substrate-ai 0.20.149 → 0.20.151

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-ByQadq3J.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-BERxzeG-.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-C2CAZDep.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-knD2uWkz.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-BAUlPom3.js";
-import "../errors-Db8EIM9w.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-BOvY53EG.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-Dgqfz9HY.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-CMBlj6UF.js";
+import "../interactive-prompt-UWLccCqL.js";
 import "../recovery-engine-BKGBeBnW.js";
 import "../version-manager-impl-qFBiO4Eh.js";
-import { registerUpgradeCommand } from "../upgrade-DOmKCyOY.js";
+import { registerUpgradeCommand } from "../upgrade-Dw6jKkH3.js";
 import { Command } from "commander";
 import { fileURLToPath } from "url";
 import { dirname, join, resolve } from "path";
@@ -624,6 +624,7 @@ const SubstrateConfigSchema = z.object({
 	supervisor_poll_interval_seconds: z.number().int().positive().optional(),
 	retry_budget: z.number().int().positive().optional(),
 	epics_path: z.string().optional(),
+	dispatch: z.object({ permission_profile: z.enum(["skip", "scoped"]).optional() }).strict().optional(),
 	finalization: z.object({
 		mode: z.enum([
 			"merge",
@@ -656,6 +657,7 @@ const PartialSubstrateConfigSchema = z.object({
 	supervisor_poll_interval_seconds: z.number().int().positive().optional(),
 	retry_budget: z.number().int().positive().optional(),
 	epics_path: z.string().optional(),
+	dispatch: z.object({ permission_profile: z.enum(["skip", "scoped"]).optional() }).strict().optional(),
 	finalization: z.object({
 		mode: z.enum([
 			"merge",
@@ -1523,6 +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"));
@@ -2276,6 +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"];
@@ -7078,7 +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-WGcvcIYK.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-CoJ3nBWL.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -8026,7 +8074,7 @@ function defaultSupervisorDeps() {
 				if (cached === null) {
 					const { AdapterRegistry: AR } = await import(
 						/* @vite-ignore */
-						"../adapter-registry-CauYNA1U.js"
+						"../adapter-registry-BsBP3j5i.js"
 );
 					cached = new AR();
 					await cached.discoverAndRegister();
@@ -8593,11 +8641,11 @@ async function runSupervisorAction(options, deps = {}) {
 						try {
 							const { createExperimenter } = await import(
 								/* @vite-ignore */
-								"../experimenter-Dm5jUPO6.js"
+								"../experimenter-CyA9K5u6.js"
 );
 							const { getLatestRun: getLatest } = await import(
 								/* @vite-ignore */
-								"../decisions-De43bvYq.js"
+								"../decisions-DH12X_94.js"
 );
 							const expAdapter = createDatabaseAdapter({
 								backend: "auto",
@@ -8607,7 +8655,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-CtIc7_rK.js"
+									"../run-Csg27VHs.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -9132,7 +9180,7 @@ async function runMetricsAction(options) {
 			const routingConfigPath = join(dbDir, "routing.yml");
 			let routingConfig = null;
 			if (existsSync$1(routingConfigPath)) try {
-				const { loadModelRoutingConfig } = await import("../routing-B3sgH5MZ.js");
+				const { loadModelRoutingConfig } = await import("../routing-pCkRxj09.js");
 				routingConfig = loadModelRoutingConfig(routingConfigPath);
 			} catch {}
 			if (routingConfig === null) routingConfig = {
@@ -13104,7 +13152,9 @@ function assembleReport(runId, manifest, halts, storyOutputTokens) {
 		completed_at: completedAt,
 		wall_clock_ms: totalWallMs
 	};
-	const spent = manifest.cost_accumulation?.run_total ?? 0;
+	const runTotal = manifest.cost_accumulation?.run_total ?? 0;
+	const perStoryCostSum = Object.values(perStoryState).reduce((sum, st) => sum + (typeof st?.cost_usd === "number" ? st.cost_usd : 0), 0);
+	const spent = runTotal > 0 ? runTotal : perStoryCostSum;
 	const ceiling = manifest.cost_accumulation != null ? manifest.cli_flags?.cost_ceiling : void 0;
 	const utilization = ceiling != null && ceiling > 0 ? `${(spent / ceiling * 100).toFixed(1)}%` : void 0;
 	const overCeiling = ceiling != null ? spent > ceiling : false;
@@ -13458,8 +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-B3iamwjO.js").then(async () => {
-		const { createVersionManager } = await import("../version-manager-impl-DizCvYy8.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-De43bvYq.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-C2CAZDep.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-C2CAZDep.js → dist-90byyGPp.js}

@@ -4,6 +4,7 @@ import { EventEmitter } from "node:events";
 import yaml, { dump, load } from "js-yaml";
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
 import { exec, execFile, execSync, spawn, spawnSync } from "node:child_process";
+import * as path$3 from "node:path";
 import * as path$2 from "node:path";
 import * as path$1 from "node:path";
 import path, { dirname as dirname$1, join as join$1, resolve as resolve$1 } from "node:path";
@@ -1302,7 +1303,8 @@ var DispatcherImpl = class {
 			...storyKey !== void 0 ? { storyKey } : {},
 			...optimizationDirectives !== void 0 ? { optimizationDirectives } : {},
 			taskType,
-			dispatchId: id
+			dispatchId: id,
+			...this._config.permissionProfile !== void 0 ? { permissionProfile: this._config.permissionProfile } : {}
 		});
 		const baseTimeoutMs = timeout ?? this._config.defaultTimeouts[taskType] ?? DEFAULT_TIMEOUTS[taskType] ?? 3e5;
 		const timeoutMultiplier = capabilities.timeoutMultiplier ?? 1;
@@ -1314,6 +1316,29 @@ var DispatcherImpl = class {
 		env["GIT_CEILING_DIRECTORIES"] = dirname$1(worktreePath);
 		if (cmd.env !== void 0) Object.assign(env, cmd.env);
 		if (cmd.unsetEnvKeys !== void 0) for (const key of cmd.unsetEnvKeys) delete env[key];
+		if (cmd.executionMode !== void 0 && cmd.executionMode !== "spawn") {
+			this._logger.error({
+				id,
+				agent,
+				executionMode: cmd.executionMode
+			}, "dispatch rejected: execution mode not implemented");
+			this._running.delete(id);
+			this._drainQueue();
+			resolve$2({
+				id,
+				status: "failed",
+				exitCode: -1,
+				output: "",
+				parsed: null,
+				parseError: `executionMode "${cmd.executionMode}" is not implemented — only 'spawn' is available (H4.4 seam)`,
+				durationMs: 0,
+				tokenEstimate: {
+					input: Math.ceil(prompt.length / CHARS_PER_TOKEN$3),
+					output: 0
+				}
+			});
+			return;
+		}
 		const proc = spawn(cmd.binary, cmd.args, {
 			cwd: cmd.cwd,
 			env,
@@ -3198,10 +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,
@@ -3218,6 +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,
@@ -6302,6 +6332,7 @@ const SubstrateConfigSchema = z.object({
 	telemetry: TelemetryConfigSchema.optional(),
 	worktree: WorktreeConfigSchema.optional(),
 	trivialOutputThreshold: z.number().int().nonnegative().optional(),
+	dispatch: z.object({ permission_profile: z.enum(["skip", "scoped"]).optional() }).strict().optional(),
 	finalization: z.object({
 		mode: z.enum([
 			"merge",
@@ -6328,6 +6359,7 @@ const PartialSubstrateConfigSchema = z.object({
 	telemetry: TelemetryConfigSchema.partial().optional(),
 	worktree: WorktreeConfigSchema.partial().optional(),
 	trivialOutputThreshold: z.number().int().nonnegative().optional(),
+	dispatch: z.object({ permission_profile: z.enum(["skip", "scoped"]).optional() }).strict().optional(),
 	finalization: z.object({
 		mode: z.enum([
 			"merge",
@@ -6668,8 +6700,8 @@ function readEnvOverrides(logger) {
 /**
 * Get a value from a nested object using dot-notation key.
 */
-function getByPath(obj, path$3) {
-	const parts = path$3.split(".");
+function getByPath(obj, path$4) {
+	const parts = path$4.split(".");
 	let cursor = obj;
 	for (const part of parts) {
 		if (cursor === null || cursor === void 0 || typeof cursor !== "object") return void 0;
@@ -6681,8 +6713,8 @@ function getByPath(obj, path$3) {
 * Return a deep clone of `obj` with `path` set to `value`.
 * Creates intermediate objects as needed.
 */
-function setByPath(obj, path$3, value) {
-	const parts = path$3.split(".");
+function setByPath(obj, path$4, value) {
+	const parts = path$4.split(".");
 	const result = { ...obj };
 	let cursor = result;
 	for (let i = 0; i < parts.length - 1; i++) {
@@ -9528,6 +9560,40 @@ function checkAdapterVersionCompat(adapterName, actualVersion, tested) {
 //#endregion
 //#region packages/core/dist/adapters/claude-adapter.js
 const execAsync$2 = promisify(exec);
+/**
+* H4.3: generate the per-worktree Claude Code settings file for the
+* 'scoped' permission profile. Written NEXT TO the worktree (its parent
+* directory — the worktree base, outside any repo after H4.2) so it can
+* never be committed by commit-first.
+*
+* Rules: reads/search/bash allowed everywhere (verification needs the
+* suite + git); file MUTATION allowed only under the worktree — anything
+* else falls to "ask", which headless -p mode denies visibly (there is no
+* interactive prompt to stall on).
+*/
+function writeScopedPermissionSettings(worktreePath) {
+	const wt = path$3.resolve(worktreePath);
+	const settings = { permissions: {
+		allow: [
+			"Read",
+			"Glob",
+			"Grep",
+			"Bash",
+			"WebFetch",
+			"WebSearch",
+			"TodoWrite",
+			"Task",
+			`Edit(${wt}/**)`,
+			`Write(${wt}/**)`,
+			`NotebookEdit(${wt}/**)`
+		],
+		deny: []
+	} };
+	const settingsPath = path$3.join(path$3.dirname(wt), `.agent-settings-${path$3.basename(wt)}.json`);
+	mkdirSync(path$3.dirname(settingsPath), { recursive: true });
+	writeFileSync(settingsPath, JSON.stringify(settings, null, 2));
+	return settingsPath;
+}
 /** Default model used when none is specified */
 const DEFAULT_MODEL$1 = "claude-sonnet-4-6";
 /**
@@ -9650,9 +9716,12 @@ var ClaudeCodeAdapter = class ClaudeCodeAdapter {
 		const args = [
 			"-p",
 			"--model",
-			model,
-			"--dangerously-skip-permissions"
+			model
 		];
+		if (options.permissionProfile === "scoped") {
+			const settingsPath = writeScopedPermissionSettings(options.worktreePath);
+			args.push("--permission-mode", "acceptEdits", "--settings", settingsPath);
+		} else args.push("--dangerously-skip-permissions");
 		args.push("--output-format", "stream-json", "--verbose");
 		if (options.additionalFlags && options.additionalFlags.length > 0) args.push(...options.additionalFlags);
 		const systemPromptParts = [BASE_SYSTEM_PROMPT];
@@ -11974,9 +12043,9 @@ var VersionManagerImpl = class {
 		try {
 			const _require = createRequire(import.meta.url);
 			const fs = _require("fs");
-			const path$3 = _require("path");
+			const path$4 = _require("path");
 			const yaml$1 = _require("js-yaml");
-			const configPath = path$3.join(process.cwd(), ".substrate", "config.yaml");
+			const configPath = path$4.join(process.cwd(), ".substrate", "config.yaml");
 			try {
 				const raw = fs.readFileSync(configPath, "utf-8");
 				configObj = yaml$1.load(raw) ?? {};
@@ -12531,4 +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-C2CAZDep.js.map
+//# sourceMappingURL=dist-90byyGPp.js.map

package/dist/{errors-Db8EIM9w.js → errors-ST3E8qWc.js}

@@ -1,4 +1,4 @@
-import { AdtError } from "./dist-C2CAZDep.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-Db8EIM9w.js.map
+//# sourceMappingURL=errors-ST3E8qWc.js.map

package/dist/{experimenter-Dm5jUPO6.js → experimenter-CyA9K5u6.js}

@@ -1,3 +1,3 @@
-import { buildAuditLogEntry, buildBranchName, buildModificationDirective, buildPRBody, buildWorktreePath, createExperimenter, determineVerdict, resolvePromptFile } from "./dist-C2CAZDep.js";
+import { buildAuditLogEntry, buildBranchName, buildModificationDirective, buildPRBody, buildWorktreePath, createExperimenter, determineVerdict, resolvePromptFile } from "./dist-90byyGPp.js";
 
 export { createExperimenter };

package/dist/{health-ByQadq3J.js → health-BERxzeG-.js}

@@ -1,6 +1,6 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { DoltClient, DoltQueryError, createDatabaseAdapter$1 as createDatabaseAdapter, getLatestRun, getPipelineRunById, initSchema } from "./dist-C2CAZDep.js";
-import { resolveMainRepoRoot, resolveRunManifest } from "./manifest-read-knD2uWkz.js";
+import { DoltClient, DoltQueryError, createDatabaseAdapter$1 as createDatabaseAdapter, getLatestRun, getPipelineRunById, initSchema } from "./dist-90byyGPp.js";
+import { resolveMainRepoRoot, resolveRunManifest } from "./manifest-read-BOvY53EG.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-ByQadq3J.js.map
+//# sourceMappingURL=health-BERxzeG-.js.map

package/dist/{health-WGcvcIYK.js → health-CoJ3nBWL.js}

@@ -1,7 +1,7 @@
-import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-ByQadq3J.js";
+import { DEFAULT_STALL_THRESHOLD_SECONDS, getAllDescendantPids, getAutoHealthData, inspectProcessTree, isOrchestratorProcessLine, registerHealthCommand, runHealthAction } from "./health-BERxzeG-.js";
 import "./logger-KeHncl-f.js";
-import "./dist-C2CAZDep.js";
-import "./manifest-read-knD2uWkz.js";
+import "./dist-90byyGPp.js";
+import "./manifest-read-BOvY53EG.js";
 import "./work-graph-repository-DZyJv5pV.js";
 import "./decisions-CzSIEeGP.js";
 

package/dist/{index-DxeIRBBf.d.ts → index-CnV5PcSR.d.ts}

@@ -296,6 +296,12 @@ declare const SubstrateConfigSchema: z.ZodObject<{
     }>>;
   }, z.core.$strict>>;
   trivialOutputThreshold: z.ZodOptional<z.ZodNumber>;
+  dispatch: z.ZodOptional<z.ZodObject<{
+    permission_profile: z.ZodOptional<z.ZodEnum<{
+      skip: "skip";
+      scoped: "scoped";
+    }>>;
+  }, z.core.$strict>>;
   finalization: z.ZodOptional<z.ZodObject<{
     mode: z.ZodOptional<z.ZodEnum<{
       merge: "merge";
@@ -860,6 +866,15 @@ interface SpawnCommand {
   stdin?: string;
   /** Optional timeout in milliseconds */
   timeoutMs?: number;
+  /**
+   * H4.4 (container-ready seam): how this command is executed.
+   * 'spawn' (default, and the only implemented mode) = child_process.spawn on
+   * the host. 'container' is RESERVED for a future backend that runs the
+   * agent in a container with the worktree bind-mounted at the same path —
+   * the dispatcher MUST reject it until that backend exists. Mirrors the
+   * direct-API adapter design's `executionMode: 'spawn' | 'direct'` seam.
+   */
+  executionMode?: 'spawn' | 'container';
 }
 /**
  * Options passed to adapter methods for each invocation.
@@ -909,6 +924,13 @@ interface AdapterOptions {
   taskType?: string;
   /** Dispatch context: unique dispatch ID for per-dispatch telemetry correlation */
   dispatchId?: string;
+  /**
+   * H4.3: permission profile for the spawned agent. 'skip' (default) uses
+   * --dangerously-skip-permissions; 'scoped' generates a per-worktree
+   * settings file (mutation allowed only under the worktree) and runs with
+   * --permission-mode acceptEdits. Config: `dispatch.permission_profile`.
+   */
+  permissionProfile?: 'skip' | 'scoped';
 }
 /**
  * Capabilities reported by an adapter for this CLI agent.
@@ -1600,4 +1622,4 @@ interface Recommendation {
 
 //#endregion
 export { AdapterDiscoveryResult, AdapterRegistry as AdapterRegistry$1, AdtError as AdtError$1, ClaudeCodeAdapter as ClaudeCodeAdapter$1, CodexCLIAdapter as CodexCLIAdapter$1, ConfigError as ConfigError$1, ConfigIncompatibleFormatError as ConfigIncompatibleFormatError$1, CoreEvents, DatabaseAdapter, DiscoveryReport, GeminiCLIAdapter as GeminiCLIAdapter$1, Recommendation, TypedEventBus };
-//# sourceMappingURL=index-DxeIRBBf.d.ts.map
+//# sourceMappingURL=index-CnV5PcSR.d.ts.map

package/dist/index.d.ts

@@ -1,4 +1,4 @@
-import { AdapterDiscoveryResult, AdapterRegistry$1 as AdapterRegistry, AdtError$1 as AdtError, ClaudeCodeAdapter$1 as ClaudeCodeAdapter, CodexCLIAdapter$1 as CodexCLIAdapter, ConfigError$1 as ConfigError, ConfigIncompatibleFormatError$1 as ConfigIncompatibleFormatError, DiscoveryReport, GeminiCLIAdapter$1 as GeminiCLIAdapter, Recommendation, TypedEventBus } from "./index-DxeIRBBf.js";
+import { AdapterDiscoveryResult, AdapterRegistry$1 as AdapterRegistry, AdtError$1 as AdtError, ClaudeCodeAdapter$1 as ClaudeCodeAdapter, CodexCLIAdapter$1 as CodexCLIAdapter, ConfigError$1 as ConfigError, ConfigIncompatibleFormatError$1 as ConfigIncompatibleFormatError, DiscoveryReport, GeminiCLIAdapter$1 as GeminiCLIAdapter, Recommendation, TypedEventBus } from "./index-CnV5PcSR.js";
 import pino from "pino";
 import { z } from "zod";
 import { Readable, Writable } from "node:stream";
@@ -1068,6 +1068,12 @@ declare const SubstrateConfigSchema: z.ZodObject<{
   supervisor_poll_interval_seconds: z.ZodOptional<z.ZodNumber>;
   retry_budget: z.ZodOptional<z.ZodNumber>;
   epics_path: z.ZodOptional<z.ZodString>;
+  dispatch: z.ZodOptional<z.ZodObject<{
+    permission_profile: z.ZodOptional<z.ZodEnum<{
+      skip: "skip";
+      scoped: "scoped";
+    }>>;
+  }, z.core.$strict>>;
   finalization: z.ZodOptional<z.ZodObject<{
     mode: z.ZodOptional<z.ZodEnum<{
       merge: "merge";
@@ -2165,6 +2171,15 @@ interface SpawnCommand {
   stdin?: string;
   /** Optional timeout in milliseconds */
   timeoutMs?: number;
+  /**
+   * H4.4 (container-ready seam): how this command is executed.
+   * 'spawn' (default, and the only implemented mode) = child_process.spawn on
+   * the host. 'container' is RESERVED for a future backend that runs the
+   * agent in a container with the worktree bind-mounted at the same path —
+   * the dispatcher MUST reject it until that backend exists. Mirrors the
+   * direct-API adapter design's `executionMode: 'spawn' | 'direct'` seam.
+   */
+  executionMode?: 'spawn' | 'container';
 }
 /**
  * Options passed to adapter methods for each invocation.
@@ -2214,6 +2229,13 @@ interface AdapterOptions {
   taskType?: string;
   /** Dispatch context: unique dispatch ID for per-dispatch telemetry correlation */
   dispatchId?: string;
+  /**
+   * H4.3: permission profile for the spawned agent. 'skip' (default) uses
+   * --dangerously-skip-permissions; 'scoped' generates a per-worktree
+   * settings file (mutation allowed only under the worktree) and runs with
+   * --permission-mode acceptEdits. Config: `dispatch.permission_profile`.
+   */
+  permissionProfile?: 'skip' | 'scoped';
 }
 /**
  * Capabilities reported by an adapter for this CLI agent.

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-C2CAZDep.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-Db8EIM9w.js";
+import { BudgetExceededError, GitError, RecoveryError, TaskConfigError, TaskGraphCycleError, TaskGraphError, TaskGraphIncompatibleFormatError, WorkerError, WorkerNotFoundError } from "./errors-ST3E8qWc.js";
 
 //#region src/core/di.ts
 /**

package/dist/{interactive-prompt-CMBlj6UF.js → interactive-prompt-UWLccCqL.js}

@@ -1,5 +1,5 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { readCurrentRunId, resolveMainRepoRoot } from "./manifest-read-knD2uWkz.js";
+import { readCurrentRunId, resolveMainRepoRoot } from "./manifest-read-BOvY53EG.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-CMBlj6UF.js.map
+//# sourceMappingURL=interactive-prompt-UWLccCqL.js.map

package/dist/{manifest-read-knD2uWkz.js → manifest-read-BOvY53EG.js}

@@ -1,5 +1,5 @@
 import { createLogger } from "./logger-KeHncl-f.js";
-import { LEARNING_FINDING, createDecision, getDecisionsByCategory } from "./dist-C2CAZDep.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";
@@ -3449,9 +3449,13 @@ 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 +6304,4 @@ 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-knD2uWkz.js.map
+//# sourceMappingURL=manifest-read-BOvY53EG.js.map

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

@@ -1,6 +1,6 @@
 import "../../logger-KeHncl-f.js";
-import "../../dist-C2CAZDep.js";
-import "../../manifest-read-knD2uWkz.js";
-import { runInteractivePrompt } from "../../interactive-prompt-CMBlj6UF.js";
+import "../../dist-90byyGPp.js";
+import "../../manifest-read-BOvY53EG.js";
+import { runInteractivePrompt } from "../../interactive-prompt-UWLccCqL.js";
 
 export { runInteractivePrompt };

package/dist/{routing-B3sgH5MZ.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-C2CAZDep.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-CtIc7_rK.js → run-Csg27VHs.js}

@@ -1,14 +1,14 @@
-import "./health-ByQadq3J.js";
+import "./health-BERxzeG-.js";
 import "./logger-KeHncl-f.js";
 import "./helpers-CElYrONe.js";
-import "./dist-C2CAZDep.js";
-import "./manifest-read-knD2uWkz.js";
-import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, runRunAction, wireNdjsonEmitter } from "./run-BAUlPom3.js";
+import "./dist-90byyGPp.js";
+import "./manifest-read-BOvY53EG.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, resolveProbeAuthorStateIntegrating, runRunAction, wireNdjsonEmitter } from "./run-Dgqfz9HY.js";
 import "./routing-DFxoKHDt.js";
 import "./work-graph-repository-DZyJv5pV.js";
 import "./decisions-CzSIEeGP.js";
 import "./decision-router-BAPpON_C.js";
-import "./interactive-prompt-CMBlj6UF.js";
+import "./interactive-prompt-UWLccCqL.js";
 import "./recovery-engine-BKGBeBnW.js";
 
 export { runRunAction };

package/dist/{run-BAUlPom3.js → run-Dgqfz9HY.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-ByQadq3J.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-BERxzeG-.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-C2CAZDep.js";
-import { FindingsInjector, RunManifest, RuntimeProbeListSchema, applyConfigToGraph, createDefaultVerificationPipeline, createGraphOrchestrator, createSdlcCodeReviewHandler, createSdlcCreateStoryHandler, createSdlcDevStoryHandler, createSdlcPhaseHandler, detectsEventDrivenAC, detectsStateIntegratingAC, extractTargetFilesFromStoryContent, parseRuntimeProbes, renderFindings, resolveGraphPath, resolveMainRepoRoot, runAcTraceabilityCheck, runStaleVerificationRecovery } from "./manifest-read-knD2uWkz.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-BOvY53EG.js";
 import { WorkGraphRepository, detectCycles } from "./work-graph-repository-DZyJv5pV.js";
 import { deriveExitCode, routeDecision } from "./decision-router-BAPpON_C.js";
-import { runInteractivePrompt } from "./interactive-prompt-CMBlj6UF.js";
+import { runInteractivePrompt } from "./interactive-prompt-UWLccCqL.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);
@@ -16449,23 +16498,26 @@ 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;
@@ -46317,6 +46369,7 @@ async function runRunAction(options) {
 	let configFinalizationMode;
 	let configMergeStrategy;
 	let configEpicGateCommand;
+	let configPermissionProfile;
 	let configWorktreeCopyFiles;
 	try {
 		const configSystem = createConfigSystem({ projectConfigDir: dbDir });
@@ -46346,6 +46399,7 @@ async function runRunAction(options) {
 		if (cfg.finalization?.mode !== void 0) configFinalizationMode = cfg.finalization.mode;
 		if (cfg.finalization?.merge_strategy !== void 0) configMergeStrategy = cfg.finalization.merge_strategy;
 		if (cfg.finalization?.epic_gate_command !== void 0) configEpicGateCommand = cfg.finalization.epic_gate_command;
+		if (cfg.dispatch?.permission_profile !== void 0) configPermissionProfile = cfg.dispatch.permission_profile;
 		if (Array.isArray(cfg.worktree?.copy_files) && cfg.worktree.copy_files.length > 0) {
 			configWorktreeCopyFiles = [...cfg.worktree.copy_files];
 			logger.info({ copyFiles: configWorktreeCopyFiles }, "Loaded worktree.copy_files from config");
@@ -46448,6 +46502,7 @@ async function runRunAction(options) {
 		...finalization !== void 0 ? { finalizationMode: finalization } : configFinalizationMode !== void 0 ? { finalizationMode: configFinalizationMode } : {},
 		...configMergeStrategy !== void 0 ? { mergeStrategy: configMergeStrategy } : {},
 		...configEpicGateCommand !== void 0 ? { epicGateCommand: configEpicGateCommand } : {},
+		...configPermissionProfile !== void 0 ? { permissionProfile: configPermissionProfile } : {},
 		...configWorktreeCopyFiles !== void 0 ? { worktreeCopyFiles: configWorktreeCopyFiles } : {}
 	});
 	let storyKeys = [...parsedStoryKeys];
@@ -46696,7 +46751,8 @@ async function runRunAction(options) {
 			adapterRegistry: injectedRegistry,
 			config: {
 				routingResolver,
-				...dispatchTimeouts ? { defaultTimeouts: dispatchTimeouts } : {}
+				...dispatchTimeouts ? { defaultTimeouts: dispatchTimeouts } : {},
+				...configPermissionProfile !== void 0 ? { permissionProfile: configPermissionProfile } : {}
 			}
 		});
 		eventBus.on("orchestrator:story-phase-complete", (payload) => {
@@ -47237,7 +47293,7 @@ async function runRunAction(options) {
 	}
 }
 async function runFullPipeline(options) {
-	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, projectRoot, events: eventsFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, skipVerification, maxReviewCycles = 2, retryBudget, registry: injectedRegistry, tokenCeilings, stories: explicitStories, telemetryEnabled: fullTelemetryEnabled, telemetryPort: fullTelemetryPort, agentId, meshUrl: fpMeshUrl, meshProjectId: fpMeshProjectId, engineType: fpEngineType, probeAuthor, probeAuthorStateIntegrating: fpProbeAuthorStateIntegrating, noWorktree, worktreeCopyFiles: fpWorktreeCopyFiles, finalizationMode: fpFinalizationMode, mergeStrategy: fpMergeStrategy, epicGateCommand: fpEpicGateCommand } = options;
+	const { packName, packPath, dbDir, dbPath, startPhase, stopAfter, concept, concurrency, outputFormat, projectRoot, events: eventsFlag, skipUx, research: researchFlag, skipResearch: skipResearchFlag, skipPreflight, skipVerification, maxReviewCycles = 2, retryBudget, registry: injectedRegistry, tokenCeilings, stories: explicitStories, telemetryEnabled: fullTelemetryEnabled, telemetryPort: fullTelemetryPort, agentId, meshUrl: fpMeshUrl, meshProjectId: fpMeshProjectId, engineType: fpEngineType, probeAuthor, probeAuthorStateIntegrating: fpProbeAuthorStateIntegrating, noWorktree, worktreeCopyFiles: fpWorktreeCopyFiles, finalizationMode: fpFinalizationMode, mergeStrategy: fpMergeStrategy, epicGateCommand: fpEpicGateCommand, permissionProfile: fpPermissionProfile } = options;
 	if (!existsSync$1(dbDir)) mkdirSync$1(dbDir, { recursive: true });
 	let doltServerFull = null;
 	try {
@@ -47278,7 +47334,10 @@ async function runFullPipeline(options) {
 		const dispatcher = createDispatcher({
 			eventBus,
 			adapterRegistry: injectedRegistry,
-			config: { routingResolver }
+			config: {
+				routingResolver,
+				...fpPermissionProfile !== void 0 ? { permissionProfile: fpPermissionProfile } : {}
+			}
 		});
 		const phaseDeps = {
 			db: adapter,
@@ -47720,7 +47779,7 @@ async function runFullPipeline(options) {
 */
 async function emitPreDispatchVersionAdvisory(currentVersion) {
 	if (process.env["SUBSTRATE_NO_UPDATE_CHECK"] === "1") return;
-	const { createVersionManager } = await import("./version-manager-impl-DizCvYy8.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);
@@ -47827,4 +47886,4 @@ 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-BAUlPom3.js.map
+//# sourceMappingURL=run-Dgqfz9HY.js.map

package/dist/src/modules/recovery-engine/index.d.ts

@@ -1,4 +1,4 @@
-import { CoreEvents, DatabaseAdapter, TypedEventBus } from "../../../index-DxeIRBBf.js";
+import { CoreEvents, DatabaseAdapter, TypedEventBus } from "../../../index-CnV5PcSR.js";
 import { z } from "zod";
 
 //#region packages/sdlc/dist/verification/findings.d.ts

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

@@ -1,4 +1,4 @@
-import { createVersionManager } from "./dist-C2CAZDep.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-DOmKCyOY.js.map
+//# sourceMappingURL=upgrade-Dw6jKkH3.js.map

package/dist/{upgrade-B3iamwjO.js → upgrade-unZndH-S.js}

@@ -1,5 +1,5 @@
-import "./dist-C2CAZDep.js";
+import "./dist-90byyGPp.js";
 import "./version-manager-impl-qFBiO4Eh.js";
-import { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand } from "./upgrade-DOmKCyOY.js";
+import { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand } from "./upgrade-Dw6jKkH3.js";
 
 export { isGlobalInstall, registerUpgradeCommand, runUpgradeCommand };

package/dist/{version-manager-impl-DizCvYy8.js → version-manager-impl--XXnwjMd.js}

@@ -1,4 +1,4 @@
-import { VersionManagerImpl, createVersionManager } from "./dist-C2CAZDep.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": "0.20.149",
+  "version": "0.20.151",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",

package/dist/adapter-registry-CauYNA1U.js

@@ -1,4 +0,0 @@
-import { AdapterRegistry } from "./dist-C2CAZDep.js";
-import "./adapter-registry-DXLMTmfD.js";
-
-export { AdapterRegistry };