substrate-ai 0.20.150 → 0.20.152

package/dist/adapter-registry-BsBP3j5i.js

@@ -0,0 +1,4 @@
+import { AdapterRegistry } from "./dist-90byyGPp.js";
+import "./adapter-registry-DXLMTmfD.js";
+
+export { AdapterRegistry };

package/dist/cli/index.js

@@ -1,20 +1,20 @@
 #!/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-CcOYQsgZ.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-Bj5OYB7r.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-C6pEdj12.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-90byyGPp.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-8oNapRvD.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-B9lhuahO.js";
-import "../errors-1xcRMTz_.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-BAN_-QKy.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-DbT2-Wzg.js";
+import "../errors-ST3E8qWc.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-BVTTIU3t.js";
+import "../interactive-prompt-Du_Yt_N4.js";
 import "../recovery-engine-BKGBeBnW.js";
 import "../version-manager-impl-qFBiO4Eh.js";
-import { registerUpgradeCommand } from "../upgrade-DcvPseav.js";
+import { registerUpgradeCommand } from "../upgrade-Dw6jKkH3.js";
 import { Command } from "commander";
 import { fileURLToPath } from "url";
 import { dirname, join, resolve } from "path";
@@ -1525,6 +1525,51 @@ async function scaffoldClaudeSettings(projectRoot) {
 	await writeFile(settingsPath, JSON.stringify(merged, null, 2) + "\n", "utf8");
 	logger$18.info({ settingsPath }, "Wrote substrate settings to .claude/settings.json");
 }
+/**
+* H5.2 (field finding #2): write substrate's own slash commands
+* (/substrate-run, /substrate-supervisor, /substrate-metrics) into
+* `.claude/commands/`. Pre-fix, the init summary ADVERTISED these commands
+* but nothing ever wrote them — the bmad generator populates `.claude/skills/`
+* only, so operators found an empty (or user-files-only) commands dir.
+*
+* Only files named `substrate-*.md` are owned (overwritten); user files are
+* never touched. Works with pre-existing / gitignored `.claude/` dirs —
+* mkdirSync recursive + per-file writes make no assumptions about state.
+*/
+function scaffoldSubstrateSlashCommands(projectRoot) {
+	try {
+		const pkgRoot = findPackageRoot(__dirname);
+		let templatesDir = join(pkgRoot, "dist", "cli", "templates", "claude-commands");
+		if (!existsSync$1(templatesDir)) templatesDir = join(pkgRoot, "src", "cli", "templates", "claude-commands");
+		if (!existsSync$1(templatesDir)) {
+			logger$18.warn({ templatesDir }, "substrate slash-command templates not found; skipping");
+			return 0;
+		}
+		const commandsDir = join(projectRoot, ".claude", "commands");
+		mkdirSync$1(commandsDir, { recursive: true });
+		let written = 0;
+		for (const file of readdirSync$1(templatesDir)) {
+			if (!file.startsWith("substrate-") || !file.endsWith(".md")) continue;
+			try {
+				writeFileSync$1(join(commandsDir, file), readFileSync$1(join(templatesDir, file), "utf8"));
+				written += 1;
+			} catch (err) {
+				logger$18.warn({
+					file,
+					err
+				}, "failed to write substrate slash command (init continues)");
+			}
+		}
+		logger$18.info({
+			written,
+			commandsDir
+		}, "Scaffolded substrate slash commands");
+		return written;
+	} catch (err) {
+		logger$18.warn({ err }, "scaffoldSubstrateSlashCommands failed; init continues");
+		return 0;
+	}
+}
 function resolveBmadMethodInstallerLibPath(fromDir = __dirname) {
 	try {
 		const _require = createRequire(join(fromDir, "synthetic.js"));
@@ -2278,6 +2323,7 @@ async function runInitAction(options) {
 		await scaffoldStatuslineScript(projectRoot);
 		await scaffoldClaudeSettings(projectRoot);
 		await scaffoldClaudeCommands(projectRoot, outputFormat);
+		scaffoldSubstrateSlashCommands(projectRoot);
 		scaffoldCodexProject(projectRoot, outputFormat);
 		if (options.installUserScope) {
 			const homeDir = process.env["HOME"] ?? process.env["USERPROFILE"];
@@ -7080,7 +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-Bhwd_HX9.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-DK5Kk5Bi.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -8028,7 +8074,7 @@ function defaultSupervisorDeps() {
 				if (cached === null) {
 					const { AdapterRegistry: AR } = await import(
 						/* @vite-ignore */
-						"../adapter-registry-DPE1OgrZ.js"
+						"../adapter-registry-BsBP3j5i.js"
 );
 					cached = new AR();
 					await cached.discoverAndRegister();
@@ -8595,11 +8641,11 @@ async function runSupervisorAction(options, deps = {}) {
 						try {
 							const { createExperimenter } = await import(
 								/* @vite-ignore */
-								"../experimenter-CRt7RrrW.js"
+								"../experimenter-CyA9K5u6.js"
 );
 							const { getLatestRun: getLatest } = await import(
 								/* @vite-ignore */
-								"../decisions-7ALaVvR9.js"
+								"../decisions-DH12X_94.js"
 );
 							const expAdapter = createDatabaseAdapter({
 								backend: "auto",
@@ -8609,7 +8655,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-B_G9KCd-.js"
+									"../run-BbXX6gY5.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -9134,7 +9180,7 @@ async function runMetricsAction(options) {
 			const routingConfigPath = join(dbDir, "routing.yml");
 			let routingConfig = null;
 			if (existsSync$1(routingConfigPath)) try {
-				const { loadModelRoutingConfig } = await import("../routing-BCXJlbUS.js");
+				const { loadModelRoutingConfig } = await import("../routing-pCkRxj09.js");
 				routingConfig = loadModelRoutingConfig(routingConfigPath);
 			} catch {}
 			if (routingConfig === null) routingConfig = {
@@ -13106,7 +13152,9 @@ function assembleReport(runId, manifest, halts, storyOutputTokens) {
 		completed_at: completedAt,
 		wall_clock_ms: totalWallMs
 	};
-	const spent = manifest.cost_accumulation?.run_total ?? 0;
+	const runTotal = manifest.cost_accumulation?.run_total ?? 0;
+	const perStoryCostSum = Object.values(perStoryState).reduce((sum, st) => sum + (typeof st?.cost_usd === "number" ? st.cost_usd : 0), 0);
+	const spent = runTotal > 0 ? runTotal : perStoryCostSum;
 	const ceiling = manifest.cost_accumulation != null ? manifest.cli_flags?.cost_ceiling : void 0;
 	const utilization = ceiling != null && ceiling > 0 ? `${(spent / ceiling * 100).toFixed(1)}%` : void 0;
 	const overCeiling = ceiling != null ? spent > ceiling : false;
@@ -13460,8 +13508,8 @@ 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-CT6TGMup.js").then(async () => {
-		const { createVersionManager } = await import("../version-manager-impl-zazA11ph.js");
+	import("../upgrade-unZndH-S.js").then(async () => {
+		const { createVersionManager } = await import("../version-manager-impl--XXnwjMd.js");
 		const vm = createVersionManager();
 		const result = await vm.checkForUpdates();
 		if (result.updateAvailable) {

package/dist/cli/templates/__tests__/docs-match-behavior.test.ts

@@ -0,0 +1,69 @@
+/**
+ * H5.3: docs-match-behavior gate for the consumer CLAUDE.md template.
+ *
+ * The template (`claude-md-substrate-section.md`) is what every consumer
+ * project's Claude session reads before driving substrate — when it drifts
+ * from the code, agents act on behavior that no longer exists (the
+ * income-sources run repeatedly hit this class). This suite pins the
+ * load-bearing claims to their code-side sources of truth:
+ *
+ *   - every finalization mode in the config schema is documented
+ *   - the ff-only merge default and the three-way opt-in are stated
+ *   - the external worktree base default (H4.2) is stated
+ *   - every `story:*` / `pipeline:*` event the template names exists in
+ *     EVENT_TYPE_NAMES (no phantom events)
+ *
+ * Ship rule (execution-plan H5.3 AC1): a change to finalizeStory /
+ * merge-to-main / verification-check registration that alters documented
+ * behavior must update the template in the same commit — this suite is the
+ * enforcement for the pinned claims; reviewers enforce the rest.
+ */
+
+import { describe, it, expect } from 'vitest'
+import { readFileSync } from 'node:fs'
+import { resolve, dirname } from 'node:path'
+import { fileURLToPath } from 'node:url'
+import { EVENT_TYPE_NAMES } from '../../../modules/implementation-orchestrator/event-types.js'
+
+const HERE = dirname(fileURLToPath(import.meta.url))
+const TEMPLATE = readFileSync(resolve(HERE, '..', 'claude-md-substrate-section.md'), 'utf-8')
+const CONFIG_SCHEMA = readFileSync(
+  resolve(HERE, '..', '..', '..', 'modules', 'config', 'config-schema.ts'),
+  'utf-8',
+)
+
+describe('consumer CLAUDE.md template ↔ behavior parity (H5.3)', () => {
+  it('documents every finalization mode the config schema accepts', () => {
+    const enumMatch = /finalization:[\s\S]*?mode: z\.enum\(\[([^\]]+)\]\)/.exec(CONFIG_SCHEMA)
+    expect(enumMatch).not.toBeNull()
+    const modes = [...enumMatch![1]!.matchAll(/'([a-z]+)'/g)].map((m) => m[1]!)
+    expect(modes.length).toBeGreaterThanOrEqual(3)
+    for (const mode of modes) {
+      expect(TEMPLATE, `finalization mode "${mode}" missing from template`).toContain(`\`${mode}\``)
+    }
+  })
+
+  it('states the ff-only merge default and the three-way opt-in (H3.3)', () => {
+    expect(TEMPLATE).toContain('fast-forward-only')
+    expect(TEMPLATE).toContain('merge_strategy: three-way')
+    expect(TEMPLATE).toContain('ff-only-merge-not-possible')
+  })
+
+  it('states the external worktree base default (H4.2)', () => {
+    expect(TEMPLATE).toContain('~/.substrate/worktrees/')
+    expect(TEMPLATE).toContain('worktree.base: in-repo')
+  })
+
+  it('every event name the template cites exists in EVENT_TYPE_NAMES', () => {
+    const cited = [...TEMPLATE.matchAll(/`((?:story|pipeline):[a-z-]+)`/g)].map((m) => m[1]!)
+    expect(cited.length).toBeGreaterThan(0)
+    const known = new Set<string>(EVENT_TYPE_NAMES)
+    const phantom = cited.filter((e) => !known.has(e))
+    expect(phantom, `template cites events that do not exist: ${phantom.join(', ')}`).toEqual([])
+  })
+
+  it('documents the commit-first discipline (H0.1) — the branch is the durable copy', () => {
+    expect(TEMPLATE).toContain('commit-first')
+    expect(TEMPLATE).toContain('wip(story-')
+  })
+})

package/dist/cli/templates/claude-commands/substrate-metrics.md

@@ -0,0 +1,12 @@
+---
+description: Show substrate run metrics and the latest completion report
+---
+
+Report on substrate pipeline outcomes for this project:
+
+1. `substrate report --run latest` — per-story outcomes, cost, escalation diagnostics, halt notifications. Add `--verify-ac` for the AC-to-test traceability matrix.
+2. `substrate metrics --output-format json` — historical run metrics.
+
+Summarize conversationally: how many stories verified/recovered/escalated/failed, total cost, and anything the operator must act on (escalations, halts, unmerged deliverable branches listed under "Finalization").
+
+$ARGUMENTS

package/dist/cli/templates/claude-commands/substrate-run.md

@@ -0,0 +1,21 @@
+---
+description: Run the substrate implementation pipeline (guided)
+---
+
+Run the substrate pipeline for this project.
+
+**Before dispatching, confirm scope with the user if they did not name stories.** Without `--stories`, substrate auto-discovers ALL pending stories and may dispatch 30+ at once.
+
+Steps:
+
+1. If the user named stories (e.g. "1-1,1-2"), run:
+   `substrate run --events --stories <keys>`
+   Otherwise ask which stories to run, or confirm a full auto-discovery run is intended.
+2. Pipeline runs take 5–40 minutes. Use a background invocation or a timeout of at least 10 minutes — the default 2-minute tool timeout WILL kill the pipeline. NEVER pipe substrate output through `head`/`tail`/`grep` (EPIPE stalls).
+3. Poll `substrate status --output-format json` every 60–90s while it runs; `substrate health --output-format json` if it goes quiet for 15+ minutes.
+4. When it completes, summarize per-story outcomes and run `substrate report --run latest`.
+
+Autonomy: default halts on critical+fatal. For fully autonomous runs use:
+`substrate run --halt-on none --non-interactive --events --output-format json`
+
+$ARGUMENTS

package/dist/cli/templates/claude-commands/substrate-supervisor.md

@@ -0,0 +1,15 @@
+---
+description: Attach the substrate supervisor to an active pipeline run
+---
+
+Attach the substrate supervisor to the pipeline run that is active in this project:
+
+`substrate supervisor --output-format json`
+
+Notes:
+- The supervisor monitors an active run (stall detection, kill-and-restart recovery, post-run analysis) — it does NOT start one. Start the run first (see /substrate-run).
+- Only attach to runs started in this session; attaching to another session's run risks killing healthy dispatches.
+- Long-running: use a background invocation or a generous timeout.
+- After the run, read the analysis with `substrate metrics --analysis <run_id> --output-format json`.
+
+$ARGUMENTS

package/dist/cli/templates/claude-md-substrate-section.md

@@ -81,7 +81,17 @@ The Recovery Engine runs a 3-tier auto-fix ladder before any halt — Tier A ret
 
 ### Per-Story Worktree Behavior
 
-Each dispatched story runs in `.substrate-worktrees/story-<key>` on its own branch (`substrate/story-<key>`). The agent's auto-commit (e.g., `feat(story-N-M): ...`) lands on the branch, not main. Merge to main happens after verification SHIP_IT; the worktree is then removed. After verification failure, the worktree and branch are preserved for `substrate reconcile-from-disk` inspection. Use `--no-worktree` if your project doesn't support worktrees (submodules, bare repos).
+Each dispatched story runs in an isolated git worktree on its own branch (`substrate/story-<key>`). By default the worktree lives OUTSIDE the repo at `~/.substrate/worktrees/<projectname>-<hash8>/<key>/`; set `worktree.base: in-repo` in `.substrate/config.yaml` to restore the legacy `.substrate-worktrees/<key>/` location. Substrate auto-commits the story's work to the branch (`feat(story-N-M): ...`) at dev-story completion — commit-first, before review — so the branch is always the durable copy; failure paths add `wip(story-<key>)` checkpoints. After verification failure, the worktree and branch are preserved for `substrate reconcile-from-disk` inspection. Use `--no-worktree` if your project doesn't support worktrees (submodules, bare repos).
+
+### Finalization — how verified work integrates
+
+`finalization.mode` in `.substrate/config.yaml` (or `--finalization <mode>` per run):
+
+- **`merge`** (default): local merge into the branch the run started from. The merge is **fast-forward-only by default** — if the base branch moved during the run, the story escalates `ff-only-merge-not-possible` instead of synthesizing a merge commit. Set `finalization.merge_strategy: three-way` to allow merge commits — **required for concurrent multi-story runs** (later stories cannot fast-forward past earlier merges). A dirty parent tree whose changes intersect the story's diff escalates `parent-tree-dirtied-by-run` naming the files.
+- **`branch`**: verified work stays on `substrate/story-<key>` — nothing self-merges; the branch is the deliverable. The safe brownfield mode.
+- **`pr`**: branch + `git push` + `gh pr create` (one PR per story). Degrades to `branch` with a warning when push/gh fail — never blocks the story.
+
+Lifecycle events on the NDJSON stream: `story:committed` → (`story:merged`) → `story:finalized {mode, branch, sha, pr_url?}`. `substrate report` lists unmerged deliverable branches under "Finalization". Optional `finalization.epic_gate_command` runs before the LAST story of an epic integrates (non-zero exit → `epic-gate-failed`, branch preserved).
 
 ### Key Commands Reference
 
@@ -92,6 +102,7 @@ Each dispatched story runs in `.substrate-worktrees/story-<key>` on its own bran
 | `substrate run --non-interactive` | Suppress stdin prompts; combine with `--halt-on none` for fully autonomous |
 | `substrate run --verify-ac` | On-demand AC-to-Test traceability matrix |
 | `substrate run --no-worktree` | Disable per-story git worktrees (use for submodules or bare repos) |
+| `substrate run --finalization <mode>` | Integration mode: `merge` (default) / `branch` (never self-merge) / `pr` |
 | `substrate report [--run <id\|latest>]` | Per-run completion report — outcomes, cost, escalation diagnostics, halt notifications |
 | `substrate report --verify-ac` | Append AC-to-Test traceability matrix to the report |
 | `substrate reconcile-from-disk [--dry-run] [--yes]` | Path A reconciliation when pipeline reports failed but tree is coherent |
@@ -120,6 +131,8 @@ Substrate writes per-project state under `.substrate/` in a few flavors:
 
 The defensible default for most projects is to ignore everything under `.substrate/` except the operator config. Local telemetry stays on each developer's machine — operators see their own corpus locally via `substrate metrics`; cross-machine sharing of routing telemetry is a future feature, not currently supported.
 
+Besides `.substrate/`, `substrate init` also scaffolds project-root artifacts that ARE intentional and worth tracking in git: `CLAUDE.md`, `AGENTS.md`, `GEMINI.md` (pipeline instructions per agent CLI), `packs/<pack-name>/` (the methodology pack's prompts — the pipeline reads these at dispatch time), `.claude/commands/substrate-*.md` + `.claude/skills/`, and `.codex/` mirrors. Track them; they are inputs to every run, not state. If your team prefers not to commit the non-Claude agent files (`AGENTS.md`, `GEMINI.md`, `.codex/`), gitignore them explicitly — substrate regenerates them on `substrate init`.
+
 ```gitignore
 # Substrate state — track only the operator config; everything else is
 # per-process, per-run, or local-machine accumulation

package/dist/{decisions-7ALaVvR9.js → decisions-DH12X_94.js}

@@ -1,4 +1,4 @@
-import { addTokenUsage, createDecision, createPipelineRun, createRequirement, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunningPipelineRuns, getTokenUsageSummary, listRequirements, registerArtifact, updateDecision, updatePipelineRun, updatePipelineRunConfig, upsertDecision } from "./dist-C6pEdj12.js";
+import { addTokenUsage, createDecision, createPipelineRun, createRequirement, getArtifactByTypeForRun, getArtifactsByRun, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestRun, getPipelineRunById, getRunningPipelineRuns, getTokenUsageSummary, listRequirements, registerArtifact, updateDecision, updatePipelineRun, updatePipelineRunConfig, upsertDecision } from "./dist-90byyGPp.js";
 import "./decisions-CzSIEeGP.js";
 
 export { getLatestRun };

package/dist/{dist-C6pEdj12.js → dist-90byyGPp.js}

@@ -3223,10 +3223,12 @@ async function initTelemetrySchema(adapter) {
       cache_hit_sub_score           DOUBLE       NOT NULL DEFAULT 0,
       io_ratio_sub_score            DOUBLE       NOT NULL DEFAULT 0,
       context_management_sub_score  DOUBLE       NOT NULL DEFAULT 0,
+      token_density_sub_score       DOUBLE       NOT NULL DEFAULT 0,
       avg_cache_hit_rate            DOUBLE       NOT NULL DEFAULT 0,
       avg_io_ratio                  DOUBLE       NOT NULL DEFAULT 0,
       context_spike_count           INTEGER      NOT NULL DEFAULT 0,
       total_turns                   INTEGER      NOT NULL DEFAULT 0,
+      cold_start_turns_excluded     INTEGER      NOT NULL DEFAULT 0,
       per_model_json                TEXT         NOT NULL DEFAULT '[]',
       per_source_json               TEXT         NOT NULL DEFAULT '[]',
       dispatch_id                   TEXT,
@@ -3243,6 +3245,9 @@ async function initTelemetrySchema(adapter) {
 	]) try {
 		await adapter.exec(`ALTER TABLE efficiency_scores ADD COLUMN ${col} TEXT`);
 	} catch {}
+	for (const [col, ddl] of [["token_density_sub_score", "DOUBLE NOT NULL DEFAULT 0"], ["cold_start_turns_excluded", "INTEGER NOT NULL DEFAULT 0"]]) try {
+		await adapter.exec(`ALTER TABLE efficiency_scores ADD COLUMN ${col} ${ddl}`);
+	} catch {}
 	await adapter.exec(`
     CREATE TABLE IF NOT EXISTS recommendations (
       id                       VARCHAR(16)   NOT NULL,
@@ -12595,4 +12600,4 @@ async function callLLM(params) {
 
 //#endregion
 export { ADVISORY_NOTES, AdapterRegistry, AdtError, BRANCH_PREFIX, BudgetConfigSchema, CLAUDE_AUTH_FAILURE_HINT, CODEX_SANDBOX_BLOCK_HINT, CURRENT_CONFIG_FORMAT_VERSION, CURRENT_TASK_GRAPH_VERSION, Categorizer, ClaudeCodeAdapter, CodexCLIAdapter, ConfigError, ConfigIncompatibleFormatError, ConsumerAnalyzer, CostTrackerConfigSchema, DEFAULT_CONFIG, DEFAULT_GLOBAL_SETTINGS, DispatcherImpl, DoltClient, DoltNotInstalled, DoltQueryError, ESCALATION_DIAGNOSIS, EXPERIMENT_RESULT, EfficiencyScorer, GeminiCLIAdapter, GlobalSettingsSchema, InMemoryDatabaseAdapter, IngestionServer, LEARNING_FINDING, LogTurnAnalyzer, ModelRoutingConfigSchema, MonitorDatabaseImpl, OPERATIONAL_FINDING, PartialGlobalSettingsSchema, PartialProviderConfigSchema, ProviderPolicySchema, ProvidersSchema, Recommender, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, STORY_METRICS, STORY_OUTCOME, SubstrateConfigSchema, TASK_TYPE_PHASE_MAP, TEST_EXPANSION_FINDING, TEST_PLAN, TelemetryConfigSchema, TelemetryNormalizer, TelemetryPipeline, TurnAnalyzer, VersionManagerImpl, addTokenUsage, aggregateTokenUsageForRun, aggregateTokenUsageForStory, buildAuditLogEntry, buildBranchName, buildModificationDirective, buildPRBody, buildWorktreePath, callLLM, checkDoltInstalled, classifyVersionGap, compareRunMetrics, createAmendmentRun, createConfigSystem, createDatabaseAdapter as createDatabaseAdapter$1, createDecision, createExperimenter, createGitWorktreeManager, createPipelineRun, createRequirement, createStderrLogger, createVersionManager, detectClaudeAuthFailure, detectCodexSandboxBlock, detectInterfaceChanges, determineVerdict, getActiveDecisions, getAllCostEntriesFiltered, getArtifactByTypeForRun, getArtifactsByRun, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhase, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getModelTier, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initWorkGraphSchema, initializeDolt, listRequirements, listRunMetrics, loadModelRoutingConfig, loadParentRunDecisions, registerArtifact, resolvePromptFile, supersedeDecision, swallowDebug, tagRunAsBaseline, updateDecision, updatePipelineRun, updatePipelineRunConfig, upsertDecision, writeRunMetrics, writeStoryMetrics };
-//# sourceMappingURL=dist-C6pEdj12.js.map
+//# sourceMappingURL=dist-90byyGPp.js.map

package/dist/{errors-1xcRMTz_.js → errors-ST3E8qWc.js}

@@ -1,4 +1,4 @@
-import { AdtError } from "./dist-C6pEdj12.js";
+import { AdtError } from "./dist-90byyGPp.js";
 
 //#region src/core/errors.ts
 /** Error thrown when task configuration is invalid */
@@ -71,4 +71,4 @@ var TaskGraphIncompatibleFormatError = class extends AdtError {
 
 //#endregion
 export { BudgetExceededError, GitError, RecoveryError, TaskConfigError, TaskGraphCycleError, TaskGraphError, TaskGraphIncompatibleFormatError, WorkerError, WorkerNotFoundError };
-//# sourceMappingURL=errors-1xcRMTz_.js.map
+//# sourceMappingURL=errors-ST3E8qWc.js.map

package/dist/{experimenter-CRt7RrrW.js → experimenter-CyA9K5u6.js}

@@ -1,3 +1,3 @@
-import { buildAuditLogEntry, buildBranchName, buildModificationDirective, buildPRBody, buildWorktreePath, createExperimenter, determineVerdict, resolvePromptFile } from "./dist-C6pEdj12.js";
+import { buildAuditLogEntry, buildBranchName, buildModificationDirective, buildPRBody, buildWorktreePath, createExperimenter, determineVerdict, resolvePromptFile } from "./dist-90byyGPp.js";
 
 export { createExperimenter };

package/dist/{health-CcOYQsgZ.js → health-Bj5OYB7r.js}

@@ -1,6 +1,6 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { DoltClient, DoltQueryError, createDatabaseAdapter$1 as createDatabaseAdapter, getLatestRun, getPipelineRunById, initSchema } from "./dist-C6pEdj12.js";
-import { resolveMainRepoRoot, resolveRunManifest } from "./manifest-read-8oNapRvD.js";
+import { DoltClient, DoltQueryError, createDatabaseAdapter$1 as createDatabaseAdapter, getLatestRun, getPipelineRunById, initSchema } from "./dist-90byyGPp.js";
+import { resolveMainRepoRoot, resolveRunManifest } from "./manifest-read-BAN_-QKy.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-CcOYQsgZ.js.map
+//# sourceMappingURL=health-Bj5OYB7r.js.map

package/dist/{health-Bhwd_HX9.js → health-DK5Kk5Bi.js}

@@ -1,7 +1,7 @@
-import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-CcOYQsgZ.js";
+import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-Bj5OYB7r.js";
 import "./logger-KeHncl-f.js";
-import "./dist-C6pEdj12.js";
-import "./manifest-read-8oNapRvD.js";
+import "./dist-90byyGPp.js";
+import "./manifest-read-BAN_-QKy.js";
 import "./work-graph-repository-DZyJv5pV.js";
 import "./decisions-CzSIEeGP.js";
 

package/dist/index.js

@@ -1,8 +1,8 @@
 import { childLogger, createLogger, logger } from "./logger-KeHncl-f.js";
 import { assertDefined, createEventBus, createTuiApp, deepClone, formatDuration, generateId, isPlainObject, isTuiCapable, printNonTtyWarning, sleep, withRetry } from "./helpers-CElYrONe.js";
-import { AdapterRegistry, AdtError, ClaudeCodeAdapter, CodexCLIAdapter, ConfigError, ConfigIncompatibleFormatError, GeminiCLIAdapter } from "./dist-C6pEdj12.js";
+import { AdapterRegistry, AdtError, ClaudeCodeAdapter, CodexCLIAdapter, ConfigError, ConfigIncompatibleFormatError, GeminiCLIAdapter } from "./dist-90byyGPp.js";
 import "./adapter-registry-DXLMTmfD.js";
-import { BudgetExceededError, GitError, RecoveryError, TaskConfigError, TaskGraphCycleError, TaskGraphError, TaskGraphIncompatibleFormatError, WorkerError, WorkerNotFoundError } from "./errors-1xcRMTz_.js";
+import { BudgetExceededError, GitError, RecoveryError, TaskConfigError, TaskGraphCycleError, TaskGraphError, TaskGraphIncompatibleFormatError, WorkerError, WorkerNotFoundError } from "./errors-ST3E8qWc.js";
 
 //#region src/core/di.ts
 /**

package/dist/{interactive-prompt-BVTTIU3t.js → interactive-prompt-Du_Yt_N4.js}

@@ -1,5 +1,5 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { readCurrentRunId, resolveMainRepoRoot } from "./manifest-read-8oNapRvD.js";
+import { readCurrentRunId, resolveMainRepoRoot } from "./manifest-read-BAN_-QKy.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-BVTTIU3t.js.map
+//# sourceMappingURL=interactive-prompt-Du_Yt_N4.js.map

package/dist/{manifest-read-8oNapRvD.js → manifest-read-BAN_-QKy.js}

@@ -1,5 +1,5 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { LEARNING_FINDING, createDecision, getDecisionsByCategory } from "./dist-C6pEdj12.js";
+import { LEARNING_FINDING, createDecision, getDecisionsByCategory } from "./dist-90byyGPp.js";
 import * as path$1 from "path";
 import { join } from "path";
 import { readFile } from "fs/promises";
@@ -2235,6 +2235,20 @@ function detectTestCommand(workingDir) {
 	} catch {}
 	return void 0;
 }
+/**
+* H7 (trust-boundary hardening): detect exit-code LAUNDERING in a resolved test
+* command — a wrapper that forces exit 0 regardless of the real suite result
+* (`… || true`, `… || :`, `… || exit 0`, `… ; true`, `… ; exit 0`). A
+* reward-hacking agent used this to make a genuinely-red suite report pass
+* (verified against compiled dist in the red-team review). Legitimate commands
+* do not mask their own exit code, so this is a tampering signal, not a style
+* nit. Note: cannot catch arbitrary in-language masking (e.g. `python -c
+* "...sys.exit(0)"`) — the trusted-profile read is the primary defense; this is
+* belt-and-braces for the shell-wrapper class and the --no-worktree path.
+*/
+function detectsExitCodeLaundering(command) {
+	return /(\|\||;)\s*(true|:|exit\s+0)(\s|;|$)/.test(command);
+}
 var TestSuiteCheck = class {
 	name = "test-suite";
 	tier = "A";
@@ -2255,6 +2269,19 @@ var TestSuiteCheck = class {
 				findings
 			};
 		}
+		if (cmd !== void 0 && cmd !== "" && detectsExitCodeLaundering(cmd)) {
+			const findings = [{
+				category: "test-command-tampered",
+				severity: "error",
+				message: `test command masks its own exit code (\`${cmd}\`) — a wrapper like \`|| true\` / \`; exit 0\` forces a pass regardless of the real suite result. Remove the exit-code mask; the suite must fail the story when tests fail.`
+			}];
+			return {
+				status: "fail",
+				details: renderFindings(findings),
+				duration_ms: Date.now() - start,
+				findings
+			};
+		}
 		if (cmd === void 0 || cmd === "") {
 			const findings = [{
 				category: "test-suite-skip",
@@ -2486,7 +2513,7 @@ var ContaminationCheck = class {
 			duration_ms: Date.now() - start,
 			findings: []
 		};
-		const allowedLanguages = readProfileLanguages(context.workingDir);
+		const allowedLanguages = context.trustedLanguages ?? readProfileLanguages(context.workingDir);
 		if (allowedLanguages.length === 0) {
 			const findings$1 = [{
 				category: "contamination-skip",
@@ -3449,9 +3476,13 @@ var RuntimeProbeCheck = class {
 			});
 		}
 		const status = findings.some((f) => f.severity === "error") ? "fail" : findings.some((f) => f.severity === "warn") ? "warn" : "pass";
+		const deferredCount = findings.filter((f) => f.category === CATEGORY_DEFERRED).length;
+		const failedCount = findings.filter((f) => f.severity === "error").length;
+		const ranCount = parsed.probes.filter((probe) => probe.sandbox !== "twin").length;
+		const summaryLine = `runtime-probes: ${ranCount} ran (${ranCount - failedCount} passed, ${failedCount} failed)` + (deferredCount > 0 ? `, ${deferredCount} deferred (sandbox=twin, Phase 3)` : "");
 		return {
 			status,
-			details: findings.length > 0 ? renderFindings(findings) : `runtime-probes: ${parsed.probes.length} probe(s) passed`,
+			details: findings.length > 0 ? `${summaryLine}\n${renderFindings(findings)}` : summaryLine,
 			duration_ms: Date.now() - start,
 			findings
 		};
@@ -6300,4 +6331,4 @@ 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-8oNapRvD.js.map
+//# sourceMappingURL=manifest-read-BAN_-QKy.js.map

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

@@ -1,6 +1,6 @@
 import "../../logger-KeHncl-f.js";
-import "../../dist-C6pEdj12.js";
-import "../../manifest-read-8oNapRvD.js";
-import { runInteractivePrompt } from "../../interactive-prompt-BVTTIU3t.js";
+import "../../dist-90byyGPp.js";
+import "../../manifest-read-BAN_-QKy.js";
+import { runInteractivePrompt } from "../../interactive-prompt-Du_Yt_N4.js";
 
 export { runInteractivePrompt };

package/dist/{routing-BCXJlbUS.js → routing-pCkRxj09.js}

@@ -1,4 +1,4 @@
-import { ModelRoutingConfigSchema, ProviderPolicySchema, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, TASK_TYPE_PHASE_MAP, getModelTier, loadModelRoutingConfig } from "./dist-C6pEdj12.js";
+import { ModelRoutingConfigSchema, ProviderPolicySchema, RoutingConfigError, RoutingRecommender, RoutingResolver, RoutingTelemetry, RoutingTokenAccumulator, RoutingTuner, TASK_TYPE_PHASE_MAP, getModelTier, loadModelRoutingConfig } from "./dist-90byyGPp.js";
 import "./routing-DFxoKHDt.js";
 
 export { loadModelRoutingConfig };

package/dist/{run-B_G9KCd-.js → run-BbXX6gY5.js}

@@ -1,14 +1,14 @@
-import "./health-CcOYQsgZ.js";
+import "./health-Bj5OYB7r.js";
 import "./logger-KeHncl-f.js";
 import "./helpers-CElYrONe.js";
-import "./dist-C6pEdj12.js";
-import "./manifest-read-8oNapRvD.js";
-import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, runRunAction, wireNdjsonEmitter } from "./run-B9lhuahO.js";
+import "./dist-90byyGPp.js";
+import "./manifest-read-BAN_-QKy.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, runRunAction, wireNdjsonEmitter } from "./run-DbT2-Wzg.js";
 import "./routing-DFxoKHDt.js";
 import "./work-graph-repository-DZyJv5pV.js";
 import "./decisions-CzSIEeGP.js";
 import "./decision-router-BAPpON_C.js";
-import "./interactive-prompt-BVTTIU3t.js";
+import "./interactive-prompt-Du_Yt_N4.js";
 import "./recovery-engine-BKGBeBnW.js";
 
 export { runRunAction };

package/dist/{run-B9lhuahO.js → run-DbT2-Wzg.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-CcOYQsgZ.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-Bj5OYB7r.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-C6pEdj12.js";
-import { FindingsInjector, RunManifest, RuntimeProbeListSchema, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, parseRuntimeProbes, renderFindings, resolveGraphPath, resolveMainRepoRoot, runAcTraceabilityCheck, runStaleVerificationRecovery } from "./manifest-read-8oNapRvD.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-90byyGPp.js";
+import { FindingsInjector, RunManifest, RuntimeProbeListSchema, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, parseRuntimeProbes, renderFindings, resolveGraphPath, resolveMainRepoRoot, runAcTraceabilityCheck, runStaleVerificationRecovery } from "./manifest-read-BAN_-QKy.js";
 import { WorkGraphRepository, detectCycles } from "./work-graph-repository-DZyJv5pV.js";
 import { deriveExitCode, routeDecision } from "./decision-router-BAPpON_C.js";
-import { runInteractivePrompt } from "./interactive-prompt-BVTTIU3t.js";
+import { runInteractivePrompt } from "./interactive-prompt-Du_Yt_N4.js";
 import { runRecoveryEngine } from "./recovery-engine-BKGBeBnW.js";
 import { basename, dirname, extname, join } from "path";
 import { access, readFile, readdir, stat } from "fs/promises";
@@ -951,7 +951,7 @@ const PIPELINE_EVENT_METADATA = [
 			{
 				name: "reason",
 				type: "string",
-				description: "Escalation reason. Common values: review-cycles-exhausted (default review-loop max hit); create-story-no-file (create-story phase did not write a story artifact); dev-story-no-commit (substrate auto-commit found no committable changes — agent produced nothing or all changes were outside the worktree); dev-story-commit-failed (substrate auto-commit failed — typically a pre-commit hook rejected the commit; stderr captured in issues); merge-to-main-error (unexpected error in the merge-to-main phase); merge-conflict-detected (story branch could not be merged due to conflicts). v0.20.87+."
+				description: "Escalation reason. Common values: review-cycles-exhausted (default review-loop max hit); create-story-no-file (create-story phase did not write a story artifact); dev-story-no-commit (substrate auto-commit found no committable changes — agent produced nothing or all changes were outside the worktree); dev-story-commit-failed (substrate auto-commit failed — typically a pre-commit hook rejected the commit; stderr captured in issues); merge-to-main-error (unexpected error in the merge-to-main phase); merge-conflict-detected (story branch could not be merged due to conflicts); parent-tree-dirtied-by-run (uncommitted parent changes intersect the story diff — merge refused, H3.3); ff-only-merge-not-possible (base moved and merge_strategy is ff-only — set finalization.merge_strategy: three-way or integrate manually, H3.3); epic-gate-failed (finalization.epic_gate_command exited non-zero before the last story of an epic integrated, H3.4); story-file-missing (story artifact gone from working tree AND branch HEAD — check wip/feat commits on the story branch, H5.5). v0.20.87+."
 			},
 			{
 				name: "cycles",
@@ -7304,6 +7304,41 @@ async function stageIntentToAdd(files, workingDirectory) {
 * Run a git command in the specified directory and return its stdout output.
 * Returns '' on any error and logs a warning.
 */
+/**
+* H5.5 (story-artifact resilience): recover a story file from the branch
+* HEAD when the working-tree copy has gone missing (live-smoke incident
+* 2026-07-06: a fix-phase agent DELETED the committed story artifact; the
+* re-review hit ENOENT and was misclassified `consecutive-review-timeouts`
+* while the file sat safely in the H0.1 feat commit the whole time).
+*
+* Reads `git show HEAD:<relpath>` in the worktree and, on success, WRITES
+* the content back to the working tree so downstream phases find it too.
+* Returns the content, or undefined when the file isn't in HEAD either.
+*/
+async function recoverStoryFileFromBranch(storyFilePath, workingDirectory) {
+	const rel = relative(workingDirectory, resolve$1(workingDirectory, storyFilePath));
+	if (rel.startsWith("..")) {
+		logger$20.warn({
+			storyFilePath,
+			workingDirectory
+		}, "recoverStoryFileFromBranch: path outside the worktree — not recoverable");
+		return void 0;
+	}
+	const content = await runGitCommand(["show", `HEAD:${rel}`], workingDirectory, "recover-story-file");
+	if (content.trim().length === 0) return void 0;
+	try {
+		const abs = resolve$1(workingDirectory, rel);
+		await mkdir$1(dirname$1(abs), { recursive: true });
+		await writeFile$1(abs, content, "utf-8");
+		logger$20.warn({ storyFilePath: abs }, "H5.5: story file restored to the working tree from branch HEAD");
+	} catch (writeErr) {
+		logger$20.warn({
+			storyFilePath,
+			err: writeErr
+		}, "H5.5: recovered story content but could not restore the file (continuing with in-memory content)");
+	}
+	return content;
+}
 async function runGitCommand(args, cwd, logLabel) {
 	return new Promise((resolve$6) => {
 		let stdout = "";
@@ -7746,20 +7781,28 @@ async function runDevStory(deps, params) {
 	try {
 		storyContent = await readFile$1(storyFilePath, "utf-8");
 	} catch (err) {
-		if (err.code === "ENOENT") {
+		const recovered = await recoverStoryFileFromBranch(storyFilePath, deps.projectRoot ?? process.cwd());
+		if (recovered !== void 0) {
+			logger$18.warn({
+				storyKey,
+				storyFilePath
+			}, "story file missing from working tree — recovered from branch HEAD (H5.5)");
+			storyContent = recovered;
+		} else if (err.code === "ENOENT") {
 			logger$18.error({
 				storyKey,
 				storyFilePath
 			}, "Story file not found");
 			return makeFailureResult("story_file_not_found");
+		} else {
+			const error = err instanceof Error ? err.message : String(err);
+			logger$18.error({
+				storyKey,
+				storyFilePath,
+				error
+			}, "Failed to read story file");
+			return makeFailureResult(`story_file_read_error: ${error}`);
 		}
-		const error = err instanceof Error ? err.message : String(err);
-		logger$18.error({
-			storyKey,
-			storyFilePath,
-			error
-		}, "Failed to read story file");
-		return makeFailureResult(`story_file_read_error: ${error}`);
 	}
 	if (storyContent.trim().length === 0) {
 		logger$18.error({
@@ -8525,14 +8568,20 @@ async function runCodeReview(deps, params) {
 		storyContent = await readFile$1(storyFilePath, "utf-8");
 	} catch (err) {
 		const error = err instanceof Error ? err.message : String(err);
-		logger$17.error({
-			storyFilePath,
-			error
-		}, "Failed to read story file");
-		return defaultFailResult(`Failed to read story file: ${error}`, {
-			input: 0,
-			output: 0
-		});
+		const recovered = await recoverStoryFileFromBranch(storyFilePath, cwd);
+		if (recovered !== void 0) {
+			logger$17.warn({ storyFilePath }, "story file missing from working tree — recovered from branch HEAD (H5.5)");
+			storyContent = recovered;
+		} else {
+			logger$17.error({
+				storyFilePath,
+				error
+			}, "Failed to read story file (absent from working tree AND branch HEAD)");
+			return defaultFailResult(`story-file-missing: ${storyFilePath} absent from working tree and branch HEAD (${error})`, {
+				input: 0,
+				output: 0
+			});
+		}
 	}
 	const archConstraintsContent = await getArchConstraints$2(deps);
 	const templateTokens = countTokens(template);
@@ -12041,8 +12090,10 @@ function assembleVerificationContext(opts) {
 	} catch {
 		commitSha = "unknown";
 	}
-	const profileBuildCommand = readProfileKey(opts.workingDir, "buildCommand");
-	const profileTestCommand = readProfileKey(opts.workingDir, "testCommand");
+	const trustedDir = opts.trustedProfileDir ?? opts.workingDir;
+	const profileBuildCommand = readProfileKey(trustedDir, "buildCommand");
+	const profileTestCommand = readProfileKey(trustedDir, "testCommand");
+	const trustedLanguages = readProfileLanguagesLocal(trustedDir);
 	return {
 		storyKey: opts.storyKey,
 		workingDir: opts.workingDir,
@@ -12057,13 +12108,26 @@ function assembleVerificationContext(opts) {
 		...opts.changedFiles !== void 0 ? { changedFiles: opts.changedFiles } : {},
 		...opts.modifiedTrackedFiles !== void 0 ? { modifiedTrackedFiles: opts.modifiedTrackedFiles } : {},
 		...profileBuildCommand !== void 0 ? { buildCommand: profileBuildCommand } : {},
-		...profileTestCommand !== void 0 ? { testCommand: profileTestCommand } : {}
+		...profileTestCommand !== void 0 ? { testCommand: profileTestCommand } : {},
+		...trustedLanguages.length > 0 ? { trustedLanguages } : {}
 	};
 }
 /**
 * Read a single `<key>: value` line from `.substrate/project-profile.yaml`
 * under `workingDir` (H1.2). Line-based parse — no yaml dependency.
 */
+function readProfileLanguagesLocal(dir) {
+	const profilePath = join$1(dir, ".substrate", "project-profile.yaml");
+	if (!existsSync(profilePath)) return [];
+	try {
+		const content = readFileSync(profilePath, "utf-8");
+		const langs = new Set();
+		for (const m of content.matchAll(/^\s*(?:-\s+)?language:\s*['"]?([a-z]+)['"]?\s*$/gm)) if (m[1] !== void 0) langs.add(m[1]);
+		return [...langs];
+	} catch {
+		return [];
+	}
+}
 function readProfileKey(workingDir, key) {
 	const profilePath = join$1(workingDir, ".substrate", "project-profile.yaml");
 	if (!existsSync(profilePath)) return void 0;
@@ -15591,6 +15655,7 @@ function createImplementationOrchestrator(deps) {
 				const verifContext = assembleVerificationContext({
 					storyKey,
 					workingDir: effectiveProjectRoot ?? process.cwd(),
+					...projectRoot !== void 0 ? { trustedProfileDir: projectRoot } : {},
 					reviewResult: latestReviewSignals,
 					storyContent: storyContentForVerification,
 					devStoryResult: devStorySignals,
@@ -15681,6 +15746,7 @@ function createImplementationOrchestrator(deps) {
 								const retryVerifContext = assembleVerificationContext({
 									storyKey,
 									workingDir: effectiveProjectRoot ?? process.cwd(),
+									...projectRoot !== void 0 ? { trustedProfileDir: projectRoot } : {},
 									reviewResult: latestReviewSignals,
 									storyContent: storyContentForVerification,
 									devStoryResult: devStorySignals,
@@ -16449,23 +16515,26 @@ function createImplementationOrchestrator(deps) {
 					continue;
 				}
 				if (isPhantomReview && timeoutRetried) {
+					const isStoryFileMissing = (reviewResult.error ?? "").includes("story-file-missing");
+					const escalationReason = isStoryFileMissing ? "story-file-missing" : "consecutive-review-timeouts";
 					logger$27.warn({
 						storyKey,
 						reviewCycles,
-						error: reviewResult.error
-					}, "Consecutive review timeouts detected (original + retry both failed) — escalating immediately");
+						error: reviewResult.error,
+						reason: escalationReason
+					}, "Consecutive review failures (original + retry) — escalating immediately");
 					endPhase(storyKey, "code-review");
 					updateStory(storyKey, {
 						phase: "ESCALATED",
-						error: "consecutive-review-timeouts",
+						error: escalationReason,
 						completedAt: new Date().toISOString()
 					});
 					await writeStoryMetricsBestEffort(storyKey, "escalated", reviewCycles + 1);
 					await emitEscalation({
 						storyKey,
-						lastVerdict: "consecutive-review-timeouts",
+						lastVerdict: escalationReason,
 						reviewCycles: reviewCycles + 1,
-						issues: ["Review dispatch failed twice consecutively (original + phantom-retry). Likely resource-constrained or diff too large for reviewer."]
+						issues: [isStoryFileMissing ? `Story artifact is missing from BOTH the working tree and the branch HEAD (${reviewResult.error ?? ""}). An agent deleted it and it was never committed — check the wip/feat commits on the story branch for the last good copy.` : "Review dispatch failed twice consecutively (original + phantom-retry). Likely resource-constrained or diff too large for reviewer."]
 					});
 					await persistState();
 					return;
@@ -47727,7 +47796,7 @@ async function runFullPipeline(options) {
 */
 async function emitPreDispatchVersionAdvisory(currentVersion) {
 	if (process.env["SUBSTRATE_NO_UPDATE_CHECK"] === "1") return;
-	const { createVersionManager } = await import("./version-manager-impl-zazA11ph.js");
+	const { createVersionManager } = await import("./version-manager-impl--XXnwjMd.js");
 	const vm = createVersionManager();
 	const result = await vm.checkForUpdates(true);
 	const gap = classifyVersionGap(currentVersion, result.latestVersion);
@@ -47834,4 +47903,4 @@ 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-B9lhuahO.js.map
+//# sourceMappingURL=run-DbT2-Wzg.js.map

package/dist/{upgrade-DcvPseav.js → upgrade-Dw6jKkH3.js}

@@ -1,4 +1,4 @@
-import { createVersionManager } from "./dist-C6pEdj12.js";
+import { createVersionManager } from "./dist-90byyGPp.js";
 import { execSync, spawn } from "child_process";
 import * as readline from "readline";
 
@@ -123,4 +123,4 @@ function registerUpgradeCommand(program) {
 
 //#endregion
 export { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand };
-//# sourceMappingURL=upgrade-DcvPseav.js.map
+//# sourceMappingURL=upgrade-Dw6jKkH3.js.map

package/dist/{upgrade-CT6TGMup.js → upgrade-unZndH-S.js}

@@ -1,5 +1,5 @@
-import "./dist-C6pEdj12.js";
+import "./dist-90byyGPp.js";
 import "./version-manager-impl-qFBiO4Eh.js";
-import { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand } from "./upgrade-DcvPseav.js";
+import { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand } from "./upgrade-Dw6jKkH3.js";
 
 export { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand };

package/dist/{version-manager-impl-zazA11ph.js → version-manager-impl--XXnwjMd.js}

@@ -1,4 +1,4 @@
-import { VersionManagerImpl, createVersionManager } from "./dist-C6pEdj12.js";
+import { VersionManagerImpl, createVersionManager } from "./dist-90byyGPp.js";
 import "./version-manager-impl-qFBiO4Eh.js";
 
 export { createVersionManager };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.20.150",
+  "version": "0.20.152",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",

package/dist/adapter-registry-DPE1OgrZ.js

@@ -1,4 +0,0 @@
-import { AdapterRegistry } from "./dist-C6pEdj12.js";
-import "./adapter-registry-DXLMTmfD.js";
-
-export { AdapterRegistry };