substrate-ai 0.20.90 → 0.20.92

package/dist/cli/index.js

@@ -1,20 +1,20 @@
 #!/usr/bin/env node
-import { FileStateStore, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createDatabaseAdapter, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion } from "../health-fVo5FGun.js";
+import { FileStateStore, SUBSTRATE_OWNED_SETTINGS_KEYS, VALID_PHASES, buildPipelineStatusOutput, createDatabaseAdapter, createDoltOperatorReader, createStateStore, findPackageRoot, formatOutput, formatPipelineStatusHuman, formatPipelineSummary, formatTokenTelemetry, getAllDescendantPids, getAutoHealthData, getSubstrateDefaultSettings, inspectProcessTree, parseDbTimestampAsUtc, registerHealthCommand, resolveBmadMethodSrcPath, resolveBmadMethodVersion } from "../health-dWYa13k4.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, createDoltClient, createPipelineRun, getActiveDecisions, getAllCostEntriesFiltered, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, swallowDebug, tagRunAsBaseline, updatePipelineRun } from "../dist-i8Re6HlE.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, createGitWorktreeManager, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, escape, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runProbeAuthor, runSolutioningPhase, unescape, validateStopAfterFromConflict } from "../run-CC_c9n-U.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, createDoltClient, createPipelineRun, getActiveDecisions, getAllCostEntriesFiltered, getBaselineRunMetrics, getDecisionsByCategory, getDecisionsByPhaseForRun, getLatestCompletedRun, getLatestRun, getPipelineRunById, getPlanningCostTotal, getRetryableEscalations, getRunMetrics, getRunningPipelineRuns, getSessionCostSummary, getSessionCostSummaryFiltered, getStoryMetricsForRun, getTokenUsageSummary, incrementRunRestarts, initSchema, initializeDolt, listRunMetrics, loadParentRunDecisions, supersedeDecision, swallowDebug, tagRunAsBaseline, updatePipelineRun } from "../dist-l0pA6zZF.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, createGitWorktreeManager, createImplementationOrchestrator, createPackLoader, createPhaseOrchestrator, createStopAfterGate, createTelemetryAdvisor, escape, formatPhaseCompletionSummary, getFactoryRunSummaries, getScenarioResultsForRun, getTwinRunsForRun, listGraphRuns, registerExportCommand, registerFactoryCommand, registerRunCommand, registerScenariosCommand, resolveStoryKeys, runAnalysisPhase, runPlanningPhase, runProbeAuthor, runSolutioningPhase, unescape, validateStopAfterFromConflict } from "../run-BXRwQRst.js";
 import "../adapter-registry-DIcrxjH8.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-BKmGNnh4.js";
-import "../errors-DPIwiYIO.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-CSmDEOWH.js";
+import "../errors-DZuD2tVU.js";
 import "../routing-DFxoKHDt.js";
 import { WorkGraphRepository } from "../work-graph-repository-DZyJv5pV.js";
 import "../decisions-CzSIEeGP.js";
 import "../decision-router-DblHY8se.js";
-import "../interactive-prompt-CPVsakLe.js";
+import "../interactive-prompt-DY-PFko-.js";
 import "../recovery-engine-BKGBeBnW.js";
 import "../version-manager-impl-qFBiO4Eh.js";
-import { registerUpgradeCommand } from "../upgrade-bldRqYko.js";
+import { registerUpgradeCommand } from "../upgrade-BP0P3qr9.js";
 import { Command } from "commander";
 import { fileURLToPath } from "url";
 import { dirname, join, resolve } from "path";
@@ -6787,14 +6787,14 @@ function buildWorkGraphFromManifest(perStoryState) {
 	};
 }
 async function runStatusAction(options) {
-	const { outputFormat, runId, projectRoot, stateStore, history } = options;
+	const { outputFormat, runId, projectRoot, historyReader, history } = options;
 	if (history === true) {
-		if (!stateStore) {
+		if (!historyReader) {
 			process.stdout.write("History not available with file backend. Use Dolt backend for state history.\n");
 			return 0;
 		}
 		try {
-			const entries = await stateStore.getHistory(20);
+			const entries = await historyReader.getHistory(20);
 			if (outputFormat === "json") {
 				process.stdout.write(JSON.stringify(entries, null, 2) + "\n");
 				return 0;
@@ -6890,7 +6890,7 @@ 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-DzquK08l.js");
+			const { inspectProcessTree: inspectProcessTree$1 } = await import("../health-CgY9akax.js");
 			const substrateDirPath = join(projectRoot, ".substrate");
 			const processInfo = inspectProcessTree$1({
 				projectRoot,
@@ -6916,12 +6916,6 @@ async function runStatusAction(options) {
 		const decisionsCount = decisionsCountRows[0]?.cnt ?? 0;
 		const storiesCountRows = await adapter.query(`SELECT COUNT(*) as cnt FROM requirements WHERE pipeline_run_id = ? AND source = 'solutioning-phase'`, [run.id]);
 		const storiesCount = storiesCountRows[0]?.cnt ?? 0;
-		let storeStories = [];
-		if (stateStore) try {
-			storeStories = await stateStore.queryStories({});
-		} catch (err) {
-			logger$15.debug({ err }, "StateStore query failed, continuing without store data");
-		}
 		if (outputFormat === "json") {
 			const statusOutput = buildPipelineStatusOutput(run, tokenSummary, decisionsCount, storiesCount);
 			const storyMetricsRows = await getStoryMetricsForRun(adapter, run.id);
@@ -6988,7 +6982,6 @@ async function runStatusAction(options) {
 					stories_per_hour: storiesPerHour,
 					cost_usd: totalCostUsd
 				},
-				story_states: storeStories,
 				workGraph: workGraph ?? null,
 				latest_heartbeat_per_story_state: latestHeartbeatPerStoryState ?? {}
 			};
@@ -7032,13 +7025,6 @@ async function runStatusAction(options) {
 					}
 				}
 			}
-			if (storeStories.length > 0) {
-				process.stdout.write("\nStateStore Story States:\n");
-				for (const s of storeStories) if (s.phase === "CHECKPOINT") {
-					const filesCount = s.checkpointFilesCount ?? 0;
-					process.stdout.write(`  ${s.storyKey}: ${s.phase} (${filesCount} files modified)\n`);
-				} else process.stdout.write(`  ${s.storyKey}: ${s.phase} (${s.reviewCycles} review cycles)\n`);
-			}
 			if (workGraph !== void 0) {
 				const { summary, readyStories, blockedStories } = workGraph;
 				process.stdout.write("\nWork Graph:\n");
@@ -7075,29 +7061,26 @@ function registerStatusCommand(program, _version = "0.0.0", projectRoot = proces
 	program.command("status").description("Show status of the most recent (or specified) pipeline run").option("--run-id <id>", "Pipeline run ID to query (defaults to latest)").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").option("--history", "Show Dolt commit history for the state store").action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		const root = opts.projectRoot;
-		let stateStore;
+		let historyReader;
 		const doltStatePath = join(root, ".substrate", "state", ".dolt");
 		if (existsSync$1(doltStatePath)) try {
-			stateStore = createStateStore({
-				backend: "dolt",
-				basePath: join(root, ".substrate", "state")
-			});
-			await stateStore.initialize();
+			historyReader = createDoltOperatorReader({ basePath: join(root, ".substrate", "state") });
+			await historyReader.initialize();
 		} catch {
-			stateStore = void 0;
+			historyReader = void 0;
 		}
 		try {
 			const exitCode = await runStatusAction({
 				outputFormat,
 				runId: opts.runId,
 				projectRoot: root,
-				stateStore,
+				...historyReader !== void 0 && { historyReader },
 				history: opts.history
 			});
 			process.exitCode = exitCode;
 		} finally {
 			try {
-				await stateStore?.close();
+				await historyReader?.close();
 			} catch {}
 		}
 	});
@@ -7855,7 +7838,7 @@ function defaultSupervisorDeps() {
 				if (cached === null) {
 					const { AdapterRegistry: AR } = await import(
 						/* @vite-ignore */
-						"../adapter-registry-B6px5DpL.js"
+						"../adapter-registry-BZ0cVi8C.js"
 );
 					cached = new AR();
 					await cached.discoverAndRegister();
@@ -8422,11 +8405,11 @@ async function runSupervisorAction(options, deps = {}) {
 						try {
 							const { createExperimenter } = await import(
 								/* @vite-ignore */
-								"../experimenter-DgeyT6XB.js"
+								"../experimenter-GfhQpMis.js"
 );
 							const { getLatestRun: getLatest } = await import(
 								/* @vite-ignore */
-								"../decisions-CMUW6gO5.js"
+								"../decisions-CsNAM-T-.js"
 );
 							const expAdapter = createDatabaseAdapter({
 								backend: "auto",
@@ -8436,7 +8419,7 @@ async function runSupervisorAction(options, deps = {}) {
 								await initSchema(expAdapter);
 								const { runRunAction: runPipeline } = await import(
 									/* @vite-ignore */
-									"../run-AN24Jark.js"
+									"../run-DPQ4DT5Q.js"
 );
 								const runStoryFn = async (opts) => {
 									const exitCode = await runPipeline({
@@ -8790,7 +8773,7 @@ function printFactoryRunTable(runs) {
 	}
 }
 async function runMetricsAction(options) {
-	const { outputFormat, projectRoot, limit = 10, compare, tagBaseline, analysis, sprint, story, taskType, since, aggregate, efficiency, recommendations, turns, consumers, categories, compareStories, routingRecommendations, run, factory, probeAuthorSummary, probeAuthorClassSummary } = options;
+	const { outputFormat, projectRoot, limit = 10, compare, tagBaseline, analysis, story, efficiency, recommendations, turns, consumers, categories, compareStories, routingRecommendations, run, factory, probeAuthorSummary, probeAuthorClassSummary } = options;
 	const telemetryModes = [
 		efficiency,
 		recommendations,
@@ -8944,13 +8927,9 @@ async function runMetricsAction(options) {
 	if (routingRecommendations === true) {
 		const dbRoot$1 = await resolveMainRepoRoot(projectRoot);
 		const dbDir = join(dbRoot$1, ".substrate");
-		const doltStatePath = join(dbDir, "state", ".dolt");
-		const doltExists = existsSync$1(doltStatePath);
-		const stateBackend = doltExists ? "dolt" : "file";
-		const stateBasePath = join(dbDir, "state");
 		const stateStore = createStateStore({
-			backend: stateBackend,
-			basePath: stateBasePath
+			backend: "file",
+			basePath: dbDir
 		});
 		await stateStore.initialize();
 		try {
@@ -8968,7 +8947,7 @@ async function runMetricsAction(options) {
 			const routingConfigPath = join(dbDir, "routing.yml");
 			let routingConfig = null;
 			if (existsSync$1(routingConfigPath)) try {
-				const { loadModelRoutingConfig } = await import("../routing-BdwJkF3S.js");
+				const { loadModelRoutingConfig } = await import("../routing-CD5PGDLe.js");
 				routingConfig = loadModelRoutingConfig(routingConfigPath);
 			} catch {}
 			if (routingConfig === null) routingConfig = {
@@ -9141,26 +9120,6 @@ async function runMetricsAction(options) {
 			return 0;
 		}
 		const runs = await listRunMetrics(adapter, limit);
-		let doltMetrics;
-		const doltStatePath = join(dbRoot, ".substrate", "state", ".dolt");
-		const hasDoltFilters = sprint !== void 0 || story !== void 0 || taskType !== void 0 || since !== void 0 || aggregate === true;
-		if (existsSync$1(doltStatePath) && hasDoltFilters) try {
-			const stateStore = createStateStore({
-				backend: "dolt",
-				basePath: join(dbRoot, ".substrate", "state")
-			});
-			await stateStore.initialize();
-			const doltFilter = {};
-			if (sprint !== void 0) doltFilter.sprint = sprint;
-			if (story !== void 0) doltFilter.storyKey = story;
-			if (taskType !== void 0) doltFilter.taskType = taskType;
-			if (since !== void 0) doltFilter.since = since;
-			if (aggregate !== void 0) doltFilter.aggregate = aggregate;
-			doltMetrics = await stateStore.queryMetrics(doltFilter);
-			await stateStore.close();
-		} catch (doltErr) {
-			logger$13.warn({ err: doltErr }, "StateStore query failed — falling back to SQLite metrics only");
-		}
 		const storyMetricDecisions = await getDecisionsByCategory(adapter, STORY_METRICS);
 		const storyMetrics = storyMetricDecisions.map((d) => {
 			const colonIdx = d.key.indexOf(":");
@@ -9250,8 +9209,8 @@ async function runMetricsAction(options) {
 			};
 			if (probeAuthorSummary) {
 				const allMetrics = storyMetricsWithFindings.map((sm) => sm.probe_author);
-				const aggregate$1 = aggregateProbeAuthorMetrics(allMetrics, storyMetricsWithFindings.length);
-				jsonPayload.probe_author_summary = aggregate$1;
+				const aggregate = aggregateProbeAuthorMetrics(allMetrics, storyMetricsWithFindings.length);
+				jsonPayload.probe_author_summary = aggregate;
 			}
 			if (probeAuthorClassSummary) {
 				const classSummaryEntries = storyMetricsWithFindings.map((sm) => {
@@ -9263,26 +9222,9 @@ async function runMetricsAction(options) {
 				});
 				jsonPayload.probe_author_class_summary = rollupProbeAuthorByClass(classSummaryEntries);
 			}
-			if (doltMetrics !== void 0) if (aggregate) {
-				const aggregateResults = doltMetrics.map((m) => ({
-					task_type: m.taskType,
-					count: m.count ?? 0,
-					avg_cost_usd: m.costUsd ?? 0,
-					sum_tokens_in: m.tokensIn ?? 0,
-					sum_tokens_out: m.tokensOut ?? 0
-				}));
-				const aggregateTotals = {
-					total_count: aggregateResults.reduce((sum, r) => sum + r.count, 0),
-					total_avg_cost_usd: aggregateResults.reduce((sum, r) => sum + r.avg_cost_usd, 0),
-					total_tokens_in: aggregateResults.reduce((sum, r) => sum + r.sum_tokens_in, 0),
-					total_tokens_out: aggregateResults.reduce((sum, r) => sum + r.sum_tokens_out, 0)
-				};
-				jsonPayload.aggregate_metrics = aggregateResults;
-				jsonPayload.aggregate_totals = aggregateTotals;
-			} else jsonPayload.dolt_metrics = doltMetrics;
 			process.stdout.write(formatOutput(jsonPayload, "json", true) + "\n");
 		} else {
-			if (runs.length === 0 && storyMetrics.length === 0 && (doltMetrics === void 0 || doltMetrics.length === 0) && factoryRuns.length === 0) {
+			if (runs.length === 0 && storyMetrics.length === 0 && factoryRuns.length === 0) {
 				process.stdout.write("No run metrics recorded yet. Run `substrate run` to generate metrics.\n");
 				return 0;
 			}
@@ -9317,41 +9259,6 @@ async function runMetricsAction(options) {
 					process.stdout.write(`  ${sm.story_key.padEnd(16)} ${runShort.padEnd(12)} ${String(sm.wall_clock_seconds).padStart(8)} ${sm.input_tokens.toLocaleString().padStart(10)} ${sm.output_tokens.toLocaleString().padStart(11)} ${String(sm.review_cycles).padStart(7)} ${stalledStr.padStart(8)}${costStr}\n`);
 				}
 			}
-			if (doltMetrics !== void 0 && doltMetrics.length > 0) if (aggregate) {
-				process.stdout.write(`\nStateStore Aggregate Metrics (by task type)\n`);
-				process.stdout.write("─".repeat(80) + "\n");
-				process.stdout.write(`  ${"Task Type".padEnd(20)} ${"Count".padStart(8)} ${"Avg Cost".padStart(12)} ${"Sum Tokens In".padStart(14)} ${"Sum Tokens Out".padStart(15)}\n`);
-				process.stdout.write("  " + "─".repeat(72) + "\n");
-				let totalCount = 0;
-				let totalCost = 0;
-				let totalTokensIn = 0;
-				let totalTokensOut = 0;
-				for (const m of doltMetrics) {
-					const count = m.count ?? 0;
-					const avgCost = m.costUsd !== void 0 ? `$${m.costUsd.toFixed(4)}` : "-";
-					const sumIn = m.tokensIn !== void 0 ? m.tokensIn.toLocaleString() : "-";
-					const sumOut = m.tokensOut !== void 0 ? m.tokensOut.toLocaleString() : "-";
-					totalCount += count;
-					totalCost += m.costUsd ?? 0;
-					totalTokensIn += m.tokensIn ?? 0;
-					totalTokensOut += m.tokensOut ?? 0;
-					process.stdout.write(`  ${m.taskType.padEnd(20)} ${String(count).padStart(8)} ${avgCost.padStart(12)} ${sumIn.padStart(14)} ${sumOut.padStart(15)}\n`);
-				}
-				process.stdout.write("  " + "─".repeat(72) + "\n");
-				process.stdout.write(`  ${"TOTAL".padEnd(20)} ${String(totalCount).padStart(8)} ${`$${totalCost.toFixed(4)}`.padStart(12)} ${totalTokensIn.toLocaleString().padStart(14)} ${totalTokensOut.toLocaleString().padStart(15)}\n`);
-			} else {
-				process.stdout.write(`\nStateStore Metrics (${doltMetrics.length} records)\n`);
-				process.stdout.write("─".repeat(80) + "\n");
-				process.stdout.write(`  ${"Story".padEnd(16)} ${"Task Type".padEnd(16)} ${"Tokens In".padStart(10)} ${"Tokens Out".padStart(11)} ${"Wall(ms)".padStart(10)} ${"Result".padEnd(12)}\n`);
-				process.stdout.write("  " + "─".repeat(76) + "\n");
-				for (const m of doltMetrics) {
-					const tokIn = m.tokensIn !== void 0 ? m.tokensIn.toLocaleString() : "-";
-					const tokOut = m.tokensOut !== void 0 ? m.tokensOut.toLocaleString() : "-";
-					const wall = m.wallClockMs !== void 0 ? String(m.wallClockMs) : "-";
-					const res = m.result ?? "-";
-					process.stdout.write(`  ${m.storyKey.padEnd(16)} ${m.taskType.padEnd(16)} ${tokIn.padStart(10)} ${tokOut.padStart(11)} ${wall.padStart(10)} ${res.padEnd(12)}\n`);
-				}
-			}
 			if (factoryRuns.length > 0) printFactoryRunTable(factoryRuns);
 		}
 		return 0;
@@ -9368,7 +9275,7 @@ async function runMetricsAction(options) {
 	}
 }
 function registerMetricsCommand(program, _version = "0.0.0", projectRoot = process.cwd()) {
-	program.command("metrics").description("Show historical pipeline run metrics and cross-run comparison").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").option("--limit <n>", "Number of runs to show (default: 10)", (v) => parseInt(v, 10), 10).option("--compare <run-id-a,run-id-b>", "Compare two runs side-by-side (comma-separated IDs, e.g. abc123,def456)").option("--tag-baseline <run-id>", "Mark a run as the performance baseline").option("--analysis <run-id>", "Read and output the analysis report for the specified run (AC5 of Story 17-3)").option("--sprint <sprint>", "Filter StateStore metrics by sprint (e.g. sprint-1)").option("--story <story-key>", "Filter StateStore metrics by story key (e.g. 26-1)").option("--task-type <type>", "Filter StateStore metrics by task type (e.g. dev-story)").option("--since <iso-date>", "Filter StateStore metrics at or after this ISO timestamp").option("--aggregate", "Aggregate StateStore metrics grouped by task_type").option("--efficiency", "Show telemetry efficiency scores for recent stories").option("--recommendations", "Show all telemetry recommendations across stories").option("--turns <storyKey>", "Show per-turn analysis for a specific story").option("--consumers <storyKey>", "Show consumer stats for a specific story").option("--categories", "Show category stats (optionally scoped by --story <storyKey>)").option("--compare-stories <storyA,storyB>", "Compare efficiency scores of two stories side-by-side (comma-separated keys)").option("--routing-recommendations", "Show routing recommendations derived from phase token breakdown history").option("--run <run-id>", "Show per-iteration score history for a specific factory run").option("--factory", "Show only factory graph run metrics (excludes SDLC runs)").option("--probe-author-summary", "Print cross-run probe-author KPI aggregate (Story 60-15)").option("--probe-author-class-summary", "Print cross-run probe-author KPI aggregate broken down by trigger class (Story 65-6)").action(async (opts) => {
+	program.command("metrics").description("Show historical pipeline run metrics and cross-run comparison").option("--project-root <path>", "Project root directory", projectRoot).option("--output-format <format>", "Output format: human (default) or json", "human").option("--limit <n>", "Number of runs to show (default: 10)", (v) => parseInt(v, 10), 10).option("--compare <run-id-a,run-id-b>", "Compare two runs side-by-side (comma-separated IDs, e.g. abc123,def456)").option("--tag-baseline <run-id>", "Mark a run as the performance baseline").option("--analysis <run-id>", "Read and output the analysis report for the specified run (AC5 of Story 17-3)").option("--story <story-key>", "Filter recommendations by story key (e.g. 26-1)").option("--efficiency", "Show telemetry efficiency scores for recent stories").option("--recommendations", "Show all telemetry recommendations across stories").option("--turns <storyKey>", "Show per-turn analysis for a specific story").option("--consumers <storyKey>", "Show consumer stats for a specific story").option("--categories", "Show category stats (optionally scoped by --story <storyKey>)").option("--compare-stories <storyA,storyB>", "Compare efficiency scores of two stories side-by-side (comma-separated keys)").option("--routing-recommendations", "Show routing recommendations derived from phase token breakdown history").option("--run <run-id>", "Show per-iteration score history for a specific factory run").option("--factory", "Show only factory graph run metrics (excludes SDLC runs)").option("--probe-author-summary", "Print cross-run probe-author KPI aggregate (Story 60-15)").option("--probe-author-class-summary", "Print cross-run probe-author KPI aggregate broken down by trigger class (Story 65-6)").action(async (opts) => {
 		const outputFormat = opts.outputFormat === "json" ? "json" : "human";
 		let compareIds;
 		if (opts.compare !== void 0) {
@@ -9392,11 +9299,7 @@ function registerMetricsCommand(program, _version = "0.0.0", projectRoot = proce
 			...compareIds !== void 0 && { compare: compareIds },
 			...opts.tagBaseline !== void 0 && { tagBaseline: opts.tagBaseline },
 			...opts.analysis !== void 0 && { analysis: opts.analysis },
-			...opts.sprint !== void 0 && { sprint: opts.sprint },
 			...opts.story !== void 0 && { story: opts.story },
-			...opts.taskType !== void 0 && { taskType: opts.taskType },
-			...opts.since !== void 0 && { since: opts.since },
-			...opts.aggregate !== void 0 && { aggregate: opts.aggregate },
 			...opts.efficiency !== void 0 && { efficiency: opts.efficiency },
 			...opts.recommendations !== void 0 && { recommendations: opts.recommendations },
 			...opts.turns !== void 0 && { turns: opts.turns },
@@ -11451,207 +11354,6 @@ function registerCancelCommand(program, projectRoot = process.cwd()) {
 	});
 }
 
-//#endregion
-//#region src/cli/commands/contracts.ts
-function registerContractsCommand(program) {
-	program.command("contracts").description("Show contract declarations and verification status").option("--output-format <format>", "Output format: text or json", "text").action(async (options) => {
-		const dbRoot = await resolveMainRepoRoot(process.cwd());
-		const statePath = join$1(dbRoot, ".substrate", "state");
-		const doltStatePath = join$1(statePath, ".dolt");
-		const storeConfig = existsSync(doltStatePath) ? {
-			backend: "dolt",
-			basePath: statePath
-		} : {
-			backend: "file",
-			basePath: statePath
-		};
-		const store = createStateStore(storeConfig);
-		try {
-			await store.initialize();
-			const contracts = await store.queryContracts();
-			if (contracts.length === 0) {
-				console.log("No contracts stored. Run a pipeline to populate contract data.");
-				return;
-			}
-			const storyKeys = [...new Set(contracts.map((c) => c.storyKey))];
-			const verificationMap = new Map();
-			for (const sk of storyKeys) {
-				const verifications = await store.getContractVerification(sk);
-				const contractVerdicts = new Map();
-				for (const v of verifications) contractVerdicts.set(v.contractName, v.verdict);
-				verificationMap.set(sk, contractVerdicts);
-			}
-			const mergedRecords = contracts.map((c) => {
-				const verdicts = verificationMap.get(c.storyKey);
-				const verdict = verdicts?.get(c.contractName);
-				return {
-					storyKey: c.storyKey,
-					contractName: c.contractName,
-					direction: c.direction,
-					schemaPath: c.schemaPath,
-					verificationStatus: verdict === "pass" ? "✓ pass" : verdict === "fail" ? "✗ fail" : "? pending",
-					verdict: verdict ?? "pending"
-				};
-			});
-			if (options.outputFormat === "json") {
-				console.log(JSON.stringify(mergedRecords, null, 2));
-				return;
-			}
-			const headers = [
-				"Story Key",
-				"Contract Name",
-				"Direction",
-				"Schema Path",
-				"Status"
-			];
-			const rows = mergedRecords.map((r) => [
-				r.storyKey,
-				r.contractName,
-				r.direction,
-				r.schemaPath,
-				r.verificationStatus
-			]);
-			const colWidths = headers.map((h, i) => Math.max(h.length, ...rows.map((r) => (r[i] ?? "").length)));
-			const formatRow$1 = (cells) => cells.map((c, i) => c.padEnd(colWidths[i])).join("  ");
-			console.log(formatRow$1(headers));
-			console.log(colWidths.map((w) => "-".repeat(w)).join("  "));
-			for (const row of rows) console.log(formatRow$1(row));
-		} finally {
-			await store.close();
-		}
-	});
-}
-
-//#endregion
-//#region src/utils/degraded-mode-hint.ts
-/**
-* Determine the appropriate degraded-mode hint message based on whether Dolt
-* is installed and/or initialized at the given state path.
-*
-* @param statePath - Absolute path to the substrate state directory
-*                    (e.g. `/project/.substrate/state`).
-*/
-async function getDegradedModeHint(statePath) {
-	try {
-		await checkDoltInstalled();
-		if (!existsSync(join$1(statePath, ".dolt"))) return {
-			hint: "Note: Dolt is installed but not initialized. Run `substrate init --dolt` to enable diff and history features.",
-			doltInstalled: true
-		};
-		return {
-			hint: "Note: Running on file backend. Diff and history require Dolt.",
-			doltInstalled: true
-		};
-	} catch (err) {
-		if (err instanceof DoltNotInstalled) return {
-			hint: "Note: Dolt is not installed. Install it from https://docs.dolthub.com/introduction/installation, then run `substrate init --dolt` to enable diff and history features.",
-			doltInstalled: false
-		};
-		throw err;
-	}
-}
-/**
-* Emit a degraded-mode hint for the given command.
-*
-* - **Text mode**: writes the hint to `process.stderr` (not stdout).
-* - **JSON mode**: does NOT write to stderr; the caller is responsible for
-*   writing the returned `hint` field to stdout as part of its JSON envelope.
-*
-* @param options - Hint options including output format, command name, and
-*                  the resolved state directory path.
-* @returns The hint message and a flag indicating whether Dolt is installed.
-*/
-async function emitDegradedModeHint(options) {
-	const { hint, doltInstalled } = await getDegradedModeHint(options.statePath);
-	if (options.outputFormat !== "json") process.stderr.write(`\n${hint}\n`);
-	return {
-		hint,
-		doltInstalled
-	};
-}
-
-//#endregion
-//#region src/cli/commands/diff.ts
-function registerDiffCommand(program) {
-	program.command("diff [storyKey]").description("Show stat-based diff of database changes for a story or sprint").option("--sprint <sprintId>", "Diff all stories in the specified sprint").option("--output-format <format>", "Output format: text or json", "text").action(async (storyKey, options) => {
-		if (storyKey === void 0 && options.sprint === void 0) {
-			console.error("Error: provide a story key or --sprint <sprintId>");
-			process.exitCode = 1;
-			return;
-		}
-		const dbRoot = await resolveMainRepoRoot(process.cwd());
-		const statePath = join$1(dbRoot, ".substrate", "state");
-		const doltStatePath = join$1(statePath, ".dolt");
-		const storeConfig = existsSync(doltStatePath) ? {
-			backend: "dolt",
-			basePath: statePath
-		} : {
-			backend: "file",
-			basePath: statePath
-		};
-		const store = createStateStore(storeConfig);
-		try {
-			await store.initialize();
-			if (store instanceof FileStateStore) {
-				const result = await emitDegradedModeHint({
-					outputFormat: options.outputFormat,
-					command: "diff",
-					statePath
-				});
-				if (options.outputFormat === "json") console.log(JSON.stringify({
-					backend: "file",
-					hint: result.hint,
-					diff: null
-				}));
-				return;
-			}
-			if (storyKey !== void 0) {
-				const diff = await store.diffStory(storyKey);
-				if (options.outputFormat === "json") {
-					console.log(JSON.stringify(diff, null, 2));
-					return;
-				}
-				console.log(`Diff for story ${storyKey}:`);
-				if (diff.tables.length === 0) console.log("  (no changes)");
-				else for (const t of diff.tables) console.log(`  ${t.table}: +${t.added.length} -${t.deleted.length} ~${t.modified.length}`);
-			} else {
-				const stories = await store.queryStories({ sprint: options.sprint });
-				const tableMap = new Map();
-				for (const story of stories) {
-					const diff = await store.diffStory(story.storyKey);
-					for (const t of diff.tables) {
-						const existing = tableMap.get(t.table);
-						if (existing === void 0) tableMap.set(t.table, {
-							table: t.table,
-							added: [...t.added],
-							deleted: [...t.deleted],
-							modified: [...t.modified]
-						});
-						else {
-							existing.added = [...existing.added, ...t.added];
-							existing.deleted = [...existing.deleted, ...t.deleted];
-							existing.modified = [...existing.modified, ...t.modified];
-						}
-					}
-				}
-				const aggregated = Array.from(tableMap.values());
-				if (options.outputFormat === "json") {
-					console.log(JSON.stringify({
-						sprint: options.sprint,
-						tables: aggregated
-					}, null, 2));
-					return;
-				}
-				console.log(`Diff for sprint ${options.sprint}:`);
-				if (aggregated.length === 0) console.log("  (no changes)");
-				else for (const t of aggregated) console.log(`  ${t.table}: +${t.added.length} -${t.deleted.length} ~${t.modified.length}`);
-			}
-		} finally {
-			await store.close();
-		}
-	});
-}
-
 //#endregion
 //#region src/cli/commands/probes-diff.ts
 /**
@@ -11980,6 +11682,54 @@ function emitError(format, message) {
 	return 1;
 }
 
+//#endregion
+//#region src/utils/degraded-mode-hint.ts
+/**
+* Determine the appropriate degraded-mode hint message based on whether Dolt
+* is installed and/or initialized at the given state path.
+*
+* @param statePath - Absolute path to the substrate state directory
+*                    (e.g. `/project/.substrate/state`).
+*/
+async function getDegradedModeHint(statePath) {
+	try {
+		await checkDoltInstalled();
+		if (!existsSync(join$1(statePath, ".dolt"))) return {
+			hint: "Note: Dolt is installed but not initialized. Run `substrate init --dolt` to enable history.",
+			doltInstalled: true
+		};
+		return {
+			hint: "Note: Running on file backend. History requires Dolt.",
+			doltInstalled: true
+		};
+	} catch (err) {
+		if (err instanceof DoltNotInstalled) return {
+			hint: "Note: Dolt is not installed. Install it from https://docs.dolthub.com/introduction/installation, then run `substrate init --dolt` to enable history.",
+			doltInstalled: false
+		};
+		throw err;
+	}
+}
+/**
+* Emit a degraded-mode hint for the given command.
+*
+* - **Text mode**: writes the hint to `process.stderr` (not stdout).
+* - **JSON mode**: does NOT write to stderr; the caller is responsible for
+*   writing the returned `hint` field to stdout as part of its JSON envelope.
+*
+* @param options - Hint options including output format, command name, and
+*                  the resolved state directory path.
+* @returns The hint message and a flag indicating whether Dolt is installed.
+*/
+async function emitDegradedModeHint(options) {
+	const { hint, doltInstalled } = await getDegradedModeHint(options.statePath);
+	if (options.outputFormat !== "json") process.stderr.write(`\n${hint}\n`);
+	return {
+		hint,
+		doltInstalled
+	};
+}
+
 //#endregion
 //#region src/cli/commands/history.ts
 function registerHistoryCommand(program) {
@@ -11988,29 +11738,22 @@ function registerHistoryCommand(program) {
 		const dbRoot = await resolveMainRepoRoot(process.cwd());
 		const statePath = join$1(dbRoot, ".substrate", "state");
 		const doltStatePath = join$1(statePath, ".dolt");
-		const storeConfig = existsSync(doltStatePath) ? {
-			backend: "dolt",
-			basePath: statePath
-		} : {
-			backend: "file",
-			basePath: statePath
-		};
-		const store = createStateStore(storeConfig);
+		if (!existsSync(doltStatePath)) {
+			const result = await emitDegradedModeHint({
+				outputFormat: options.outputFormat,
+				command: "history",
+				statePath
+			});
+			if (options.outputFormat === "json") console.log(JSON.stringify({
+				backend: "file",
+				hint: result.hint,
+				entries: []
+			}));
+			return;
+		}
+		const store = createDoltOperatorReader({ basePath: statePath });
 		try {
 			await store.initialize();
-			if (store instanceof FileStateStore) {
-				const result = await emitDegradedModeHint({
-					outputFormat: options.outputFormat,
-					command: "history",
-					statePath
-				});
-				if (options.outputFormat === "json") console.log(JSON.stringify({
-					backend: "file",
-					hint: result.hint,
-					entries: []
-				}));
-				return;
-			}
 			const entries = await store.getHistory(limit);
 			if (entries.length === 0) {
 				console.log("No history available.");
@@ -12182,16 +11925,7 @@ const logger$3 = createLogger("cli:routing");
 function registerRoutingCommand(program) {
 	program.command("routing").description("Show routing configuration and auto-tune history").option("--history", "Show the routing auto-tune log (model changes applied)").option("--output-format <format>", "Output format: text or json", "text").action(async (options) => {
 		const dbRoot = await resolveMainRepoRoot(process.cwd());
-		const statePath = join$1(dbRoot, ".substrate", "state");
-		const doltStatePath = join$1(statePath, ".dolt");
-		const storeConfig = existsSync(doltStatePath) ? {
-			backend: "dolt",
-			basePath: statePath
-		} : {
-			backend: "file",
-			basePath: statePath
-		};
-		const store = createStateStore(storeConfig);
+		const store = new FileStateStore({ basePath: join$1(dbRoot, ".substrate") });
 		try {
 			await store.initialize();
 			if (options.history === true) {
@@ -13562,8 +13296,6 @@ async function createProgram() {
 	registerMetricsCommand(program, version);
 	registerRetryEscalatedCommand(program, version, process.cwd(), registry);
 	registerCancelCommand(program, process.cwd());
-	registerContractsCommand(program);
-	registerDiffCommand(program);
 	registerHistoryCommand(program);
 	registerMigrateCommand(program);
 	registerProbesCommand(program);
@@ -13589,8 +13321,8 @@ 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-BeqdIFCx.js").then(async () => {
-		const { createVersionManager } = await import("../version-manager-impl-CZ1AbRt3.js");
+	import("../upgrade-DCDe5u0P.js").then(async () => {
+		const { createVersionManager } = await import("../version-manager-impl-B8MpvZQz.js");
 		const vm = createVersionManager();
 		const result = await vm.checkForUpdates();
 		if (result.updateAvailable) {