substrate-ai 0.19.51 → 0.19.53

package/dist/cli/index.js

@@ -4,7 +4,7 @@ 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, IngestionServer, MonitorDatabaseImpl, OPERATIONAL_FINDING, PartialGlobalSettingsSchema, PartialProviderConfigSchema, ProvidersSchema, RoutingRecommender, STORY_METRICS, TelemetryConfigSchema, addTokenUsage, aggregateTokenUsageForRun, checkDoltInstalled, compareRunMetrics, createAmendmentRun, createConfigSystem, createDecision, createDoltClient, createPipelineRun, getActiveDecisions, getAllCostEntriesFiltered, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, tagRunAsBaseline, updatePipelineRun } from "../dist-sNh9XQ6V.js";
 import "../adapter-registry-DXLMTmfD.js";
-import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-BbwMFNWQ.js";
+import { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runSolutioningPhase, validateStopAfterFromConflict } from "../run-BUKozIHS.js";
 import "../errors-RupuC-ES.js";
 import "../routing-CcBOCuC9.js";
 import "../decisions-C0pz9Clx.js";
@@ -2284,6 +2284,164 @@ async function scaffoldClaudeCommands(projectRoot, outputFormat) {
 		logger$15.warn({ err }, "scaffoldClaudeCommands failed; init continues");
 	}
 }
+/**
+* Sync every `.md` file from a source commands directory into a target prompts
+* directory, flat. Codex CLI loads `<root>/.codex/prompts/*.md` as slash
+* commands, so the already-generated Claude command files map 1:1.
+*
+* On re-runs, any `.md` file in the target that matches `ownershipPrefixes`
+* but is no longer present in the source is removed, so stale substrate-
+* generated prompts don't accumulate. `.md` files without a matching prefix
+* are left untouched (protecting user-authored content in `~/.codex/`).
+*
+* Returns the number of prompt files written.
+*/
+function syncCommandsAsPrompts(commandsDir, promptsDir, ownershipPrefixes, namePrefix) {
+	if (!existsSync$1(commandsDir)) return 0;
+	mkdirSync$1(promptsDir, { recursive: true });
+	const sourceEntries = readdirSync$1(commandsDir, { withFileTypes: true }).filter((e) => e.isFile() && e.name.endsWith(".md"));
+	const destNames = new Set(sourceEntries.map((e) => namePrefix && !e.name.startsWith(namePrefix) ? `${namePrefix}${e.name}` : e.name));
+	try {
+		for (const entry of readdirSync$1(promptsDir, { withFileTypes: true })) {
+			if (!entry.isFile() || !entry.name.endsWith(".md")) continue;
+			const isOwned = ownershipPrefixes.some((p) => entry.name.startsWith(p));
+			if (!isOwned) continue;
+			if (destNames.has(entry.name)) continue;
+			unlinkSync$1(join(promptsDir, entry.name));
+		}
+	} catch (err) {
+		logger$15.debug({
+			err,
+			promptsDir
+		}, "Failed to prune stale prompts");
+	}
+	let count = 0;
+	for (const entry of sourceEntries) {
+		const destName = namePrefix && !entry.name.startsWith(namePrefix) ? `${namePrefix}${entry.name}` : entry.name;
+		cpSync(join(commandsDir, entry.name), join(promptsDir, destName));
+		count++;
+	}
+	return count;
+}
+/**
+* Sync skill directories from a source skills root into a target skills root,
+* optionally namespaced under `namePrefix`.
+*
+* Every direct child directory of `srcSkillsDir` is treated as a skill bundle
+* (no SKILL.md check — the source is always `.claude/skills/` which has
+* already been sanitized by `prepareSkillsDir`). On re-runs, any skill
+* directory in the target whose name starts with one of `ownershipPrefixes`
+* but is no longer present in the source is removed.
+*
+* Returns the number of skill directories copied.
+*/
+function syncSkillsToTarget(srcSkillsDir, destSkillsDir, ownershipPrefixes, namePrefix) {
+	if (!existsSync$1(srcSkillsDir)) return 0;
+	mkdirSync$1(destSkillsDir, { recursive: true });
+	const sourceEntries = readdirSync$1(srcSkillsDir, { withFileTypes: true }).filter((e) => e.isDirectory());
+	const destNames = new Set(sourceEntries.map((e) => namePrefix && !e.name.startsWith(namePrefix) ? `${namePrefix}${e.name}` : e.name));
+	try {
+		for (const entry of readdirSync$1(destSkillsDir, { withFileTypes: true })) {
+			if (!entry.isDirectory()) continue;
+			const isOwned = ownershipPrefixes.some((p) => entry.name.startsWith(p));
+			if (!isOwned) continue;
+			if (destNames.has(entry.name)) continue;
+			rmSync$1(join(destSkillsDir, entry.name), {
+				recursive: true,
+				force: true
+			});
+		}
+	} catch (err) {
+		logger$15.debug({
+			err,
+			destSkillsDir
+		}, "Failed to prune stale skills");
+	}
+	let count = 0;
+	for (const entry of sourceEntries) {
+		const destName = namePrefix && !entry.name.startsWith(namePrefix) ? `${namePrefix}${entry.name}` : entry.name;
+		const dest = join(destSkillsDir, destName);
+		rmSync$1(dest, {
+			recursive: true,
+			force: true
+		});
+		cpSync(join(srcSkillsDir, entry.name), dest, { recursive: true });
+		count++;
+	}
+	return count;
+}
+const PROJECT_OWNERSHIP_PREFIXES = ["bmad-", "substrate-"];
+/**
+* Scaffold project-scoped Codex content from the already-generated
+* `.claude/commands/` and `.claude/skills/`. Must run AFTER
+* `scaffoldClaudeCommands`.
+*
+* Writes:
+*   - <projectRoot>/.codex/prompts/*.md  (slash commands)
+*   - <projectRoot>/.codex/skills/<skill>/  (skill bundles)
+*
+* Stale substrate-owned entries (bmad-*, substrate-*) from previous runs are
+* pruned before new content is written. Non-owned files (e.g., `ship.md` from
+* a plugin) are left alone.
+*/
+function scaffoldCodexProject(projectRoot, outputFormat) {
+	const claudeCommandsDir = join(projectRoot, ".claude", "commands");
+	const claudeSkillsDir = join(projectRoot, ".claude", "skills");
+	const codexDir = join(projectRoot, ".codex");
+	const codexPromptsDir = join(codexDir, "prompts");
+	const codexSkillsDir = join(codexDir, "skills");
+	try {
+		const promptCount = syncCommandsAsPrompts(claudeCommandsDir, codexPromptsDir, PROJECT_OWNERSHIP_PREFIXES, "");
+		const skillCount = syncSkillsToTarget(claudeSkillsDir, codexSkillsDir, PROJECT_OWNERSHIP_PREFIXES, "");
+		const total = promptCount + skillCount;
+		if (outputFormat !== "json" && total > 0) process.stdout.write(`Generated ${String(total)} Codex artifacts (${String(promptCount)} prompts, ${String(skillCount)} skills)\n`);
+		if (total > 0) logger$15.info({
+			promptCount,
+			skillCount,
+			codexDir
+		}, "Generated .codex/");
+		else logger$15.debug({ codexDir }, "No Codex artifacts generated; source Claude content not found");
+	} catch (err) {
+		const msg = err instanceof Error ? err.message : String(err);
+		if (outputFormat !== "json") process.stderr.write(`Warning: .codex/ generation failed: ${msg}\n`);
+		logger$15.warn({ err }, "scaffoldCodexProject failed; init continues");
+	}
+}
+/**
+* Install Codex content user-wide at `~/.codex/`, namespaced under
+* `substrate-` to avoid colliding with user-installed content.
+*
+* Writes:
+*   - ~/.codex/prompts/substrate-<slug>.md  (slash commands)
+*   - ~/.codex/skills/substrate-<name>/     (skill bundles)
+*
+* Stale `substrate-*` entries from previous runs are pruned before new
+* content is written. Files/directories without the `substrate-` prefix
+* are never touched.
+*/
+function scaffoldCodexUser(projectRoot, homeDir, outputFormat) {
+	const claudeCommandsDir = join(projectRoot, ".claude", "commands");
+	const claudeSkillsDir = join(projectRoot, ".claude", "skills");
+	const userCodexDir = join(homeDir, ".codex");
+	const userPromptsDir = join(userCodexDir, "prompts");
+	const userSkillsDir = join(userCodexDir, "skills");
+	try {
+		const promptCount = syncCommandsAsPrompts(claudeCommandsDir, userPromptsDir, ["substrate-"], "substrate-");
+		const skillCount = syncSkillsToTarget(claudeSkillsDir, userSkillsDir, ["substrate-"], "substrate-");
+		const total = promptCount + skillCount;
+		if (outputFormat !== "json" && total > 0) process.stdout.write(`Installed ${String(total)} Codex artifacts to ${userCodexDir} (${String(promptCount)} prompts, ${String(skillCount)} skills)\n`);
+		if (total > 0) logger$15.info({
+			promptCount,
+			skillCount,
+			userCodexDir
+		}, "Installed user-scope Codex content");
+		else logger$15.debug({ userCodexDir }, "No user-scope Codex content installed; source Claude content not found");
+	} catch (err) {
+		const msg = err instanceof Error ? err.message : String(err);
+		if (outputFormat !== "json") process.stderr.write(`Warning: user-scope Codex install failed: ${msg}\n`);
+		logger$15.warn({ err }, "scaffoldCodexUser failed; init continues");
+	}
+}
 const PROVIDER_DEFAULTS = DEFAULT_CONFIG.providers;
 const ADAPTER_TO_PROVIDER = {
 	"claude-code": "claude",
@@ -2512,6 +2670,12 @@ async function runInitAction(options) {
 		await scaffoldStatuslineScript(projectRoot);
 		await scaffoldClaudeSettings(projectRoot);
 		await scaffoldClaudeCommands(projectRoot, outputFormat);
+		scaffoldCodexProject(projectRoot, outputFormat);
+		if (options.installUserScope) {
+			const homeDir = process.env["HOME"] ?? process.env["USERPROFILE"];
+			if (homeDir) scaffoldCodexUser(projectRoot, homeDir, outputFormat);
+			else if (outputFormat !== "json") process.stderr.write("Warning: --install-user-scope requested but HOME/USERPROFILE is not set\n");
+		}
 		const gitignorePath = join(projectRoot, ".gitignore");
 		const runtimeEntries = [
 			".substrate/orchestrator.pid",
@@ -2519,7 +2683,9 @@ async function runInitAction(options) {
 			".substrate/scenarios/",
 			".substrate/state/",
 			".substrate/substrate.db",
-			".substrate/substrate.db-journal"
+			".substrate/substrate.db-journal",
+			".codex/prompts/",
+			".codex/skills/"
 		];
 		try {
 			const existing = existsSync$1(gitignorePath) ? readFileSync$1(gitignorePath, "utf-8") : "";
@@ -2583,6 +2749,8 @@ async function runInitAction(options) {
 			process.stdout.write(`    AGENTS.md             pipeline instructions for Codex CLI\n`);
 			process.stdout.write(`    GEMINI.md             pipeline instructions for Gemini CLI\n`);
 			process.stdout.write(`    .claude/commands/     /substrate-run, /substrate-supervisor, /substrate-metrics\n`);
+			process.stdout.write(`    .codex/prompts/       Codex slash commands (mirror of .claude/commands/)\n`);
+			process.stdout.write(`    .codex/skills/        Codex skill bundles (mirror of .claude/skills/)\n`);
 			process.stdout.write(`    .substrate/           config, database, routing policy\n`);
 			if (doltInitialized) process.stdout.write(`✓ Dolt state store initialized at .substrate/state/\n`);
 			else if (doltMode !== "skip") process.stdout.write(`ℹ  Dolt not detected — install Dolt for versioned state, \`substrate diff\`, and observability persistence. See: https://docs.dolthub.com/introduction/installation\n`);
@@ -2598,7 +2766,7 @@ async function runInitAction(options) {
 	}
 }
 function registerInitCommand(program, _version, registry) {
-	program.command("init").description("Initialize Substrate — creates config, scaffolds methodology pack, and sets up database").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", process.cwd()).option("-y, --yes", "Skip all interactive prompts and use defaults", false).option("--force", "Overwrite existing files and packs", false).option("--output-format <format>", "Output format: human (default) or json", "human").option("--dolt", "Initialize Dolt state database as part of init (forces Dolt bootstrapping)", false).option("--no-dolt", "Skip Dolt state store initialization even if Dolt is installed").action(async (opts) => {
+	program.command("init").description("Initialize Substrate — creates config, scaffolds methodology pack, and sets up database").option("--pack <name>", "Methodology pack name", "bmad").option("--project-root <path>", "Project root directory", process.cwd()).option("-y, --yes", "Skip all interactive prompts and use defaults", false).option("--force", "Overwrite existing files and packs", false).option("--output-format <format>", "Output format: human (default) or json", "human").option("--dolt", "Initialize Dolt state database as part of init (forces Dolt bootstrapping)", false).option("--no-dolt", "Skip Dolt state store initialization even if Dolt is installed").option("--install-user-scope", "Also install Codex prompts/skills into ~/.codex/ (namespaced substrate-*)", false).action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		const doltMode = opts.noDolt ? "skip" : opts.dolt ? "force" : "auto";
 		const exitCode = await runInitAction({
@@ -2608,6 +2776,7 @@ function registerInitCommand(program, _version, registry) {
 			force: opts.force,
 			yes: opts.yes,
 			doltMode,
+			installUserScope: opts.installUserScope,
 			...registry !== void 0 && { registry }
 		});
 		process.exitCode = exitCode;
@@ -5022,7 +5191,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-d6XoJl27.js"
+									"../run-BwMDKH66.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({

package/dist/{run-BbwMFNWQ.js → run-BUKozIHS.js}

@@ -13374,7 +13374,8 @@ function createImplementationOrchestrator(deps) {
 							workingDirectory: projectRoot,
 							pipelineRunId: config.pipelineRunId,
 							filesModified: group.files,
-							buildPassed: _buildPassed
+							buildPassed: _buildPassed,
+							...baselineHeadSha ? { baselineCommit: baselineHeadSha } : {}
 						});
 						if (batchReview.tokenUsage) {
 							aggregateTokens.input += batchReview.tokenUsage.input;
@@ -43076,4 +43077,4 @@ function registerRunCommand(program, _version = "0.0.0", projectRoot = process.c
 
 //#endregion
 export { AdapterTelemetryPersistence, AppError, DoltRepoMapMetaRepository, DoltSymbolRepository, ERR_REPO_MAP_STORAGE_WRITE, EpicIngester, GitClient, GrammarLoader, RepoMapInjector, RepoMapModule, RepoMapQueryEngine, RepoMapStorage, SymbolParser, createContextCompiler, createDispatcher, createEventEmitter, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, normalizeGraphSummaryToStatus, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveMaxReviewCycles, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runRunAction, runSolutioningPhase, validateStopAfterFromConflict, wireNdjsonEmitter };
-//# sourceMappingURL=run-BbwMFNWQ.js.map
+//# sourceMappingURL=run-BUKozIHS.js.map

package/dist/{run-d6XoJl27.js → run-BwMDKH66.js}

@@ -2,7 +2,7 @@ import "./health-DrZiqv4h.js";
 import "./logger-KeHncl-f.js";
 import "./helpers-CElYrONe.js";
 import "./dist-sNh9XQ6V.js";
-import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, runRunAction, wireNdjsonEmitter } from "./run-BbwMFNWQ.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, runRunAction, wireNdjsonEmitter } from "./run-BUKozIHS.js";
 import "./routing-CcBOCuC9.js";
 import "./decisions-C0pz9Clx.js";
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.19.51",
+  "version": "0.19.53",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",