substrate-ai 0.2.20 → 0.2.21

package/dist/cli/index.js

@@ -1,11 +1,11 @@
 #!/usr/bin/env node
-import { DatabaseWrapper, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createContextCompiler, createDispatcher, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, findPackageRoot, formatOutput, formatPhaseCompletionSummary, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, registerHealthCommand, registerRunCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, runAnalysisPhase, runMigrations, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-CcWb6Kb-.js";
+import { DatabaseWrapper, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createContextCompiler, createDispatcher, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, findPackageRoot, formatOutput, formatPhaseCompletionSummary, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, registerHealthCommand, registerRunCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, runAnalysisPhase, runMigrations, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-BLIgARum.js";
 import { createLogger, deepMask } from "../logger-D2fS2ccL.js";
 import { AdapterRegistry, createEventBus } from "../event-bus-BMxhfxfT.js";
 import { CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, PartialSubstrateConfigSchema, SUPPORTED_CONFIG_FORMAT_VERSIONS, SubstrateConfigSchema, defaultConfigMigrator } from "../version-manager-impl-CZ6KF1Ds.js";
 import { ConfigError, ConfigIncompatibleFormatError } from "../errors-BPqtzQ4U.js";
-import { addTokenUsage, createDecision, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestRun, getTokenUsageSummary, listRequirements, updatePipelineRun } from "../decisions-Dq4cAA2L.js";
-import { EXPERIMENT_RESULT, OPERATIONAL_FINDING, STORY_METRICS, aggregateTokenUsageForRun, compareRunMetrics, getBaselineRunMetrics, getRunMetrics, getStoryMetricsForRun, incrementRunRestarts, listRunMetrics, tagRunAsBaseline } from "../operational-Dq4IfJzE.js";
+import { addTokenUsage, createDecision, createPipelineRun, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestRun, getTokenUsageSummary, listRequirements, updatePipelineRun } from "../decisions-Dq4cAA2L.js";
+import { ESCALATION_DIAGNOSIS, EXPERIMENT_RESULT, OPERATIONAL_FINDING, STORY_METRICS, aggregateTokenUsageForRun, compareRunMetrics, getBaselineRunMetrics, getRunMetrics, getStoryMetricsForRun, incrementRunRestarts, listRunMetrics, tagRunAsBaseline } from "../operational-CnMlvWqc.js";
 import { abortMerge, createWorktree, getConflictingFiles, getMergedFiles, getOrphanedWorktrees, performMerge, removeBranch, removeWorktree, simulateMerge, verifyGitVersion } from "../git-utils-CtmrZrHS.js";
 import { registerUpgradeCommand } from "../upgrade-CjjAx5kD.js";
 import { Command } from "commander";
@@ -324,7 +324,7 @@ const DEFAULT_CONFIG = {
 
 //#endregion
 //#region src/cli/commands/init.ts
-const logger$16 = createLogger("init");
+const logger$17 = createLogger("init");
 const __dirname = dirname(new URL(import.meta.url).pathname);
 const INIT_EXIT_SUCCESS = 0;
 const INIT_EXIT_ERROR = 1;
@@ -345,7 +345,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 	const version = resolveBmadMethodVersion();
 	if (force && bmadExists) process.stderr.write(`Warning: Replacing existing _bmad/ framework with bmad-method@${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");
@@ -355,7 +355,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 			const destDir = join(bmadDest, dir);
 			mkdirSync(destDir, { recursive: true });
 			cpSync(srcDir, destDir, { recursive: true });
-			logger$16.info({
+			logger$17.info({
 				dir,
 				dest: destDir
 			}, "Scaffolded BMAD framework directory");
@@ -374,7 +374,7 @@ 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 -->";
@@ -389,7 +389,7 @@ async function scaffoldClaudeMd(projectRoot) {
 	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;
 	}
 	if (!sectionContent.endsWith("\n")) sectionContent += "\n";
@@ -407,7 +407,7 @@ async function scaffoldClaudeMd(projectRoot) {
 		newContent = existingContent + separator + sectionContent;
 	}
 	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 scaffoldStatuslineScript(projectRoot) {
 	const pkgRoot = findPackageRoot(__dirname);
@@ -418,7 +418,7 @@ 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");
@@ -426,7 +426,7 @@ async function scaffoldStatuslineScript(projectRoot) {
 	mkdirSync(claudeDir, { recursive: true });
 	await writeFile(statuslinePath, content, "utf8");
 	chmodSync(statuslinePath, 493);
-	logger$16.info({ statuslinePath }, "Wrote .claude/statusline.sh");
+	logger$17.info({ statuslinePath }, "Wrote .claude/statusline.sh");
 }
 async function scaffoldClaudeSettings(projectRoot) {
 	const claudeDir = join(projectRoot, ".claude");
@@ -442,7 +442,7 @@ async function scaffoldClaudeSettings(projectRoot) {
 	if (!merged["$schema"]) merged["$schema"] = "https://json.schemastore.org/claude-code-settings.json";
 	mkdirSync(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 {
@@ -512,7 +512,7 @@ async function compileBmadAgents(bmadDir) {
 				writeFileSync(mdPath, result.xml, "utf-8");
 				compiled++;
 			} catch (compileErr) {
-				logger$16.debug({
+				logger$17.debug({
 					err: compileErr,
 					file
 				}, "Failed to compile agent YAML");
@@ -533,9 +533,9 @@ 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 { AgentCommandGenerator } = _require(join(installerLibPath, "ide", "shared", "agent-command-generator.js"));
 		const { WorkflowCommandGenerator } = _require(join(installerLibPath, "ide", "shared", "workflow-command-generator.js"));
@@ -547,7 +547,7 @@ 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(commandsDir, { recursive: true });
@@ -563,7 +563,7 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		const taskToolCount = await taskToolGen.writeDashArtifacts(commandsDir, taskToolArtifacts);
 		const total = agentCount + workflowCount + taskToolCount;
 		if (outputFormat !== "json") 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,
@@ -573,7 +573,7 @@ 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");
 	}
 }
 const PROVIDER_DEFAULTS = DEFAULT_CONFIG.providers;
@@ -647,7 +647,7 @@ 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;
@@ -696,12 +696,12 @@ async function runInitAction(options) {
 				return INIT_EXIT_ERROR;
 			}
 			if (force && existsSync(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(dirname(packPath), { recursive: true });
 			cpSync(bundledPackPath, packPath, { recursive: true });
-			logger$16.info({
+			logger$17.info({
 				pack: packName,
 				dest: packPath
 			}, "Scaffolded methodology pack");
@@ -754,7 +754,7 @@ 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;
 	}
 }
@@ -800,7 +800,7 @@ function formatUnsupportedVersionError(formatType, version, supported) {
 
 //#endregion
 //#region src/modules/config/config-system-impl.ts
-const logger$15 = createLogger("config");
+const logger$16 = createLogger("config");
 function deepMerge(base, override) {
 	const result = { ...base };
 	for (const [key, val] of Object.entries(override)) if (val !== null && val !== void 0 && typeof val === "object" && !Array.isArray(val) && typeof result[key] === "object" && result[key] !== null && !Array.isArray(result[key])) result[key] = deepMerge(result[key], val);
@@ -845,7 +845,7 @@ function readEnvOverrides() {
 	}
 	const parsed = PartialSubstrateConfigSchema.safeParse(overrides);
 	if (!parsed.success) {
-		logger$15.warn({ errors: parsed.error.issues }, "Invalid environment variable overrides ignored");
+		logger$16.warn({ errors: parsed.error.issues }, "Invalid environment variable overrides ignored");
 		return {};
 	}
 	return parsed.data;
@@ -909,7 +909,7 @@ var ConfigSystemImpl = class {
 			throw new ConfigError(`Configuration validation failed:\n${issues}`, { issues: result.error.issues });
 		}
 		this._config = result.data;
-		logger$15.debug("Configuration loaded successfully");
+		logger$16.debug("Configuration loaded successfully");
 	}
 	getConfig() {
 		if (this._config === null) throw new ConfigError("Configuration has not been loaded. Call load() before getConfig().", {});
@@ -972,7 +972,7 @@ var ConfigSystemImpl = class {
 				if (version !== void 0 && typeof version === "string" && !isVersionSupported(version, SUPPORTED_CONFIG_FORMAT_VERSIONS)) if (defaultConfigMigrator.canMigrate(version, CURRENT_CONFIG_FORMAT_VERSION)) {
 					const migrationOutput = defaultConfigMigrator.migrate(rawObj, version, CURRENT_CONFIG_FORMAT_VERSION, filePath);
 					if (migrationOutput.result.success) {
-						logger$15.info({
+						logger$16.info({
 							from: version,
 							to: CURRENT_CONFIG_FORMAT_VERSION,
 							backup: migrationOutput.result.backupPath
@@ -1015,7 +1015,7 @@ function createConfigSystem(options = {}) {
 
 //#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;
@@ -1041,7 +1041,7 @@ 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;
 	}
@@ -1115,7 +1115,7 @@ 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;
 	}
@@ -1269,9 +1269,9 @@ function registerConfigCommand(program, _version) {
 
 //#endregion
 //#region src/cli/commands/resume.ts
-const logger$13 = createLogger("resume-cmd");
+const logger$14 = createLogger("resume-cmd");
 async function runResumeAction(options) {
-	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName } = options;
+	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName, registry } = options;
 	if (stopAfter !== void 0 && !VALID_PHASES.includes(stopAfter)) {
 		const errorMsg = `Invalid phase: "${stopAfter}". Valid phases: ${VALID_PHASES.join(", ")}`;
 		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
@@ -1345,13 +1345,14 @@ async function runResumeAction(options) {
 			concurrency,
 			outputFormat,
 			existingRunId: runId,
-			projectRoot
+			projectRoot,
+			registry
 		});
 	} catch (err) {
 		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 {
@@ -1360,7 +1361,7 @@ async function runResumeAction(options) {
 	}
 }
 async function runFullPipelineFromPhase(options) {
-	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, existingRunId, projectRoot } = options;
+	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, existingRunId, projectRoot, registry: injectedRegistry } = options;
 	if (!existsSync(dbDir)) mkdirSync(dbDir, { recursive: true });
 	const dbWrapper = new DatabaseWrapper(dbPath);
 	try {
@@ -1380,8 +1381,8 @@ async function runFullPipelineFromPhase(options) {
 		}
 		const eventBus = createEventBus();
 		const contextCompiler = createContextCompiler({ db });
-		const adapterRegistry = new AdapterRegistry();
-		await adapterRegistry.discoverAndRegister();
+		const adapterRegistry = injectedRegistry ?? new AdapterRegistry();
+		if (injectedRegistry === void 0) await adapterRegistry.discoverAndRegister();
 		const dispatcher = createDispatcher({
 			eventBus,
 			adapterRegistry
@@ -1502,7 +1503,7 @@ async function runFullPipelineFromPhase(options) {
 							});
 						}
 					} catch (err) {
-						logger$13.warn({ err }, "Failed to record token usage");
+						logger$14.warn({ err }, "Failed to record token usage");
 					}
 				});
 				const storyDecisions = db.prepare(`SELECT description FROM requirements WHERE pipeline_run_id = ? AND source = 'solutioning-phase'`).all(runId);
@@ -1561,7 +1562,7 @@ 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 {
@@ -1569,7 +1570,7 @@ async function runFullPipelineFromPhase(options) {
 		} catch {}
 	}
 }
-function registerResumeCommand(program, _version = "0.0.0", projectRoot = process.cwd()) {
+function registerResumeCommand(program, _version = "0.0.0", projectRoot = process.cwd(), registry) {
 	program.command("resume").description("Resume a previously interrupted pipeline run").option("--run-id <id>", "Pipeline run ID to resume (defaults to latest)").option("--pack <name>", "Methodology pack name", "bmad").option("--stop-after <phase>", "Stop pipeline after this phase completes (overrides saved state)").option("--concurrency <n>", "Maximum parallel conflict groups", (v) => parseInt(v, 10), 3).option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		const exitCode = await runResumeAction({
@@ -1578,7 +1579,8 @@ function registerResumeCommand(program, _version = "0.0.0", projectRoot = proces
 			outputFormat,
 			projectRoot: opts.projectRoot,
 			concurrency: opts.concurrency,
-			pack: opts.pack
+			pack: opts.pack,
+			registry
 		});
 		process.exitCode = exitCode;
 	});
@@ -1586,7 +1588,7 @@ 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");
 async function runStatusAction(options) {
 	const { outputFormat, runId, projectRoot } = options;
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
@@ -1663,7 +1665,7 @@ 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 {
@@ -2087,7 +2089,7 @@ 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.
 *
@@ -2118,7 +2120,7 @@ function runPostPhaseSupersessionDetection(db, amendmentRunId, currentPhase, han
 			});
 		} catch (err) {
 			const msg = err instanceof Error ? err.message : String(err);
-			logger$11.warn({
+			logger$12.warn({
 				err,
 				originalId: parentMatch.id,
 				supersedingId: newDec.id
@@ -2127,7 +2129,7 @@ function runPostPhaseSupersessionDetection(db, amendmentRunId, currentPhase, han
 	}
 }
 async function runAmendAction(options) {
-	const { concept: conceptArg, conceptFile, runId: specifiedRunId, stopAfter, from: startPhase, projectRoot, pack: packName } = options;
+	const { concept: conceptArg, conceptFile, runId: specifiedRunId, stopAfter, from: startPhase, projectRoot, pack: packName, registry: injectedRegistry } = options;
 	let concept;
 	if (conceptFile !== void 0 && conceptFile !== "") try {
 		concept = await readFile(conceptFile, "utf-8");
@@ -2214,8 +2216,8 @@ async function runAmendAction(options) {
 		}
 		const eventBus = createEventBus();
 		const contextCompiler = createContextCompiler({ db });
-		const adapterRegistry = new AdapterRegistry();
-		await adapterRegistry.discoverAndRegister();
+		const adapterRegistry = injectedRegistry ?? new AdapterRegistry();
+		if (injectedRegistry === void 0) await adapterRegistry.discoverAndRegister();
 		const dispatcher = createDispatcher({
 			eventBus,
 			adapterRegistry
@@ -2253,7 +2255,7 @@ 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");
@@ -2373,7 +2375,7 @@ 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 {
@@ -2381,7 +2383,7 @@ async function runAmendAction(options) {
 		} catch {}
 	}
 }
-function registerAmendCommand(program, _version = "0.0.0", projectRoot = process.cwd()) {
+function registerAmendCommand(program, _version = "0.0.0", projectRoot = process.cwd(), registry) {
 	program.command("amend").description("Run an amendment pipeline against a completed run and an existing run").option("--concept <text>", "Amendment concept description (inline)").option("--concept-file <path>", "Path to concept file").option("--run-id <id>", "Parent run ID (defaults to latest completed run)").option("--stop-after <phase>", "Stop pipeline after this phase completes").option("--from <phase>", "Start pipeline from this phase").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").action(async (opts) => {
 		const exitCode = await runAmendAction({
 			concept: opts.concept,
@@ -2390,7 +2392,8 @@ function registerAmendCommand(program, _version = "0.0.0", projectRoot = process
 			stopAfter: opts.stopAfter,
 			from: opts.from,
 			projectRoot: opts.projectRoot,
-			pack: opts.pack
+			pack: opts.pack,
+			registry
 		});
 		process.exitCode = exitCode;
 	});
@@ -2828,7 +2831,7 @@ async function runSupervisorAction(options, deps = {}) {
 						try {
 							const { createExperimenter } = await import(
 								/* @vite-ignore */
-								"../experimenter-prkFLFPw.js"
+								"../experimenter-bc40oi8p.js"
 );
 							const { getLatestRun: getLatest } = await import(
 								/* @vite-ignore */
@@ -2842,7 +2845,7 @@ async function runSupervisorAction(options, deps = {}) {
 								const expDb = expDbWrapper.db;
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-C5zfaWYN.js"
+									"../run-gmS6DsGT.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -3085,7 +3088,7 @@ 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 runMetricsAction(options) {
 	const { outputFormat, projectRoot, limit = 10, compare, tagBaseline, analysis } = options;
 	if (analysis !== void 0) {
@@ -3237,7 +3240,7 @@ 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 {
@@ -3491,7 +3494,7 @@ function getPlanningCostTotal(db, sessionId) {
 function getLatestSessionId(_db) {
 	return null;
 }
-const logger$9 = createLogger("cost-cmd");
+const logger$10 = createLogger("cost-cmd");
 const COST_EXIT_SUCCESS = 0;
 const COST_EXIT_ERROR = 1;
 /**
@@ -3737,7 +3740,7 @@ 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 (wrapper !== null) try {
@@ -3839,7 +3842,7 @@ function applyMonitorSchema(db) {
 
 //#endregion
 //#region src/persistence/monitor-database.ts
-const logger$8 = createLogger("persistence:monitor-db");
+const logger$9 = createLogger("persistence:monitor-db");
 var MonitorDatabaseImpl = class {
 	_db = null;
 	_path;
@@ -3850,10 +3853,10 @@ var MonitorDatabaseImpl = class {
 		this._open();
 	}
 	_open() {
-		logger$8.info({ path: this._path }, "Opening monitor database");
+		logger$9.info({ path: this._path }, "Opening monitor database");
 		this._db = new BetterSqlite3(this._path);
 		const walResult = this._db.pragma("journal_mode = WAL");
-		if (walResult?.[0]?.journal_mode !== "wal") logger$8.warn({ result: walResult?.[0]?.journal_mode }, "Monitor DB: WAL pragma did not confirm wal mode");
+		if (walResult?.[0]?.journal_mode !== "wal") logger$9.warn({ result: walResult?.[0]?.journal_mode }, "Monitor DB: WAL pragma did not confirm wal mode");
 		this._db.pragma("synchronous = NORMAL");
 		this._db.pragma("busy_timeout = 5000");
 		this._db.pragma("foreign_keys = ON");
@@ -3888,7 +3891,7 @@ var MonitorDatabaseImpl = class {
         total_retries       = total_retries + @retries,
         last_updated        = @lastUpdated
     `);
-		logger$8.info({ path: this._path }, "Monitor database ready");
+		logger$9.info({ path: this._path }, "Monitor database ready");
 	}
 	_assertOpen() {
 		if (this._db === null) throw new Error("MonitorDatabase: connection is closed");
@@ -4037,7 +4040,7 @@ var MonitorDatabaseImpl = class {
 		const db = this._assertOpen();
 		const cutoff = new Date(Date.now() - retentionDays * 24 * 60 * 60 * 1e3).toISOString();
 		const result = db.prepare("DELETE FROM task_metrics WHERE recorded_at < @cutoff").run({ cutoff });
-		logger$8.info({
+		logger$9.info({
 			cutoff,
 			deleted: result.changes
 		}, "Pruned old task_metrics rows");
@@ -4076,13 +4079,13 @@ var MonitorDatabaseImpl = class {
 			db.exec("ROLLBACK");
 			throw err;
 		}
-		logger$8.info("Rebuilt performance_aggregates from task_metrics");
+		logger$9.info("Rebuilt performance_aggregates from task_metrics");
 	}
 	resetAllData() {
 		const db = this._assertOpen();
 		db.exec("DELETE FROM task_metrics");
 		db.exec("DELETE FROM performance_aggregates");
-		logger$8.info({ path: this._path }, "Monitor data reset — all rows deleted");
+		logger$9.info({ path: this._path }, "Monitor data reset — all rows deleted");
 	}
 	getTaskMetricsDateRange() {
 		const db = this._assertOpen();
@@ -4099,7 +4102,7 @@ var MonitorDatabaseImpl = class {
 		if (this._db === null) return;
 		this._db.close();
 		this._db = null;
-		logger$8.info({ path: this._path }, "Monitor database closed");
+		logger$9.info({ path: this._path }, "Monitor database closed");
 	}
 	/**
 	* Access the raw underlying database for testing purposes only.
@@ -4112,7 +4115,7 @@ var MonitorDatabaseImpl = class {
 
 //#endregion
 //#region src/modules/monitor/recommendation-engine.ts
-const logger$7 = createLogger("monitor:recommendations");
+const logger$8 = createLogger("monitor:recommendations");
 var RecommendationEngine = class {
 	_monitorDb;
 	_filters;
@@ -4145,7 +4148,7 @@ var RecommendationEngine = class {
 		const sinceDate = new Date(Date.now() - this._historyDays * 24 * 60 * 60 * 1e3).toISOString();
 		const aggregates = this._monitorDb.getAggregates({ sinceDate });
 		if (aggregates.length === 0) {
-			logger$7.debug("No performance aggregates found — no recommendations to generate");
+			logger$8.debug("No performance aggregates found — no recommendations to generate");
 			return [];
 		}
 		const byTaskType = new Map();
@@ -4210,7 +4213,7 @@ var RecommendationEngine = class {
 			if (confDiff !== 0) return confDiff;
 			return b.improvement_percentage - a.improvement_percentage;
 		});
-		logger$7.debug({ count: recommendations.length }, "Generated routing recommendations");
+		logger$8.debug({ count: recommendations.length }, "Generated routing recommendations");
 		return recommendations;
 	}
 	/**
@@ -4376,7 +4379,7 @@ function generateMonitorReport(monitorDb, options = {}) {
 
 //#endregion
 //#region src/cli/commands/monitor.ts
-const logger$6 = createLogger("monitor-cmd");
+const logger$7 = createLogger("monitor-cmd");
 const MONITOR_EXIT_SUCCESS = 0;
 const MONITOR_EXIT_ERROR = 1;
 /**
@@ -4579,7 +4582,7 @@ async function runMonitorReportAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$6.error({ err }, "runMonitorReportAction failed");
+		logger$7.error({ err }, "runMonitorReportAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -4641,7 +4644,7 @@ async function runMonitorStatusAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$6.error({ err }, "runMonitorStatusAction failed");
+		logger$7.error({ err }, "runMonitorStatusAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -4676,7 +4679,7 @@ async function runMonitorResetAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$6.error({ err }, "runMonitorResetAction failed");
+		logger$7.error({ err }, "runMonitorResetAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -4724,7 +4727,7 @@ async function runMonitorRecommendationsAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$6.error({ err }, "runMonitorRecommendationsAction failed");
+		logger$7.error({ err }, "runMonitorRecommendationsAction failed");
 		return MONITOR_EXIT_ERROR;
 	} finally {
 		if (monitorDb !== null) try {
@@ -4802,7 +4805,7 @@ function registerMonitorCommand(program, version = "0.0.0", projectRoot = proces
 
 //#endregion
 //#region src/modules/git-worktree/git-worktree-manager-impl.ts
-const logger$5 = createLogger("git-worktree");
+const logger$6 = createLogger("git-worktree");
 const BRANCH_PREFIX = "substrate/task-";
 const DEFAULT_WORKTREE_BASE = ".substrate-worktrees";
 var GitWorktreeManagerImpl = class {
@@ -4821,7 +4824,7 @@ var GitWorktreeManagerImpl = class {
 		this._db = db;
 		this._onTaskReady = ({ taskId }) => {
 			this._handleTaskReady(taskId).catch((err) => {
-				logger$5.error({
+				logger$6.error({
 					taskId,
 					err
 				}, "Unhandled error in _handleTaskReady");
@@ -4835,40 +4838,40 @@ var GitWorktreeManagerImpl = class {
 		};
 	}
 	async initialize() {
-		logger$5.info({ projectRoot: this._projectRoot }, "GitWorktreeManager.initialize()");
+		logger$6.info({ projectRoot: this._projectRoot }, "GitWorktreeManager.initialize()");
 		await this.verifyGitVersion();
 		const cleaned = await this.cleanupAllWorktrees();
-		if (cleaned > 0) logger$5.info({ cleaned }, "Recovered orphaned worktrees on startup");
+		if (cleaned > 0) logger$6.info({ cleaned }, "Recovered orphaned worktrees on startup");
 		this._eventBus.on("task:ready", this._onTaskReady);
 		this._eventBus.on("task:complete", this._onTaskComplete);
 		this._eventBus.on("task:failed", this._onTaskFailed);
-		logger$5.info("GitWorktreeManager initialized");
+		logger$6.info("GitWorktreeManager initialized");
 	}
 	async shutdown() {
-		logger$5.info("GitWorktreeManager.shutdown()");
+		logger$6.info("GitWorktreeManager.shutdown()");
 		this._eventBus.off("task:ready", this._onTaskReady);
 		this._eventBus.off("task:complete", this._onTaskComplete);
 		this._eventBus.off("task:failed", this._onTaskFailed);
 		await this.cleanupAllWorktrees();
-		logger$5.info("GitWorktreeManager shutdown complete");
+		logger$6.info("GitWorktreeManager shutdown complete");
 	}
 	async _handleTaskReady(taskId) {
-		logger$5.debug({ taskId }, "task:ready — creating worktree");
+		logger$6.debug({ taskId }, "task:ready — creating worktree");
 		try {
 			await this.createWorktree(taskId);
 		} catch (err) {
-			logger$5.error({
+			logger$6.error({
 				taskId,
 				err
 			}, "Failed to create worktree for task");
 		}
 	}
 	async _handleTaskDone(taskId) {
-		logger$5.debug({ taskId }, "task done — cleaning up worktree");
+		logger$6.debug({ taskId }, "task done — cleaning up worktree");
 		try {
 			await this.cleanupWorktree(taskId);
 		} catch (err) {
-			logger$5.warn({
+			logger$6.warn({
 				taskId,
 				err
 			}, "Failed to cleanup worktree for task");
@@ -4878,7 +4881,7 @@ var GitWorktreeManagerImpl = class {
 		if (!taskId || taskId.trim().length === 0) throw new Error("createWorktree: taskId must be a non-empty string");
 		const branchName = BRANCH_PREFIX + taskId;
 		const worktreePath = this.getWorktreePath(taskId);
-		logger$5.debug({
+		logger$6.debug({
 			taskId,
 			branchName,
 			worktreePath,
@@ -4898,7 +4901,7 @@ var GitWorktreeManagerImpl = class {
 			worktreePath,
 			createdAt
 		};
-		logger$5.info({
+		logger$6.info({
 			taskId,
 			branchName,
 			worktreePath
@@ -4908,7 +4911,7 @@ var GitWorktreeManagerImpl = class {
 	async cleanupWorktree(taskId) {
 		const branchName = BRANCH_PREFIX + taskId;
 		const worktreePath = this.getWorktreePath(taskId);
-		logger$5.debug({
+		logger$6.debug({
 			taskId,
 			branchName,
 			worktreePath
@@ -4918,7 +4921,7 @@ var GitWorktreeManagerImpl = class {
 			await access$1(worktreePath);
 			worktreeExists = true;
 		} catch {
-			logger$5.debug({
+			logger$6.debug({
 				taskId,
 				worktreePath
 			}, "cleanupWorktree: worktree does not exist, skipping removal");
@@ -4926,7 +4929,7 @@ var GitWorktreeManagerImpl = class {
 		if (worktreeExists) try {
 			await removeWorktree(worktreePath, this._projectRoot);
 		} catch (err) {
-			logger$5.warn({
+			logger$6.warn({
 				taskId,
 				worktreePath,
 				err
@@ -4935,7 +4938,7 @@ var GitWorktreeManagerImpl = class {
 		try {
 			await removeBranch(branchName, this._projectRoot);
 		} catch (err) {
-			logger$5.warn({
+			logger$6.warn({
 				taskId,
 				branchName,
 				err
@@ -4945,13 +4948,13 @@ var GitWorktreeManagerImpl = class {
 			taskId,
 			branchName
 		});
-		logger$5.info({
+		logger$6.info({
 			taskId,
 			branchName
 		}, "Worktree cleaned up");
 	}
 	async cleanupAllWorktrees() {
-		logger$5.debug({ projectRoot: this._projectRoot }, "cleanupAllWorktrees");
+		logger$6.debug({ projectRoot: this._projectRoot }, "cleanupAllWorktrees");
 		const orphanedPaths = await getOrphanedWorktrees(this._projectRoot, this._baseDirectory);
 		let cleaned = 0;
 		for (const worktreePath of orphanedPaths) {
@@ -4960,12 +4963,12 @@ var GitWorktreeManagerImpl = class {
 			try {
 				await removeWorktree(worktreePath, this._projectRoot);
 				worktreeRemoved = true;
-				logger$5.debug({
+				logger$6.debug({
 					taskId,
 					worktreePath
 				}, "cleanupAllWorktrees: removed orphaned worktree");
 			} catch (err) {
-				logger$5.warn({
+				logger$6.warn({
 					taskId,
 					worktreePath,
 					err
@@ -4975,12 +4978,12 @@ var GitWorktreeManagerImpl = class {
 			let branchRemoved = false;
 			try {
 				branchRemoved = await removeBranch(branchName, this._projectRoot);
-				if (branchRemoved) logger$5.debug({
+				if (branchRemoved) logger$6.debug({
 					taskId,
 					branchName
 				}, "cleanupAllWorktrees: removed orphaned branch");
 			} catch (err) {
-				logger$5.warn({
+				logger$6.warn({
 					taskId,
 					branchName,
 					err
@@ -4988,14 +4991,14 @@ var GitWorktreeManagerImpl = class {
 			}
 			if (worktreeRemoved) cleaned++;
 		}
-		if (cleaned > 0) logger$5.info({ cleaned }, "cleanupAllWorktrees: recovered orphaned worktrees");
+		if (cleaned > 0) logger$6.info({ cleaned }, "cleanupAllWorktrees: recovered orphaned worktrees");
 		return cleaned;
 	}
 	async detectConflicts(taskId, targetBranch = "main") {
 		if (!taskId || taskId.trim().length === 0) throw new Error("detectConflicts: taskId must be a non-empty string");
 		const branchName = BRANCH_PREFIX + taskId;
 		const worktreePath = this.getWorktreePath(taskId);
-		logger$5.debug({
+		logger$6.debug({
 			taskId,
 			branchName,
 			targetBranch
@@ -5023,7 +5026,7 @@ var GitWorktreeManagerImpl = class {
 			branch: branchName,
 			conflictingFiles: report.conflictingFiles
 		});
-		logger$5.info({
+		logger$6.info({
 			taskId,
 			hasConflicts: report.hasConflicts,
 			conflictCount: conflictingFiles.length
@@ -5033,14 +5036,14 @@ var GitWorktreeManagerImpl = class {
 	async mergeWorktree(taskId, targetBranch = "main") {
 		if (!taskId || taskId.trim().length === 0) throw new Error("mergeWorktree: taskId must be a non-empty string");
 		const branchName = BRANCH_PREFIX + taskId;
-		logger$5.debug({
+		logger$6.debug({
 			taskId,
 			branchName,
 			targetBranch
 		}, "mergeWorktree");
 		const conflictReport = await this.detectConflicts(taskId, targetBranch);
 		if (conflictReport.hasConflicts) {
-			logger$5.info({
+			logger$6.info({
 				taskId,
 				conflictCount: conflictReport.conflictingFiles.length
 			}, "Merge skipped due to conflicts");
@@ -5062,7 +5065,7 @@ var GitWorktreeManagerImpl = class {
 			success: true,
 			mergedFiles
 		};
-		logger$5.info({
+		logger$6.info({
 			taskId,
 			branchName,
 			mergedFileCount: mergedFiles.length
@@ -5070,7 +5073,7 @@ var GitWorktreeManagerImpl = class {
 		return result;
 	}
 	async listWorktrees() {
-		logger$5.debug({
+		logger$6.debug({
 			projectRoot: this._projectRoot,
 			baseDirectory: this._baseDirectory
 		}, "listWorktrees");
@@ -5094,7 +5097,7 @@ var GitWorktreeManagerImpl = class {
 				createdAt
 			});
 		}
-		logger$5.debug({ count: results.length }, "listWorktrees: found worktrees");
+		logger$6.debug({ count: results.length }, "listWorktrees: found worktrees");
 		return results;
 	}
 	getWorktreePath(taskId) {
@@ -5114,7 +5117,7 @@ function createGitWorktreeManager(options) {
 
 //#endregion
 //#region src/cli/commands/merge.ts
-const logger$4 = createLogger("merge-cmd");
+const logger$5 = createLogger("merge-cmd");
 const MERGE_EXIT_SUCCESS = 0;
 const MERGE_EXIT_CONFLICT = 1;
 const MERGE_EXIT_ERROR = 2;
@@ -5152,7 +5155,7 @@ async function mergeTask(taskId, targetBranch, projectRoot) {
 		projectRoot
 	});
 	try {
-		logger$4.info({
+		logger$5.info({
 			taskId,
 			targetBranch
 		}, "Running conflict detection...");
@@ -5174,7 +5177,7 @@ async function mergeTask(taskId, targetBranch, projectRoot) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		console.error(`Error merging task "${taskId}": ${message}`);
-		logger$4.error({
+		logger$5.error({
 			taskId,
 			err
 		}, "merge --task failed");
@@ -5228,7 +5231,7 @@ async function mergeAll(targetBranch, projectRoot, taskIds) {
 			error: message
 		});
 		console.log(`  Error for task "${taskId}": ${message}`);
-		logger$4.error({
+		logger$5.error({
 			taskId,
 			err
 		}, "merge --all: task failed");
@@ -5281,7 +5284,7 @@ function registerMergeCommand(program, projectRoot = process.cwd()) {
 
 //#endregion
 //#region src/cli/commands/worktrees.ts
-const logger$3 = createLogger("worktrees-cmd");
+const logger$4 = createLogger("worktrees-cmd");
 const WORKTREES_EXIT_SUCCESS = 0;
 const WORKTREES_EXIT_ERROR = 1;
 /** Valid task statuses for filtering */
@@ -5408,7 +5411,7 @@ async function listWorktreesAction(options) {
 		try {
 			worktreeInfos = await manager.listWorktrees();
 		} catch (err) {
-			logger$3.error({ err }, "Failed to list worktrees");
+			logger$4.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;
@@ -5435,7 +5438,7 @@ async function listWorktreesAction(options) {
 	} catch (err) {
 		const message = err instanceof Error ? err.message : String(err);
 		process.stderr.write(`Error: ${message}\n`);
-		logger$3.error({ err }, "listWorktreesAction failed");
+		logger$4.error({ err }, "listWorktreesAction failed");
 		return WORKTREES_EXIT_ERROR;
 	}
 }
@@ -5476,7 +5479,7 @@ function registerWorktreesCommand(program, version = "0.0.0", projectRoot = proc
 
 //#endregion
 //#region src/cli/commands/brainstorm.ts
-const logger$2 = createLogger("brainstorm-cmd");
+const logger$3 = createLogger("brainstorm-cmd");
 /**
 * Detect whether the project has existing planning artifacts that indicate
 * this is an amendment session (vs. a brand-new project brainstorm).
@@ -5522,13 +5525,13 @@ async function loadAmendmentContextDocuments(projectRoot) {
 	try {
 		brief = await readFile(briefPath, "utf-8");
 	} catch {
-		logger$2.warn({ briefPath }, "product-brief.md not found — continuing without brief context");
+		logger$3.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$2.warn({ prdPath }, "requirements.md not found — continuing without PRD context");
+		logger$3.warn({ prdPath }, "requirements.md not found — continuing without PRD context");
 		process.stderr.write(`Warning: requirements.md not found at ${prdPath}\n`);
 	}
 	return {
@@ -5737,7 +5740,7 @@ async function dispatchToPersonas(userPrompt, context, llmDispatch) {
 		}
 	];
 	const defaultDispatch = async (prompt, personaName) => {
-		logger$2.debug({
+		logger$3.debug({
 			personaName,
 			promptLength: prompt.length
 		}, "Dispatching to persona (stub mode)");
@@ -5754,7 +5757,7 @@ async function dispatchToPersonas(userPrompt, context, llmDispatch) {
 			};
 		} catch (err) {
 			const msg = err instanceof Error ? err.message : String(err);
-			logger$2.error({
+			logger$3.error({
 				err,
 				personaName: persona.name
 			}, "Persona dispatch failed");
@@ -5906,7 +5909,7 @@ async function runBrainstormSession(options, llmDispatch, rlInterface) {
 			}
 		});
 		rl.on("error", (err) => {
-			logger$2.error({ err }, "readline error");
+			logger$3.error({ err }, "readline error");
 			if (!sessionEnded) endSession(false);
 		});
 	});
@@ -6496,7 +6499,7 @@ function renderReadinessReport(decisions) {
 
 //#endregion
 //#region src/cli/commands/export.ts
-const logger$1 = createLogger("export-cmd");
+const logger$2 = createLogger("export-cmd");
 /**
 * Execute the export action.
 * Returns an exit code (0 = success, 1 = error).
@@ -6623,7 +6626,7 @@ async function runExportAction(options) {
 		const msg = err instanceof Error ? err.message : String(err);
 		if (outputFormat === "json") process.stdout.write(JSON.stringify({ error: msg }) + "\n");
 		else process.stderr.write(`Error: ${msg}\n`);
-		logger$1.error({ err }, "export action failed");
+		logger$2.error({ err }, "export action failed");
 		return 1;
 	} finally {
 		if (dbWrapper !== void 0) try {
@@ -6645,6 +6648,220 @@ function registerExportCommand(program, _version = "0.0.0", projectRoot = proces
 	});
 }
 
+//#endregion
+//#region src/persistence/queries/retry-escalated.ts
+/**
+* Query the decision store for escalation-diagnosis decisions and classify
+* each story key as retryable or skipped.
+*
+* Key format in the DB: `{storyKey}:{runId}`
+*
+* - When `runId` is provided, only decisions whose key contains that runId
+*   are considered (AC5 scoping).
+* - When `runId` is omitted, the runId of the last (most recently created)
+*   escalation-diagnosis decision is used as the default (AC1 defaulting).
+*
+* @param db    The SQLite database connection
+* @param runId Optional run ID to scope the query
+*/
+function getRetryableEscalations(db, runId) {
+	const decisions = getDecisionsByCategory(db, ESCALATION_DIAGNOSIS);
+	const result = {
+		retryable: [],
+		skipped: []
+	};
+	if (decisions.length === 0) return result;
+	const parsed = [];
+	for (const decision of decisions) {
+		const colonIdx = decision.key.indexOf(":");
+		if (colonIdx === -1) continue;
+		const storyKey = decision.key.slice(0, colonIdx);
+		const decisionRunId = decision.key.slice(colonIdx + 1);
+		let diagnosis;
+		try {
+			diagnosis = JSON.parse(decision.value);
+		} catch {
+			continue;
+		}
+		parsed.push({
+			storyKey,
+			decisionRunId,
+			diagnosis
+		});
+	}
+	if (parsed.length === 0) return result;
+	const effectiveRunId = runId ?? parsed[parsed.length - 1].decisionRunId;
+	const lastEntryByKey = new Map();
+	for (const entry of parsed) {
+		if (entry.decisionRunId !== effectiveRunId) continue;
+		lastEntryByKey.set(entry.storyKey, entry);
+	}
+	for (const [storyKey, entry] of lastEntryByKey.entries()) {
+		const { recommendedAction } = entry.diagnosis;
+		if (recommendedAction === "retry-targeted") result.retryable.push(storyKey);
+		else if (recommendedAction === "human-intervention") result.skipped.push({
+			key: storyKey,
+			reason: "needs human review"
+		});
+		else if (recommendedAction === "split-story") result.skipped.push({
+			key: storyKey,
+			reason: "story should be split"
+		});
+	}
+	return result;
+}
+
+//#endregion
+//#region src/cli/commands/retry-escalated.ts
+const logger$1 = createLogger("retry-escalated-cmd");
+async function runRetryEscalatedAction(options) {
+	const { runId, dryRun, outputFormat, projectRoot, concurrency, pack: packName, registry: injectedRegistry } = options;
+	const dbRoot = await resolveMainRepoRoot(projectRoot);
+	const dbPath = join(dbRoot, ".substrate", "substrate.db");
+	if (!existsSync(dbPath)) {
+		const errorMsg = `Decision store not initialized. Run 'substrate init' first.`;
+		if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
+		else process.stderr.write(`Error: ${errorMsg}\n`);
+		return 1;
+	}
+	const dbWrapper = new DatabaseWrapper(dbPath);
+	try {
+		dbWrapper.open();
+		runMigrations(dbWrapper.db);
+		const db = dbWrapper.db;
+		const { retryable, skipped } = getRetryableEscalations(db, runId);
+		if (retryable.length === 0) {
+			if (outputFormat === "json") process.stdout.write(formatOutput({
+				retryKeys: [],
+				skippedKeys: skipped
+			}, "json", true) + "\n");
+			else process.stdout.write("No retry-targeted escalations found.\n");
+			return 0;
+		}
+		if (dryRun) {
+			if (outputFormat === "json") process.stdout.write(formatOutput({
+				retryKeys: retryable,
+				skippedKeys: skipped
+			}, "json", true) + "\n");
+			else {
+				const count = retryable.length;
+				process.stdout.write(`Retrying: ${count} ${count === 1 ? "story" : "stories"} — ${retryable.join(", ")}\n`);
+				for (const s of skipped) process.stdout.write(`Skipping: ${s.key} (${s.reason})\n`);
+			}
+			return 0;
+		}
+		const packPath = join(projectRoot, "packs", packName);
+		const packLoader = createPackLoader();
+		let pack;
+		try {
+			pack = await packLoader.load(packPath);
+		} catch (err) {
+			const msg = err instanceof Error ? err.message : String(err);
+			const errorMsg = `Methodology pack '${packName}' not found. Run 'substrate init' first.\n${msg}`;
+			if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, errorMsg) + "\n");
+			else process.stderr.write(`Error: ${errorMsg}\n`);
+			return 1;
+		}
+		if (outputFormat === "human") {
+			const count = retryable.length;
+			process.stdout.write(`Retrying: ${count} ${count === 1 ? "story" : "stories"} — ${retryable.join(", ")}\n`);
+			for (const s of skipped) process.stdout.write(`Skipping: ${s.key} (${s.reason})\n`);
+		}
+		const pipelineRun = createPipelineRun(db, {
+			methodology: pack.manifest.name,
+			start_phase: "implementation",
+			config_json: JSON.stringify({
+				storyKeys: retryable,
+				concurrency,
+				retryRun: true
+			})
+		});
+		const eventBus = createEventBus();
+		const contextCompiler = createContextCompiler({ db });
+		const adapterRegistry = injectedRegistry ?? new AdapterRegistry();
+		if (injectedRegistry === void 0) await adapterRegistry.discoverAndRegister();
+		const dispatcher = createDispatcher({
+			eventBus,
+			adapterRegistry
+		});
+		const orchestrator = createImplementationOrchestrator({
+			db,
+			pack,
+			contextCompiler,
+			dispatcher,
+			eventBus,
+			config: {
+				maxConcurrency: concurrency,
+				maxReviewCycles: 2,
+				pipelineRunId: pipelineRun.id
+			},
+			projectRoot
+		});
+		eventBus.on("orchestrator:story-phase-complete", (payload) => {
+			try {
+				const result = payload.result;
+				if (result?.tokenUsage !== void 0) {
+					const { input, output } = result.tokenUsage;
+					const costUsd = (input * 3 + output * 15) / 1e6;
+					addTokenUsage(db, pipelineRun.id, {
+						phase: payload.phase,
+						agent: "claude-code",
+						input_tokens: input,
+						output_tokens: output,
+						cost_usd: costUsd
+					});
+				}
+			} catch (err) {
+				logger$1.warn({ err }, "Failed to record token usage");
+			}
+		});
+		if (outputFormat === "human") {
+			eventBus.on("orchestrator:story-complete", (payload) => {
+				process.stdout.write(`  [COMPLETE] ${payload.storyKey} (${payload.reviewCycles} review cycle(s))\n`);
+			});
+			eventBus.on("orchestrator:story-escalated", (payload) => {
+				process.stdout.write(`  [ESCALATED] ${payload.storyKey}: ${payload.lastVerdict}\n`);
+			});
+		}
+		await orchestrator.run(retryable);
+		if (outputFormat === "json") process.stdout.write(formatOutput({
+			retryKeys: retryable,
+			skippedKeys: skipped
+		}, "json", true) + "\n");
+		else process.stdout.write("[RETRY] Complete\n");
+		return 0;
+	} catch (err) {
+		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$1.error({ err }, "retry-escalated failed");
+		return 1;
+	} finally {
+		try {
+			dbWrapper.close();
+		} catch {}
+	}
+}
+function registerRetryEscalatedCommand(program, _version = "0.0.0", projectRoot = process.cwd(), registry) {
+	program.command("retry-escalated").description("Retry escalated stories flagged as retry-targeted by escalation diagnosis").option("--run-id <id>", "Scope to a specific pipeline run ID (defaults to latest run with escalations)").option("--dry-run", "Print retryable and skipped stories without invoking the orchestrator").option("--concurrency <n>", "Maximum parallel story executions", (v) => {
+		const n = parseInt(v, 10);
+		if (isNaN(n) || n < 1) throw new Error(`--concurrency must be a positive integer, got: ${v}`);
+		return n;
+	}, 3).option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").action(async (opts) => {
+		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
+		const exitCode = await runRetryEscalatedAction({
+			runId: opts.runId,
+			dryRun: opts.dryRun === true,
+			outputFormat,
+			projectRoot: opts.projectRoot,
+			concurrency: opts.concurrency,
+			pack: opts.pack,
+			registry
+		});
+		process.exitCode = exitCode;
+	});
+}
+
 //#endregion
 //#region src/cli/index.ts
 process.setMaxListeners(20);
@@ -6680,16 +6897,19 @@ async function createProgram() {
 	const version = await getPackageVersion();
 	const program = new Command();
 	program.name("substrate").description("Substrate - Autonomous implementation pipeline for AI coding agents").version(version, "-v, --version", "Output the current version");
-	registerAdaptersCommand(program, version);
+	const registry = new AdapterRegistry();
+	await registry.discoverAndRegister();
+	registerAdaptersCommand(program, version, registry);
 	registerInitCommand(program, version);
 	registerConfigCommand(program, version);
-	registerRunCommand(program, version);
-	registerResumeCommand(program, version);
+	registerRunCommand(program, version, process.cwd(), registry);
+	registerResumeCommand(program, version, process.cwd(), registry);
 	registerStatusCommand(program, version);
-	registerAmendCommand(program, version);
+	registerAmendCommand(program, version, process.cwd(), registry);
 	registerHealthCommand(program, version);
 	registerSupervisorCommand(program, version);
 	registerMetricsCommand(program, version);
+	registerRetryEscalatedCommand(program, version, process.cwd(), registry);
 	registerCostCommand(program, version);
 	registerMonitorCommand(program, version);
 	registerMergeCommand(program);