substrate-ai 0.19.49 → 0.19.51

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-DI5SzKf5.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 "../errors-RupuC-ES.js";
 import "../routing-CcBOCuC9.js";
 import "../decisions-C0pz9Clx.js";
@@ -1862,6 +1862,72 @@ async function scaffoldClaudeMd(projectRoot, profile) {
 	await writeFile(claudeMdPath, newContent, "utf8");
 	logger$15.info({ claudeMdPath }, "Wrote substrate section to CLAUDE.md");
 }
+async function scaffoldAgentsMd(projectRoot, profile) {
+	const agentsMdPath = join(projectRoot, "AGENTS.md");
+	const pkgRoot = findPackageRoot(__dirname);
+	const templateName = "agents-md-substrate-section.md";
+	let templatePath = join(pkgRoot, "dist", "cli", "templates", templateName);
+	if (!existsSync$1(templatePath)) templatePath = join(pkgRoot, "src", "cli", "templates", templateName);
+	let sectionContent;
+	try {
+		sectionContent = await readFile(templatePath, "utf8");
+	} catch {
+		logger$15.warn({ templatePath }, "AGENTS.md substrate section template not found; skipping");
+		return;
+	}
+	const substrateVersion = readSubstrateVersion(pkgRoot);
+	sectionContent = sectionContent.replace("{{SUBSTRATE_VERSION}}", substrateVersion);
+	if (!sectionContent.endsWith("\n")) sectionContent += "\n";
+	const devNotesSection = buildStackAwareDevNotes(profile ?? null);
+	let existingContent = "";
+	let fileExists$1 = false;
+	try {
+		existingContent = await readFile(agentsMdPath, "utf8");
+		fileExists$1 = true;
+	} catch {}
+	let newContent;
+	if (!fileExists$1) newContent = devNotesSection ? devNotesSection + "\n\n" + sectionContent : sectionContent;
+	else if (existingContent.includes(CLAUDE_MD_START_MARKER)) newContent = existingContent.replace(new RegExp(`${CLAUDE_MD_START_MARKER.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}[\\s\\S]*?${CLAUDE_MD_END_MARKER.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}`), sectionContent.trimEnd());
+	else {
+		const separator = existingContent.endsWith("\n") ? "\n" : "\n\n";
+		newContent = existingContent + separator + sectionContent;
+	}
+	await writeFile(agentsMdPath, newContent, "utf8");
+	logger$15.info({ agentsMdPath }, "Wrote substrate section to AGENTS.md");
+}
+async function scaffoldGeminiMd(projectRoot, profile) {
+	const geminiMdPath = join(projectRoot, "GEMINI.md");
+	const pkgRoot = findPackageRoot(__dirname);
+	const templateName = "gemini-md-substrate-section.md";
+	let templatePath = join(pkgRoot, "dist", "cli", "templates", templateName);
+	if (!existsSync$1(templatePath)) templatePath = join(pkgRoot, "src", "cli", "templates", templateName);
+	let sectionContent;
+	try {
+		sectionContent = await readFile(templatePath, "utf8");
+	} catch {
+		logger$15.warn({ templatePath }, "GEMINI.md substrate section template not found; skipping");
+		return;
+	}
+	const substrateVersion = readSubstrateVersion(pkgRoot);
+	sectionContent = sectionContent.replace("{{SUBSTRATE_VERSION}}", substrateVersion);
+	if (!sectionContent.endsWith("\n")) sectionContent += "\n";
+	const devNotesSection = buildStackAwareDevNotes(profile ?? null);
+	let existingContent = "";
+	let fileExists$1 = false;
+	try {
+		existingContent = await readFile(geminiMdPath, "utf8");
+		fileExists$1 = true;
+	} catch {}
+	let newContent;
+	if (!fileExists$1) newContent = devNotesSection ? devNotesSection + "\n\n" + sectionContent : sectionContent;
+	else if (existingContent.includes(CLAUDE_MD_START_MARKER)) newContent = existingContent.replace(new RegExp(`${CLAUDE_MD_START_MARKER.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}[\\s\\S]*?${CLAUDE_MD_END_MARKER.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}`), sectionContent.trimEnd());
+	else {
+		const separator = existingContent.endsWith("\n") ? "\n" : "\n\n";
+		newContent = existingContent + separator + sectionContent;
+	}
+	await writeFile(geminiMdPath, newContent, "utf8");
+	logger$15.info({ geminiMdPath }, "Wrote substrate section to GEMINI.md");
+}
 async function scaffoldStatuslineScript(projectRoot) {
 	const pkgRoot = findPackageRoot(__dirname);
 	const templateName = "statusline.sh";
@@ -2441,6 +2507,8 @@ async function runInitAction(options) {
 		await initSchema(dbAdapter);
 		await dbAdapter.close();
 		await scaffoldClaudeMd(projectRoot, detectedProfile);
+		await scaffoldAgentsMd(projectRoot, detectedProfile);
+		await scaffoldGeminiMd(projectRoot, detectedProfile);
 		await scaffoldStatuslineScript(projectRoot);
 		await scaffoldClaudeSettings(projectRoot);
 		await scaffoldClaudeCommands(projectRoot, outputFormat);
@@ -2512,6 +2580,8 @@ async function runInitAction(options) {
 			}
 			process.stdout.write(`  Scaffolded:\n`);
 			process.stdout.write(`    CLAUDE.md             pipeline instructions for Claude Code\n`);
+			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(`    .substrate/           config, database, routing policy\n`);
 			if (doltInitialized) process.stdout.write(`✓ Dolt state store initialized at .substrate/state/\n`);
@@ -4952,7 +5022,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-zENUXBXk.js"
+									"../run-d6XoJl27.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({

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

@@ -0,0 +1,63 @@
+<!-- substrate:start -->
+<!-- substrate:version={{SUBSTRATE_VERSION}} -->
+## Substrate Pipeline
+
+This project uses Substrate for automated implementation pipelines. When asked to implement, build, or run the pipeline, go straight to running substrate. Do not explore the codebase, read source files, or plan the implementation yourself. Substrate orchestrates sub-agents that handle all of that.
+
+### Running the Pipeline
+
+Substrate auto-detects which pipeline phase to start from (analysis, planning, solutioning, implementation) and auto-discovers pending stories.
+
+```
+substrate run --events
+```
+
+To target specific stories:
+```
+substrate run --events --stories 1-1,1-2,1-3
+```
+
+If substrate needs input it can't auto-detect (e.g., a project concept for analysis), it will exit with a clear error message telling you what to provide.
+
+Scope warning: Without `--stories`, substrate auto-discovers ALL pending stories across ALL epics and may dispatch 30+ stories at once. For controlled runs, always specify story keys explicitly with `--stories`.
+
+Execution rules:
+- Pipeline runs take 5-40 minutes. Use long timeouts.
+- Never pipe substrate output to head, tail, grep, or any command that may close the pipe early.
+- For full event protocol and command reference: `substrate run --help-agent`
+
+### Monitoring
+
+Poll status periodically (every 60-90s):
+```
+substrate status --output-format json
+```
+
+Check process health:
+```
+substrate health --output-format json
+```
+
+### After Pipeline Completes
+
+1. Summarize results: X succeeded, Y failed, Z escalated
+2. Check metrics: `substrate metrics --output-format json`
+
+### Handling Escalations
+
+- On story escalation: read the flagged files and issues, propose a fix, ask the user before applying
+- On minor fix verdict (NEEDS_MINOR_FIXES): offer to fix automatically
+- On build verification failure: read the build output, diagnose the error, propose a fix
+- Never re-run a failed story without explicit user confirmation
+
+### Key Commands
+
+| Command | Purpose |
+|---|---|
+| `substrate run --events` | Run pipeline with NDJSON event stream |
+| `substrate status --output-format json` | Poll current pipeline state |
+| `substrate health --output-format json` | Check process health |
+| `substrate metrics --output-format json` | View historical run metrics |
+| `substrate resume` | Resume an interrupted pipeline run |
+| `substrate run --help-agent` | Full agent instruction reference |
+<!-- substrate:end -->

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

@@ -0,0 +1,63 @@
+<!-- substrate:start -->
+<!-- substrate:version={{SUBSTRATE_VERSION}} -->
+## Substrate Pipeline
+
+This project uses Substrate for automated implementation pipelines. When asked to implement, build, or run the pipeline, go straight to running substrate. Do not explore the codebase, read source files, or plan the implementation yourself. Substrate orchestrates sub-agents that handle all of that.
+
+### Running the Pipeline
+
+Substrate auto-detects which pipeline phase to start from (analysis, planning, solutioning, implementation) and auto-discovers pending stories.
+
+```
+substrate run --events
+```
+
+To target specific stories:
+```
+substrate run --events --stories 1-1,1-2,1-3
+```
+
+If substrate needs input it can't auto-detect (e.g., a project concept for analysis), it will exit with a clear error message telling you what to provide.
+
+Scope warning: Without `--stories`, substrate auto-discovers ALL pending stories across ALL epics and may dispatch 30+ stories at once. For controlled runs, always specify story keys explicitly with `--stories`.
+
+Execution rules:
+- Pipeline runs take 5-40 minutes. Use long timeouts.
+- Never pipe substrate output to head, tail, grep, or any command that may close the pipe early.
+- For full event protocol and command reference: `substrate run --help-agent`
+
+### Monitoring
+
+Poll status periodically (every 60-90s):
+```
+substrate status --output-format json
+```
+
+Check process health:
+```
+substrate health --output-format json
+```
+
+### After Pipeline Completes
+
+1. Summarize results: X succeeded, Y failed, Z escalated
+2. Check metrics: `substrate metrics --output-format json`
+
+### Handling Escalations
+
+- On story escalation: read the flagged files and issues, propose a fix, ask the user before applying
+- On minor fix verdict (NEEDS_MINOR_FIXES): offer to fix automatically
+- On build verification failure: read the build output, diagnose the error, propose a fix
+- Never re-run a failed story without explicit user confirmation
+
+### Key Commands
+
+| Command | Purpose |
+|---|---|
+| `substrate run --events` | Run pipeline with NDJSON event stream |
+| `substrate status --output-format json` | Poll current pipeline state |
+| `substrate health --output-format json` | Check process health |
+| `substrate metrics --output-format json` | View historical run metrics |
+| `substrate resume` | Resume an interrupted pipeline run |
+| `substrate run --help-agent` | Full agent instruction reference |
+<!-- substrate:end -->

package/dist/{run-DI5SzKf5.js → run-BbwMFNWQ.js}

@@ -6213,6 +6213,29 @@ async function getGitDiffStatSummary(workingDirectory = process.cwd()) {
 	], workingDirectory, "git-diff-stat");
 }
 /**
+* Capture the diff between two commits (e.g., baseline..HEAD).
+* Used when the dev-story agent committed its work, making `git diff HEAD`
+* empty. This shows what was actually changed.
+*
+* @param baseCommit - Starting commit SHA
+* @param endCommit - Ending commit SHA (defaults to 'HEAD')
+* @param workingDirectory - Directory to run git in
+* @returns The diff string, or '' on error
+*/
+async function getGitDiffBetweenCommits(baseCommit, endCommit = "HEAD", workingDirectory = process.cwd()) {
+	return runGitCommand(["diff", `${baseCommit}..${endCommit}`], workingDirectory, "git-diff-commits");
+}
+/**
+* Capture the stat-only diff between two commits.
+*/
+async function getGitDiffStatBetweenCommits(baseCommit, endCommit = "HEAD", workingDirectory = process.cwd()) {
+	return runGitCommand([
+		"diff",
+		"--stat",
+		`${baseCommit}..${endCommit}`
+	], workingDirectory, "git-diff-stat-commits");
+}
+/**
 * Capture the git diff scoped to specific files.
 *
 * Runs `git diff HEAD -- file1.ts file2.ts ...` to produce a diff
@@ -7738,7 +7761,7 @@ async function countTestMetrics(filesModified, cwd) {
 * @returns Promise resolving to CodeReviewResult
 */
 async function runCodeReview(deps, params) {
-	const { storyKey, storyFilePath, workingDirectory, pipelineRunId, filesModified, previousIssues, buildPassed } = params;
+	const { storyKey, storyFilePath, workingDirectory, pipelineRunId, filesModified, previousIssues, buildPassed, baselineCommit } = params;
 	const cwd = workingDirectory ?? process.cwd();
 	logger$14.debug({
 		storyKey,
@@ -7814,6 +7837,22 @@ async function runCodeReview(deps, params) {
 			gitDiffContent = await getGitDiffStatSummary(cwd);
 		}
 	}
+	if (gitDiffContent.trim().length === 0 && baselineCommit) {
+		logger$14.info({
+			storyKey,
+			baselineCommit
+		}, "Working tree diff empty — diffing against baseline commit");
+		const commitDiff = await getGitDiffBetweenCommits(baselineCommit, "HEAD", cwd);
+		const commitTotal = nonDiffTokens + countTokens(commitDiff);
+		if (commitDiff.trim().length > 0) if (commitTotal <= TOKEN_CEILING) gitDiffContent = commitDiff;
+		else {
+			logger$14.warn({
+				estimatedTotal: commitTotal,
+				ceiling: TOKEN_CEILING
+			}, "Baseline..HEAD diff exceeds token ceiling — using stat-only summary");
+			gitDiffContent = await getGitDiffStatBetweenCommits(baselineCommit, "HEAD", cwd);
+		}
+	}
 	if (gitDiffContent.trim().length === 0) {
 		logger$14.info({ storyKey }, "Empty git diff — skipping review with SHIP_IT");
 		return {
@@ -12974,11 +13013,26 @@ function createImplementationOrchestrator(deps) {
 					}).trim();
 					hasNewCommits = currentHead !== baselineHeadSha;
 				} catch {}
-				if (hasNewCommits) logger$24.info({
-					storyKey,
-					baselineHeadSha
-				}, "Working tree clean but new commits detected since dispatch — skipping zero-diff escalation");
-				else {
+				if (hasNewCommits && baselineHeadSha) {
+					try {
+						const committedFiles = execSync(`git diff --name-only ${baselineHeadSha}..HEAD`, {
+							cwd: projectRoot ?? process.cwd(),
+							encoding: "utf-8",
+							timeout: 5e3,
+							stdio: [
+								"ignore",
+								"pipe",
+								"pipe"
+							]
+						}).trim();
+						if (committedFiles.length > 0) gitDiffFiles = committedFiles.split("\n").filter(Boolean);
+					} catch {}
+					logger$24.info({
+						storyKey,
+						baselineHeadSha,
+						committedFileCount: gitDiffFiles?.length ?? 0
+					}, "Working tree clean but new commits detected since dispatch — skipping zero-diff escalation");
+				} else {
 					logger$24.warn({ storyKey }, "Zero-diff detected after COMPLETE dev-story — no file changes and no new commits");
 					eventBus.emit("orchestrator:zero-diff-escalation", {
 						storyKey,
@@ -13367,7 +13421,8 @@ function createImplementationOrchestrator(deps) {
 						pipelineRunId: config.pipelineRunId,
 						filesModified: devFilesModified,
 						buildPassed: _buildPassed,
-						...previousIssueList.length > 0 ? { previousIssues: previousIssueList } : {}
+						...previousIssueList.length > 0 ? { previousIssues: previousIssueList } : {},
+						...baselineHeadSha ? { baselineCommit: baselineHeadSha } : {}
 					});
 				}
 				if (config.pipelineRunId !== void 0 && reviewResult.tokenUsage !== void 0) try {
@@ -43021,4 +43076,4 @@ 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-DI5SzKf5.js.map
+//# sourceMappingURL=run-BbwMFNWQ.js.map

package/dist/{run-zENUXBXk.js → run-d6XoJl27.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-DI5SzKf5.js";
+import { normalizeGraphSummaryToStatus, registerRunCommand, resolveMaxReviewCycles, runRunAction, wireNdjsonEmitter } from "./run-BbwMFNWQ.js";
 import "./routing-CcBOCuC9.js";
 import "./decisions-C0pz9Clx.js";
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "substrate-ai",
-  "version": "0.19.49",
+  "version": "0.19.51",
   "description": "Substrate — multi-agent orchestration daemon for AI coding agents",
   "type": "module",
   "license": "MIT",