substrate-ai 0.20.154 → 0.20.156

package/dist/cli/index.js

@@ -1,17 +1,17 @@
 #!/usr/bin/env node
-import { FileKvStore, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createDatabaseAdapter, createDoltOperatorReader, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion } from "../health-BmBd4zyE.js";
+import { FileKvStore, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createDatabaseAdapter, createDoltOperatorReader, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion } from "../health-CoJWnndU.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, createGitWorktreeManager, createPipelineRun, createStderrLogger, getActiveDecisions, getAllCostEntriesFiltered, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initWorkGraphSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, swallowDebug, tagRunAsBaseline, updatePipelineRun } from "../dist-Dl3vBZil.js";
 import "../adapter-registry-DXLMTmfD.js";
-import { RunManifest, SupervisorLock, ZERO_FINDINGS_BY_AUTHOR, ZERO_FINDING_COUNTS, ZERO_PROBE_AUTHOR_METRICS, aggregateProbeAuthorMetrics, parseRuntimeProbes, readCurrentRunId, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, rollupFindingsByAuthor, rollupProbeAuthorByClass, rollupProbeAuthorMetrics, runAcTraceabilityCheck } from "../manifest-read-Dan3I0ea.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-CNzfjk92.js";
+import { RunManifest, SupervisorLock, ZERO_FINDINGS_BY_AUTHOR, ZERO_FINDING_COUNTS, ZERO_PROBE_AUTHOR_METRICS, aggregateProbeAuthorMetrics, parseRuntimeProbes, readCurrentRunId, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, rollupFindingsByAuthor, rollupProbeAuthorByClass, rollupProbeAuthorMetrics, runAcTraceabilityCheck } from "../manifest-read-DFpujDzP.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-hO_G3pBQ.js";
 import "../errors-Dyyei2ah.js";
 import "../routing-DFxoKHDt.js";
 import { WorkGraphRepository } from "../work-graph-repository-DZyJv5pV.js";
 import "../decisions-CzSIEeGP.js";
 import "../decision-router-BAPpON_C.js";
-import "../interactive-prompt-Cj0Od5XZ.js";
+import "../interactive-prompt-BuoVYIgS.js";
 import "../recovery-engine-BKGBeBnW.js";
 import "../version-manager-impl-qFBiO4Eh.js";
 import { registerUpgradeCommand } from "../upgrade-DGqUA_5f.js";
@@ -7126,7 +7126,7 @@ async function runStatusAction(options) {
 			logger$15.debug({ err }, "Work graph query failed, continuing without work graph data");
 		}
 		if (run === void 0) {
-			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-BwXD8UBv.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-D_taFoP2.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -8655,7 +8655,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-6x92Moln.js"
+									"../run-DJ7P6y4z.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({

package/dist/{health-BmBd4zyE.js → health-CoJWnndU.js}

@@ -1,6 +1,6 @@
 import { createLogger } from "./logger-KeHncl-f.js";
 import { DoltClient, DoltQueryError, createDatabaseAdapter$1 as createDatabaseAdapter, getLatestRun, getPipelineRunById, initSchema } from "./dist-Dl3vBZil.js";
-import { resolveMainRepoRoot, resolveRunManifest } from "./manifest-read-Dan3I0ea.js";
+import { resolveMainRepoRoot, resolveRunManifest } from "./manifest-read-DFpujDzP.js";
 import { createRequire } from "module";
 import { dirname, join } from "path";
 import { existsSync, readFileSync } from "node:fs";
@@ -1000,4 +1000,4 @@ function registerHealthCommand(program, _version = "0.0.0", projectRoot = proces
 
 //#endregion
 export { BMAD_BASELINE_TOKENS_FULL, DEFAULT_STALL_THRESHOLD_SECONDS, FileKvStore, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, __commonJS, __require, __toESM, buildPipelineStatusOutput, createDatabaseAdapter$1 as createDatabaseAdapter, createDoltOperatorReader, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, isOrchestratorProcessLine, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion, runHealthAction, validateStoryKey };
-//# sourceMappingURL=health-BmBd4zyE.js.map
+//# sourceMappingURL=health-CoJWnndU.js.map

package/dist/{health-BwXD8UBv.js → health-D_taFoP2.js}

@@ -1,7 +1,7 @@
-import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-BmBd4zyE.js";
+import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-CoJWnndU.js";
 import "./logger-KeHncl-f.js";
 import "./dist-Dl3vBZil.js";
-import "./manifest-read-Dan3I0ea.js";
+import "./manifest-read-DFpujDzP.js";
 import "./work-graph-repository-DZyJv5pV.js";
 import "./decisions-CzSIEeGP.js";
 

package/dist/{interactive-prompt-Cj0Od5XZ.js → interactive-prompt-BuoVYIgS.js}

@@ -1,5 +1,5 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { readCurrentRunId, resolveMainRepoRoot } from "./manifest-read-Dan3I0ea.js";
+import { readCurrentRunId, resolveMainRepoRoot } from "./manifest-read-DFpujDzP.js";
 import { join } from "node:path";
 import { mkdir, readFile, writeFile } from "node:fs/promises";
 import * as readline from "node:readline";
@@ -180,4 +180,4 @@ async function runInteractivePrompt(decisionContext) {
 
 //#endregion
 export { runInteractivePrompt };
-//# sourceMappingURL=interactive-prompt-Cj0Od5XZ.js.map
+//# sourceMappingURL=interactive-prompt-BuoVYIgS.js.map

package/dist/{manifest-read-Dan3I0ea.js → manifest-read-DFpujDzP.js}

@@ -2244,10 +2244,10 @@ function detectTestCommand(workingDir) {
 * do not mask their own exit code, so this is a tampering signal, not a style
 * nit. Note: cannot catch arbitrary in-language masking (e.g. `python -c
 * "...sys.exit(0)"`) — the trusted-profile read is the primary defense; this is
-* belt-and-braces for the shell-wrapper class and the --no-worktree path.
+* belt-and-braces for common shell-wrapper masks; NOT a complete parser.
 */
 function detectsExitCodeLaundering(command) {
-	return /(\|\||;)\s*(true|:|exit\s+0)(\s|;|$)/.test(command);
+	return /(\|\||;)\s*(true|:|exit\s+0|return\s+0|exec\s+true)(?!\w)/.test(command) || /\{\s*(exit\s+0|true|:)\s*;?\s*\}/.test(command);
 }
 var TestSuiteCheck = class {
 	name = "test-suite";
@@ -2415,11 +2415,35 @@ const LANGUAGE_EXTENSIONS = {
 		".mjs",
 		".cjs"
 	],
-	python: [".py"],
+	python: [".py", ".pyi"],
 	go: [".go"],
 	rust: [".rs"],
 	java: [".java"],
-	kotlin: [".kt", ".kts"]
+	kotlin: [".kt", ".kts"],
+	ruby: [".rb", ".rake"],
+	php: [".php"],
+	csharp: [".cs"],
+	cpp: [
+		".cpp",
+		".cc",
+		".cxx",
+		".hpp",
+		".hh",
+		".h",
+		".hxx"
+	],
+	c: [".c", ".h"],
+	swift: [".swift"],
+	scala: [".scala", ".sc"],
+	elixir: [".ex", ".exs"],
+	clojure: [
+		".clj",
+		".cljs",
+		".cljc"
+	],
+	perl: [".pl", ".pm"],
+	lua: [".lua"],
+	dart: [".dart"]
 };
 /** JS-family toolchain manifests whose appearance flips build detection. */
 const JS_TOOLCHAIN_MANIFESTS = [
@@ -2436,7 +2460,18 @@ const JS_TOOLCHAIN_MANIFESTS = [
 const ALWAYS_DENY_SEGMENTS = [
 	"node_modules",
 	".venv",
-	"__pycache__"
+	"venv",
+	"__pycache__",
+	".gradle",
+	".tox",
+	".mypy_cache",
+	".pytest_cache",
+	".ruff_cache",
+	".next",
+	".nuxt",
+	".svelte-kit",
+	"coverage",
+	".turbo"
 ];
 /**
 * Collect every `language: <x>` declaration in the profile (single-project
@@ -2477,7 +2512,21 @@ function classifyContamination(changedFiles, allowedLanguages) {
 			droppings.push(file);
 			continue;
 		}
-		if (!allowJs && segments.includes("dist")) {
+		if (segments.some((seg) => seg.endsWith(".egg-info"))) {
+			droppings.push(file);
+			continue;
+		}
+		if (!allowJs && segments.some((seg) => seg === "dist" || seg === "build" || seg === "out")) {
+			droppings.push(file);
+			continue;
+		}
+		const allowGoVendor = allowedLanguages.includes("go");
+		const allowJvmTarget = allowedLanguages.some((l) => l === "rust" || l === "java" || l === "kotlin" || l === "scala");
+		if (!allowGoVendor && segments.includes("vendor")) {
+			droppings.push(file);
+			continue;
+		}
+		if (!allowJvmTarget && segments.includes("target")) {
 			droppings.push(file);
 			continue;
 		}
@@ -2568,6 +2617,8 @@ function isTestPath(file) {
 	if (/(^|\/)(__tests__|tests?)\//.test(norm)) return true;
 	if (/\.(test|spec)\.[a-z]+$/.test(base)) return true;
 	if (/^test_.*\.py$/.test(base) || /_test\.(py|go)$/.test(base)) return true;
+	if (base === "conftest.py") return true;
+	if (/(^|\/)(fixtures|factories|testsupport|test-support|test_support|__mocks__|__fixtures__)\//.test(norm)) return true;
 	return false;
 }
 var TestMutationCheck = class {
@@ -6331,4 +6382,4 @@ async function resolveRunManifest(dbRoot, runId) {
 
 //#endregion
 export { FindingsInjector, RunManifest, RuntimeProbeListSchema, SupervisorLock, ZERO_FINDINGS_BY_AUTHOR, ZERO_FINDING_COUNTS, ZERO_PROBE_AUTHOR_METRICS, aggregateProbeAuthorMetrics, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, parseRuntimeProbes, readCurrentRunId, renderFindings, resolveGraphPath, resolveMainRepoRoot, resolveRunManifest, rollupFindingCounts, rollupFindingsByAuthor, rollupProbeAuthorByClass, rollupProbeAuthorMetrics, runAcTraceabilityCheck, runStaleVerificationRecovery };
-//# sourceMappingURL=manifest-read-Dan3I0ea.js.map
+//# sourceMappingURL=manifest-read-DFpujDzP.js.map

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

@@ -1,6 +1,6 @@
 import "../../logger-KeHncl-f.js";
 import "../../dist-Dl3vBZil.js";
-import "../../manifest-read-Dan3I0ea.js";
-import { runInteractivePrompt } from "../../interactive-prompt-Cj0Od5XZ.js";
+import "../../manifest-read-DFpujDzP.js";
+import { runInteractivePrompt } from "../../interactive-prompt-BuoVYIgS.js";
 
 export { runInteractivePrompt };

package/dist/{run-6x92Moln.js → run-DJ7P6y4z.js}

@@ -1,14 +1,14 @@
-import "./health-BmBd4zyE.js";
+import "./health-CoJWnndU.js";
 import "./logger-KeHncl-f.js";
 import "./helpers-CElYrONe.js";
 import "./dist-Dl3vBZil.js";
-import "./manifest-read-Dan3I0ea.js";
-import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, runRunAction, wireNdjsonEmitter } from "./run-CNzfjk92.js";
+import "./manifest-read-DFpujDzP.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, runRunAction, wireNdjsonEmitter } from "./run-hO_G3pBQ.js";
 import "./routing-DFxoKHDt.js";
 import "./work-graph-repository-DZyJv5pV.js";
 import "./decisions-CzSIEeGP.js";
 import "./decision-router-BAPpON_C.js";
-import "./interactive-prompt-Cj0Od5XZ.js";
+import "./interactive-prompt-BuoVYIgS.js";
 import "./recovery-engine-BKGBeBnW.js";
 
 export { runRunAction };

package/dist/{run-CNzfjk92.js → run-hO_G3pBQ.js}

@@ -1,11 +1,11 @@
-import { BMAD_BASELINE_TOKENS_FULL, FileKvStore, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, VALID_PHASES, __commonJS, __require, __toESM, buildPipelineStatusOutput, createDatabaseAdapter, formatOutput, formatPipelineSummary, formatTokenTelemetry, inspectProcessTree, parseDbTimestampAsUtc, validateStoryKey } from "./health-BmBd4zyE.js";
+import { BMAD_BASELINE_TOKENS_FULL, FileKvStore, STOP_AFTER_VALID_PHASES, STORY_KEY_PATTERN, VALID_PHASES, __commonJS, __require, __toESM, buildPipelineStatusOutput, createDatabaseAdapter, formatOutput, formatPipelineSummary, formatTokenTelemetry, inspectProcessTree, parseDbTimestampAsUtc, validateStoryKey } from "./health-CoJWnndU.js";
 import { createLogger } from "./logger-KeHncl-f.js";
 import { TypedEventBusImpl, createEventBus, createTuiApp, isTuiCapable, printNonTtyWarning, sleep } from "./helpers-CElYrONe.js";
 import { ADVISORY_NOTES, BRANCH_PREFIX, CLAUDE_AUTH_FAILURE_HINT, CODEX_SANDBOX_BLOCK_HINT, Categorizer, ConsumerAnalyzer, DEFAULT_GLOBAL_SETTINGS, DispatcherImpl, DoltClient, ESCALATION_DIAGNOSIS, EXPERIMENT_RESULT, EfficiencyScorer, IngestionServer, LogTurnAnalyzer, OPERATIONAL_FINDING, Recommender, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, STORY_METRICS, STORY_OUTCOME, SubstrateConfigSchema, TEST_EXPANSION_FINDING, TEST_PLAN, TelemetryNormalizer, TelemetryPipeline, TurnAnalyzer, addTokenUsage, aggregateTokenUsageForRun, aggregateTokenUsageForStory, callLLM, classifyVersionGap, createConfigSystem, createDatabaseAdapter$1, createDecision, createGitWorktreeManager, createPipelineRun, createRequirement, detectClaudeAuthFailure, detectCodexSandboxBlock, detectInterfaceChanges, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunMetrics, getRunningPipelineRuns, getStoryMetricsForRun, getTokenUsageSummary, initSchema, listRequirements, loadModelRoutingConfig, registerArtifact, swallowDebug, updatePipelineRun, updatePipelineRunConfig, upsertDecision, writeRunMetrics, writeStoryMetrics } from "./dist-Dl3vBZil.js";
-import { FindingsInjector, RunManifest, RuntimeProbeListSchema, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, parseRuntimeProbes, renderFindings, resolveGraphPath, resolveMainRepoRoot, runAcTraceabilityCheck, runStaleVerificationRecovery } from "./manifest-read-Dan3I0ea.js";
+import { FindingsInjector, RunManifest, RuntimeProbeListSchema, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, parseRuntimeProbes, renderFindings, resolveGraphPath, resolveMainRepoRoot, runAcTraceabilityCheck, runStaleVerificationRecovery } from "./manifest-read-DFpujDzP.js";
 import { WorkGraphRepository, detectCycles } from "./work-graph-repository-DZyJv5pV.js";
 import { deriveExitCode, routeDecision } from "./decision-router-BAPpON_C.js";
-import { runInteractivePrompt } from "./interactive-prompt-Cj0Od5XZ.js";
+import { runInteractivePrompt } from "./interactive-prompt-BuoVYIgS.js";
 import { runRecoveryEngine } from "./recovery-engine-BKGBeBnW.js";
 import { basename, dirname, extname, join } from "path";
 import { access, readFile, readdir, stat } from "fs/promises";
@@ -5340,7 +5340,7 @@ function checkGitModifiedTrackedFiles(workingDir = process.cwd(), baselineSha) {
 		return [];
 	}
 	const diffs = ["git diff --name-only HEAD", "git diff --cached --name-only"];
-	if (baselineSha !== void 0 && baselineSha.length > 0) diffs.push(`git diff --name-only --diff-filter=MD ${baselineSha}..HEAD`);
+	if (baselineSha !== void 0 && baselineSha.length > 0) diffs.push(`git diff --name-only --diff-filter=MDR ${baselineSha}..HEAD`);
 	for (const args of diffs) try {
 		execSync(args, {
 			cwd: workingDir,
@@ -6901,8 +6901,12 @@ async function commitDevStoryOutput(storyKey, storyTitle, filesModified, working
 	const COMMIT_DENY_SEGMENTS = [
 		"node_modules",
 		".venv",
+		"venv",
 		"__pycache__",
-		".substrate-worktrees"
+		".substrate-worktrees",
+		".mypy_cache",
+		".pytest_cache",
+		".ruff_cache"
 	];
 	const insideWorktree = [];
 	for (const p of filesModified) {
@@ -6931,7 +6935,7 @@ async function commitDevStoryOutput(storyKey, storyTitle, filesModified, working
 		reason: "no-files-inside-worktree"
 	};
 	try {
-		execSync(`git add ${insideWorktree.map((p) => JSON.stringify(p)).join(" ")}`, {
+		execFileSync("git", ["add", ...insideWorktree], {
 			cwd: workingDir,
 			stdio: [
 				"ignore",
@@ -6970,7 +6974,11 @@ async function commitDevStoryOutput(storyKey, storyTitle, filesModified, working
 	const title = storyTitle ?? "implementation";
 	const message = `feat(story-${storyKey}): ${title}`;
 	try {
-		execSync(`git commit -m ${JSON.stringify(message)}`, {
+		execFileSync("git", [
+			"commit",
+			"-m",
+			message
+		], {
 			cwd: workingDir,
 			stdio: [
 				"ignore",
@@ -7074,7 +7082,12 @@ async function checkpointStoryWorktree(storyKey, reason, workingDir) {
 	const cleanReason = (reason.split("\n")[0] ?? "checkpoint").split("").filter((ch) => ch.charCodeAt(0) >= 32).join("").slice(0, 100);
 	const message = `wip(story-${storyKey}): ${cleanReason}`;
 	try {
-		execSync(`git commit --no-verify -m ${JSON.stringify(message)}`, {
+		execFileSync("git", [
+			"commit",
+			"--no-verify",
+			"-m",
+			message
+		], {
 			cwd: workingDir,
 			stdio: [
 				"ignore",
@@ -14219,7 +14232,20 @@ function createImplementationOrchestrator(deps) {
 				}
 				if (effectiveProjectRoot !== void 0 && effectiveProjectRoot !== projectRoot) {
 					const resolvedStoryFile = isAbsolute(createResult.story_file) ? createResult.story_file : resolve$1(effectiveProjectRoot, createResult.story_file);
-					const relToWorktree = relative(effectiveProjectRoot, resolvedStoryFile);
+					const canonicalize = (p) => {
+						let cur = p;
+						for (let i = 0; i < 64; i++) try {
+							return join$1(realpathSync(cur), relative(cur, p));
+						} catch {
+							const parent = dirname$1(cur);
+							if (parent === cur) break;
+							cur = parent;
+						}
+						return p;
+					};
+					const realWorktree = canonicalize(effectiveProjectRoot);
+					const realStoryFile = canonicalize(resolvedStoryFile);
+					const relToWorktree = relative(realWorktree, realStoryFile);
 					const outsideWorktree = relToWorktree.startsWith("..") || isAbsolute(relToWorktree);
 					if (outsideWorktree) {
 						const errMsg = `create-story wrote its artifact OUTSIDE the story worktree: ${createResult.story_file} (resolved: ${resolvedStoryFile}) (worktree: ${effectiveProjectRoot}). The agent escaped its working directory — this is the parent/home-directory write-leak class (field finding #15). The stray file was NOT adopted; inspect and remove it.`;
@@ -15267,6 +15293,72 @@ function createImplementationOrchestrator(deps) {
 		}
 		if (devStoryWasSuccess && gitDiffFiles !== void 0 && gitDiffFiles.length > 0) {
 			const implClassification = classifyImplementationDiff(gitDiffFiles);
+			let implAddedLines;
+			if (implClassification.hasImplementation && baselineHeadSha) {
+				const numstatCwd = effectiveProjectRoot ?? process.cwd();
+				try {
+					execSync("git add -N -A", {
+						cwd: numstatCwd,
+						timeout: 5e3,
+						stdio: [
+							"ignore",
+							"pipe",
+							"pipe"
+						]
+					});
+					const numstat = execSync("git diff -w --numstat HEAD", {
+						cwd: numstatCwd,
+						encoding: "utf-8",
+						timeout: 5e3,
+						stdio: [
+							"ignore",
+							"pipe",
+							"pipe"
+						]
+					});
+					try {
+						execSync("git reset -q", {
+							cwd: numstatCwd,
+							timeout: 5e3,
+							stdio: [
+								"ignore",
+								"pipe",
+								"pipe"
+							]
+						});
+					} catch {}
+					const isArtifactPath = (f$1) => {
+						const n$1 = f$1.replace(/\\/g, "/").replace(/^\.\//, "");
+						return n$1.startsWith("_bmad-output/") || n$1.startsWith(".substrate/");
+					};
+					const implRows = numstat.split("\n").map((line) => line.split("	")).filter((cols) => cols.length === 3 && cols[0] !== "-" && !isArtifactPath(cols[2]));
+					implAddedLines = implRows.length > 0 ? implRows.reduce((sum, cols) => sum + (Number.parseInt(cols[0], 10) || 0), 0) : void 0;
+				} catch {
+					implAddedLines = void 0;
+				}
+			}
+			if (implClassification.hasImplementation && implAddedLines === 0) {
+				logger$27.warn({
+					storyKey,
+					changed: gitDiffFiles.slice(0, 10)
+				}, "dev-story reported success but its implementation files added zero non-whitespace lines (empty stub / whitespace-only / pure deletion) — escalating no-implementation");
+				endPhase(storyKey, "dev-story", devStoryModel);
+				updateStory(storyKey, {
+					phase: "ESCALATED",
+					error: "no-implementation",
+					completedAt: new Date().toISOString()
+				});
+				await writeStoryMetricsBestEffort(storyKey, "escalated", 0);
+				await emitEscalation({
+					storyKey,
+					lastVerdict: "no-implementation",
+					reviewCycles: 0,
+					issues: [`dev-story reported COMPLETE and touched non-artifact files, but added ZERO non-whitespace lines to any of them (${gitDiffFiles.slice(0, 10).join(", ")}) — the "implementation" is an empty stub, a whitespace-only edit, or a pure deletion.`],
+					escalationReason: "no-implementation"
+				});
+				await persistState();
+				return;
+			}
 			if (!implClassification.hasImplementation) {
 				logger$27.warn({
 					storyKey,
@@ -15756,7 +15848,7 @@ function createImplementationOrchestrator(deps) {
 									outputTokenCount: devOutputTokenCount,
 									sourceEpicContent,
 									...effectiveProjectRoot !== void 0 ? { changedFiles: recaptureChangedFiles(effectiveProjectRoot) } : {},
-									...modifiedTrackedFiles !== void 0 ? { modifiedTrackedFiles } : {},
+									...effectiveProjectRoot !== void 0 ? { modifiedTrackedFiles: checkGitModifiedTrackedFiles(effectiveProjectRoot, baselineHeadSha) } : {},
 									runId: config.pipelineRunId
 								});
 								const retryVerifSummary = await verificationPipeline.run(retryVerifContext, "A");
@@ -16194,7 +16286,12 @@ function createImplementationOrchestrator(deps) {
 				if (finalizationMode === "branch" || finalizationMode === "pr") {
 					let prUrl;
 					if (finalizationMode === "pr") try {
-						execSync(`git push -u origin ${branchName}`, {
+						execFileSync("git", [
+							"push",
+							"-u",
+							"origin",
+							branchName
+						], {
 							cwd: projectRoot,
 							stdio: [
 								"ignore",
@@ -16204,7 +16301,16 @@ function createImplementationOrchestrator(deps) {
 							timeout: 6e4
 						});
 						const shortSha = (storyDeliverableSha ?? "").slice(0, 10);
-						const ghOutput = execSync(`gh pr create --head ${branchName} --title ${JSON.stringify(`story ${storyKey}: ${_capturedStoryTitle ?? "implementation"}`)} --body ${JSON.stringify(`Substrate story ${storyKey} (commit ${shortSha}). Verified by the Tier-A pipeline; see the run manifest for the full verification record.`)}`, {
+						const ghOutput = execFileSync("gh", [
+							"pr",
+							"create",
+							"--head",
+							branchName,
+							"--title",
+							`story ${storyKey}: ${_capturedStoryTitle ?? "implementation"}`,
+							"--body",
+							`Substrate story ${storyKey} (commit ${shortSha}). Verified by the Tier-A pipeline; see the run manifest for the full verification record.`
+						], {
 							cwd: projectRoot,
 							encoding: "utf-8",
 							stdio: [
@@ -16546,6 +16652,26 @@ function createImplementationOrchestrator(deps) {
 					continue;
 				}
 				if (isPhantomReview && timeoutRetried) {
+					const phantomAuthSignature = detectClaudeAuthFailure(reviewResult.error ?? "");
+					if (phantomAuthSignature !== null) {
+						endPhase(storyKey, "code-review");
+						updateStory(storyKey, {
+							phase: "ESCALATED",
+							error: "auth-failure",
+							completedAt: new Date().toISOString()
+						});
+						await writeStoryMetricsBestEffort(storyKey, "escalated", reviewCycles + 1);
+						await emitEscalation({
+							storyKey,
+							lastVerdict: "auth-failure",
+							reviewCycles: reviewCycles + 1,
+							issues: [reviewResult.error ?? "", CLAUDE_AUTH_FAILURE_HINT],
+							escalationReason: "auth-failure"
+						});
+						await triggerAuthFailureHalt(storyKey, phantomAuthSignature);
+						await persistState();
+						return;
+					}
 					const isStoryFileMissing = (reviewResult.error ?? "").includes("story-file-missing");
 					const escalationReason = isStoryFileMissing ? "story-file-missing" : "consecutive-review-timeouts";
 					logger$27.warn({
@@ -16625,6 +16751,25 @@ function createImplementationOrchestrator(deps) {
 			} catch (err) {
 				const errMsg = err instanceof Error ? err.message : String(err);
 				endPhase(storyKey, "code-review");
+				const reviewAuthSignature = detectClaudeAuthFailure(errMsg);
+				if (reviewAuthSignature !== null) {
+					updateStory(storyKey, {
+						phase: "ESCALATED",
+						error: "auth-failure",
+						completedAt: new Date().toISOString()
+					});
+					await writeStoryMetricsBestEffort(storyKey, "failed", reviewCycles);
+					await emitEscalation({
+						storyKey,
+						lastVerdict: "auth-failure",
+						reviewCycles,
+						issues: [errMsg, CLAUDE_AUTH_FAILURE_HINT],
+						escalationReason: "auth-failure"
+					});
+					await triggerAuthFailureHalt(storyKey, reviewAuthSignature);
+					await persistState();
+					return;
+				}
 				updateStory(storyKey, {
 					phase: "ESCALATED",
 					error: errMsg,
@@ -16850,6 +16995,10 @@ function createImplementationOrchestrator(deps) {
 						storyKey
 					});
 					const fixResult = await handle.result;
+					{
+						const fixFiles = fixResult.parsed?.files_modified;
+						if (Array.isArray(fixFiles)) devFilesModified = Array.from(new Set([...devFilesModified, ...fixFiles.filter((f$1) => typeof f$1 === "string")]));
+					}
 					eventBus.emit("orchestrator:story-phase-complete", {
 						storyKey,
 						phase: "IN_MINOR_FIX",
@@ -17057,6 +17206,10 @@ function createImplementationOrchestrator(deps) {
 				});
 				const fixResult = await handle.result;
 				endPhase(storyKey, "fix");
+				{
+					const fixFiles = fixResult.parsed?.files_modified;
+					if (Array.isArray(fixFiles)) devFilesModified = Array.from(new Set([...devFilesModified, ...fixFiles.filter((f$1) => typeof f$1 === "string")]));
+				}
 				eventBus.emit("orchestrator:story-phase-complete", {
 					storyKey,
 					phase: taskType === "minor-fixes" ? "IN_MINOR_FIX" : "IN_MAJOR_FIX",
@@ -47934,4 +48087,4 @@ function registerRunCommand(program, version = "0.0.0", projectRoot = process.cw
 
 //#endregion
 export { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GLOBSTAR$1 as GLOBSTAR, GitClient, GrammarLoader, Minimatch$1 as Minimatch, Minipass, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, escape$1 as escape, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, normalizeGraphSummaryToStatus, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runProbeAuthor, runRunAction, runSolutioningPhase, unescape$1 as unescape, validateStopAfterFromConflict, wireNdjsonEmitter };
-//# sourceMappingURL=run-CNzfjk92.js.map
+//# sourceMappingURL=run-hO_G3pBQ.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.20.154",
+  "version": "0.20.156",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",