree-sitter-javascript tree-sitter-python` in the substrate installation directory.";
 				if (options.outputFormat === "json") console.log(JSON.stringify({
@@ -12708,15 +12710,15 @@ function registerRepoMapCommand(program) {
 				process.exitCode = 1;
 				return;
 			}
-			const parser = new SymbolParser(grammarLoader, logger$2);
-			const storage = new RepoMapStorage(symbolRepo, metaRepo, gitClient, logger$2);
+			const parser = new SymbolParser(grammarLoader, logger$3);
+			const storage = new RepoMapStorage(symbolRepo, metaRepo, gitClient, logger$3);
 			let updateWarning;
 			try {
 				await storage.incrementalUpdate(dbRoot, parser);
 			} catch (err) {
 				if (err instanceof AppError && err.code === ERR_REPO_MAP_STORAGE_WRITE) {
 					updateWarning = err.message;
-					logger$2.warn({ err }, "repo-map --update: storage write error (partial update)");
+					logger$3.warn({ err }, "repo-map --update: storage write error (partial update)");
 				} else throw err;
 			}
 			const meta = await metaRepo.getMeta();
@@ -12736,7 +12738,7 @@ function registerRepoMapCommand(program) {
 			return;
 		}
 		if (options.query !== void 0) {
-			logger$2.debug({ symbol: options.query }, "repo-map --query");
+			logger$3.debug({ symbol: options.query }, "repo-map --query");
 			const result = await queryEngine.query({
 				symbols: [options.query],
 				maxTokens: 4e3
@@ -12758,7 +12760,7 @@ function registerRepoMapCommand(program) {
 				process.exitCode = 1;
 				return;
 			}
-			const injector = new RepoMapInjector(queryEngine, logger$2);
+			const injector = new RepoMapInjector(queryEngine, logger$3);
 			const injectionResult = await injector.buildContext(storyContent, 2e3);
 			console.log(JSON.stringify({
 				text: injectionResult.text,
@@ -12772,7 +12774,7 @@ function registerRepoMapCommand(program) {
 
 //#endregion
 //#region src/cli/commands/routing.ts
-const logger$1 = createLogger("cli:routing");
+const logger$2 = createLogger("cli:routing");
 function registerRoutingCommand(program) {
 	program.command("routing").description("Show routing configuration and auto-tune history").option("--history", "Show the routing auto-tune log (model changes applied)").option("--output-format <format>", "Output format: text or json", "text").action(async (options) => {
 		const dbRoot = await resolveMainRepoRoot(process.cwd());
@@ -12789,7 +12791,7 @@ function registerRoutingCommand(program) {
 		try {
 			await store.initialize();
 			if (options.history === true) {
-				logger$1.debug("routing --history: fetching tune log");
+				logger$2.debug("routing --history: fetching tune log");
 				const raw$1 = await store.getMetric("global", "routing_tune_log");
 				let entries = [];
 				if (Array.isArray(raw$1)) entries = raw$1.sort((a, b) => b.appliedAt.localeCompare(a.appliedAt));
@@ -13124,6 +13126,405 @@ function registerFactoryCommand$1(program) {
 	}) });
 }
 
+//#endregion
+//#region src/cli/commands/reconcile-from-disk.ts
+const logger$1 = createLogger("reconcile-from-disk");
+/** 64KB tail window for capturing subprocess stderr/stdout (Story 66-5 pattern). */
+const MAX_OUTPUT_BYTES = 64 * 1024;
+/**
+* Gate chain definition — each gate runs in order. On any failure the chain
+* halts and emits pipeline:reconcile-gate-failed before exiting with code 1.
+*/
+const GATE_CHAIN = [
+	{
+		name: "build",
+		cmd: "npm",
+		args: ["run", "build"],
+		timeoutMs: 18e4
+	},
+	{
+		name: "check:circular",
+		cmd: "npm",
+		args: ["run", "check:circular"],
+		timeoutMs: 6e4
+	},
+	{
+		name: "typecheck:gate",
+		cmd: "npm",
+		args: ["run", "typecheck:gate"],
+		timeoutMs: 12e4
+	},
+	{
+		name: "test:fast",
+		cmd: "npm",
+		args: ["run", "test:fast"],
+		timeoutMs: 3e5
+	}
+];
+/**
+* Truncate a string to the last N bytes (tail-window pattern from Story 66-5).
+* Preserves the END of the string, which contains the most recent diagnostic output.
+*/
+function tailWindow(s, maxBytes = MAX_OUTPUT_BYTES) {
+	if (!s) return "";
+	if (Buffer.byteLength(s, "utf-8") <= maxBytes) return s;
+	const buf = Buffer.from(s, "utf-8");
+	return buf.slice(buf.length - maxBytes).toString("utf-8");
+}
+/**
+* Read and parse the reconcile manifest index from .substrate/runs/manifest.json.
+* Returns null if the file doesn't exist or fails to parse.
+*/
+async function readReconcileManifest(dbRoot) {
+	const manifestPath = join(dbRoot, ".substrate", "runs", "manifest.json");
+	try {
+		const content = await readFile(manifestPath, "utf-8");
+		const parsed = JSON.parse(content);
+		if (parsed !== null && typeof parsed === "object" && "runs" in parsed && Array.isArray(parsed.runs)) return parsed;
+		return null;
+	} catch {
+		return null;
+	}
+}
+/**
+* Find a specific run entry from the manifest by runId.
+* When runId is not provided, returns the last (most recent) entry.
+*/
+function findRunEntry(manifest, runId) {
+	if (manifest.runs.length === 0) return null;
+	if (runId) return manifest.runs.find((r) => r.runId === runId) ?? null;
+	return manifest.runs[manifest.runs.length - 1] ?? null;
+}
+/**
+* Detect an auto-committed SHA for a story using git log.
+*
+* Searches commits matching `feat(story-<storyKey>)` since started_at using
+* git's --grep filter. Returns the first matching SHA, or undefined if none found.
+*
+* Git operations use `cwd: projectRoot` (not process.cwd()) to avoid the
+* bash-session-drift footgun documented in obs_025.
+*/
+function detectAutoCommit(storyKey, startedAt, projectRoot) {
+	const grepPattern = `feat(story-${storyKey})`;
+	const result = spawnSync("git", [
+		"log",
+		"--oneline",
+		`--since=${startedAt}`,
+		`--grep=${grepPattern}`
+	], {
+		cwd: projectRoot,
+		encoding: "utf-8",
+		timeout: 1e4
+	});
+	if (result.status !== 0 || !result.stdout?.trim()) return void 0;
+	const lines = result.stdout.trim().split("\n").filter(Boolean);
+	for (const line of lines) {
+		const sha = line.split(" ")[0];
+		if (sha) return sha;
+	}
+	return void 0;
+}
+/**
+* Detect working-tree changes for files declared in targetFiles.
+*
+* Runs `git status --porcelain` and cross-references with targetFiles.
+* Returns the list of matching modified/added/deleted paths.
+*/
+function detectWorkingTreeChanges(targetFiles, projectRoot) {
+	if (targetFiles.length === 0) return [];
+	const result = spawnSync("git", ["status", "--porcelain"], {
+		cwd: projectRoot,
+		encoding: "utf-8",
+		timeout: 1e4
+	});
+	if (result.status !== 0 || !result.stdout?.trim()) return [];
+	const modifiedPaths = [];
+	const lines = result.stdout.split("\n").filter((l) => l.trim().length > 0);
+	for (const line of lines) {
+		const path$4 = line.length > 3 ? line.slice(3).trim() : line.trim();
+		for (const tf of targetFiles) if (path$4 === tf || path$4.endsWith(`/${tf}`) || tf.endsWith(`/${path$4}`) || path$4.endsWith(tf) || tf.endsWith(path$4)) {
+			modifiedPaths.push(path$4);
+			break;
+		}
+	}
+	return modifiedPaths;
+}
+/**
+* Run the validation gate chain: build → check:circular → typecheck:gate → test:fast.
+*
+* Each gate uses child_process.spawnSync with an explicit timeout. On any gate
+* failure, stderr/stdout are captured with a 64KB tail-window (Story 66-5 pattern)
+* and the chain halts.
+*/
+function runGateChain(projectRoot) {
+	const gateResults = [];
+	for (const gate of GATE_CHAIN) {
+		const startMs = Date.now();
+		const result = spawnSync(gate.cmd, gate.args, {
+			cwd: projectRoot,
+			encoding: "utf-8",
+			timeout: gate.timeoutMs
+		});
+		const durationMs = Date.now() - startMs;
+		const stderrTail = tailWindow(result.stderr ?? "");
+		const stdoutTail = tailWindow(result.stdout ?? "");
+		const exitCode = result.status ?? (result.signal ? 128 : -1);
+		const passed = result.status === 0 && !result.signal;
+		gateResults.push({
+			gate: gate.name,
+			passed,
+			exitCode,
+			durationMs,
+			...stderrTail ? { stderrTail } : {},
+			...stdoutTail ? { stdoutTail } : {}
+		});
+		if (!passed) return {
+			passed: false,
+			gateResults
+		};
+	}
+	return {
+		passed: true,
+		gateResults
+	};
+}
+/**
+* Prompt the operator for confirmation before making Dolt writes.
+* Returns true if the operator responds 'y' or 'Y'.
+*/
+async function promptOperator(storyCount) {
+	return new Promise((resolve$2) => {
+		const rl = readline.createInterface({
+			input: process.stdin,
+			output: process.stdout
+		});
+		rl.question(`Reconcile ${storyCount} stories to status='complete'? [y/N] `, (answer) => {
+			rl.close();
+			resolve$2(answer.toLowerCase() === "y");
+		});
+	});
+}
+/**
+* Run the reconcile-from-disk action.
+* Returns exit code: 0 = success/no-op, 1 = error/gate-failure.
+*/
+async function runReconcileFromDiskAction(options) {
+	const { runId, dryRun = false, yes = false, outputFormat, projectRoot, _dbRoot, _skipGates = false } = options;
+	const startMs = Date.now();
+	const dbRoot = _dbRoot ?? await resolveMainRepoRoot(projectRoot);
+	const indexManifest = await readReconcileManifest(dbRoot);
+	let resolvedRunId = null;
+	let runEntry = null;
+	if (runId) {
+		resolvedRunId = runId;
+		if (indexManifest) runEntry = findRunEntry(indexManifest, runId);
+	} else if (indexManifest && indexManifest.runs.length > 0) {
+		runEntry = findRunEntry(indexManifest);
+		resolvedRunId = runEntry?.runId ?? null;
+	} else resolvedRunId = await readCurrentRunId(dbRoot);
+	if (!resolvedRunId) {
+		const errorMsg = "No runs found. Use `substrate metrics --output-format json` for run history.";
+		if (outputFormat === "json") process.stdout.write(JSON.stringify({ error: errorMsg }) + "\n");
+		else process.stderr.write(`Error: ${errorMsg}\n`);
+		return 1;
+	}
+	if (!runEntry) {
+		const { manifest: fullManifest } = await resolveRunManifest(dbRoot, resolvedRunId);
+		if (fullManifest) try {
+			const data = await fullManifest.read();
+			const stories = Object.entries(data.per_story_state).map(([key, state]) => ({
+				storyKey: key,
+				status: state.status
+			}));
+			runEntry = {
+				runId: resolvedRunId,
+				started_at: data.created_at,
+				stories
+			};
+		} catch {
+			logger$1.debug({ runId: resolvedRunId }, "failed to read individual run manifest");
+		}
+	}
+	if (!runEntry) {
+		const errorMsg = runId ? `Run '${runId}' not found. Use \`substrate metrics --output-format json\` for run history.` : "No runs found. Use `substrate metrics --output-format json` for run history.";
+		if (outputFormat === "json") process.stdout.write(JSON.stringify({ error: errorMsg }) + "\n");
+		else process.stderr.write(`Error: ${errorMsg}\n`);
+		return 1;
+	}
+	const candidateStories = runEntry.stories.filter((s) => s.status !== "complete" && s.status !== "cancelled");
+	if (candidateStories.length === 0) {
+		const output$1 = {
+			runId: resolvedRunId,
+			candidates: [],
+			gateResults: [],
+			reconciled: false,
+			affectedStoryKeys: []
+		};
+		if (outputFormat === "json") process.stdout.write(JSON.stringify(output$1) + "\n");
+		else process.stdout.write(`All stories already complete or cancelled for run ${resolvedRunId}.\n`);
+		return 0;
+	}
+	const diffRecords = [];
+	for (const story of candidateStories) {
+		const autoCommittedSha = detectAutoCommit(story.storyKey, runEntry.started_at, projectRoot);
+		const modifiedFiles = detectWorkingTreeChanges(story.targetFiles ?? [], projectRoot);
+		const reconcilable = !!(autoCommittedSha || modifiedFiles.length > 0);
+		diffRecords.push({
+			storyKey: story.storyKey,
+			autoCommittedSha,
+			modifiedFiles,
+			reconcilable
+		});
+	}
+	if (dryRun) {
+		const output$1 = {
+			runId: resolvedRunId,
+			candidates: diffRecords,
+			gateResults: [],
+			reconciled: false,
+			affectedStoryKeys: []
+		};
+		if (outputFormat === "json") process.stdout.write(JSON.stringify(output$1) + "\n");
+		else {
+			process.stdout.write(`[DRY RUN] Run: ${resolvedRunId}\n`);
+			process.stdout.write(`Would run gates: ${GATE_CHAIN.map((g) => g.name).join(" → ")}\n`);
+			const reconcilable = diffRecords.filter((r) => r.reconcilable);
+			process.stdout.write(`Would reconcile ${reconcilable.length} of ${diffRecords.length} candidate stories\n`);
+			for (const r of diffRecords) {
+				const status = r.reconcilable ? "✓ reconcilable" : "✗ not reconcilable";
+				const detail = r.autoCommittedSha ? ` (commit: ${r.autoCommittedSha})` : "";
+				process.stdout.write(`  ${r.storyKey}: ${status}${detail}\n`);
+			}
+		}
+		return 0;
+	}
+	const { passed, gateResults } = _skipGates ? {
+		passed: true,
+		gateResults: []
+	} : runGateChain(projectRoot);
+	if (!passed) {
+		const failedGateResult = gateResults.find((g) => !g.passed);
+		const failedGateName = failedGateResult?.gate ?? "unknown";
+		const durationMs$1 = Date.now() - startMs;
+		const localBus$1 = new EventEmitter();
+		localBus$1.emit("pipeline:reconcile-gate-failed", {
+			runId: resolvedRunId,
+			failedGate: failedGateName,
+			stderrTail: failedGateResult?.stderrTail,
+			stdoutTail: failedGateResult?.stdoutTail,
+			durationMs: durationMs$1
+		});
+		logger$1.info({
+			runId: resolvedRunId,
+			failedGate: failedGateName,
+			exitCode: failedGateResult?.exitCode
+		}, "reconcile-from-disk gate failed");
+		const output$1 = {
+			runId: resolvedRunId,
+			candidates: diffRecords,
+			gateResults,
+			reconciled: false,
+			affectedStoryKeys: []
+		};
+		if (outputFormat === "json") process.stdout.write(JSON.stringify(output$1) + "\n");
+		else {
+			process.stderr.write(`Gate '${failedGateName}' failed (exit ${failedGateResult?.exitCode ?? -1}). No Dolt changes made.\n`);
+			if (failedGateResult?.stderrTail) process.stderr.write(`--- stderr ---\n${failedGateResult.stderrTail}\n`);
+		}
+		return 1;
+	}
+	const reconcilableRecords = diffRecords.filter((r) => r.reconcilable);
+	if (!yes) {
+		if (outputFormat === "human") {
+			process.stdout.write(`\nRun: ${resolvedRunId}\n`);
+			process.stdout.write(`Stories to reconcile (${reconcilableRecords.length}):\n`);
+			for (const r of reconcilableRecords) {
+				const detail = r.autoCommittedSha ? ` (commit: ${r.autoCommittedSha})` : "";
+				process.stdout.write(`  ${r.storyKey}${detail}\n`);
+			}
+			process.stdout.write("\n");
+		}
+		const confirmed = await promptOperator(reconcilableRecords.length);
+		if (!confirmed) {
+			const output$1 = {
+				runId: resolvedRunId,
+				candidates: diffRecords,
+				gateResults,
+				reconciled: false,
+				affectedStoryKeys: []
+			};
+			if (outputFormat === "json") process.stdout.write(JSON.stringify(output$1) + "\n");
+			else process.stdout.write("Reconciliation declined.\n");
+			return 0;
+		}
+	}
+	const adapter = createDatabaseAdapter({
+		backend: "auto",
+		basePath: dbRoot
+	});
+	try {
+		await initSchema(adapter);
+		const now = new Date().toISOString();
+		await adapter.transaction(async (tx) => {
+			for (const record of reconcilableRecords) await tx.query("UPDATE wg_stories SET status='complete', updated_at=? WHERE story_key=? AND run_id=?", [
+				now,
+				record.storyKey,
+				resolvedRunId
+			]);
+		});
+		logger$1.info({
+			runId: resolvedRunId,
+			affectedStories: reconcilableRecords.map((r) => r.storyKey)
+		}, "reconcile-from-disk: Dolt update complete");
+	} finally {
+		await adapter.close().catch(() => {});
+	}
+	const durationMs = Date.now() - startMs;
+	const affectedStoryKeys = reconcilableRecords.map((r) => r.storyKey);
+	const localBus = new EventEmitter();
+	localBus.emit("pipeline:reconcile-from-disk", {
+		runId: resolvedRunId,
+		affectedStories: affectedStoryKeys,
+		gatesPassed: true,
+		operatorConfirmed: !yes,
+		durationMs
+	});
+	const output = {
+		runId: resolvedRunId,
+		candidates: diffRecords,
+		gateResults,
+		reconciled: true,
+		affectedStoryKeys
+	};
+	if (outputFormat === "json") process.stdout.write(JSON.stringify(output) + "\n");
+	else {
+		process.stdout.write(`Reconciled ${affectedStoryKeys.length} stories to 'complete' in ${durationMs}ms.\n`);
+		for (const key of affectedStoryKeys) process.stdout.write(`  ✓ ${key}\n`);
+	}
+	return 0;
+}
+/**
+* Register the `reconcile-from-disk` subcommand with the CLI program.
+*
+* Command shape:
+*   substrate reconcile-from-disk [--run-id <id>] [--dry-run] [--yes]
+*                                  [--output-format <human|json>]
+*                                  [--project-root <path>]
+*/
+function registerReconcileFromDiskCommand(program, _version = "0.0.0", projectRoot = process.cwd(), _registry) {
+	program.command("reconcile-from-disk").description("Reconcile wg_stories.status against working-tree and git history (Path A recovery)").option("--run-id <id>", "Pipeline run ID to reconcile (defaults to most recent run in .substrate/runs/manifest.json)").option("--dry-run", "Print discovery output and would-update list without running gates or writing Dolt").option("--yes", "Skip operator confirmation prompt (gates still run; gate failure still aborts)").option("--output-format <format>", "Output format: human (default) or json", "human").option("--project-root <path>", "Project root directory", projectRoot).action(async (opts) => {
+		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
+		const exitCode = await runReconcileFromDiskAction({
+			runId: opts.runId,
+			dryRun: opts.dryRun,
+			yes: opts.yes,
+			outputFormat,
+			projectRoot: opts.projectRoot
+		});
+		process.exitCode = exitCode;
+	});
+}
+
 //#endregion
 //#region src/cli/index.ts
 process.setMaxListeners(20);
@@ -13192,6 +13593,7 @@ async function createProgram() {
 	registerEpicStatusCommand(program);
 	registerScenariosCommand(program);
 	registerFactoryCommand$1(program);
+	registerReconcileFromDiskCommand(program, version, process.cwd(), registry);
 	registerUpgradeCommand(program);
 	return program;
 }