@iowarp/clio-coder 0.4.0 → 0.4.1

package/src/cli/run.ts

@@ -148,7 +148,7 @@ async function assemblePrompt(parsed: RunCliArgs): Promise<{
  * path, not a skill package, or validation failure such as a missing
  * description). Exported for contracts tests.
  */
-export function explicitSkillPathErrors(skillPaths: ReadonlyArray<string>): string[] {
+function explicitSkillPathErrors(skillPaths: ReadonlyArray<string>): string[] {
 	const errors: string[] = [];
 	for (const skillPath of skillPaths) {
 		const list = loadSkills({ disableDiscovery: true, explicitSkillPaths: [skillPath] });
@@ -187,7 +187,7 @@ export function explicitSkillPathErrors(skillPaths: ReadonlyArray<string>): stri
  * closure sits on. Boundaries rule6 in `tests/boundaries/check-boundaries.ts`
  * holds both halves of that.
  */
-export async function unknownSlashCommandRefusal(task: string): Promise<string | null> {
+async function unknownSlashCommandRefusal(task: string): Promise<string | null> {
 	if (!task.trim().startsWith("/")) return null;
 	const { parseSlashCommand } = await import("../interactive/slash-commands.js");
 	const command = parseSlashCommand(task);
@@ -376,9 +376,9 @@ async function runDispatch(
 	// does. The journal never reads settings.yaml itself: it sits on the
 	// dispatch event path, where a settings read would be both a cost and a
 	// throw site.
-	configureRunEventJournal(baseSettings.panes.journal);
-	effectiveSettings =
-		parsed.autonomy === undefined ? baseSettings : { ...structuredClone(baseSettings), autonomy: parsed.autonomy };
+	configureRunEventJournal(baseSettings.fleet.history.journal);
+	effectiveSettings = structuredClone(baseSettings);
+	if (parsed.autonomy !== undefined) effectiveSettings.safety.autonomy = parsed.autonomy;
 	const dispatch = loaded.getContract<DispatchContract>("dispatch");
 	if (!dispatch) {
 		process.stderr.write("dispatch domain unavailable\n");
@@ -394,19 +394,15 @@ async function runDispatch(
 			return 1;
 		}
 		const settings = effectiveSettings;
-		const profileTargetId = parsed.agentProfile ? settings.workers?.profiles?.[parsed.agentProfile]?.target : undefined;
+		const profileTargetId = parsed.agentProfile ? settings.fleet?.profiles?.[parsed.agentProfile]?.target : undefined;
 		const runtimeByTarget = new Map(settings.targets.map((target) => [target.id, target.runtime] as const));
 		const runtimeTargetId = parsed.agentRuntime
-			? [settings.workers?.default, ...Object.values(settings.workers?.profiles ?? {})].find(
+			? [settings.fleet?.default, ...Object.values(settings.fleet?.profiles ?? {})].find(
 					(profile) => profile?.target && runtimeByTarget.get(profile.target) === parsed.agentRuntime,
 				)?.target
 			: undefined;
 		const targetId =
-			parsed.target ??
-			profileTargetId ??
-			runtimeTargetId ??
-			settings.workers?.default?.target ??
-			settings.orchestrator?.target;
+			parsed.target ?? profileTargetId ?? runtimeTargetId ?? settings.fleet?.default?.target ?? settings.chat?.target;
 		const target = targetId ? providers.getTarget(targetId) : null;
 		const runtime = target ? providers.getRuntime(target.runtime) : null;
 		if (!target || !runtime) {
@@ -441,7 +437,7 @@ async function runDispatch(
 	if (skillPaths.length > 0) dispatchReq.skillPaths = skillPaths;
 	try {
 		const settings = effectiveSettings;
-		if (settings.skills?.trustProjectCompatRoots) {
+		if (settings.integrations.projectResources?.trustProjectImports) {
 			dispatchReq.trustProjectCompatRoots = true;
 		}
 	} catch {
@@ -451,8 +447,8 @@ async function runDispatch(
 	let memorySection = "";
 	try {
 		const records = loadMemoryRecordsSync(clioDataDir());
-		const boundProfileName = parsed.agentProfile ?? effectiveSettings.workers.agentBindings[parsed.agentId];
-		const boundProfile = boundProfileName ? effectiveSettings.workers.profiles[boundProfileName] : undefined;
+		const boundProfileName = parsed.agentProfile ?? effectiveSettings.fleet.agentProfiles[parsed.agentId];
+		const boundProfile = boundProfileName ? effectiveSettings.fleet.profiles[boundProfileName] : undefined;
 		const configuredRuntime = (targetId: string | null | undefined): string | undefined =>
 			effectiveSettings.targets.find((target) => target.id === targetId)?.runtime;
 		const profileRuntimeId = configuredRuntime(boundProfile?.target);

package/src/cli/share.ts

@@ -233,7 +233,7 @@ export function runShareCommand(argv: ReadonlyArray<string>): number {
 				const archive = plan.archive;
 				if (archive) {
 					process.stdout.write(
-						`archive: ${archive.manifest.format} clio=${archive.manifest.clioVersion} files=${archive.files.length} created=${archive.manifest.createdAt}\n`,
+						`archive: ${archive.manifest.format} clio-coder=${archive.manifest.clioCoderVersion} files=${archive.files.length} created=${archive.manifest.createdAt}\n`,
 					);
 				}
 			}

package/src/cli/skills-eval.ts

@@ -311,7 +311,7 @@ type EvalArm = "baseline" | "treatment" | "judge";
  *
  * @internal Exported for contract tests.
  */
-export function armRunArgs(
+function armRunArgs(
 	arm: EvalArm,
 	prompt: string,
 	options: { target?: string | undefined; skillBaseDir?: string | undefined } = {},
@@ -335,7 +335,7 @@ export function armRunArgs(
  *
  * @internal Exported for contract tests.
  */
-export function permissionWallReason(arm: EvalArm, run: CapturedRun): string | null {
+function permissionWallReason(arm: EvalArm, run: CapturedRun): string | null {
 	const haystack = `${run.transcript}\n${run.finalText}`;
 	let blocked = 0;
 	let at = haystack.indexOf(HEADLESS_PERMISSION_DENIED_MARKER);
@@ -360,7 +360,7 @@ function unmeasuredBullets(scenario: SkillEvalScenario, reason: string): ScoredB
  *
  * @internal Exported for contract tests.
  */
-export function evalChildEnv(allowNetwork: boolean, env: NodeJS.ProcessEnv = process.env): NodeJS.ProcessEnv {
+function evalChildEnv(allowNetwork: boolean, env: NodeJS.ProcessEnv = process.env): NodeJS.ProcessEnv {
 	const childEnv: NodeJS.ProcessEnv = { ...env };
 	if (allowNetwork) Reflect.deleteProperty(childEnv, NO_NETWORK_TOOLS_ENV);
 	else childEnv[NO_NETWORK_TOOLS_ENV] = "1";
@@ -378,7 +378,7 @@ export function evalChildEnv(allowNetwork: boolean, env: NodeJS.ProcessEnv = pro
  * the catalog answers only for a name no root installed, which is the skill
  * author's case in this repository.
  */
-export function resolveSkillBaseDir(
+function resolveSkillBaseDir(
 	nameOrPath: string,
 	cwd: string,
 ): { baseDir: string | null; origin?: string; error?: string } {
@@ -442,7 +442,7 @@ async function runScenario(
 	// Published per-scenario figure: monotonic so a clock correction during a
 	// long sweep cannot land in one row's wall time.
 	const scenarioStart = performance.now();
-	const workspace = await mkdtemp(join(tmpdir(), "clio-skill-eval-seed-"));
+	const workspace = await mkdtemp(join(tmpdir(), "clio-coder-skill-eval-seed-"));
 	let runWorkspaces: MaterializedSkillEvalWorkspaces | null = null;
 	try {
 		if (workspaceOverride !== null) await copyWorkspace(workspaceOverride, workspace);
@@ -570,7 +570,7 @@ export interface MaterializedSkillEvalWorkspaces {
  * cooperative model, not as an isolation guarantee.
  */
 async function armWorkspace(created: string[]): Promise<string> {
-	const root = await mkdtemp(join(tmpdir(), "clio-skill-eval-"));
+	const root = await mkdtemp(join(tmpdir(), "clio-coder-skill-eval-"));
 	created.push(root);
 	const workspace = join(root, "workspace");
 	await mkdir(workspace, { recursive: true });
@@ -578,7 +578,7 @@ async function armWorkspace(created: string[]): Promise<string> {
 }
 
 /** @internal Exported for contract tests. */
-export async function materializeSkillEvalWorkspaces(seedWorkspace: string): Promise<MaterializedSkillEvalWorkspaces> {
+async function materializeSkillEvalWorkspaces(seedWorkspace: string): Promise<MaterializedSkillEvalWorkspaces> {
 	const created: string[] = [];
 	try {
 		const baseline = await armWorkspace(created);
@@ -814,7 +814,7 @@ function loadsSkillBody(tool: string, args: unknown): boolean {
 }
 
 /** @internal Exported for contract tests. */
-export function parseRunStdout(stdout: string): { sessionId: string | null; transcript: string; finalText: string } {
+function parseRunStdout(stdout: string): { sessionId: string | null; transcript: string; finalText: string } {
 	let sessionId: string | null = null;
 	const lines: string[] = [];
 	let finalText = "";
@@ -938,7 +938,7 @@ function judgeVerdictAbsenceReason(judge: CapturedRun): string {
 }
 
 /** Exported for contracts tests. */
-export function parseJudgeVerdicts(scenario: SkillEvalScenario, judge: CapturedRun): ScoredBullet[] {
+function parseJudgeVerdicts(scenario: SkillEvalScenario, judge: CapturedRun): ScoredBullet[] {
 	const parsed = extractBulletsObject(judge.finalText) ?? extractBulletsObject(judge.transcript);
 	// No verdict object anywhere in the judge run. The scenario was not scored,
 	// which is a fact about the judge, so every bullet stays unmeasured rather
@@ -982,7 +982,7 @@ export function parseJudgeVerdicts(scenario: SkillEvalScenario, judge: CapturedR
  * content, so this walks candidate `{` openers around the first "bullets" key
  * and balance-scans to the matching close brace.
  */
-export function extractBulletsObject(text: string): Record<string, unknown> | null {
+function extractBulletsObject(text: string): Record<string, unknown> | null {
 	const stripped = text.replace(/```(?:json)?/g, "");
 	const bulletsAt = stripped.indexOf('"bullets"');
 	if (bulletsAt < 0) return null;
@@ -1085,7 +1085,7 @@ function synthesizeArtifact(
 		evalId,
 		taskFile: evalsPath,
 		taskFileHash: contentHash,
-		clio: evalClioProvenance(),
+		clioCoder: evalClioProvenance(),
 		environment: evalEnvironmentProvenance(),
 		target: target ?? null,
 		model: null,

package/src/cli/targets.ts

@@ -205,8 +205,7 @@ export async function runTargetsCommand(args: ReadonlyArray<string>): Promise<nu
 	if (parsed.json) {
 		const settings = readSettings();
 		const candidateFor = (status: TargetStatus): string | null => {
-			const orchestratorModel =
-				settings.orchestrator?.target === status.target.id ? (settings.orchestrator?.model ?? null) : null;
+			const orchestratorModel = settings.chat?.target === status.target.id ? (settings.chat?.model ?? null) : null;
 			return orchestratorModel ?? status.target.defaultModel ?? null;
 		};
 		const rows = filtered.map((status) => {
@@ -467,11 +466,11 @@ function runProfileRemove(args: ReadonlyArray<string>): number {
 	}
 	ensureClioState();
 	const settings = readSettings();
-	if (!settings.workers.profiles[parsed.name]) {
+	if (!settings.fleet.profiles[parsed.name]) {
 		printError(`no fleet profile named ${parsed.name}`);
 		return 1;
 	}
-	const boundAgents = Object.entries(settings.workers.agentBindings)
+	const boundAgents = Object.entries(settings.fleet.agentProfiles)
 		.filter(([, profileName]) => profileName === parsed.name)
 		.map(([agentId]) => agentId);
 	if (boundAgents.length > 0 && !parsed.force) {
@@ -510,23 +509,23 @@ function runProfileRename(args: ReadonlyArray<string>): number {
 	}
 	ensureClioState();
 	const settings = readSettings();
-	if (!settings.workers.profiles[parsed.oldName]) {
+	if (!settings.fleet.profiles[parsed.oldName]) {
 		printError(`no fleet profile named ${parsed.oldName}`);
 		return 1;
 	}
-	if (settings.workers.profiles[parsed.newName]) {
+	if (settings.fleet.profiles[parsed.newName]) {
 		printError(`fleet profile already exists: ${parsed.newName}`);
 		return 2;
 	}
 	let updatedBindings = 0;
 	updateSettings((fresh) => {
-		const profile = fresh.workers.profiles[parsed.oldName];
+		const profile = fresh.fleet.profiles[parsed.oldName];
 		if (!profile) return;
-		fresh.workers.profiles[parsed.newName] = profile;
-		delete fresh.workers.profiles[parsed.oldName];
-		for (const [agentId, profileName] of Object.entries(fresh.workers.agentBindings)) {
+		fresh.fleet.profiles[parsed.newName] = profile;
+		delete fresh.fleet.profiles[parsed.oldName];
+		for (const [agentId, profileName] of Object.entries(fresh.fleet.agentProfiles)) {
 			if (profileName !== parsed.oldName) continue;
-			fresh.workers.agentBindings[agentId] = parsed.newName;
+			fresh.fleet.agentProfiles[agentId] = parsed.newName;
 			updatedBindings += 1;
 		}
 	});
@@ -551,13 +550,13 @@ function runProfileBind(args: ReadonlyArray<string>): number {
 	}
 	ensureClioState();
 	const settings = readSettings();
-	if (settings.delegation.agents.some((agent) => agent.id === parsed.agentId)) {
+	if (settings.integrations.externalAgents.entries.some((agent) => agent.id === parsed.agentId)) {
 		printError(
 			`cannot bind ACP delegation agent '${parsed.agentId}' to a fleet profile; ACP agents use their own runner and ignore native target routing`,
 		);
 		return 1;
 	}
-	if (!settings.workers.profiles[parsed.profileName]) {
+	if (!settings.fleet.profiles[parsed.profileName]) {
 		process.stderr.write(
 			`${chalk.yellow("warning:")} fleet profile '${parsed.profileName}' is not configured; binding will resolve after the profile exists\n`,
 		);
@@ -581,12 +580,12 @@ function runProfileUnbind(args: ReadonlyArray<string>): number {
 	}
 	ensureClioState();
 	const settings = readSettings();
-	if (!settings.workers.agentBindings[parsed]) {
+	if (!settings.fleet.agentProfiles[parsed]) {
 		printError(`agent ${parsed} is not bound to a fleet profile`);
 		return 1;
 	}
 	updateSettings((fresh) => {
-		delete fresh.workers.agentBindings[parsed];
+		delete fresh.fleet.agentProfiles[parsed];
 	});
 	printOk(`unbound agent ${parsed}`);
 	return 0;
@@ -608,10 +607,10 @@ function runProfileBindings(args: ReadonlyArray<string>): number {
 	}
 	ensureClioState();
 	const settings = readSettings();
-	const rows = Object.entries(settings.workers.agentBindings)
+	const rows = Object.entries(settings.fleet.agentProfiles)
 		.sort(([a], [b]) => a.localeCompare(b))
 		.map(([agentId, profileName]) => {
-			const profile = settings.workers.profiles[profileName];
+			const profile = settings.fleet.profiles[profileName];
 			return {
 				agentId,
 				profile: profileName,
@@ -686,7 +685,7 @@ function runFleet(args: ReadonlyArray<string>, usage = "clio-coder targets fleet
 	ensureClioState();
 	const settings = readSettings();
 	const byId = new Map(settings.targets.map((target) => [target.id, target] as const));
-	const rows = Object.entries(settings.workers.profiles).map(([name, profile]) => {
+	const rows = Object.entries(settings.fleet.profiles).map(([name, profile]) => {
 		const target = profile.target ? byId.get(profile.target) : undefined;
 		return {
 			name,
@@ -782,7 +781,7 @@ function runConvert(args: ReadonlyArray<string>): number {
 		printOk(`target ${id} already uses runtime ${runtimeId}`);
 		return 0;
 	}
-	if (settings.orchestrator.target === id && !isOrchestratorEligibleRuntime(runtime)) {
+	if (settings.chat.target === id && !isOrchestratorEligibleRuntime(runtime)) {
 		printError(`cannot convert orchestrator target '${id}' to non-HTTP/native runtime '${runtime.id}'`);
 		return 1;
 	}
@@ -917,7 +916,7 @@ function tableWidths(rows: ReadonlyArray<TargetTableRow>, width: number): Target
  * cut to its width, marked the same way. Colour is dropped on those rows because
  * the ansi bytes would sit inside the cut; a wrapped row costs more than colour.
  */
-export function formatTargetTable(
+function formatTargetTable(
 	rows: ReadonlyArray<TargetTableRow>,
 	width: number,
 	paintHealth: (cell: string, row: TargetTableRow) => string = (cell) => cell,
@@ -972,7 +971,7 @@ function renderTable(providers: ProvidersContract, entries: ReadonlyArray<Target
 	}
 }
 
-export function targetTableRow(providers: ProvidersContract, status: TargetStatus): TargetTableRow {
+function targetTableRow(providers: ProvidersContract, status: TargetStatus): TargetTableRow {
 	const diagnostic = degradedHealthDiagnostic(status);
 	return {
 		id: status.target.id,
@@ -1034,7 +1033,7 @@ function capabilityBadges(caps: CapabilityFlags): string {
  * no states (cloud targets); "resident: none" when states are known and
  * nothing is loaded, so a cold box is distinguishable from an unknown one.
  */
-export function residentModelsSummary(states: TargetStatus["discoveredModelStates"]): string | null {
+function residentModelsSummary(states: TargetStatus["discoveredModelStates"]): string | null {
 	if (!states) return null;
 	const entries = Object.entries(states);
 	if (entries.length === 0) return null;
@@ -1049,7 +1048,7 @@ export function residentModelsSummary(states: TargetStatus["discoveredModelState
  * capability the target reported. Saying so is the difference between a number
  * a user can plan against and one they cannot.
  */
-export function formatContextWindow(
+function formatContextWindow(
 	status: Pick<TargetStatus, "capabilities" | "contextWindowProvenance"> &
 		Partial<Pick<TargetStatus, "target" | "discoveredModelStates">>,
 ): string {
@@ -1065,7 +1064,7 @@ export function formatContextWindow(
 		: `ctx ${window}`;
 }
 
-export function formatNotes(status: TargetStatus): string {
+function formatNotes(status: TargetStatus): string {
 	const parts: string[] = [];
 	const diagnostic = degradedHealthDiagnostic(status);
 	// The health diagnosis leads because gateway, context, and residency facts

package/src/cli/trace-inspect.ts

@@ -166,7 +166,7 @@ function processSummary(reader: TraceReader, runId: string): TraceInspectProcess
 }
 
 /** Pure payload builder, exported so the fixed contract is testable without subprocess capture. */
-export function traceInspectSnapshot(
+function traceInspectSnapshot(
 	now: () => number = Date.now,
 	databasePath: string = traceDatabasePath(clioStatePath()),
 ): TraceInspectSnapshot {

package/src/cli/trace.ts

@@ -4,6 +4,7 @@ import { resolve } from "node:path";
 import { fileURLToPath, pathToFileURL } from "node:url";
 import { clioStatePath } from "../core/xdg.js";
 import {
+	assertTraceSelectOnly,
 	DEFAULT_TRACE_RETENTION_POLICY,
 	resolveTraceRetentionPolicy,
 	TRACE_EVENT_POLL_LIMIT,
@@ -149,6 +150,14 @@ export async function runTraceCommand(args: string[]): Promise<number> {
 		process.stderr.write("trace sql requires a SELECT query\n");
 		return 2;
 	}
+	if (command === "sql") {
+		try {
+			assertTraceSelectOnly(sqlQuery);
+		} catch (error) {
+			process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`);
+			return 2;
+		}
+	}
 
 	if (command === "ui") return runTraceUi(parsed.db, parsed.port);
 
@@ -378,6 +387,38 @@ function missingDatabase(parsed: ParsedTraceArgs): number {
 		);
 		return 1;
 	}
+	if (parsed.json && parsed.positional[0] === "runs") {
+		process.stdout.write("[]\n");
+		return 0;
+	}
+	if (parsed.json && parsed.positional[0] === "prune") {
+		let policy: ReturnType<typeof resolveTraceRetentionPolicy>;
+		try {
+			policy = resolveTraceRetentionPolicy({
+				...(parsed.maxAgeDays === undefined ? {} : { maxAgeDays: parsed.maxAgeDays }),
+				...(parsed.maxBytes === undefined ? {} : { maxBytes: parsed.maxBytes }),
+			});
+		} catch (error) {
+			process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`);
+			return 1;
+		}
+		process.stdout.write(
+			`${JSON.stringify(
+				{
+					available: false,
+					policy,
+					runsRemoved: 0,
+					rowsRemoved: 0,
+					bytesRemoved: 0,
+					vacuumed: false,
+					protectedRuns: 0,
+				},
+				null,
+				2,
+			)}\n`,
+		);
+		return 0;
+	}
 	process.stdout.write(
 		`no trace database yet at ${parsed.db}. rows are recorded when a dispatch executes or an interactive turn runs; run \`clio-coder run "<task>"\` or start a session to create one.\n`,
 	);

package/src/cli/uninstall.ts

@@ -90,7 +90,7 @@ export interface ProjectContextInventory {
  * rather than one per session. Directories whose `.clio-coder/` is already gone are
  * dropped, because an inventory of nothing to do is noise.
  */
-export function projectContextInventory(stateDir: string): ProjectContextInventory {
+function projectContextInventory(stateDir: string): ProjectContextInventory {
 	const root = join(stateDir, "sessions");
 	let hashes: string[];
 	try {
@@ -298,7 +298,7 @@ function readNpmPrefix(): string | null {
  * that cannot be resolved is dangling, which is still something the operator
  * will hit and still not this installation.
  */
-export function otherClioOnPath(pathClio: string | null, localLink: string): string | null {
+function otherClioOnPath(pathClio: string | null, localLink: string): string | null {
 	if (pathClio === null) return null;
 	if (pathClio === localLink) return null;
 	const resolve = (path: string): string | null => {

package/src/cli/upgrade.ts

@@ -1,12 +1,8 @@
 import { spawn } from "node:child_process";
-import { loadDomains } from "../core/domain-loader.js";
 import { initializeClioHome } from "../core/init.js";
 import { clioStateDir } from "../core/xdg.js";
-import { ConfigDomainModule } from "../domains/config/index.js";
-import type { LifecycleContract } from "../domains/lifecycle/contract.js";
-import { LifecycleDomainModule } from "../domains/lifecycle/index.js";
 import { detectInstallMethod } from "../domains/lifecycle/install-method.js";
-import { listMigrations } from "../domains/lifecycle/migrations/index.js";
+import { listMigrations, runPending } from "../domains/lifecycle/migrations/index.js";
 import { readStateInfo } from "../domains/lifecycle/state.js";
 import { getVersionInfo } from "../domains/lifecycle/version.js";
 import { printError, printHeader, printOk } from "./shared.js";
@@ -229,36 +225,35 @@ export async function runUpgradeCommand(argv: ReadonlyArray<string>): Promise<nu
 	if (opts.skipMigrations) {
 		process.stdout.write("[upgrade] skipping migrations (--skip-migrations)\n");
 	} else {
-		const loaded = await loadDomains([ConfigDomainModule, LifecycleDomainModule]);
+		// Migrations run on the state tree directly rather than through the
+		// lifecycle domain. Loading that domain pulls in `config`, whose start
+		// runs the strict settings reader, and a settings-repairing migration is
+		// precisely the one that cannot get past it: `clio-coder upgrade` on a
+		// home whose settings.yaml names a retired key failed the domain load and
+		// never reached the migration that removes the key. A runner that needs
+		// valid config in order to repair invalid config can never run. The
+		// domain's `runMigrations` is a passthrough to this same function, so
+		// nothing is lost by calling it where the circularity does not exist.
+		let result: Awaited<ReturnType<typeof runPending>>;
 		try {
-			const lifecycle = loaded.getContract<LifecycleContract>("lifecycle");
-			if (!lifecycle) {
-				printError("lifecycle domain unavailable");
-				return 1;
-			}
-			let result: Awaited<ReturnType<LifecycleContract["runMigrations"]>>;
-			try {
-				result = await lifecycle.runMigrations(stateDir);
-			} catch (err) {
-				// A migration reports why it could not run, but on its own that reads
-				// as the whole upgrade being impossible. It is not: the rest of the
-				// upgrade is independent of it, and naming the flag that runs the rest
-				// is the difference between a stuck operator and a moved one.
-				printError(
-					`migration failed: ${err instanceof Error ? err.message : String(err)}`,
-					"the rest of the upgrade does not depend on it; run `clio-coder upgrade --skip-migrations` to continue, then fix the cause and re-run `clio-coder upgrade`.",
-				);
-				return 1;
-			}
-			appliedIds = [...result.applied];
-			appliedCount = appliedIds.length;
-			if (appliedCount === 0) {
-				process.stdout.write("[upgrade] no pending migrations\n");
-			} else {
-				for (const id of appliedIds) process.stdout.write(`[upgrade] applied migration ${id}\n`);
-			}
-		} finally {
-			await loaded.stop();
+			result = await runPending(stateDir);
+		} catch (err) {
+			// A migration reports why it could not run, but on its own that reads
+			// as the whole upgrade being impossible. It is not: the rest of the
+			// upgrade is independent of it, and naming the flag that runs the rest
+			// is the difference between a stuck operator and a moved one.
+			printError(
+				`migration failed: ${err instanceof Error ? err.message : String(err)}`,
+				"the rest of the upgrade does not depend on it; run `clio-coder upgrade --skip-migrations` to continue, then fix the cause and re-run `clio-coder upgrade`.",
+			);
+			return 1;
+		}
+		appliedIds = [...result.applied];
+		appliedCount = appliedIds.length;
+		if (appliedCount === 0) {
+			process.stdout.write("[upgrade] no pending migrations\n");
+		} else {
+			for (const id of appliedIds) process.stdout.write(`[upgrade] applied migration ${id}\n`);
 		}
 	}
 

package/src/cli/usage.ts

@@ -788,7 +788,7 @@ function indent(text: string): string {
 		.join("\n");
 }
 
-export function inWindow(iso: string, start: number, end: number): boolean {
+function inWindow(iso: string, start: number, end: number): boolean {
 	const value = Date.parse(iso);
 	return Number.isFinite(value) && value >= start && value <= end + USAGE_WINDOW_FUTURE_SKEW_MS;
 }
@@ -968,7 +968,7 @@ function bashCommandFromToolCallPayload(payload: unknown): string | null {
  * assignments dropped, verb plus subcommand kept, flags kept with values
  * stripped, remaining arguments dropped.
  */
-export function bashShape(command: string): string {
+function bashShape(command: string): string {
 	const firstLine = command.split("\n").find((line) => {
 		const trimmed = line.trim();
 		return trimmed.length > 0 && !trimmed.startsWith("#");

package/src/cli/validate-model.ts

@@ -39,7 +39,7 @@ function describeLiveTarget(live: LiveModelInventory): string {
 }
 
 /** The refusal `configure` prints for a model the live target does not advertise. */
-export function formatUnadvertisedModelReason(modelId: string, live: LiveModelInventory): string {
+function formatUnadvertisedModelReason(modelId: string, live: LiveModelInventory): string {
 	const resident = live.resident.length > 0 ? live.resident.join(", ") : "none";
 	return (
 		`${describeLiveTarget(live)} does not advertise model '${modelId}'. ` +

package/src/cli/verifiers-inspect.ts

@@ -283,7 +283,7 @@ function projectCheck(check: AuthoringCheck): VerifiersInspectCheck | null {
 
 const ORIGIN_RANK: Record<VerifierOrigin, number> = { "package-script": 0, catalog: 1, proposed: 2 };
 
-export function verifiersInspectSnapshot(
+function verifiersInspectSnapshot(
 	now: () => number = Date.now,
 	workspaceRoot: string = process.cwd(),
 ): VerifiersInspectSnapshot {

package/src/cli/wiki-generate.ts

@@ -149,7 +149,7 @@ async function drainDispatchEvents(
 	let firstBlockReason: string | null = null;
 	// Every event is consumed so finalization cannot block on an unread iterator.
 	for await (const event of events) {
-		if (!isRecord(event) || event.type !== "clio_tool_finish") continue;
+		if (!isRecord(event) || event.type !== "clio_coder_tool_finish") continue;
 		const tool = eventPayloadString(event, "tool");
 		if (!tool) continue;
 		const outcome = eventPayloadString(event, "outcome") ?? "done";
@@ -190,7 +190,7 @@ interface WikiDispatchOutcome {
  * throws: a failed page must not take down the pages around it, and whatever
  * the run wrote before it stopped is already on disk.
  */
-export async function runWikiDispatch(input: {
+async function runWikiDispatch(input: {
 	dispatch: DispatchContract;
 	cwd: string;
 	outputDir: string;
@@ -371,7 +371,7 @@ async function runPagePhase(
 	return next;
 }
 
-export async function generateWikiWithDocumenter(
+async function generateWikiWithDocumenter(
 	dispatch: DispatchContract,
 	input: WikiGenerateInput,
 	route: WikiModelRoute = {},
@@ -472,11 +472,11 @@ export async function resolveDocumenterModelId(route: WikiModelRoute = {}): Prom
 		const providers = loaded.getContract<ProvidersContract>("providers");
 		if (!config || !providers) return UNRESOLVED_DOCUMENTER_MODEL;
 		const settings = config.get();
-		const workers = settings.workers;
+		const workers = settings.fleet;
 		// Keyed on the dispatched agent id and nothing else, because that is what
 		// `placement.ts` reads. Falling back to another agent's binding here would
 		// record a model in wiki metadata that no dispatch ever ran.
-		const bindingProfileName = workers?.agentBindings?.[WIKI_AGENT_ID];
+		const bindingProfileName = workers?.agentProfiles?.[WIKI_AGENT_ID];
 		const profile = bindingProfileName ? workers?.profiles?.[bindingProfileName] : undefined;
 		const targetId = route.target ?? profile?.target ?? workers?.default?.target ?? settings.targets?.[0]?.id ?? null;
 		if (!targetId) return UNRESOLVED_DOCUMENTER_MODEL;

package/src/core/bash-exec.ts

@@ -75,7 +75,7 @@ const LOGIN_ENV_CAPTURE_TIMEOUT_MS = 10_000;
 let loginEnvCapture: Promise<NodeJS.ProcessEnv | null> | null = null;
 
 /** NUL-delimited `env -0` output to an env map; null when unusable (no PATH). */
-export function parseNullDelimitedEnv(raw: string): NodeJS.ProcessEnv | null {
+function parseNullDelimitedEnv(raw: string): NodeJS.ProcessEnv | null {
 	const env: NodeJS.ProcessEnv = {};
 	for (const entry of raw.split("\0")) {
 		if (entry.length === 0) continue;

package/src/core/boot-trace.ts

@@ -16,7 +16,7 @@
 const BOOT_TRACE_ENV = "CLIO_CODER_TRACE_BOOT";
 
 /** True when boot tracing is enabled for this process. */
-export function isBootTraceEnabled(): boolean {
+function isBootTraceEnabled(): boolean {
 	return process.env[BOOT_TRACE_ENV] === "1";
 }
 
@@ -24,11 +24,11 @@ export function isBootTraceEnabled(): boolean {
 export function formatBootTrace(phase: string, detail?: string): string | null {
 	if (!isBootTraceEnabled()) return null;
 	const suffix = detail !== undefined && detail.length > 0 ? ` (${detail})` : "";
-	return `[clio:boot] +${performance.now().toFixed(1)}ms ${phase}${suffix}\n`;
+	return `[clio-coder:boot] +${performance.now().toFixed(1)}ms ${phase}${suffix}\n`;
 }
 
 /**
- * Stamp a boot phase marker to stderr, e.g. `[clio:boot] +742.1ms cli entry`.
+ * Stamp a boot phase marker to stderr, e.g. `[clio-coder:boot] +742.1ms cli entry`.
  * `detail` appends a parenthetical (module counts, ids). No-op unless
  * `CLIO_CODER_TRACE_BOOT=1`. Never throws: a diagnostic must not affect boot.
  */

package/src/core/bus-trace.ts

@@ -11,7 +11,7 @@
  * orchestrator-wide observability, not a domain concern. Add channels to the
  * `TRACED_CHANNELS` list if a future front needs to observe them.
  *
- * Ordering invariant: the first `[clio:bus] shutdown.requested` line must
+ * Ordering invariant: the first `[clio-coder:bus] shutdown.requested` line must
  * never reach stderr before the `Clio Coder: received <SIGNAL>, shutting down...`
  * notice written by termination.installSignalHandlers in
  * src/core/termination.ts. Future edits to termination.ts must preserve that
@@ -47,7 +47,7 @@ export function installBusTracer(): void {
 	const bus = getSharedBus();
 	for (const channel of TRACED_CHANNELS) {
 		bus.on(channel, (payload) => {
-			process.stderr.write(`[clio:bus] ${channel}${traceSuffix(payload)}\n`);
+			process.stderr.write(`[clio-coder:bus] ${channel}${traceSuffix(payload)}\n`);
 		});
 	}
 }

package/src/core/compile-cache.ts

@@ -65,7 +65,7 @@ export interface CompileCacheHandle {
  * exercise the settle semantics without flipping the real process-global
  * cache.
  */
-export function createCompileCache(
+function createCompileCache(
 	enableFn: typeof enableCompileCache = enableCompileCache,
 	rootExists: (dir: string) => boolean = existsSync,
 ): CompileCacheHandle {