substrate-ai 0.2.16 → 0.2.17

package/dist/cli/index.js

@@ -1,21 +1,20 @@
 #!/usr/bin/env node
-import { createLogger, deepMask } from "../logger-C6n1g8uP.js";
-import { AdapterRegistry, createEventBus } from "../event-bus-J-bw-pkp.js";
-import { CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, PartialSubstrateConfigSchema, SUPPORTED_CONFIG_FORMAT_VERSIONS, SubstrateConfigSchema, defaultConfigMigrator } from "../version-manager-impl-BpVx2DkY.js";
-import { DatabaseWrapper, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createContextCompiler, createDispatcher, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, findPackageRoot, formatOutput, formatPhaseCompletionSummary, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getSubstrateDefaultSettings, parseDbTimestampAsUtc, registerRunCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, resolveMainRepoRoot, runAnalysisPhase, runMigrations, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-BrI2xzk7.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-CLpXJNQ8.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, getPipelineRunById, getTokenUsageSummary, listRequirements, updatePipelineRun } from "../decisions-SyswIRKz.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-CobuCGbM.js";
-import { abortMerge, createWorktree, getConflictingFiles, getMergedFiles, getOrphanedWorktrees, performMerge, removeBranch, removeWorktree, simulateMerge, verifyGitVersion } from "../git-utils-BtI5eNoN.js";
-import { registerUpgradeCommand } from "../upgrade-rV26kdh3.js";
-import { createRequire } from "module";
+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";
 import { fileURLToPath } from "url";
 import { dirname, join, resolve } from "path";
 import { access, mkdir, readFile, writeFile } from "fs/promises";
 import { chmodSync, cpSync, existsSync, mkdirSync, readFileSync, readdirSync, realpathSync, statSync, unlinkSync, writeFileSync } from "fs";
 import yaml from "js-yaml";
-import { createRequire as createRequire$1 } from "node:module";
+import { createRequire } from "node:module";
 import * as path$1 from "node:path";
 import { isAbsolute, join as join$1 } from "node:path";
 import BetterSqlite3 from "better-sqlite3";
@@ -26,10 +25,6 @@ import { access as access$1 } from "node:fs/promises";
 import { randomUUID } from "crypto";
 import { createInterface as createInterface$1 } from "readline";
 
-//#region rolldown:runtime
-var __require = /* @__PURE__ */ createRequire(import.meta.url);
-
-//#endregion
 //#region src/cli/utils/formatting.ts
 /**
 * Build adapter list rows from discovery results.
@@ -329,7 +324,7 @@ const DEFAULT_CONFIG = {
 
 //#endregion
 //#region src/cli/commands/init.ts
-const logger$17 = createLogger("init");
+const logger$16 = createLogger("init");
 const __dirname = dirname(new URL(import.meta.url).pathname);
 const INIT_EXIT_SUCCESS = 0;
 const INIT_EXIT_ERROR = 1;
@@ -350,7 +345,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 	const version = resolveBmadMethodVersion();
 	if (force && bmadExists) process.stderr.write(`Warning: Replacing existing _bmad/ framework with bmad-method@${version}\n`);
 	process.stdout.write(`Scaffolding BMAD framework from bmad-method@${version}\n`);
-	logger$17.info({
+	logger$16.info({
 		version,
 		dest: bmadDest
 	}, "Scaffolding BMAD framework");
@@ -360,7 +355,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 			const destDir = join(bmadDest, dir);
 			mkdirSync(destDir, { recursive: true });
 			cpSync(srcDir, destDir, { recursive: true });
-			logger$17.info({
+			logger$16.info({
 				dir,
 				dest: destDir
 			}, "Scaffolded BMAD framework directory");
@@ -379,7 +374,7 @@ async function scaffoldBmadFramework(projectRoot, force, outputFormat) {
 			"document_output_language: English"
 		].join("\n") + "\n";
 		await writeFile(configFile, configStub, "utf8");
-		logger$17.info({ configFile }, "Generated _bmad/_config/config.yaml stub");
+		logger$16.info({ configFile }, "Generated _bmad/_config/config.yaml stub");
 	}
 }
 const CLAUDE_MD_START_MARKER = "<!-- substrate:start -->";
@@ -394,7 +389,7 @@ async function scaffoldClaudeMd(projectRoot) {
 	try {
 		sectionContent = await readFile(templatePath, "utf8");
 	} catch {
-		logger$17.warn({ templatePath }, "CLAUDE.md substrate section template not found; skipping");
+		logger$16.warn({ templatePath }, "CLAUDE.md substrate section template not found; skipping");
 		return;
 	}
 	if (!sectionContent.endsWith("\n")) sectionContent += "\n";
@@ -412,7 +407,7 @@ async function scaffoldClaudeMd(projectRoot) {
 		newContent = existingContent + separator + sectionContent;
 	}
 	await writeFile(claudeMdPath, newContent, "utf8");
-	logger$17.info({ claudeMdPath }, "Wrote substrate section to CLAUDE.md");
+	logger$16.info({ claudeMdPath }, "Wrote substrate section to CLAUDE.md");
 }
 async function scaffoldStatuslineScript(projectRoot) {
 	const pkgRoot = findPackageRoot(__dirname);
@@ -423,7 +418,7 @@ async function scaffoldStatuslineScript(projectRoot) {
 	try {
 		content = await readFile(templatePath, "utf8");
 	} catch {
-		logger$17.warn({ templatePath }, "statusline.sh template not found; skipping");
+		logger$16.warn({ templatePath }, "statusline.sh template not found; skipping");
 		return;
 	}
 	const claudeDir = join(projectRoot, ".claude");
@@ -431,7 +426,7 @@ async function scaffoldStatuslineScript(projectRoot) {
 	mkdirSync(claudeDir, { recursive: true });
 	await writeFile(statuslinePath, content, "utf8");
 	chmodSync(statuslinePath, 493);
-	logger$17.info({ statuslinePath }, "Wrote .claude/statusline.sh");
+	logger$16.info({ statuslinePath }, "Wrote .claude/statusline.sh");
 }
 async function scaffoldClaudeSettings(projectRoot) {
 	const claudeDir = join(projectRoot, ".claude");
@@ -447,11 +442,11 @@ async function scaffoldClaudeSettings(projectRoot) {
 	if (!merged["$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$17.info({ settingsPath }, "Wrote substrate settings to .claude/settings.json");
+	logger$16.info({ settingsPath }, "Wrote substrate settings to .claude/settings.json");
 }
 function resolveBmadMethodInstallerLibPath(fromDir = __dirname) {
 	try {
-		const _require = createRequire$1(join(fromDir, "synthetic.js"));
+		const _require = createRequire(join(fromDir, "synthetic.js"));
 		const pkgJsonPath = _require.resolve("bmad-method/package.json");
 		return join(dirname(pkgJsonPath), "tools", "cli", "installers", "lib");
 	} catch {
@@ -482,7 +477,7 @@ function clearBmadCommandFiles(commandsDir) {
 	} catch {}
 }
 async function compileBmadAgents(bmadDir) {
-	const _require = createRequire$1(join(__dirname, "synthetic.js"));
+	const _require = createRequire(join(__dirname, "synthetic.js"));
 	let compilerPath;
 	try {
 		const pkgJsonPath = _require.resolve("bmad-method/package.json");
@@ -517,7 +512,7 @@ async function compileBmadAgents(bmadDir) {
 				writeFileSync(mdPath, result.xml, "utf-8");
 				compiled++;
 			} catch (compileErr) {
-				logger$17.debug({
+				logger$16.debug({
 					err: compileErr,
 					file
 				}, "Failed to compile agent YAML");
@@ -535,12 +530,12 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		return;
 	}
 	try {
-		const _require = createRequire$1(join(__dirname, "synthetic.js"));
+		const _require = createRequire(join(__dirname, "synthetic.js"));
 		try {
 			const compiledCount = await compileBmadAgents(bmadDir);
-			if (compiledCount > 0) logger$17.info({ compiledCount }, "Compiled agent YAML files to MD");
+			if (compiledCount > 0) logger$16.info({ compiledCount }, "Compiled agent YAML files to MD");
 		} catch (compileErr) {
-			logger$17.warn({ err: compileErr }, "Agent compilation failed; agent commands may be incomplete");
+			logger$16.warn({ err: compileErr }, "Agent compilation failed; agent commands may be incomplete");
 		}
 		const { AgentCommandGenerator } = _require(join(installerLibPath, "ide", "shared", "agent-command-generator.js"));
 		const { WorkflowCommandGenerator } = _require(join(installerLibPath, "ide", "shared", "workflow-command-generator.js"));
@@ -552,7 +547,7 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 			const manifestGen = new ManifestGenerator();
 			await manifestGen.generateManifests(bmadDir, allModules, [], { ides: ["claude-code"] });
 		} catch (manifestErr) {
-			logger$17.warn({ err: manifestErr }, "ManifestGenerator failed; workflow/task commands may be incomplete");
+			logger$16.warn({ err: manifestErr }, "ManifestGenerator failed; workflow/task commands may be incomplete");
 		}
 		const commandsDir = join(projectRoot, ".claude", "commands");
 		mkdirSync(commandsDir, { recursive: true });
@@ -568,7 +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$17.info({
+		logger$16.info({
 			agentCount,
 			workflowCount,
 			taskToolCount,
@@ -578,7 +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$17.warn({ err }, "scaffoldClaudeCommands failed; init continues");
+		logger$16.warn({ err }, "scaffoldClaudeCommands failed; init continues");
 	}
 }
 const PROVIDER_DEFAULTS = DEFAULT_CONFIG.providers;
@@ -652,7 +647,7 @@ async function runInitAction(options) {
 			discoveryReport = await registry.discoverAndRegister();
 		} catch (err) {
 			const message = err instanceof Error ? err.message : String(err);
-			logger$17.error({ err }, "Adapter discovery failed");
+			logger$16.error({ err }, "Adapter discovery failed");
 			if (outputFormat === "json") process.stdout.write(formatOutput(null, "json", false, `Adapter discovery failed: ${message}`) + "\n");
 			else process.stderr.write(`  Error: adapter discovery failed — ${message}\n`);
 			return INIT_EXIT_ERROR;
@@ -701,12 +696,12 @@ async function runInitAction(options) {
 				return INIT_EXIT_ERROR;
 			}
 			if (force && existsSync(localManifest)) {
-				logger$17.info({ pack: packName }, "Replacing existing pack with bundled version");
+				logger$16.info({ pack: packName }, "Replacing existing pack with bundled version");
 				process.stderr.write(`Warning: Replacing existing pack '${packName}' with bundled version\n`);
 			}
 			mkdirSync(dirname(packPath), { recursive: true });
 			cpSync(bundledPackPath, packPath, { recursive: true });
-			logger$17.info({
+			logger$16.info({
 				pack: packName,
 				dest: packPath
 			}, "Scaffolded methodology pack");
@@ -759,7 +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$17.error({ err }, "init failed");
+		logger$16.error({ err }, "init failed");
 		return INIT_EXIT_ERROR;
 	}
 }
@@ -805,7 +800,7 @@ function formatUnsupportedVersionError(formatType, version, supported) {
 
 //#endregion
 //#region src/modules/config/config-system-impl.ts
-const logger$16 = createLogger("config");
+const logger$15 = 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);
@@ -850,7 +845,7 @@ function readEnvOverrides() {
 	}
 	const parsed = PartialSubstrateConfigSchema.safeParse(overrides);
 	if (!parsed.success) {
-		logger$16.warn({ errors: parsed.error.issues }, "Invalid environment variable overrides ignored");
+		logger$15.warn({ errors: parsed.error.issues }, "Invalid environment variable overrides ignored");
 		return {};
 	}
 	return parsed.data;
@@ -914,7 +909,7 @@ var ConfigSystemImpl = class {
 			throw new ConfigError(`Configuration validation failed:\n${issues}`, { issues: result.error.issues });
 		}
 		this._config = result.data;
-		logger$16.debug("Configuration loaded successfully");
+		logger$15.debug("Configuration loaded successfully");
 	}
 	getConfig() {
 		if (this._config === null) throw new ConfigError("Configuration has not been loaded. Call load() before getConfig().", {});
@@ -977,7 +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$16.info({
+						logger$15.info({
 							from: version,
 							to: CURRENT_CONFIG_FORMAT_VERSION,
 							backup: migrationOutput.result.backupPath
@@ -1020,7 +1015,7 @@ function createConfigSystem(options = {}) {
 
 //#endregion
 //#region src/cli/commands/config.ts
-const logger$15 = createLogger("config-cmd");
+const logger$14 = createLogger("config-cmd");
 const CONFIG_EXIT_SUCCESS = 0;
 const CONFIG_EXIT_ERROR = 1;
 const CONFIG_EXIT_INVALID = 2;
@@ -1046,7 +1041,7 @@ 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$14.error({ err }, "Failed to load configuration");
 		process.stderr.write(`  Error loading configuration: ${message}\n`);
 		return CONFIG_EXIT_ERROR;
 	}
@@ -1120,7 +1115,7 @@ 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$14.error({ err }, "Failed to load configuration");
 		process.stderr.write(`Error loading configuration: ${message}\n`);
 		return CONFIG_EXIT_ERROR;
 	}
@@ -1274,7 +1269,7 @@ function registerConfigCommand(program, _version) {
 
 //#endregion
 //#region src/cli/commands/resume.ts
-const logger$14 = createLogger("resume-cmd");
+const logger$13 = createLogger("resume-cmd");
 async function runResumeAction(options) {
 	const { runId: specifiedRunId, stopAfter, outputFormat, projectRoot, concurrency, pack: packName } = options;
 	if (stopAfter !== void 0 && !VALID_PHASES.includes(stopAfter)) {
@@ -1356,7 +1351,7 @@ 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$13.error({ err }, "auto resume failed");
 		return 1;
 	} finally {
 		try {
@@ -1507,7 +1502,7 @@ async function runFullPipelineFromPhase(options) {
 							});
 						}
 					} catch (err) {
-						logger$14.warn({ err }, "Failed to record token usage");
+						logger$13.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);
@@ -1566,7 +1561,7 @@ 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$13.error({ err }, "pipeline from phase failed");
 		return 1;
 	} finally {
 		try {
@@ -1591,7 +1586,7 @@ function registerResumeCommand(program, _version = "0.0.0", projectRoot = proces
 
 //#endregion
 //#region src/cli/commands/status.ts
-const logger$13 = createLogger("status-cmd");
+const logger$12 = createLogger("status-cmd");
 async function runStatusAction(options) {
 	const { outputFormat, runId, projectRoot } = options;
 	const dbRoot = await resolveMainRepoRoot(projectRoot);
@@ -1668,7 +1663,7 @@ 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$12.error({ err }, "status action failed");
 		return 1;
 	} finally {
 		try {
@@ -2092,7 +2087,7 @@ 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$11 = createLogger("amend-cmd");
 /**
 * Detect and apply supersessions after a phase completes in an amendment run.
 *
@@ -2123,7 +2118,7 @@ function runPostPhaseSupersessionDetection(db, amendmentRunId, currentPhase, han
 			});
 		} catch (err) {
 			const msg = err instanceof Error ? err.message : String(err);
-			logger$12.warn({
+			logger$11.warn({
 				err,
 				originalId: parentMatch.id,
 				supersedingId: newDec.id
@@ -2258,7 +2253,7 @@ 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$11.info({
 				phase: currentPhase,
 				amendmentContextLen: amendmentContext.length
 			}, "Amendment context loaded for phase");
@@ -2378,7 +2373,7 @@ 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$11.error({ err }, "amend failed");
 		return 1;
 	} finally {
 		try {
@@ -2401,268 +2396,6 @@ function registerAmendCommand(program, _version = "0.0.0", projectRoot = process
 	});
 }
 
-//#endregion
-//#region src/cli/commands/health.ts
-const logger$11 = createLogger("health-cmd");
-/** Default stall threshold in seconds — also used by supervisor default */
-const DEFAULT_STALL_THRESHOLD_SECONDS = 600;
-/**
-* Determine whether a ps output line represents the substrate pipeline orchestrator.
-* Handles invocation via:
-*   - `substrate run` (globally installed)
-*   - `substrate-ai run`
-*   - `node dist/cli/index.js run` (npm run substrate:dev)
-*   - `npx substrate run`
-*   - any node process whose command contains `run` with `--events` or `--stories`
-*
-* When `projectRoot` is provided, additionally checks that the command line
-* contains that path (via `--project-root` flag or as part of the binary/CWD path).
-* This ensures multi-project environments match the correct orchestrator.
-*/
-function isOrchestratorProcessLine(line, projectRoot) {
-	if (line.includes("grep")) return false;
-	let isOrchestrator = false;
-	if (line.includes("substrate run")) isOrchestrator = true;
-	else if (line.includes("substrate-ai run")) isOrchestrator = true;
-	else if (line.includes("index.js run")) isOrchestrator = true;
-	else if (line.includes("node") && /\srun(\s|$)/.test(line) && (line.includes("--events") || line.includes("--stories"))) isOrchestrator = true;
-	if (!isOrchestrator) return false;
-	if (projectRoot !== void 0) return line.includes(projectRoot);
-	return true;
-}
-function inspectProcessTree(opts) {
-	const { projectRoot, execFileSync: execFileSyncOverride } = opts ?? {};
-	const result = {
-		orchestrator_pid: null,
-		child_pids: [],
-		zombies: []
-	};
-	try {
-		let psOutput;
-		if (execFileSyncOverride !== void 0) psOutput = execFileSyncOverride("ps", ["-eo", "pid,ppid,stat,command"], {
-			encoding: "utf-8",
-			timeout: 5e3
-		});
-		else {
-			const { execFileSync } = __require("node:child_process");
-			psOutput = execFileSync("ps", ["-eo", "pid,ppid,stat,command"], {
-				encoding: "utf-8",
-				timeout: 5e3
-			});
-		}
-		const lines = psOutput.split("\n");
-		for (const line of lines) if (isOrchestratorProcessLine(line, projectRoot)) {
-			const match = line.trim().match(/^(\d+)/);
-			if (match) {
-				result.orchestrator_pid = parseInt(match[1], 10);
-				break;
-			}
-		}
-		if (result.orchestrator_pid !== null) for (const line of lines) {
-			const parts = line.trim().split(/\s+/);
-			if (parts.length >= 3) {
-				const pid = parseInt(parts[0], 10);
-				const ppid = parseInt(parts[1], 10);
-				const stat$2 = parts[2];
-				if (ppid === result.orchestrator_pid && pid !== result.orchestrator_pid) {
-					result.child_pids.push(pid);
-					if (stat$2.includes("Z")) result.zombies.push(pid);
-				}
-			}
-		}
-	} catch {}
-	return result;
-}
-/**
-* Collect all descendant PIDs of the given root PIDs by walking the process
-* tree recursively. This ensures that grandchildren of the orchestrator
-* (e.g. node subprocesses spawned by `claude -p`) are also killed during
-* stall recovery, leaving no orphan processes.
-*
-* Returns only the descendants — the root PIDs themselves are NOT included.
-*/
-function getAllDescendantPids(rootPids, execFileSyncOverride) {
-	if (rootPids.length === 0) return [];
-	try {
-		let psOutput;
-		if (execFileSyncOverride !== void 0) psOutput = execFileSyncOverride("ps", ["-eo", "pid,ppid"], {
-			encoding: "utf-8",
-			timeout: 5e3
-		});
-		else {
-			const { execFileSync } = __require("node:child_process");
-			psOutput = execFileSync("ps", ["-eo", "pid,ppid"], {
-				encoding: "utf-8",
-				timeout: 5e3
-			});
-		}
-		const childrenOf = new Map();
-		for (const line of psOutput.split("\n")) {
-			const parts = line.trim().split(/\s+/);
-			if (parts.length >= 2) {
-				const pid = parseInt(parts[0], 10);
-				const ppid = parseInt(parts[1], 10);
-				if (!isNaN(pid) && !isNaN(ppid) && pid > 0) {
-					if (!childrenOf.has(ppid)) childrenOf.set(ppid, []);
-					childrenOf.get(ppid).push(pid);
-				}
-			}
-		}
-		const descendants = [];
-		const seen = new Set(rootPids);
-		const queue = [...rootPids];
-		while (queue.length > 0) {
-			const current = queue.shift();
-			const children = childrenOf.get(current) ?? [];
-			for (const child of children) if (!seen.has(child)) {
-				seen.add(child);
-				descendants.push(child);
-				queue.push(child);
-			}
-		}
-		return descendants;
-	} catch {
-		return [];
-	}
-}
-/**
-* Fetch pipeline health data as a structured object without any stdout side-effects.
-* Used by runSupervisorAction to poll health without formatting overhead.
-*
-* Returns a NO_PIPELINE_RUNNING health object for all graceful "no data" cases
-* (missing DB, missing run, terminal run status). Throws only on unexpected errors.
-*/
-async function getAutoHealthData(options) {
-	const { runId, projectRoot } = options;
-	const dbRoot = await resolveMainRepoRoot(projectRoot);
-	const dbPath = join(dbRoot, ".substrate", "substrate.db");
-	const NO_PIPELINE = {
-		verdict: "NO_PIPELINE_RUNNING",
-		run_id: null,
-		status: null,
-		current_phase: null,
-		staleness_seconds: 0,
-		last_activity: "",
-		process: {
-			orchestrator_pid: null,
-			child_pids: [],
-			zombies: []
-		},
-		stories: {
-			active: 0,
-			completed: 0,
-			escalated: 0,
-			details: {}
-		}
-	};
-	if (!existsSync(dbPath)) return NO_PIPELINE;
-	const dbWrapper = new DatabaseWrapper(dbPath);
-	try {
-		dbWrapper.open();
-		const db = dbWrapper.db;
-		let run;
-		if (runId !== void 0) run = getPipelineRunById(db, runId);
-		else run = getLatestRun(db);
-		if (run === void 0) return NO_PIPELINE;
-		const updatedAt = parseDbTimestampAsUtc(run.updated_at);
-		const stalenessSeconds = Math.round((Date.now() - updatedAt.getTime()) / 1e3);
-		let storyDetails = {};
-		let active = 0;
-		let completed = 0;
-		let escalated = 0;
-		try {
-			if (run.token_usage_json) {
-				const state = JSON.parse(run.token_usage_json);
-				if (state.stories) for (const [key, s] of Object.entries(state.stories)) {
-					storyDetails[key] = {
-						phase: s.phase,
-						review_cycles: s.reviewCycles
-					};
-					if (s.phase === "COMPLETE") completed++;
-					else if (s.phase === "ESCALATED") escalated++;
-					else if (s.phase !== "PENDING") active++;
-				}
-			}
-		} catch {}
-		const processInfo = inspectProcessTree({ projectRoot });
-		let verdict = "NO_PIPELINE_RUNNING";
-		if (run.status === "running") if (processInfo.orchestrator_pid === null && active === 0 && completed > 0) verdict = "NO_PIPELINE_RUNNING";
-		else if (processInfo.zombies.length > 0) verdict = "STALLED";
-		else if (processInfo.orchestrator_pid !== null && processInfo.child_pids.length > 0 && stalenessSeconds > DEFAULT_STALL_THRESHOLD_SECONDS) verdict = "HEALTHY";
-		else if (stalenessSeconds > DEFAULT_STALL_THRESHOLD_SECONDS) verdict = "STALLED";
-		else if (processInfo.orchestrator_pid !== null && processInfo.child_pids.length === 0 && active > 0) verdict = "STALLED";
-		else verdict = "HEALTHY";
-		else if (run.status === "completed" || run.status === "failed" || run.status === "stopped") verdict = "NO_PIPELINE_RUNNING";
-		return {
-			verdict,
-			run_id: run.id,
-			status: run.status,
-			current_phase: run.current_phase,
-			staleness_seconds: stalenessSeconds,
-			last_activity: run.updated_at,
-			process: processInfo,
-			stories: {
-				active,
-				completed,
-				escalated,
-				details: storyDetails
-			}
-		};
-	} finally {
-		try {
-			dbWrapper.close();
-		} catch {}
-	}
-}
-async function runHealthAction(options) {
-	const { outputFormat } = options;
-	try {
-		const health = await getAutoHealthData(options);
-		if (outputFormat === "json") process.stdout.write(formatOutput(health, "json", true) + "\n");
-		else {
-			const verdictLabel = health.verdict === "HEALTHY" ? "HEALTHY" : health.verdict === "STALLED" ? "STALLED" : "NO PIPELINE RUNNING";
-			process.stdout.write(`\nPipeline Health: ${verdictLabel}\n`);
-			if (health.run_id !== null) {
-				process.stdout.write(`  Run:          ${health.run_id}\n`);
-				process.stdout.write(`  Status:       ${health.status}\n`);
-				process.stdout.write(`  Phase:        ${health.current_phase ?? "N/A"}\n`);
-				process.stdout.write(`  Last Active:  ${health.last_activity} (${health.staleness_seconds}s ago)\n`);
-				const processInfo = health.process;
-				if (processInfo.orchestrator_pid !== null) {
-					process.stdout.write(`  Orchestrator: PID ${processInfo.orchestrator_pid}\n`);
-					process.stdout.write(`  Children:     ${processInfo.child_pids.length} active`);
-					if (processInfo.zombies.length > 0) process.stdout.write(` (${processInfo.zombies.length} ZOMBIE)`);
-					process.stdout.write("\n");
-				} else process.stdout.write("  Orchestrator: not running\n");
-				const storyDetails = health.stories.details;
-				if (Object.keys(storyDetails).length > 0) {
-					process.stdout.write("\n  Stories:\n");
-					for (const [key, s] of Object.entries(storyDetails)) process.stdout.write(`    ${key}: ${s.phase} (${s.review_cycles} review cycles)\n`);
-					process.stdout.write(`\n  Summary: ${health.stories.active} active, ${health.stories.completed} completed, ${health.stories.escalated} escalated\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$11.error({ err }, "health action failed");
-		return 1;
-	}
-}
-function registerHealthCommand(program, _version = "0.0.0", projectRoot = process.cwd()) {
-	program.command("health").description("Check pipeline health: process status, stall detection, and verdict").option("--run-id <id>", "Pipeline run ID to query (defaults to latest)").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 runHealthAction({
-			outputFormat,
-			runId: opts.runId,
-			projectRoot: opts.projectRoot
-		});
-		process.exitCode = exitCode;
-	});
-}
-
 //#endregion
 //#region src/cli/commands/supervisor.ts
 function defaultSupervisorDeps() {
@@ -3095,11 +2828,11 @@ async function runSupervisorAction(options, deps = {}) {
 						try {
 							const { createExperimenter } = await import(
 								/* @vite-ignore */
-								"../experimenter-Cd04gAWQ.js"
+								"../experimenter-CHRVkV3d.js"
 );
 							const { getLatestRun: getLatest } = await import(
 								/* @vite-ignore */
-								"../decisions-BmqXQ3Se.js"
+								"../decisions-DxgMpQpz.js"
 );
 							const dbPath = join(projectRoot, ".substrate", "substrate.db");
 							const expDbWrapper = new DatabaseWrapper(dbPath);
@@ -3109,7 +2842,7 @@ async function runSupervisorAction(options, deps = {}) {
 								const expDb = expDbWrapper.db;
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-fjuwOUib.js"
+									"../run-DPrhfU2T.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -6969,8 +6702,8 @@ async function createProgram() {
 /** Fire-and-forget startup version check (story 8.3, AC3/AC5) */
 function checkForUpdatesInBackground(currentVersion) {
 	if (process.env.SUBSTRATE_NO_UPDATE_CHECK === "1") return;
-	import("../upgrade-BjYVeC6G.js").then(async () => {
-		const { createVersionManager } = await import("../version-manager-impl-9N_519Ey.js");
+	import("../upgrade-CF8EjNuO.js").then(async () => {
+		const { createVersionManager } = await import("../version-manager-impl-C6jmvble.js");
 		const vm = createVersionManager();
 		const result = await vm.checkForUpdates();
 		if (result.updateAvailable) {