@mcoda/mswarm 0.1.57 → 0.1.60

package/dist/vendor/codali/cli/RunCommand.js

@@ -0,0 +1,2261 @@
+import { randomUUID } from "node:crypto";
+import { spawnSync } from "node:child_process";
+import { createWriteStream, existsSync } from "node:fs";
+import { readFile, mkdir } from "node:fs/promises";
+import path from "node:path";
+import { createInterface } from "node:readline/promises";
+import process from "node:process";
+import { loadConfig } from "../config/ConfigLoader.js";
+import { createProvider } from "../providers/ProviderRegistry.js";
+import { OpenAiCompatibleProvider } from "../providers/OpenAiCompatibleProvider.js";
+import { OllamaRemoteProvider } from "../providers/OllamaRemoteProvider.js";
+import { CodexCliProvider } from "../providers/CodexCliProvider.js";
+import { ToolRegistry } from "../tools/ToolRegistry.js";
+import { createFileTools } from "../tools/filesystem/FileTools.js";
+import { createDiffTool } from "../tools/diff/DiffTool.js";
+import { createSearchTool } from "../tools/search/SearchTool.js";
+import { createShellTool } from "../tools/shell/ShellTool.js";
+import { DocdexClient } from "../docdex/DocdexClient.js";
+import { createDocdexTools } from "../tools/docdex/DocdexTools.js";
+import { RunContext } from "../runtime/RunContext.js";
+import { WorkspaceLock } from "../runtime/WorkspaceLock.js";
+import { runCodaliTask } from "../runtime/CodaliRuntime.js";
+import { RunLogger } from "../runtime/RunLogger.js";
+import { RunLogReader } from "../runtime/RunLogReader.js";
+import { registerProvider } from "../providers/ProviderRegistry.js";
+import { ContextAssembler } from "../cognitive/ContextAssembler.js";
+import { ArchitectPlanner } from "../cognitive/ArchitectPlanner.js";
+import { BuilderRunner } from "../cognitive/BuilderRunner.js";
+import { CriticEvaluator } from "../cognitive/CriticEvaluator.js";
+import { ValidationRunner } from "../cognitive/ValidationRunner.js";
+import { MemoryWriteback } from "../cognitive/MemoryWriteback.js";
+import { PatchApplier } from "../cognitive/PatchApplier.js";
+import { PatchInterpreter } from "../cognitive/PatchInterpreter.js";
+import { SmartPipeline } from "../cognitive/SmartPipeline.js";
+import { buildRoutedProvider } from "../cognitive/ProviderRouting.js";
+import { ContextManager } from "../cognitive/ContextManager.js";
+import { ContextStore } from "../cognitive/ContextStore.js";
+import { ContextSummarizer } from "../cognitive/ContextSummarizer.js";
+import { ContextRedactor } from "../cognitive/ContextRedactor.js";
+import { estimateCostFromChars, estimateCostFromUsage, estimateUsageCostTelemetry, resolvePricing, } from "../cognitive/CostEstimator.js";
+import { getGlobalWorkspaceDir } from "../runtime/StoragePaths.js";
+import { resolveAgentConfig } from "../agents/AgentResolver.js";
+import { selectPhaseAgents } from "../agents/PhaseAgentSelector.js";
+export const parseArgs = (argv) => {
+    const parseNumberArg = (value) => {
+        if (!value)
+            return undefined;
+        const parsed = Number(value);
+        return Number.isFinite(parsed) ? parsed : undefined;
+    };
+    const parseBooleanArg = (value) => {
+        if (!value)
+            return undefined;
+        const normalized = value.trim().toLowerCase();
+        if (["1", "true", "yes", "on"].includes(normalized))
+            return true;
+        if (["0", "false", "no", "off"].includes(normalized))
+            return false;
+        return undefined;
+    };
+    const parseListArg = (value) => {
+        if (!value)
+            return undefined;
+        const items = value
+            .split(",")
+            .map((entry) => entry.trim())
+            .filter(Boolean);
+        return items.length ? items : undefined;
+    };
+    const parsed = {};
+    const positionals = [];
+    for (let i = 0; i < argv.length; i += 1) {
+        const arg = argv[i];
+        const next = argv[i + 1];
+        if (arg === "--workspace-root" && next) {
+            parsed.workspaceRoot = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--project" && next) {
+            parsed.project = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--command" && next) {
+            parsed.command = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--command-run-id" && next) {
+            parsed.commandRunId = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--job-id" && next) {
+            parsed.jobId = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--run-id" && next) {
+            parsed.runId = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--task-id" && next) {
+            parsed.taskId = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--task-key" && next) {
+            parsed.taskKey = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--agent" && next) {
+            parsed.agent = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--agent-id" && next) {
+            parsed.agentId = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--agent-slug" && next) {
+            parsed.agentSlug = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--agent-librarian" && next) {
+            parsed.agentLibrarian = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--agent-architect" && next) {
+            parsed.agentArchitect = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--agent-builder" && next) {
+            parsed.agentBuilder = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--agent-critic" && next) {
+            parsed.agentCritic = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--agent-interpreter" && next) {
+            parsed.agentInterpreter = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--plan-hint" && next) {
+            parsed.planHint = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--smart") {
+            parsed.smart = true;
+            continue;
+        }
+        if (arg === "--no-deep-investigation") {
+            parsed.deepInvestigationEnabled = false;
+            continue;
+        }
+        if (arg === "--provider" && next) {
+            parsed.provider = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--model" && next) {
+            parsed.model = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--api-key" && next) {
+            parsed.apiKey = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--base-url" && next) {
+            parsed.baseUrl = next;
+            i += 1;
+            continue;
+        }
+        if ((arg === "--workflow-profile" || arg === "--profile") && next) {
+            parsed.workflowProfile = next;
+            i += 1;
+            continue;
+        }
+        if ((arg === "--task" || arg === "--task-file") && next) {
+            parsed.taskFile = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--config" && next) {
+            parsed.configPath = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--docdex-base-url" && next) {
+            parsed.docdexBaseUrl = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--docdex-repo-id" && next) {
+            parsed.docdexRepoId = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--docdex-repo-root" && next) {
+            parsed.docdexRepoRoot = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-mode" && next) {
+            if (next === "bundle_text" || next === "json")
+                parsed.contextMode = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-max-files" && next) {
+            parsed.contextMaxFiles = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-max-total-bytes" && next) {
+            parsed.contextMaxTotalBytes = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-token-budget" && next) {
+            parsed.contextTokenBudget = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-focus-max-bytes" && next) {
+            parsed.contextFocusMaxBytes = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-periphery-max-bytes" && next) {
+            parsed.contextPeripheryMaxBytes = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-include-repo-map" && next) {
+            parsed.contextIncludeRepoMap = parseBooleanArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-include-impact" && next) {
+            parsed.contextIncludeImpact = parseBooleanArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-include-snippets" && next) {
+            parsed.contextIncludeSnippets = parseBooleanArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-read-strategy" && next) {
+            if (next === "docdex" || next === "fs")
+                parsed.contextReadStrategy = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-max-refreshes" && next) {
+            parsed.contextMaxRefreshes = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-skeletonize" && next) {
+            parsed.contextSkeletonize = parseBooleanArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-redact-secrets" && next) {
+            parsed.contextRedactSecrets = parseBooleanArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--context-ignore-files-from" && next) {
+            parsed.contextIgnoreFilesFrom = parseListArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--security-redact-patterns" && next) {
+            parsed.securityRedactPatterns = parseListArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--builder-mode" && next) {
+            if (next === "tool_calls" || next === "patch_json" || next === "freeform") {
+                parsed.builderMode = next;
+            }
+            i += 1;
+            continue;
+        }
+        if (arg === "--builder-patch-format" && next) {
+            if (next === "search_replace" || next === "file_writes")
+                parsed.builderPatchFormat = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--interpreter-provider" && next) {
+            parsed.interpreterProvider = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--interpreter-model" && next) {
+            parsed.interpreterModel = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--interpreter-format" && next) {
+            parsed.interpreterFormat = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--interpreter-grammar" && next) {
+            parsed.interpreterGrammar = next;
+            i += 1;
+            continue;
+        }
+        if (arg === "--interpreter-max-retries" && next) {
+            parsed.interpreterMaxRetries = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--interpreter-timeout-ms" && next) {
+            parsed.interpreterTimeoutMs = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--streaming-flush-ms" && next) {
+            parsed.streamingFlushMs = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--cost-max" && next) {
+            parsed.costMaxPerRun = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--cost-char-per-token" && next) {
+            parsed.costCharPerToken = parseNumberArg(next);
+            i += 1;
+            continue;
+        }
+        if (arg === "--cost-pricing-overrides" && next) {
+            parsed.costPricingOverrides = next;
+            i += 1;
+            continue;
+        }
+        if (!arg.startsWith("-")) {
+            positionals.push(arg);
+        }
+    }
+    if (positionals.length) {
+        parsed.inlineTask = positionals.join(" ");
+    }
+    return parsed;
+};
+const ROOT_MARKERS = [
+    ".git",
+    "package.json",
+    "pnpm-workspace.yaml",
+    "yarn.lock",
+    "bun.lockb",
+    "go.mod",
+    "Cargo.toml",
+    "pyproject.toml",
+    "requirements.txt",
+    "Gemfile",
+    "composer.json",
+    "pom.xml",
+    "build.gradle",
+    "build.gradle.kts",
+    "codali.config.json",
+    ".codalirc",
+];
+export const resolveWorkspaceRoot = (cwd, explicitRoot) => {
+    if (explicitRoot) {
+        return path.resolve(cwd, explicitRoot);
+    }
+    let current = path.resolve(cwd);
+    let previous = "";
+    while (current !== previous) {
+        for (const marker of ROOT_MARKERS) {
+            if (existsSync(path.join(current, marker))) {
+                return current;
+            }
+        }
+        previous = current;
+        current = path.dirname(current);
+    }
+    return path.resolve(cwd);
+};
+const formatCost = (cost) => {
+    if (cost === undefined)
+        return "unknown";
+    return `$${cost.toFixed(4)}`;
+};
+const toSummaryPhase = (phase) => {
+    if (phase === "librarian" || phase === "plan")
+        return "plan";
+    if (phase === "architect" || phase === "retrieve")
+        return "retrieve";
+    if (phase === "builder" || phase === "act")
+        return "act";
+    if (phase === "critic" || phase === "verify" || phase === "architect_review")
+        return "verify";
+    return undefined;
+};
+const uniqueStrings = (values) => Array.from(new Set(values.map((value) => value.trim()).filter((value) => value.length > 0))).sort((left, right) => left.localeCompare(right));
+const inferFailureClass = (stage, reasons, errorMessage) => {
+    const haystack = [stage ?? "", ...reasons, errorMessage ?? ""].join(" ").toLowerCase();
+    if (haystack.includes("verification"))
+        return "verification_failure";
+    if (haystack.includes("policy") || haystack.includes("guardrail"))
+        return "policy_failure";
+    if (haystack.includes("safety"))
+        return "safety_failure";
+    if (haystack.includes("patch"))
+        return "patch_failure";
+    if (haystack.includes("provider") || haystack.includes("rate limit") || haystack.includes("auth")) {
+        return "provider_failure";
+    }
+    if (haystack.includes("execution") || haystack.includes("runner") || haystack.includes("timeout")) {
+        return "execution_failure";
+    }
+    return "unknown_failure";
+};
+const summarizeContext = (context, fallbackContent) => {
+    const files = context?.files ?? [];
+    const focusCount = files.filter((file) => file.role === "focus").length;
+    const peripheryCount = files.filter((file) => file.role === "periphery").length;
+    const content = context?.serialized?.content ?? fallbackContent ?? "";
+    return {
+        focusCount,
+        peripheryCount,
+        content,
+        charCount: content.length,
+    };
+};
+const confirmOverage = async (message) => {
+    if (!process.stdin.isTTY) {
+        return false;
+    }
+    const rl = createInterface({ input: process.stdin, output: process.stderr });
+    try {
+        const answer = await rl.question(message);
+        const normalized = answer.trim().toLowerCase();
+        return normalized === "y" || normalized === "yes";
+    }
+    finally {
+        rl.close();
+    }
+};
+const createStreamState = (flushEveryMs, outputStream) => {
+    let buffer = "";
+    let lastFlush = Date.now();
+    let didStream = false;
+    const forceColor = process.env.FORCE_COLOR;
+    const supportsColor = (forceColor && forceColor !== "0") || (!!process.stderr.isTTY && !process.env.NO_COLOR);
+    const colorize = (code, text) => supportsColor ? `\u001b[${code}m${text}\u001b[0m` : text;
+    const indent = "  ";
+    const statusColor = (phase) => {
+        if (phase === "executing")
+            return "35";
+        if (phase === "patching")
+            return "33";
+        if (phase === "done")
+            return "32";
+        return "36";
+    };
+    const tag = (phase) => colorize(statusColor(phase), `[${phase}]`);
+    const toolTag = (name) => colorize("34", `[tool:${name}]`);
+    const toolLead = () => colorize("34", "[tool]");
+    const okTag = () => colorize("32", "ok");
+    const errTag = () => colorize("31", "error");
+    const errorLine = (message) => colorize("31", message);
+    const flush = () => {
+        if (buffer.length > 0) {
+            process.stdout.write(buffer);
+            outputStream?.write(buffer);
+            buffer = "";
+        }
+        lastFlush = Date.now();
+    };
+    const writeStatus = (line) => {
+        flush();
+        process.stderr.write(`${line}\n`);
+        outputStream?.write(`${line.replace(/\u001b\[[0-9;]*m/g, "")}\n`);
+    };
+    const onEvent = (event) => {
+        if (event.type === "token") {
+            didStream = true;
+            buffer += event.content;
+            const now = Date.now();
+            if (now - lastFlush >= flushEveryMs) {
+                flush();
+            }
+            return;
+        }
+        if (event.type === "status") {
+            const suffix = event.message ? ` ${event.message}` : "";
+            writeStatus(`${indent}${tag(event.phase)}${suffix}`);
+            return;
+        }
+        if (event.type === "tool_call") {
+            writeStatus(`${indent}${toolLead()} ${event.name}`);
+            return;
+        }
+        if (event.type === "tool_result") {
+            const outcome = event.ok === false ? errTag() : okTag();
+            const suffix = event.ok === false && event.errorCode
+                ? ` ${colorize("31", `(${event.errorCode}${event.retryable ? ",retryable" : ""})`)}`
+                : "";
+            writeStatus(`${indent}${toolTag(event.name)} ${outcome}${suffix}`);
+            return;
+        }
+        if (event.type === "error") {
+            writeStatus(`${indent}${colorize("31", "[error]")} ${errorLine(event.message)}`);
+        }
+    };
+    const onToken = (token) => {
+        didStream = true;
+        buffer += token;
+        const now = Date.now();
+        if (now - lastFlush >= flushEveryMs) {
+            flush();
+        }
+    };
+    return {
+        onEvent,
+        onToken,
+        flush,
+        didStream: () => didStream,
+        writeOutput: (text) => {
+            outputStream?.write(text);
+        },
+    };
+};
+const createPatchValidator = (workspaceRoot, allowShell, shellAllowlist) => {
+    if (!allowShell)
+        return undefined;
+    const allowlist = new Set(shellAllowlist ?? []);
+    return async (filePath) => {
+        const ext = path.extname(filePath).toLowerCase();
+        if (![".js", ".mjs", ".cjs"].includes(ext)) {
+            return;
+        }
+        if (!allowlist.has("node")) {
+            return;
+        }
+        const result = spawnSync("node", ["--check", filePath], {
+            cwd: workspaceRoot,
+            encoding: "utf8",
+        });
+        if (result.error) {
+            throw result.error;
+        }
+        if (result.status !== 0) {
+            throw new Error(result.stderr?.toString() || "node --check failed");
+        }
+    };
+};
+const isPhaseProvider = (value) => value === "librarian" ||
+    value === "architect" ||
+    value === "builder" ||
+    value === "critic" ||
+    value === "interpreter";
+const resolveInterpreterRoute = (config, phaseRoutes) => {
+    const requestedProvider = config.interpreter.provider?.trim() || "auto";
+    const requestedModel = config.interpreter.model?.trim() || "auto";
+    const fallbackRoute = phaseRoutes.interpreter ??
+        phaseRoutes.critic ??
+        phaseRoutes.architect ??
+        phaseRoutes.builder ??
+        phaseRoutes.librarian;
+    const routed = requestedProvider === "auto"
+        ? fallbackRoute
+        : isPhaseProvider(requestedProvider)
+            ? phaseRoutes[requestedProvider]
+            : undefined;
+    const provider = routed?.provider ?? requestedProvider;
+    const baseConfig = routed
+        ? { ...routed.config }
+        : {
+            model: config.model,
+            apiKey: config.apiKey,
+            baseUrl: config.baseUrl,
+            timeoutMs: config.interpreter.timeoutMs,
+        };
+    if (!baseConfig.baseUrl) {
+        const sameProviderBaseUrl = Object.values(phaseRoutes)
+            .map((route) => (route.provider === provider ? route.config.baseUrl : undefined))
+            .find((value) => typeof value === "string" && value.length > 0);
+        baseConfig.baseUrl = sameProviderBaseUrl ?? config.baseUrl ?? baseConfig.baseUrl;
+    }
+    const resolvedModel = requestedModel !== "auto"
+        ? requestedModel
+        : baseConfig.model ?? fallbackRoute?.config.model ?? config.model;
+    return {
+        provider,
+        config: {
+            ...baseConfig,
+            model: resolvedModel,
+            timeoutMs: config.interpreter.timeoutMs ?? baseConfig.timeoutMs,
+        },
+        temperature: routed?.temperature,
+    };
+};
+export const isToolEnabled = (name, tools) => {
+    if (name === "run_shell" && !tools.allowShell) {
+        return false;
+    }
+    const enabled = tools.enabled?.length ? new Set(tools.enabled) : undefined;
+    if (!enabled)
+        return true;
+    return enabled.has(name);
+};
+const PATCH_JSON_STRUCTURED_CAPABILITIES = [
+    "strict_instruction_following",
+    "json_formatting",
+    "schema_adherence",
+    "structured_output",
+];
+const PATCH_JSON_CODE_CAPABILITIES = [
+    "code_write",
+    "iterative_coding",
+    "simple_refactor",
+    "minimal_diff_generation",
+    "migration_scripts",
+    "debugging",
+    "refactor_support",
+];
+const countCapabilityMatches = (capabilities, required) => required.filter((capability) => capabilities.includes(capability)).length;
+export const assessPhaseFallbackSuitability = (phase, builderMode, selection) => {
+    if (phase !== "builder") {
+        return { ok: true, reason: "not_builder_phase", builderMode };
+    }
+    if (builderMode !== "patch_json") {
+        return { ok: true, reason: "builder_mode_not_patch_json", builderMode };
+    }
+    const capabilities = selection.capabilities ?? [];
+    const structuredHits = countCapabilityMatches(capabilities, PATCH_JSON_STRUCTURED_CAPABILITIES);
+    const codeHits = countCapabilityMatches(capabilities, PATCH_JSON_CODE_CAPABILITIES);
+    if (codeHits <= 0) {
+        return {
+            ok: false,
+            reason: "missing_patch_code_capability",
+            details: { codeHits },
+        };
+    }
+    if (structuredHits > 0) {
+        return {
+            ok: true,
+            reason: "capability_requirements_met",
+            details: { structuredHits, codeHits },
+            builderMode: "patch_json",
+        };
+    }
+    const hasToolRunner = capabilities.includes("tool_runner");
+    if (selection.supportsTools || hasToolRunner) {
+        return {
+            ok: true,
+            reason: "fallback_patch_json_without_structured_capability",
+            details: { structuredHits, codeHits, hasToolRunner: hasToolRunner ? 1 : 0 },
+            // Keep patch_json mode so fallback builders stay in the same patch contract path.
+            builderMode: "patch_json",
+        };
+    }
+    return {
+        ok: false,
+        reason: "missing_structured_output_capability",
+        details: { structuredHits, codeHits },
+    };
+};
+const readStdin = async () => {
+    const chunks = [];
+    return new Promise((resolve, reject) => {
+        process.stdin.on("data", (chunk) => chunks.push(Buffer.from(chunk)));
+        process.stdin.on("end", () => resolve(Buffer.concat(chunks).toString("utf8")));
+        process.stdin.on("error", reject);
+    });
+};
+const resolveTaskInput = async (parsed) => {
+    if (parsed.taskFile) {
+        return readFile(parsed.taskFile, "utf8");
+    }
+    if (parsed.inlineTask) {
+        return parsed.inlineTask;
+    }
+    if (process.stdin.isTTY) {
+        return "";
+    }
+    return readStdin();
+};
+const isTrivialRequest = (request) => {
+    const normalized = request.trim().toLowerCase();
+    if (normalized.length === 0)
+        return false;
+    const shortEnough = normalized.length <= 120;
+    const signals = ["typo", "spelling", "format", "whitespace", "rename", "readme", "comment"];
+    return shortEnough && signals.some((signal) => normalized.includes(signal));
+};
+const buildWorkflowTaskInput = (request, profile) => {
+    if (!profile || profile.name === "run") {
+        return request;
+    }
+    const outputInstruction = profile.outputContract === "patch_summary"
+        ? "Return a patch/change-focused summary with changed files and verification notes."
+        : profile.outputContract === "review_findings"
+            ? "Return risk/findings-oriented review output. Do not propose write-oriented changes."
+            : profile.outputContract === "verification_summary"
+                ? "Return verification-first output with test/validation summary."
+                : "Return explanation-first output. Do not propose write-oriented changes.";
+    const writePolicy = profile.allowWrites ? "writes_allowed" : "no_writes";
+    return [
+        `WORKFLOW PROFILE: ${profile.name}`,
+        `OUTPUT CONTRACT: ${profile.outputContract}`,
+        `VERIFICATION POLICY: ${profile.verificationPolicy}`,
+        `VERIFICATION MIN CHECKS: ${profile.verificationMinimumChecks}`,
+        `VERIFICATION HIGH-CONFIDENCE ENFORCEMENT: ${profile.verificationEnforceHighConfidence ? "strict" : "off"}`,
+        `WRITE POLICY: ${writePolicy}`,
+        outputInstruction,
+        "",
+        "USER TASK:",
+        request,
+    ].join("\n");
+};
+const collectPhaseDurations = (artifacts) => {
+    const durations = {};
+    for (const artifact of artifacts) {
+        if (artifact.kind !== "summary")
+            continue;
+        const phase = toSummaryPhase(artifact.phase);
+        if (!phase)
+            continue;
+        if (typeof artifact.duration_ms !== "number" || !Number.isFinite(artifact.duration_ms))
+            continue;
+        durations[phase] = artifact.duration_ms;
+    }
+    return durations;
+};
+const buildArtifactReferences = (phaseArtifactEvents, requiredArtifacts) => {
+    const references = [];
+    for (const event of phaseArtifactEvents) {
+        if (!event.phase || !event.kind)
+            continue;
+        const phase = toSummaryPhase(event.phase) ?? event.phase;
+        references.push({
+            phase,
+            kind: event.kind,
+            path: event.path ?? null,
+            status: "present",
+        });
+    }
+    const seen = new Set(references.map((entry) => `${entry.phase}:${entry.kind}`));
+    const missing = [];
+    for (const required of requiredArtifacts) {
+        if (seen.has(required))
+            continue;
+        missing.push(required);
+        const [phase, kind] = required.split(":");
+        references.push({
+            phase: phase ?? "unknown",
+            kind: kind ?? "unknown",
+            status: "missing",
+            reason_code: "artifact_not_emitted",
+        });
+    }
+    references.sort((left, right) => `${left.phase}:${left.kind}:${left.status}`.localeCompare(`${right.phase}:${right.kind}:${right.status}`));
+    return { references, missing: uniqueStrings(missing) };
+};
+const buildQualityDimensions = (artifactReferences, disposition) => {
+    const hasPresent = (phase) => artifactReferences.some((entry) => entry.phase === phase && entry.status === "present");
+    const retrieval = hasPresent("retrieve")
+        ? "available"
+        : disposition === "pass"
+            ? "degraded"
+            : "missing";
+    const plan = hasPresent("plan")
+        ? "available"
+        : disposition === "pass"
+            ? "degraded"
+            : "missing";
+    const patch = hasPresent("act")
+        ? "available"
+        : disposition === "pass"
+            ? "degraded"
+            : "missing";
+    const verification = hasPresent("verify")
+        ? "available"
+        : disposition === "pass"
+            ? "degraded"
+            : "missing";
+    return {
+        plan,
+        retrieval,
+        patch,
+        verification,
+        final_disposition: "available",
+    };
+};
+const buildPhaseTelemetry = (params) => {
+    const phaseOrder = ["plan", "retrieve", "act", "verify"];
+    const usage = params.usage;
+    const usageTotals = usage
+        ? {
+            input_tokens: usage.inputTokens,
+            output_tokens: usage.outputTokens,
+            total_tokens: usage.totalTokens
+                ?? ((usage.inputTokens ?? 0) + (usage.outputTokens ?? 0) || undefined),
+        }
+        : undefined;
+    const costTelemetry = estimateUsageCostTelemetry(usage, params.pricingSpec);
+    return phaseOrder
+        .filter((phase) => {
+        const providerInfo = params.phaseProviders[phase];
+        return Boolean(providerInfo?.provider || providerInfo?.model || params.phaseDurations[phase] !== undefined);
+    })
+        .map((phase) => {
+        const providerInfo = params.phaseProviders[phase] ?? {};
+        if (phase === "act") {
+            return {
+                run_id: params.runId,
+                phase,
+                provider: providerInfo.provider,
+                model: providerInfo.model,
+                duration_ms: params.phaseDurations[phase],
+                usage: usageTotals,
+                cost: costTelemetry.costUsd !== undefined
+                    ? {
+                        usd: costTelemetry.costUsd,
+                        source: costTelemetry.source,
+                        pricing_source: params.pricingSource,
+                    }
+                    : undefined,
+                missing_usage_reason: usageTotals === undefined
+                    ? "usage_missing"
+                    : undefined,
+                missing_cost_reason: costTelemetry.costUsd === undefined
+                    ? costTelemetry.reasonCode ?? "cost_missing"
+                    : undefined,
+            };
+        }
+        return {
+            run_id: params.runId,
+            phase,
+            provider: providerInfo.provider,
+            model: providerInfo.model,
+            duration_ms: params.phaseDurations[phase],
+            missing_usage_reason: "provider_usage_not_exposed",
+            missing_cost_reason: "usage_missing",
+        };
+    });
+};
+class StubProvider {
+    constructor() {
+        this.name = "stub";
+    }
+    async generate(request) {
+        const last = request.messages[request.messages.length - 1];
+        const promptText = request.messages.map((message) => message.content ?? "").join("\n");
+        const lowerPrompt = promptText.toLowerCase();
+        const isArchitectPrompt = /ROLE:\s*Technical Architect/i.test(promptText);
+        const isArchitectReviewPrompt = isArchitectPrompt
+            && (/TASK:\s*Review the builder output/i.test(promptText)
+                || (/OUTPUT FORMAT \(PLAIN TEXT\):/i.test(promptText) && /STATUS:\s*PASS\|RETRY/i.test(promptText)));
+        if (isArchitectReviewPrompt) {
+            return {
+                message: {
+                    role: "assistant",
+                    content: [
+                        "STATUS: PASS",
+                        "REASONS:",
+                        "- Request intent and plan targets are covered.",
+                        "FEEDBACK:",
+                    ].join("\n"),
+                },
+            };
+        }
+        const isArchitectPlanPrompt = isArchitectPrompt
+            && (/TASK:\s*Produce an implementation plan/i.test(promptText)
+                || /PREFERRED OUTPUT SHAPE \(PLAIN TEXT\)/i.test(promptText));
+        if (isArchitectPlanPrompt) {
+            return {
+                message: {
+                    role: "assistant",
+                    content: [
+                        "WHAT IS REQUIRED:",
+                        "- Apply the requested behavior update for the current task.",
+                        "CURRENT CONTEXT:",
+                        "- Existing implementation lives in src/index.ts.",
+                        "FOLDER STRUCTURE:",
+                        "- src/index.ts",
+                        "FILES TO TOUCH:",
+                        "- src/index.ts",
+                        "IMPLEMENTATION PLAN:",
+                        "- Update src/index.ts to implement the requested behavior change.",
+                        "RISK: low scoped single-file update.",
+                        "VERIFY:",
+                        "- echo ok",
+                    ].join("\n"),
+                },
+            };
+        }
+        if (lowerPrompt.includes("\"patches\"") || lowerPrompt.includes("search_replace")) {
+            return {
+                message: {
+                    role: "assistant",
+                    content: JSON.stringify({
+                        patches: [
+                            {
+                                action: "replace",
+                                file: "src/index.ts",
+                                search_block: "const value = 1;",
+                                replace_block: "const value = 2;",
+                            },
+                        ],
+                    }),
+                },
+            };
+        }
+        if (lowerPrompt.includes("\"files\"") || lowerPrompt.includes("file_writes")) {
+            return {
+                message: {
+                    role: "assistant",
+                    content: JSON.stringify({
+                        files: [{ path: "src/index.ts", content: "const value = 2;\n" }],
+                        delete: [],
+                    }),
+                },
+            };
+        }
+        if (request.responseFormat?.type === "json" || request.responseFormat?.type === "gbnf") {
+            if (promptText.includes("\"files\"")) {
+                return {
+                    message: {
+                        role: "assistant",
+                        content: JSON.stringify({
+                            files: [{ path: "src/index.ts", content: "const value = 2;\n" }],
+                            delete: [],
+                        }),
+                    },
+                };
+            }
+            if (promptText.includes("\"patches\"")) {
+                return {
+                    message: {
+                        role: "assistant",
+                        content: JSON.stringify({
+                            patches: [
+                                {
+                                    action: "replace",
+                                    file: "src/index.ts",
+                                    search_block: "const value = 1;",
+                                    replace_block: "const value = 2;",
+                                },
+                            ],
+                        }),
+                    },
+                };
+            }
+            return {
+                message: {
+                    role: "assistant",
+                    content: JSON.stringify({
+                        steps: ["1. Apply change"],
+                        target_files: ["src/index.ts"],
+                        risk_assessment: "low",
+                        verification: ["Run unit tests: pnpm test --filter codali"],
+                    }),
+                },
+            };
+        }
+        return { message: { role: "assistant", content: `stub:${last?.content ?? ""}` } };
+    }
+}
+const registerBuiltins = () => {
+    try {
+        registerProvider("openai-compatible", (config) => new OpenAiCompatibleProvider(config));
+    }
+    catch {
+        // ignore duplicate registrations
+    }
+    try {
+        registerProvider("ollama-remote", (config) => new OllamaRemoteProvider(config));
+    }
+    catch {
+        // ignore duplicate registrations
+    }
+    try {
+        registerProvider("codex-cli", (config) => new CodexCliProvider(config));
+    }
+    catch {
+        // ignore duplicate registrations
+    }
+    try {
+        registerProvider("stub", () => new StubProvider());
+    }
+    catch {
+        // ignore duplicate registrations
+    }
+};
+export class RunCommand {
+    static async run(argv) {
+        registerBuiltins();
+        const parsed = parseArgs(argv);
+        const resolvedWorkspaceRoot = resolveWorkspaceRoot(process.cwd(), parsed.workspaceRoot);
+        const agentRef = parsed.agent ?? parsed.agentId ?? parsed.agentSlug;
+        const resolvedAgent = agentRef
+            ? await resolveAgentConfig(agentRef, {
+                provider: parsed.provider,
+                model: parsed.model,
+                baseUrl: parsed.baseUrl,
+                apiKey: parsed.apiKey,
+            })
+            : undefined;
+        const provider = parsed.provider ?? resolvedAgent?.provider;
+        const model = parsed.model ?? resolvedAgent?.model;
+        const apiKey = parsed.apiKey ?? resolvedAgent?.apiKey;
+        const baseUrl = parsed.baseUrl ?? resolvedAgent?.baseUrl;
+        const agentId = resolvedAgent?.agent.id ?? parsed.agentId;
+        const agentSlug = resolvedAgent?.agent.slug ?? parsed.agentSlug;
+        const cliConfig = {};
+        if (parsed.workspaceRoot)
+            cliConfig.workspaceRoot = parsed.workspaceRoot;
+        if (parsed.project)
+            cliConfig.project = parsed.project;
+        if (parsed.command)
+            cliConfig.command = parsed.command;
+        if (parsed.commandRunId)
+            cliConfig.commandRunId = parsed.commandRunId;
+        if (parsed.jobId)
+            cliConfig.jobId = parsed.jobId;
+        if (parsed.runId)
+            cliConfig.runId = parsed.runId;
+        if (parsed.taskId)
+            cliConfig.taskId = parsed.taskId;
+        if (parsed.taskKey)
+            cliConfig.taskKey = parsed.taskKey;
+        if (agentId)
+            cliConfig.agentId = agentId;
+        if (agentSlug)
+            cliConfig.agentSlug = agentSlug;
+        if (parsed.smart !== undefined)
+            cliConfig.smart = parsed.smart;
+        if (parsed.deepInvestigationEnabled !== undefined) {
+            cliConfig.deepInvestigation = { enabled: parsed.deepInvestigationEnabled };
+        }
+        if (parsed.planHint)
+            cliConfig.planHint = parsed.planHint;
+        if (provider)
+            cliConfig.provider = provider;
+        if (model)
+            cliConfig.model = model;
+        if (apiKey)
+            cliConfig.apiKey = apiKey;
+        if (baseUrl)
+            cliConfig.baseUrl = baseUrl;
+        if (parsed.workflowProfile) {
+            cliConfig.workflow = { profile: parsed.workflowProfile };
+        }
+        const docdexOverrides = {};
+        if (parsed.docdexBaseUrl)
+            docdexOverrides.baseUrl = parsed.docdexBaseUrl;
+        if (parsed.docdexRepoId)
+            docdexOverrides.repoId = parsed.docdexRepoId;
+        if (parsed.docdexRepoRoot)
+            docdexOverrides.repoRoot = parsed.docdexRepoRoot;
+        if (Object.keys(docdexOverrides).length) {
+            cliConfig.docdex = docdexOverrides;
+        }
+        const contextOverrides = {};
+        if (parsed.contextMode)
+            contextOverrides.mode = parsed.contextMode;
+        if (parsed.contextMaxFiles !== undefined)
+            contextOverrides.maxFiles = parsed.contextMaxFiles;
+        if (parsed.contextMaxTotalBytes !== undefined)
+            contextOverrides.maxTotalBytes = parsed.contextMaxTotalBytes;
+        if (parsed.contextTokenBudget !== undefined)
+            contextOverrides.tokenBudget = parsed.contextTokenBudget;
+        if (parsed.contextFocusMaxBytes !== undefined)
+            contextOverrides.focusMaxFileBytes = parsed.contextFocusMaxBytes;
+        if (parsed.contextPeripheryMaxBytes !== undefined)
+            contextOverrides.peripheryMaxBytes = parsed.contextPeripheryMaxBytes;
+        if (parsed.contextIncludeRepoMap !== undefined)
+            contextOverrides.includeRepoMap = parsed.contextIncludeRepoMap;
+        if (parsed.contextIncludeImpact !== undefined)
+            contextOverrides.includeImpact = parsed.contextIncludeImpact;
+        if (parsed.contextIncludeSnippets !== undefined)
+            contextOverrides.includeSnippets = parsed.contextIncludeSnippets;
+        if (parsed.contextReadStrategy)
+            contextOverrides.readStrategy = parsed.contextReadStrategy;
+        if (parsed.contextMaxRefreshes !== undefined)
+            contextOverrides.maxContextRefreshes = parsed.contextMaxRefreshes;
+        if (parsed.contextSkeletonize !== undefined)
+            contextOverrides.skeletonizeLargeFiles = parsed.contextSkeletonize;
+        if (parsed.contextRedactSecrets !== undefined)
+            contextOverrides.redactSecrets = parsed.contextRedactSecrets;
+        if (parsed.contextIgnoreFilesFrom)
+            contextOverrides.ignoreFilesFrom = parsed.contextIgnoreFilesFrom;
+        if (Object.keys(contextOverrides).length) {
+            cliConfig.context = contextOverrides;
+        }
+        const securityOverrides = {};
+        if (parsed.securityRedactPatterns)
+            securityOverrides.redactPatterns = parsed.securityRedactPatterns;
+        if (Object.keys(securityOverrides).length) {
+            cliConfig.security = securityOverrides;
+        }
+        const builderOverrides = {};
+        if (parsed.builderMode)
+            builderOverrides.mode = parsed.builderMode;
+        if (parsed.builderPatchFormat)
+            builderOverrides.patchFormat = parsed.builderPatchFormat;
+        if (Object.keys(builderOverrides).length) {
+            cliConfig.builder = builderOverrides;
+        }
+        const interpreterOverrides = {};
+        if (parsed.interpreterProvider)
+            interpreterOverrides.provider = parsed.interpreterProvider;
+        if (parsed.interpreterModel)
+            interpreterOverrides.model = parsed.interpreterModel;
+        if (parsed.interpreterFormat)
+            interpreterOverrides.format = parsed.interpreterFormat;
+        if (parsed.interpreterGrammar)
+            interpreterOverrides.grammar = parsed.interpreterGrammar;
+        if (parsed.interpreterMaxRetries !== undefined) {
+            interpreterOverrides.maxRetries = parsed.interpreterMaxRetries;
+        }
+        if (parsed.interpreterTimeoutMs !== undefined) {
+            interpreterOverrides.timeoutMs = parsed.interpreterTimeoutMs;
+        }
+        if (Object.keys(interpreterOverrides).length) {
+            cliConfig.interpreter = interpreterOverrides;
+        }
+        const streamingOverrides = {};
+        if (parsed.streamingFlushMs !== undefined)
+            streamingOverrides.flushEveryMs = parsed.streamingFlushMs;
+        if (Object.keys(streamingOverrides).length) {
+            cliConfig.streaming = streamingOverrides;
+        }
+        const costOverrides = {};
+        if (parsed.costMaxPerRun !== undefined)
+            costOverrides.maxCostPerRun = parsed.costMaxPerRun;
+        if (parsed.costCharPerToken !== undefined)
+            costOverrides.charPerToken = parsed.costCharPerToken;
+        if (parsed.costPricingOverrides) {
+            try {
+                costOverrides.pricingOverrides = JSON.parse(parsed.costPricingOverrides);
+            }
+            catch {
+                // ignore malformed pricing overrides
+            }
+        }
+        if (Object.keys(costOverrides).length) {
+            cliConfig.cost = costOverrides;
+        }
+        const routingOverrides = {};
+        const setRoutingOverride = (phase, key, value) => {
+            if (!value)
+                return;
+            routingOverrides[phase] = {
+                ...(routingOverrides[phase] ?? {}),
+                [key]: value,
+            };
+        };
+        setRoutingOverride("librarian", "agent", parsed.agentLibrarian);
+        setRoutingOverride("architect", "agent", parsed.agentArchitect);
+        setRoutingOverride("builder", "agent", parsed.agentBuilder);
+        setRoutingOverride("critic", "agent", parsed.agentCritic);
+        setRoutingOverride("interpreter", "agent", parsed.agentInterpreter);
+        if (Object.keys(routingOverrides).length) {
+            cliConfig.routing = routingOverrides;
+        }
+        const config = await loadConfig({
+            cli: cliConfig,
+            configPath: parsed.configPath,
+            cwd: resolvedWorkspaceRoot,
+        });
+        if (config.deepInvestigation?.enabled && !config.smart) {
+            throw new Error("Deep investigation requires --smart. Enable smart mode or disable deep investigation.");
+        }
+        if (!config.smart && resolvedAgent?.agent) {
+            const { contextWindow, maxOutputTokens, supportsTools } = resolvedAgent.agent;
+            if (contextWindow && model) {
+                config.localContext.modelTokenLimits = {
+                    ...config.localContext.modelTokenLimits,
+                    [model]: contextWindow,
+                };
+            }
+            if (maxOutputTokens && config.limits.maxTokens === undefined) {
+                config.limits.maxTokens = maxOutputTokens;
+            }
+            if (supportsTools === false && config.builder.mode === "tool_calls") {
+                config.builder.mode = "patch_json";
+            }
+        }
+        const taskInput = await resolveTaskInput(parsed);
+        if (!taskInput.trim()) {
+            throw new Error("Task input is empty; provide --task <file>, inline text, or pass text via stdin.");
+        }
+        const workflowProfile = config.resolvedWorkflowProfile;
+        const writesAllowed = workflowProfile?.allowWrites !== false;
+        const workflowTaskInput = buildWorkflowTaskInput(taskInput, workflowProfile);
+        const runId = config.runId ?? randomUUID();
+        const runContext = new RunContext(runId, config.workspaceRoot, {
+            request: workflowTaskInput,
+            command: config.command,
+            workspaceRoot: config.workspaceRoot,
+            smart: config.smart,
+            provider: config.provider,
+            model: config.model,
+            builderMode: config.builder.mode,
+            maxRetries: config.limits.maxRetries,
+            maxContextRefreshes: config.context.maxContextRefreshes,
+            maxSteps: config.limits.maxSteps,
+            maxToolCalls: config.limits.maxToolCalls,
+            maxTokens: config.limits.maxTokens,
+            timeoutMs: config.limits.timeoutMs,
+        });
+        const storageRoot = getGlobalWorkspaceDir(config.workspaceRoot);
+        const lock = new WorkspaceLock(storageRoot, runId);
+        await lock.acquire();
+        const logger = new RunLogger(storageRoot, config.logging.directory, runId);
+        const outputLogPath = path.join(path.dirname(logger.logPath), `${runId}.output.log`);
+        await mkdir(path.dirname(outputLogPath), { recursive: true });
+        const outputStream = createWriteStream(outputLogPath, { flags: "a" });
+        const unregisterSignals = lock.registerSignalHandlers({
+            onSignal: async (signal) => {
+                try {
+                    await logger.log("run_cancelled", {
+                        runId,
+                        signal,
+                        command: config.command,
+                        commandRunId: config.commandRunId,
+                        jobId: config.jobId,
+                        project: config.project,
+                        taskId: config.taskId,
+                        taskKey: config.taskKey,
+                    });
+                }
+                catch {
+                    // ignore logging failures during shutdown
+                }
+            },
+        });
+        await logger.log("run_start", {
+            runId,
+            fingerprint: runContext.fingerprint ?? null,
+            command: config.command,
+            commandRunId: config.commandRunId,
+            jobId: config.jobId,
+            project: config.project,
+            taskId: config.taskId,
+            taskKey: config.taskKey,
+            agentId: config.agentId,
+            agentSlug: config.agentSlug,
+            provider: config.provider,
+            model: config.model,
+            workflow: workflowProfile
+                ? {
+                    name: workflowProfile.name,
+                    source: workflowProfile.source,
+                    command: workflowProfile.command,
+                    outputContract: workflowProfile.outputContract,
+                    verificationPolicy: workflowProfile.verificationPolicy,
+                    verificationMinimumChecks: workflowProfile.verificationMinimumChecks,
+                    verificationEnforceHighConfidence: workflowProfile.verificationEnforceHighConfidence,
+                    allowWrites: workflowProfile.allowWrites,
+                }
+                : null,
+            policy: {
+                allowShell: config.tools.allowShell ?? false,
+                allowDestructiveOperations: config.tools.allowDestructiveOperations ?? false,
+                allowWrites: writesAllowed,
+            },
+        });
+        let finalMessageContent = "";
+        let usage;
+        let toolCallsExecuted = 0;
+        let pricingSpec;
+        let pricingSource;
+        let estimatedCost;
+        let estimatedTokens;
+        let estimatedChars;
+        let estimatedFocus = 0;
+        let estimatedPeriphery = 0;
+        let smartRuntimeSummary;
+        let summaryDisposition = "pass";
+        let summaryFailureClass;
+        let summaryReasonCodes = [];
+        let summaryFailureStage;
+        let summaryRetryable;
+        let summaryVerification;
+        const phaseProviders = {};
+        let summaryEmitted = false;
+        const emitRunSummary = async () => {
+            const reader = new RunLogReader(config.workspaceRoot, config.logging.directory);
+            const phaseArtifacts = await reader.getPhaseArtifacts(runId);
+            const phaseArtifactQuery = await reader.queryEvents({
+                filters: { run_id: runId, event_type: "phase_artifact" },
+                limit: 2000,
+                sort: "asc",
+            });
+            const phaseArtifactEvents = phaseArtifactQuery.events
+                .map((event) => {
+                const data = event.data;
+                return {
+                    phase: typeof data.phase === "string" ? data.phase : undefined,
+                    kind: typeof data.kind === "string" ? data.kind : undefined,
+                    path: typeof data.path === "string" ? data.path : undefined,
+                };
+            });
+            const requiredArtifacts = config.smart
+                ? [
+                    "retrieve:summary",
+                    "retrieve:retrieval_report",
+                    "plan:summary",
+                    "act:summary",
+                    "verify:plan",
+                    "verify:verification_report",
+                ]
+                : [];
+            const { references: artifactReferences, missing } = buildArtifactReferences(phaseArtifactEvents, requiredArtifacts);
+            const phaseDurations = collectPhaseDurations(phaseArtifacts);
+            const phaseTelemetry = buildPhaseTelemetry({
+                runId,
+                phaseProviders,
+                phaseDurations,
+                usage,
+                pricingSpec,
+                pricingSource,
+            });
+            for (const telemetry of phaseTelemetry) {
+                await logger.logPhaseTelemetry(telemetry);
+            }
+            const actualCost = estimateCostFromUsage(usage, pricingSpec);
+            const finalReasonCodes = uniqueStrings(summaryReasonCodes);
+            const finalFailureClass = summaryDisposition === "pass"
+                ? undefined
+                : summaryFailureClass
+                    ?? inferFailureClass(summaryFailureStage, finalReasonCodes);
+            const verificationSummary = summaryVerification
+                ? {
+                    outcome: summaryVerification.outcome,
+                    reasonCodes: summaryVerification.reason_codes,
+                    policy: summaryVerification.policy,
+                    totals: summaryVerification.totals,
+                }
+                : smartRuntimeSummary?.verification
+                    ?? null;
+            await logger.logRunSummary({
+                run_id: runId,
+                runId,
+                fingerprint: runContext.fingerprint ?? null,
+                toolCallsExecuted,
+                touchedFiles: runContext.getTouchedFiles(),
+                durationMs: Date.now() - runContext.startedAt,
+                usage,
+                costEstimate: {
+                    charCount: estimatedChars,
+                    estimatedTokens,
+                    estimatedCost,
+                    pricingSource,
+                },
+                actualCost,
+                budget: {
+                    maxSteps: config.limits.maxSteps,
+                    maxToolCalls: config.limits.maxToolCalls,
+                    maxTokens: config.limits.maxTokens ?? null,
+                    timeoutMs: config.limits.timeoutMs ?? null,
+                    consumedDurationMs: Date.now() - runContext.startedAt,
+                    consumedToolCalls: toolCallsExecuted,
+                },
+                quality_dimensions: buildQualityDimensions(artifactReferences, summaryDisposition),
+                final_disposition: {
+                    status: summaryDisposition,
+                    failure_class: finalFailureClass,
+                    reason_codes: finalReasonCodes,
+                    stage: summaryFailureStage,
+                    retryable: summaryRetryable ?? null,
+                },
+                artifact_references: artifactReferences,
+                phase_telemetry: phaseTelemetry,
+                missing_artifacts: missing,
+                smartRuntime: smartRuntimeSummary ?? null,
+                verification: verificationSummary,
+                workflow: workflowProfile
+                    ? {
+                        name: workflowProfile.name,
+                        source: workflowProfile.source,
+                        command: workflowProfile.command,
+                        outputContract: workflowProfile.outputContract,
+                        verificationPolicy: workflowProfile.verificationPolicy,
+                        verificationMinimumChecks: workflowProfile.verificationMinimumChecks,
+                        verificationEnforceHighConfidence: workflowProfile.verificationEnforceHighConfidence,
+                        allowWrites: workflowProfile.allowWrites,
+                    }
+                    : null,
+                policy: {
+                    allowShell: config.tools.allowShell ?? false,
+                    allowDestructiveOperations: config.tools.allowDestructiveOperations ?? false,
+                    allowWrites: writesAllowed,
+                },
+                command: config.command,
+                commandRunId: config.commandRunId,
+                jobId: config.jobId,
+                project: config.project,
+                taskId: config.taskId,
+                task_id: config.taskId,
+                taskKey: config.taskKey,
+                agentId: config.agentId,
+                agentSlug: config.agentSlug,
+                smart: config.smart ?? false,
+            });
+        };
+        try {
+            const registry = new ToolRegistry();
+            const registerIfEnabled = (tool) => {
+                if (!writesAllowed && tool.name === "write_file") {
+                    return;
+                }
+                if (isToolEnabled(tool.name, config.tools)) {
+                    registry.register(tool);
+                }
+            };
+            for (const tool of createFileTools())
+                registerIfEnabled(tool);
+            registerIfEnabled(createDiffTool());
+            registerIfEnabled(createSearchTool());
+            registerIfEnabled(createShellTool());
+            const docdexClient = new DocdexClient({
+                baseUrl: config.docdex.baseUrl,
+                repoId: config.docdex.repoId,
+                repoRoot: config.docdex.repoRoot ?? config.workspaceRoot,
+                dagSessionId: runId,
+            });
+            for (const tool of createDocdexTools(docdexClient))
+                registerIfEnabled(tool);
+            const toolContext = {
+                workspaceRoot: config.workspaceRoot,
+                recordTouchedFile: (filePath) => runContext.recordTouchedFile(filePath),
+                allowOutsideWorkspace: config.tools.allowOutsideWorkspace,
+                allowShell: config.tools.allowShell,
+                allowDestructiveOperations: config.tools.allowDestructiveOperations,
+                shellAllowlist: config.tools.shellAllowlist,
+            };
+            const streamState = createStreamState(config.streaming.flushEveryMs, outputStream);
+            if (config.smart) {
+                const hasRoutingAgent = Object.values(config.routing ?? {}).some((phase) => Boolean(phase?.agent));
+                const hasExplicitProvider = Boolean(parsed.provider || parsed.model || parsed.baseUrl || parsed.apiKey);
+                const shouldForceAgentDefaults = !agentRef && !hasRoutingAgent && !hasExplicitProvider;
+                const shouldSelectAgents = config.provider !== "stub";
+                const emptySelection = (phase) => ({
+                    phase,
+                    capabilities: [],
+                    source: "none",
+                });
+                const phaseOverrides = {
+                    librarian: config.routing?.librarian?.agent,
+                    architect: config.routing?.architect?.agent,
+                    builder: config.routing?.builder?.agent,
+                    critic: config.routing?.critic?.agent,
+                    interpreter: config.routing?.interpreter?.agent,
+                };
+                const phaseExclusions = {};
+                let phaseSelections = shouldSelectAgents
+                    ? await selectPhaseAgents({
+                        overrides: phaseOverrides,
+                        builderMode: config.builder.mode,
+                        fallbackAgent: resolvedAgent,
+                        allowCloudModels: config.security.allowCloudModels,
+                        excludeAgentIds: phaseExclusions,
+                    })
+                    : {
+                        librarian: emptySelection("librarian"),
+                        architect: emptySelection("architect"),
+                        builder: emptySelection("builder"),
+                        critic: emptySelection("critic"),
+                        interpreter: emptySelection("interpreter"),
+                    };
+                if (shouldSelectAgents) {
+                    const unresolvedPhases = Object.values(phaseSelections)
+                        .filter((selection) => !selection.resolved)
+                        .map((selection) => selection.phase);
+                    if (unresolvedPhases.length > 0) {
+                        throw new Error(`No eligible mcoda agents found for phase(s): ${unresolvedPhases.join(", ")}. ` +
+                            "Add/configure agents and verify with `mcoda agent list --json`.");
+                    }
+                }
+                const fallbackResolved = phaseSelections.builder.resolved ??
+                    phaseSelections.architect.resolved ??
+                    phaseSelections.critic.resolved ??
+                    phaseSelections.librarian.resolved ??
+                    phaseSelections.interpreter.resolved ??
+                    resolvedAgent;
+                if (shouldForceAgentDefaults) {
+                    if (!fallbackResolved) {
+                        throw new Error("No eligible agents found in the mcoda agent registry. Run `mcoda agent list` or supply --agent/--provider/--model.");
+                    }
+                    config.provider = fallbackResolved.provider;
+                    config.model = fallbackResolved.model;
+                    config.apiKey = fallbackResolved.apiKey;
+                    config.baseUrl = fallbackResolved.baseUrl;
+                }
+                else if (!config.provider || !config.model) {
+                    if (fallbackResolved) {
+                        config.provider = config.provider || fallbackResolved.provider;
+                        config.model = config.model || fallbackResolved.model;
+                        config.apiKey = config.apiKey ?? fallbackResolved.apiKey;
+                        config.baseUrl = config.baseUrl ?? fallbackResolved.baseUrl;
+                    }
+                }
+                if (!config.provider || !config.model) {
+                    throw new Error("Missing provider/model after agent resolution. Provide --agent or configure routing defaults.");
+                }
+                const defaults = {
+                    provider: config.provider,
+                    config: {
+                        model: config.model,
+                        apiKey: config.apiKey,
+                        baseUrl: config.baseUrl,
+                        timeoutMs: config.limits.timeoutMs,
+                    },
+                };
+                const selectedPhaseModels = new Set(Object.values(phaseSelections)
+                    .map((selection) => selection.resolved?.model)
+                    .filter((value) => Boolean(value)));
+                if (shouldSelectAgents &&
+                    config.localContext.summarize.model &&
+                    !selectedPhaseModels.has(config.localContext.summarize.model)) {
+                    throw new Error(`CODALI_LOCAL_CONTEXT_SUMMARIZE_MODEL (${config.localContext.summarize.model}) ` +
+                        "must match a model from selected mcoda agents.");
+                }
+                for (const selection of Object.values(phaseSelections)) {
+                    if (!selection.resolved)
+                        continue;
+                    const contextWindow = selection.resolved.agent.contextWindow;
+                    if (contextWindow) {
+                        config.localContext.modelTokenLimits = {
+                            ...config.localContext.modelTokenLimits,
+                            [selection.resolved.model]: contextWindow,
+                        };
+                    }
+                }
+                const builderSelection = phaseSelections.builder;
+                if (builderSelection.resolved?.agent.maxOutputTokens && config.limits.maxTokens === undefined) {
+                    config.limits.maxTokens = builderSelection.resolved.agent.maxOutputTokens;
+                }
+                if (builderSelection.resolved?.agent.supportsTools === false &&
+                    config.builder.mode === "tool_calls") {
+                    config.builder.mode = "patch_json";
+                }
+                for (const selection of Object.values(phaseSelections)) {
+                    if (!selection.resolved)
+                        continue;
+                    await logger.log("phase_agent_selected", {
+                        phase: selection.phase,
+                        agentId: selection.resolved.agent.id,
+                        agentSlug: selection.resolved.agent.slug,
+                        provider: selection.resolved.provider,
+                        model: selection.resolved.model,
+                        source: selection.source,
+                        score: selection.score,
+                        reason: selection.reason,
+                    });
+                }
+                const buildDefaultsForPhase = (phase) => {
+                    const selected = phaseSelections[phase].resolved;
+                    return selected
+                        ? {
+                            provider: selected.provider,
+                            config: {
+                                model: selected.model,
+                                apiKey: selected.apiKey,
+                                baseUrl: selected.baseUrl,
+                                timeoutMs: config.limits.timeoutMs,
+                            },
+                        }
+                        : defaults;
+                };
+                const librarianDefaults = buildDefaultsForPhase("librarian");
+                const architectDefaults = buildDefaultsForPhase("architect");
+                const builderDefaults = buildDefaultsForPhase("builder");
+                const criticDefaults = buildDefaultsForPhase("critic");
+                const interpreterDefaults = buildDefaultsForPhase("interpreter");
+                const librarianRoute = buildRoutedProvider("librarian", librarianDefaults, config.routing, Boolean(phaseSelections.librarian.resolved));
+                const architectRoute = buildRoutedProvider("architect", architectDefaults, config.routing, Boolean(phaseSelections.architect.resolved));
+                const builderRoute = buildRoutedProvider("builder", builderDefaults, config.routing, Boolean(phaseSelections.builder.resolved));
+                const criticRoute = buildRoutedProvider("critic", criticDefaults, config.routing, Boolean(phaseSelections.critic.resolved));
+                const interpreterPhaseRoute = buildRoutedProvider("interpreter", interpreterDefaults, config.routing, Boolean(phaseSelections.interpreter.resolved));
+                const phaseRoutes = {
+                    librarian: librarianRoute,
+                    architect: architectRoute,
+                    builder: builderRoute,
+                    critic: criticRoute,
+                    interpreter: interpreterPhaseRoute,
+                };
+                phaseProviders.retrieve = {
+                    provider: librarianRoute.provider,
+                    model: librarianRoute.config.model,
+                };
+                phaseProviders.plan = {
+                    provider: architectRoute.provider,
+                    model: architectRoute.config.model,
+                };
+                phaseProviders.act = {
+                    provider: builderRoute.provider,
+                    model: builderRoute.config.model,
+                };
+                phaseProviders.verify = {
+                    provider: criticRoute.provider,
+                    model: criticRoute.config.model,
+                };
+                const librarianProvider = createProvider(librarianRoute.provider, librarianRoute.config);
+                const architectProvider = createProvider(architectRoute.provider, architectRoute.config);
+                const builderProvider = createProvider(builderRoute.provider, builderRoute.config);
+                const profileAgentId = config.agentId ??
+                    config.agentSlug ??
+                    phaseSelections.architect.resolved?.agent.id ??
+                    phaseSelections.critic.resolved?.agent.id ??
+                    phaseSelections.librarian.resolved?.agent.id ??
+                    phaseSelections.builder.resolved?.agent.id ??
+                    phaseSelections.interpreter.resolved?.agent.id ??
+                    "codali";
+                const store = new ContextStore({
+                    workspaceRoot: storageRoot,
+                    storageDir: config.localContext.storageDir,
+                });
+                const redactor = config.context.redactSecrets
+                    ? new ContextRedactor({
+                        workspaceRoot: config.workspaceRoot,
+                        ignoreFilesFrom: config.context.ignoreFilesFrom,
+                        redactPatterns: config.security.redactPatterns,
+                    })
+                    : undefined;
+                if (redactor) {
+                    await redactor.loadIgnoreMatchers();
+                }
+                let summarizer;
+                if (config.localContext.enabled && config.localContext.summarize.enabled) {
+                    const providerKey = config.localContext.summarize.provider;
+                    let summarizerProviderName = providerKey;
+                    let summarizerConfig = { ...defaults.config };
+                    let summarizerTemperature;
+                    if (isPhaseProvider(providerKey)) {
+                        const route = phaseRoutes[providerKey];
+                        summarizerProviderName = route.provider;
+                        summarizerConfig = { ...route.config };
+                        summarizerTemperature = route.temperature;
+                    }
+                    if (config.localContext.summarize.model) {
+                        summarizerConfig = {
+                            ...summarizerConfig,
+                            model: config.localContext.summarize.model,
+                        };
+                    }
+                    const summarizerProvider = createProvider(summarizerProviderName, summarizerConfig);
+                    summarizer = new ContextSummarizer(summarizerProvider, {
+                        maxTokens: config.localContext.summarize.targetTokens,
+                        temperature: summarizerTemperature,
+                        logger,
+                    });
+                }
+                const contextManager = new ContextManager({
+                    config: config.localContext,
+                    store,
+                    redactor,
+                    summarizer,
+                    logger,
+                    charPerToken: config.cost.charPerToken,
+                });
+                const laneScope = {
+                    jobId: config.jobId ?? config.commandRunId,
+                    runId,
+                    taskId: config.taskId,
+                    taskKey: config.taskKey,
+                };
+                const deepMode = Boolean(config.deepInvestigation?.enabled);
+                const contextAssembler = new ContextAssembler(docdexClient, {
+                    workspaceRoot: config.workspaceRoot,
+                    queryProvider: librarianProvider,
+                    queryTemperature: librarianRoute?.temperature,
+                    agentId: profileAgentId,
+                    maxFiles: config.context.maxFiles,
+                    maxTotalBytes: config.context.maxTotalBytes,
+                    tokenBudget: config.context.tokenBudget,
+                    includeRepoMap: config.context.includeRepoMap,
+                    includeImpact: config.context.includeImpact,
+                    includeSnippets: config.context.includeSnippets,
+                    readStrategy: config.context.readStrategy,
+                    focusMaxFileBytes: config.context.focusMaxFileBytes,
+                    peripheryMaxBytes: config.context.peripheryMaxBytes,
+                    skeletonizeLargeFiles: config.context.skeletonizeLargeFiles,
+                    serializationMode: config.context.mode,
+                    redactSecrets: config.context.redactSecrets,
+                    redactPatterns: config.security.redactPatterns,
+                    ignoreFilesFrom: config.context.ignoreFilesFrom,
+                    preferredFiles: config.context.preferredFiles,
+                    recentFiles: config.context.recentFiles,
+                    readOnlyPaths: config.security.readOnlyPaths,
+                    allowDocEdits: config.security.allowDocEdits,
+                    deepMode,
+                    contextManager,
+                    laneScope,
+                    onEvent: streamState.onEvent,
+                    logger,
+                });
+                const deepScanPreset = Boolean(config.deepInvestigation?.enabled && config.deepInvestigation?.deepScanPreset);
+                if (deepScanPreset) {
+                    contextAssembler.applyDeepScanPreset();
+                }
+                const preflightContext = await contextAssembler.assemble(workflowTaskInput);
+                const pricingResolution = resolvePricing(config.cost.pricingOverrides, builderRoute.provider, builderRoute.config.model);
+                pricingSpec = pricingResolution.pricing;
+                pricingSource = pricingResolution.source;
+                const summary = summarizeContext(preflightContext, workflowTaskInput);
+                estimatedFocus = summary.focusCount;
+                estimatedPeriphery = summary.peripheryCount;
+                const estimate = estimateCostFromChars(summary.charCount, config.cost.charPerToken, pricingSpec, pricingSource);
+                estimatedCost = estimate.estimatedCost;
+                estimatedTokens = estimate.estimatedTotalTokens;
+                estimatedChars = estimate.charCount;
+                await logger.log("cost_estimate", {
+                    provider: builderRoute.provider,
+                    model: builderRoute.config.model,
+                    focusCount: estimatedFocus,
+                    peripheryCount: estimatedPeriphery,
+                    charCount: estimatedChars,
+                    estimatedTokens,
+                    estimatedCost,
+                    pricingSource,
+                });
+                process.stderr.write(`[codali] Preflight: focus=${estimatedFocus} periphery=${estimatedPeriphery} ` +
+                    `chars=${estimatedChars} tokens~${estimatedTokens} est_cost=${formatCost(estimatedCost)}\n`);
+                if (estimatedCost !== undefined && estimatedCost > config.cost.maxCostPerRun) {
+                    const proceed = await confirmOverage(`Estimated cost ${formatCost(estimatedCost)} exceeds max ${formatCost(config.cost.maxCostPerRun)}. Continue? [y/N] `);
+                    if (!proceed) {
+                        throw new Error("Run cancelled due to cost limit");
+                    }
+                }
+                const architectPlanner = new ArchitectPlanner(architectProvider, {
+                    temperature: architectRoute.temperature,
+                    logger,
+                    model: architectRoute.config.model,
+                    // Architect is intentionally plain-text first; avoid hard response-format constraints.
+                    responseFormat: undefined,
+                    planHint: config.planHint,
+                    stream: config.streaming.enabled,
+                    onEvent: streamState.onEvent,
+                });
+                const builderResponseFormat = builderRoute.responseFormat ?? (config.builder.mode === "patch_json" ? { type: "json" } : undefined);
+                const patchValidator = createPatchValidator(config.workspaceRoot, config.tools.allowShell ?? false, config.tools.shellAllowlist ?? []);
+                const needsPatchApplier = config.builder.mode === "patch_json" || config.builder.mode === "freeform" || config.builder.mode === "tool_calls";
+                const patchApplier = needsPatchApplier
+                    ? new PatchApplier({
+                        workspaceRoot: config.workspaceRoot,
+                        validateFile: patchValidator,
+                        policy: {
+                            allowDestructiveOperations: config.tools.allowDestructiveOperations ?? false,
+                            allowWrites: writesAllowed,
+                        },
+                    })
+                    : undefined;
+                const wantsInterpreter = config.builder.mode === "freeform" || config.builder.fallbackToInterpreter === true;
+                const interpreterRoute = wantsInterpreter
+                    ? resolveInterpreterRoute(config, phaseRoutes)
+                    : undefined;
+                const interpreterProvider = interpreterRoute
+                    ? createProvider(interpreterRoute.provider, {
+                        ...interpreterRoute.config,
+                        timeoutMs: config.interpreter.timeoutMs ??
+                            interpreterRoute.config.timeoutMs ??
+                            config.limits.timeoutMs,
+                    })
+                    : undefined;
+                const interpreterResponseFormat = config.interpreter.format
+                    ? {
+                        type: config.interpreter.format,
+                        grammar: config.interpreter.grammar,
+                    }
+                    : { type: "json" };
+                const patchInterpreter = interpreterProvider && wantsInterpreter
+                    ? new PatchInterpreter({
+                        provider: interpreterProvider,
+                        patchFormat: config.builder.patchFormat,
+                        responseFormat: interpreterResponseFormat,
+                        maxRetries: config.interpreter.maxRetries,
+                        timeoutMs: config.interpreter.timeoutMs,
+                        logger,
+                        model: interpreterRoute?.config.model,
+                        temperature: interpreterRoute?.temperature,
+                    })
+                    : undefined;
+                const builderRunner = new BuilderRunner({
+                    provider: builderProvider,
+                    tools: registry,
+                    context: toolContext,
+                    maxSteps: config.limits.maxSteps,
+                    maxToolCalls: config.limits.maxToolCalls,
+                    maxTokens: config.limits.maxTokens,
+                    timeoutMs: config.limits.timeoutMs,
+                    temperature: builderRoute.temperature,
+                    responseFormat: builderResponseFormat,
+                    mode: config.builder.mode,
+                    patchFormat: config.builder.patchFormat,
+                    patchApplier,
+                    interpreter: patchInterpreter,
+                    fallbackToInterpreter: config.builder.fallbackToInterpreter ?? false,
+                    allowDestructiveOperations: config.tools.allowDestructiveOperations ?? false,
+                    stream: config.streaming.enabled,
+                    onEvent: streamState.onEvent,
+                    onToken: streamState.onToken,
+                    streamFlushMs: config.streaming.flushEveryMs,
+                    logger,
+                    model: builderRoute.config.model,
+                });
+                const validator = new ValidationRunner({
+                    allowShell: config.tools.allowShell ?? false,
+                    shellAllowlist: config.tools.shellAllowlist ?? [],
+                    workspaceRoot: config.workspaceRoot,
+                    docdexClient,
+                    defaultPolicyName: workflowProfile?.verificationPolicy,
+                    defaultMinimumChecks: workflowProfile?.verificationMinimumChecks,
+                    defaultEnforceHighConfidence: workflowProfile?.verificationEnforceHighConfidence,
+                });
+                const criticEvaluator = new CriticEvaluator(validator, {
+                    model: criticRoute.config.model,
+                    logger,
+                });
+                const memoryWriteback = new MemoryWriteback(docdexClient, {
+                    agentId: profileAgentId,
+                    workspaceRoot: config.workspaceRoot,
+                    learning: config.learning,
+                    logger,
+                });
+                const phaseFallbackCounts = {};
+                const maxPhaseFallbacks = 3;
+                const recoverPhaseProvider = async (input) => {
+                    if (!shouldSelectAgents)
+                        return { switched: false };
+                    const phase = input.phase;
+                    const currentSelection = phaseSelections[phase];
+                    const currentResolved = currentSelection.resolved;
+                    if (!currentResolved)
+                        return { switched: false };
+                    const currentAgentId = currentResolved.agent.id;
+                    if (!currentAgentId)
+                        return { switched: false };
+                    const fallbackCount = phaseFallbackCounts[phase] ?? 0;
+                    if (fallbackCount >= maxPhaseFallbacks) {
+                        await logger.log("phase_agent_fallback_skipped", {
+                            phase,
+                            reason: "fallback_limit_reached",
+                            limit: maxPhaseFallbacks,
+                            error: input.error.message,
+                        });
+                        return { switched: false };
+                    }
+                    const excluded = Array.from(new Set([...(phaseExclusions[phase] ?? []), currentAgentId]));
+                    phaseExclusions[phase] = excluded;
+                    let currentExcluded = excluded;
+                    const evaluatedAgentIds = new Set();
+                    let reselection;
+                    let nextSelection;
+                    let nextResolved = undefined;
+                    let selectedBuilderMode = config.builder.mode;
+                    while (true) {
+                        reselection = await selectPhaseAgents({
+                            overrides: phaseOverrides,
+                            builderMode: config.builder.mode,
+                            fallbackAgent: resolvedAgent,
+                            allowCloudModels: config.security.allowCloudModels,
+                            excludeAgentIds: {
+                                ...phaseExclusions,
+                                [phase]: currentExcluded,
+                            },
+                        });
+                        nextSelection = reselection[phase];
+                        nextResolved = nextSelection.resolved;
+                        if (!nextResolved || nextResolved.agent.id === currentAgentId) {
+                            await logger.log("phase_agent_fallback_skipped", {
+                                phase,
+                                reason: "no_alternate_agent",
+                                currentAgentId,
+                                excluded: currentExcluded,
+                                error: input.error.message,
+                            });
+                            return { switched: false };
+                        }
+                        const nextAgentId = nextResolved.agent.id;
+                        if (evaluatedAgentIds.has(nextAgentId)) {
+                            await logger.log("phase_agent_fallback_skipped", {
+                                phase,
+                                reason: "no_eligible_alternate_agent",
+                                currentAgentId,
+                                excluded: currentExcluded,
+                                error: input.error.message,
+                            });
+                            return { switched: false };
+                        }
+                        evaluatedAgentIds.add(nextAgentId);
+                        const suitability = assessPhaseFallbackSuitability(phase, config.builder.mode, {
+                            capabilities: nextSelection.capabilities,
+                            supportsTools: nextResolved.agent.supportsTools ?? false,
+                        });
+                        if (suitability.ok) {
+                            selectedBuilderMode = suitability.builderMode ?? config.builder.mode;
+                            break;
+                        }
+                        currentExcluded = Array.from(new Set([...currentExcluded, nextAgentId]));
+                        phaseExclusions[phase] = currentExcluded;
+                        await logger.log("phase_agent_fallback_rejected", {
+                            phase,
+                            reason: suitability.reason,
+                            agentId: nextAgentId,
+                            agentSlug: nextResolved.agent.slug,
+                            currentAgentId,
+                            excluded: currentExcluded,
+                            details: suitability.details ?? null,
+                            error: input.error.message,
+                        });
+                    }
+                    phaseExclusions[phase] = currentExcluded;
+                    if (!reselection || !nextSelection || !nextResolved) {
+                        await logger.log("phase_agent_fallback_skipped", {
+                            phase,
+                            reason: "reselection_failed",
+                            currentAgentId,
+                            excluded: currentExcluded,
+                            error: input.error.message,
+                        });
+                        return { switched: false };
+                    }
+                    phaseSelections = reselection;
+                    phaseFallbackCounts[phase] = fallbackCount + 1;
+                    const phaseDefaults = {
+                        provider: nextResolved.provider,
+                        config: {
+                            model: nextResolved.model,
+                            apiKey: nextResolved.apiKey,
+                            baseUrl: nextResolved.baseUrl,
+                            timeoutMs: config.limits.timeoutMs,
+                        },
+                    };
+                    const nextRoute = buildRoutedProvider(phase, phaseDefaults, config.routing, true);
+                    const mappedPhase = toSummaryPhase(phase);
+                    if (mappedPhase) {
+                        phaseProviders[mappedPhase] = {
+                            provider: nextRoute.provider,
+                            model: nextRoute.config.model,
+                        };
+                    }
+                    if (phase === "builder") {
+                        const priorBuilderMode = config.builder.mode;
+                        if (selectedBuilderMode !== priorBuilderMode) {
+                            config.builder.mode = selectedBuilderMode;
+                            await logger.log("phase_agent_fallback_mode_change", {
+                                phase,
+                                fromMode: priorBuilderMode,
+                                toMode: selectedBuilderMode,
+                                reason: "fallback_suitability",
+                            });
+                        }
+                        const nextProvider = createProvider(nextRoute.provider, nextRoute.config);
+                        const nextResponseFormat = nextRoute.responseFormat
+                            ?? (config.builder.mode === "patch_json" ? { type: "json" } : undefined);
+                        builderRunner.setProvider(nextProvider, {
+                            model: nextRoute.config.model,
+                            temperature: nextRoute.temperature,
+                            responseFormat: nextResponseFormat,
+                            mode: config.builder.mode,
+                        });
+                    }
+                    await logger.log("phase_agent_selected", {
+                        phase,
+                        agentId: nextResolved.agent.id,
+                        agentSlug: nextResolved.agent.slug,
+                        provider: nextResolved.provider,
+                        model: nextResolved.model,
+                        source: "fallback",
+                        reason: `provider_failure_recovery:${input.error.message}`,
+                    });
+                    await logger.log("phase_agent_fallback", {
+                        phase,
+                        fromAgentId: currentAgentId,
+                        toAgentId: nextResolved.agent.id,
+                        attempt: input.attempt,
+                        fallback_count: phaseFallbackCounts[phase],
+                        error: input.error.message,
+                    });
+                    return {
+                        switched: true,
+                        note: `Provider failure (${input.error.message}). ` +
+                            `Switched ${phase} agent to ${nextResolved.agent.slug ?? nextResolved.agent.id}; continue with current plan.`,
+                    };
+                };
+                const pipeline = new SmartPipeline({
+                    contextAssembler,
+                    initialContext: preflightContext,
+                    architectPlanner,
+                    builderRunner,
+                    criticEvaluator,
+                    memoryWriteback,
+                    maxRetries: config.limits.maxRetries,
+                    maxContextRefreshes: config.context.maxContextRefreshes,
+                    fastPath: undefined,
+                    deepMode,
+                    deepScanPreset,
+                    deepInvestigation: config.deepInvestigation,
+                    getTouchedFiles: () => runContext.getTouchedFiles(),
+                    logger,
+                    contextManager,
+                    laneScope,
+                    verificationPolicyName: workflowProfile?.verificationPolicy,
+                    minimumVerificationChecks: workflowProfile?.verificationMinimumChecks,
+                    enforceVerificationHighConfidence: workflowProfile?.verificationEnforceHighConfidence,
+                    onEvent: streamState.onEvent,
+                    onPhaseProviderFailure: recoverPhaseProvider,
+                });
+                const result = await pipeline.run(workflowTaskInput);
+                for (const file of result.builderResult.touchedFiles ?? []) {
+                    runContext.recordTouchedFile(file);
+                }
+                smartRuntimeSummary = {
+                    attempts: result.attempts,
+                    maxRetries: config.limits.maxRetries,
+                    maxContextRefreshes: config.context.maxContextRefreshes,
+                    contextRefreshTerminationReason: result.contextRefreshTerminationReason ?? null,
+                    phaseTrace: result.phaseTrace,
+                    verification: result.verification
+                        ? {
+                            outcome: result.verification.outcome,
+                            reasonCodes: result.verification.reason_codes,
+                            highConfidence: result.criticResult.report?.high_confidence
+                                ?? result.criticResult.high_confidence
+                                ?? false,
+                            policy: result.verification.policy,
+                            totals: result.verification.totals,
+                        }
+                        : null,
+                };
+                summaryVerification = result.verification;
+                if (result.criticResult.status !== "PASS") {
+                    const failureReasons = result.criticResult.reasons?.length
+                        ? result.criticResult.reasons
+                        : ["smart_pipeline_failed"];
+                    summaryDisposition = "fail";
+                    summaryFailureStage = "smart_pipeline";
+                    summaryRetryable = result.criticResult.retryable ?? null;
+                    summaryReasonCodes = uniqueStrings(failureReasons);
+                    summaryFailureClass = inferFailureClass(summaryFailureStage, summaryReasonCodes);
+                    await logger.log("run_failed", {
+                        stage: "smart_pipeline",
+                        reasons: failureReasons,
+                        failure_class: summaryFailureClass,
+                        retryable: result.criticResult.retryable ?? null,
+                        report: result.criticResult.report ?? null,
+                    });
+                    throw new Error(`Smart pipeline failed: ${failureReasons.join("; ")}`);
+                }
+                if (result.verification && result.verification.outcome !== "verified_passed") {
+                    summaryDisposition = "degraded";
+                    summaryFailureStage = "verify";
+                    summaryReasonCodes = uniqueStrings(result.verification.reason_codes.map((code) => `verification_${code}`));
+                    summaryFailureClass = "verification_failure";
+                }
+                finalMessageContent = result.builderResult.finalMessage.content;
+                usage = result.builderResult.usage;
+                toolCallsExecuted = result.builderResult.toolCallsExecuted;
+            }
+            else {
+                const pricingResolution = resolvePricing(config.cost.pricingOverrides, config.provider, config.model);
+                pricingSpec = pricingResolution.pricing;
+                pricingSource = pricingResolution.source;
+                phaseProviders.act = {
+                    provider: config.provider,
+                    model: config.model,
+                };
+                const summary = summarizeContext(undefined, workflowTaskInput);
+                estimatedFocus = summary.focusCount;
+                estimatedPeriphery = summary.peripheryCount;
+                const estimate = estimateCostFromChars(summary.charCount, config.cost.charPerToken, pricingSpec, pricingSource);
+                estimatedCost = estimate.estimatedCost;
+                estimatedTokens = estimate.estimatedTotalTokens;
+                estimatedChars = estimate.charCount;
+                await logger.log("cost_estimate", {
+                    provider: config.provider,
+                    model: config.model,
+                    focusCount: estimatedFocus,
+                    peripheryCount: estimatedPeriphery,
+                    charCount: estimatedChars,
+                    estimatedTokens,
+                    estimatedCost,
+                    pricingSource,
+                });
+                process.stderr.write(`[codali] Preflight: focus=${estimatedFocus} periphery=${estimatedPeriphery} ` +
+                    `chars=${estimatedChars} tokens~${estimatedTokens} est_cost=${formatCost(estimatedCost)}\n`);
+                if (estimatedCost !== undefined && estimatedCost > config.cost.maxCostPerRun) {
+                    const proceed = await confirmOverage(`Estimated cost ${formatCost(estimatedCost)} exceeds max ${formatCost(config.cost.maxCostPerRun)}. Continue? [y/N] `);
+                    if (!proceed) {
+                        throw new Error("Run cancelled due to cost limit");
+                    }
+                }
+                const provider = createProvider(config.provider, {
+                    model: config.model,
+                    apiKey: config.apiKey,
+                    baseUrl: config.baseUrl,
+                    timeoutMs: config.limits.timeoutMs,
+                });
+                const result = await runCodaliTask({
+                    task: workflowTaskInput,
+                    workspace: { root: config.workspaceRoot },
+                    provider: {
+                        name: config.provider,
+                        model: config.model,
+                        apiKey: config.apiKey,
+                        baseUrl: config.baseUrl,
+                        timeoutMs: config.limits.timeoutMs,
+                    },
+                    docdex: {
+                        baseUrl: config.docdex.baseUrl,
+                        repoId: config.docdex.repoId,
+                        repoRoot: config.docdex.repoRoot ?? config.workspaceRoot,
+                        dagSessionId: runId,
+                    },
+                    policy: {
+                        allowWrites: writesAllowed,
+                        allowShell: config.tools.allowShell ?? false,
+                        allowDestructiveOperations: config.tools.allowDestructiveOperations ?? false,
+                        allowOutsideWorkspace: config.tools.allowOutsideWorkspace ?? false,
+                        maxSteps: config.limits.maxSteps,
+                        maxToolCalls: config.limits.maxToolCalls,
+                        maxTokens: config.limits.maxTokens,
+                        timeoutMs: config.limits.timeoutMs,
+                        mode: "tool_loop",
+                    },
+                    streaming: config.streaming,
+                    metadata: {
+                        jobId: config.jobId,
+                        requestId: runId,
+                        tenantId: config.project,
+                        agentSlug: config.agentSlug,
+                    },
+                    providerInstance: provider,
+                    toolRegistry: registry,
+                    toolContext,
+                    logger,
+                    onEvent: (event) => {
+                        if (event.type === "usage" || event.type === "final") {
+                            return;
+                        }
+                        if (event.type === "subagent_start" || event.type === "subagent_result") {
+                            return;
+                        }
+                        if (event.type === "tool_call") {
+                            streamState.onEvent({ type: "tool_call", name: event.name, args: event.args });
+                            return;
+                        }
+                        if (event.type === "tool_result") {
+                            streamState.onEvent({
+                                type: "tool_result",
+                                name: event.name,
+                                output: event.output,
+                                ok: event.ok,
+                                errorCode: event.errorCode,
+                                retryable: event.retryable,
+                            });
+                            return;
+                        }
+                        streamState.onEvent(event);
+                    },
+                });
+                finalMessageContent = result.finalMessage;
+                usage = result.usage;
+                toolCallsExecuted = result.toolCallsExecuted;
+            }
+            streamState.flush();
+            if (streamState.didStream()) {
+                if (!finalMessageContent.endsWith("\n")) {
+                    process.stdout.write("\n");
+                    streamState.writeOutput("\n");
+                }
+            }
+            else {
+                // eslint-disable-next-line no-console
+                console.log(finalMessageContent);
+                streamState.writeOutput(`${finalMessageContent}\n`);
+            }
+            await emitRunSummary();
+            summaryEmitted = true;
+            const meta = {
+                runId,
+                fingerprint: runContext.fingerprint ?? null,
+                logPath: logger.logPath,
+                outputLogPath,
+                touchedFiles: runContext.getTouchedFiles(),
+                command: config.command,
+                commandRunId: config.commandRunId,
+                jobId: config.jobId,
+                project: config.project,
+                taskId: config.taskId,
+                taskKey: config.taskKey,
+                agentId: config.agentId,
+                agentSlug: config.agentSlug,
+                workflow: workflowProfile
+                    ? {
+                        name: workflowProfile.name,
+                        source: workflowProfile.source,
+                        outputContract: workflowProfile.outputContract,
+                        allowWrites: workflowProfile.allowWrites,
+                    }
+                    : null,
+            };
+            try {
+                process.stderr.write(`CODALI_RUN_META ${JSON.stringify(meta)}\n`);
+            }
+            catch {
+                // ignore stderr write failures
+            }
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            summaryDisposition = "fail";
+            summaryFailureStage = summaryFailureStage ?? "run_command";
+            summaryReasonCodes = summaryReasonCodes.length > 0 ? summaryReasonCodes : uniqueStrings([message]);
+            summaryFailureClass = summaryFailureClass ?? inferFailureClass(summaryFailureStage, summaryReasonCodes, message);
+            try {
+                await logger.log("run_failed", {
+                    stage: summaryFailureStage,
+                    reasons: summaryReasonCodes,
+                    failure_class: summaryFailureClass,
+                    retryable: summaryRetryable ?? null,
+                    error: message,
+                });
+                if (!summaryEmitted) {
+                    await emitRunSummary();
+                    summaryEmitted = true;
+                }
+            }
+            catch {
+                // Ignore secondary logging failures.
+            }
+            throw error;
+        }
+        finally {
+            outputStream.end();
+            unregisterSignals();
+            await lock.release();
+        }
+    }
+}