clinkx 0.3.0 → 1.1.0

package/dist/context-builder/lifecycle-reconcile.js

@@ -0,0 +1,191 @@
+import { randomBytes } from "node:crypto";
+import { hostname as osHostname } from "node:os";
+import { readdir as fsReaddir, readFile as fsReadFile } from "node:fs/promises";
+import { open as fsOpen, rename as fsRename, rm as fsRm, } from "node:fs/promises";
+import { join } from "node:path";
+import { logger } from "../logger.js";
+import { CONTEXT_BUILDER_LIFECYCLE_DIRECTORY, MAX_CONTEXT_BUILDER_LIFECYCLE_DURATION_MS, isContextBuilderOperationId, isLegalContextBuilderLifecycleTransition, isTerminalContextBuilderLifecycleStatus, parseContextBuilderLifecycleStateV1, resolveContextBuilderLifecycleLocation, } from "./lifecycle-contract.js";
+import { resolveContextBuilderRunsDir } from "./config.js";
+import { cleanupContextBuilderIncompleteRun, resolveContextBuilderRunPaths, } from "./storage.js";
+/**
+ * Terminalize standalone/refine journals frozen as pending/running whose
+ * same-host `.building.json` pid is dead. Foreign-host and missing/unparseable
+ * pid evidence is `unknown` and is never touched — same asymmetry as workflow
+ * `reconcileStaleRunDirectories`. Does not invent a dedicated worker lock;
+ * liveness is the building-json pid probe only.
+ *
+ * Writes `failed`/`terminal` + `internal_failure`. Never `cancelled`. Never
+ * rewrites curator/finalizer outcomes. Best-effort incomplete-artifact cleanup
+ * after the journal write. Idempotent. Log-and-continue on malformed rows.
+ */
+export async function reconcileStaleContextBuilderJournals(options = {}) {
+    const runsDir = await resolveContextBuilderRunsDir(options.runsDir);
+    const now = options.now ?? (() => new Date());
+    const hostname = options.hostname ?? osHostname();
+    const isAlive = options.isProcessAlive ?? isProcessAlive;
+    const journalDir = join(runsDir, CONTEXT_BUILDER_LIFECYCLE_DIRECTORY);
+    let entries = [];
+    try {
+        entries = await fsReaddir(journalDir);
+    }
+    catch {
+        return { scanned: 0, reconciled: 0, skipped: 0, failed: 0 };
+    }
+    let scanned = 0;
+    let reconciled = 0;
+    let skipped = 0;
+    let failed = 0;
+    for (const name of entries) {
+        if (!isContextBuilderOperationId(name))
+            continue;
+        scanned += 1;
+        try {
+            const location = resolveContextBuilderLifecycleLocation(runsDir, name);
+            const raw = await fsReadFile(location.state_json, "utf8");
+            const previous = parseContextBuilderLifecycleStateV1(JSON.parse(raw));
+            if (isTerminalContextBuilderLifecycleStatus(previous.status)) {
+                skipped += 1;
+                continue;
+            }
+            const observation = await observeContextRunWorker({
+                runsDir,
+                state: previous,
+                hostname,
+                isProcessAlive: isAlive,
+            });
+            if (observation !== "dead") {
+                skipped += 1;
+                continue;
+            }
+            const next = buildReconciledFailureSnapshot(previous, now());
+            if (!isLegalContextBuilderLifecycleTransition(previous, next)) {
+                logger.warn({ contextRunId: name }, "stale context run reconcile produced an illegal transition");
+                failed += 1;
+                continue;
+            }
+            await writeAtomicLifecycleSnapshot(location.state_json, next);
+            reconciled += 1;
+            await cleanupReconciledArtifact(runsDir, previous).catch((error) => {
+                logger.warn({
+                    contextRunId: name,
+                    err: error instanceof Error ? error.message : String(error),
+                }, "stale context run artifact cleanup failed");
+            });
+        }
+        catch (error) {
+            failed += 1;
+            logger.warn({
+                contextRunId: name,
+                err: error instanceof Error ? error.message : String(error),
+            }, "stale context run reconcile skipped a malformed journal");
+        }
+    }
+    return { scanned, reconciled, skipped, failed };
+}
+export async function observeContextRunWorker(input) {
+    const artifactRunId = input.state.artifact_run_id;
+    if (artifactRunId == null)
+        return "unknown";
+    let buildingRaw;
+    try {
+        const paths = resolveContextBuilderRunPaths(input.runsDir, artifactRunId);
+        buildingRaw = await fsReadFile(paths.buildingJson, "utf8");
+    }
+    catch {
+        return "unknown";
+    }
+    let parsed;
+    try {
+        parsed = JSON.parse(buildingRaw);
+    }
+    catch {
+        return "unknown";
+    }
+    if (parsed === null || typeof parsed !== "object")
+        return "unknown";
+    const building = parsed;
+    if (typeof building.hostname !== "string" || typeof building.pid !== "number") {
+        return "unknown";
+    }
+    if (!Number.isInteger(building.pid) || building.pid <= 0)
+        return "unknown";
+    if (building.hostname !== input.hostname)
+        return "unknown";
+    return input.isProcessAlive(building.pid) ? "live" : "dead";
+}
+function buildReconciledFailureSnapshot(previous, now) {
+    const completedAt = monotonicTimestamp(now.toISOString(), previous.updated_at);
+    return parseContextBuilderLifecycleStateV1({
+        ...previous,
+        status: "failed",
+        phase: "terminal",
+        updated_at: completedAt,
+        completed_at: completedAt,
+        duration_ms: boundedDuration(previous.created_at, completedAt),
+        reason_codes: [...new Set([...previous.reason_codes, "internal_failure"])],
+    });
+}
+async function cleanupReconciledArtifact(runsDir, state) {
+    const artifactRunId = state.artifact_run_id;
+    if (artifactRunId == null)
+        return;
+    const paths = resolveContextBuilderRunPaths(runsDir, artifactRunId);
+    let ownerNonce;
+    try {
+        const parsed = JSON.parse(await fsReadFile(paths.buildingJson, "utf8"));
+        if (parsed !== null &&
+            typeof parsed === "object" &&
+            typeof parsed.owner_nonce === "string") {
+            ownerNonce = parsed.owner_nonce;
+        }
+    }
+    catch {
+        return;
+    }
+    if (ownerNonce == null)
+        return;
+    await cleanupContextBuilderIncompleteRun(paths, ownerNonce);
+}
+async function writeAtomicLifecycleSnapshot(finalPath, snapshot) {
+    const tempPath = `${finalPath}.${randomBytes(8).toString("hex")}.tmp`;
+    let handle;
+    let renamed = false;
+    try {
+        handle = await fsOpen(tempPath, "wx", 0o600);
+        await handle.writeFile(`${JSON.stringify(snapshot)}\n`, { encoding: "utf8" });
+        await handle.sync();
+        await handle.close();
+        handle = undefined;
+        await fsRename(tempPath, finalPath);
+        renamed = true;
+    }
+    finally {
+        if (handle !== undefined) {
+            await handle.close().catch(() => { });
+        }
+        if (!renamed) {
+            await fsRm(tempPath, { force: true }).catch(() => { });
+        }
+    }
+}
+function monotonicTimestamp(candidate, floor) {
+    return Date.parse(candidate) < Date.parse(floor) ? floor : candidate;
+}
+function boundedDuration(createdAt, completedAt) {
+    return Math.min(MAX_CONTEXT_BUILDER_LIFECYCLE_DURATION_MS, Math.max(0, Date.parse(completedAt) - Date.parse(createdAt)));
+}
+function isProcessAlive(pid) {
+    if (pid <= 0)
+        return false;
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (error) {
+        return !(typeof error === "object" &&
+            error !== null &&
+            "code" in error &&
+            error.code === "ESRCH");
+    }
+}
+//# sourceMappingURL=lifecycle-reconcile.js.map

package/dist/context-builder/lifecycle-reconcile.js.map

@@ -0,0 +1 @@
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package/dist/context-builder/lifecycle-recovery.d.ts

@@ -0,0 +1,2 @@
+import type { ContextBuilderReceipt } from "./receipt.js";
+export declare function appendLifecycleCompletionWarning(receipt: ContextBuilderReceipt, maxWarnings: number): ContextBuilderReceipt;

package/dist/context-builder/lifecycle-recovery.js

@@ -0,0 +1,14 @@
+export function appendLifecycleCompletionWarning(receipt, maxWarnings) {
+    const warning = {
+        code: "lifecycle_completion_unavailable",
+        message: "Context Run completion could not be persisted after two attempts.",
+    };
+    return {
+        ...receipt,
+        warnings: [
+            ...receipt.warnings.slice(0, Math.max(0, maxWarnings - 1)),
+            warning,
+        ],
+    };
+}
+//# sourceMappingURL=lifecycle-recovery.js.map

package/dist/context-builder/lifecycle-recovery.js.map

@@ -0,0 +1 @@
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package/dist/context-builder/mutation-lock.d.ts

@@ -0,0 +1,32 @@
+import { type FileHandle } from "node:fs/promises";
+import type { BigIntStats } from "node:fs";
+export type ContextBuilderMutationLockTarget = {
+    runId: string;
+    runsDir: string;
+    runDir: string;
+};
+export type ContextBuilderMutationLockOps = {
+    open?(path: string, flags: string, mode?: number): Promise<FileHandle>;
+    lstat?(path: string, options: {
+        bigint: true;
+    }): Promise<BigIntStats>;
+    rm?(path: string, options: {
+        force?: boolean;
+    }): Promise<void>;
+};
+export type ContextBuilderMutationLockOptions = {
+    ownerNonce?: string | undefined;
+    /** Keep the storage default unless a best-effort caller needs a tighter bound. */
+    maxAttempts?: number | undefined;
+    /** Deterministic contention seam; production callers leave this unset. */
+    onContention?: (() => void | Promise<void>) | undefined;
+    /** Storage cleanup supplies its existing owner/manifest admission check. */
+    canRecoverStale?: (() => Promise<boolean>) | undefined;
+    /** Deterministic seam after stale-lock qualification, before final admission/removal. */
+    beforeStaleRemoval?: (() => void | Promise<void>) | undefined;
+};
+/**
+ * Serialize cooperative mutations of one context_builder run. The lock lives
+ * beside the run directory so it also survives removal of that directory.
+ */
+export declare function withContextBuilderMutationLock<T>(target: ContextBuilderMutationLockTarget, ops: ContextBuilderMutationLockOps, callback: () => Promise<T>, options?: ContextBuilderMutationLockOptions): Promise<T>;

package/dist/context-builder/mutation-lock.js

@@ -0,0 +1,321 @@
+import { lstat as fsLstat, open as fsOpen, rm as fsRm, } from "node:fs/promises";
+import { hostname } from "node:os";
+import { isAbsolute, join, relative, resolve } from "node:path";
+import { ExecutionError } from "../errors.js";
+import { validateCallerRunId } from "./run-id.js";
+const CONTEXT_BUILDER_MUTATION_LOCK_SUFFIX = ".mutation.lock";
+const CONTEXT_BUILDER_MUTATION_LOCK_RECOVERY_SUFFIX = ".recovery";
+const CONTEXT_BUILDER_MUTATION_LOCK_ATTEMPTS = 1_000;
+const CONTEXT_BUILDER_MUTATION_LOCK_RETRY_MS = 10;
+const CONTEXT_BUILDER_STALE_MUTATION_LOCK_MS = 10 * 60 * 1_000;
+/**
+ * Serialize cooperative mutations of one context_builder run. The lock lives
+ * beside the run directory so it also survives removal of that directory.
+ */
+export async function withContextBuilderMutationLock(target, ops, callback, options = {}) {
+    const lockPath = mutationLockPathForTarget(target);
+    const acquired = await acquireContextBuilderMutationLock(lockPath, ops, options);
+    try {
+        return await callback();
+    }
+    finally {
+        await removeMutationLockIfCurrent(lockPath, acquired.fingerprint, ops);
+        await acquired.handle.close().catch(() => { });
+    }
+}
+async function acquireContextBuilderMutationLock(lockPath, ops, options) {
+    const open = ops.open ?? fsOpen;
+    const maxAttempts = resolveMutationLockAttempts(options.maxAttempts);
+    for (let attempt = 0; attempt < maxAttempts; attempt += 1) {
+        try {
+            const handle = await open(lockPath, "wx", 0o600);
+            try {
+                await writeMutationLockMetadata(handle, options.ownerNonce);
+                return {
+                    handle,
+                    fingerprint: await fingerprintOpenHandle(handle),
+                };
+            }
+            catch (error) {
+                const fingerprint = await fingerprintOpenHandle(handle).catch(() => undefined);
+                if (fingerprint !== undefined) {
+                    await removeMutationLockIfCurrent(lockPath, fingerprint, ops);
+                }
+                await handle.close().catch(() => { });
+                throw error;
+            }
+        }
+        catch (error) {
+            if (isNodeError(error) && error.code === "EEXIST") {
+                await options.onContention?.();
+                if (options.canRecoverStale !== undefined
+                    && await breakStaleMutationLock(lockPath, ops, options.canRecoverStale, options.beforeStaleRemoval)) {
+                    continue;
+                }
+                await delay(CONTEXT_BUILDER_MUTATION_LOCK_RETRY_MS);
+                continue;
+            }
+            throw error;
+        }
+    }
+    throw new ExecutionError("context_builder timed out waiting for the run mutation lock");
+}
+function resolveMutationLockAttempts(value) {
+    if (value === undefined) {
+        return CONTEXT_BUILDER_MUTATION_LOCK_ATTEMPTS;
+    }
+    if (!Number.isSafeInteger(value) || value <= 0) {
+        throw new ExecutionError("context_builder mutation lock attempts must be a positive integer");
+    }
+    return value;
+}
+function mutationLockPathForTarget(target) {
+    validateCallerRunId(target.runId);
+    const resolvedRunsDir = resolve(target.runsDir);
+    const resolvedRunDir = resolve(target.runDir);
+    if (!isPathInsideDirectory(resolvedRunDir, resolvedRunsDir)) {
+        throw new ExecutionError("context_builder refused mutation lock outside runs directory");
+    }
+    return join(resolvedRunsDir, `.${target.runId}${CONTEXT_BUILDER_MUTATION_LOCK_SUFFIX}`);
+}
+async function writeMutationLockMetadata(handle, ownerNonce) {
+    const metadata = {
+        pid: process.pid,
+        hostname: hostname(),
+        created_at: new Date().toISOString(),
+        ...(ownerNonce == null ? {} : { owner_nonce: ownerNonce }),
+    };
+    await handle.writeFile(`${JSON.stringify(metadata)}\n`, { encoding: "utf8" });
+}
+async function breakStaleMutationLock(lockPath, ops, canRecoverStale, beforeStaleRemoval) {
+    const candidate = await observeMutationLock(lockPath, ops);
+    if (candidate === undefined) {
+        return false;
+    }
+    try {
+        if (!isRecoverableStaleMutationLock(candidate)) {
+            return false;
+        }
+    }
+    finally {
+        await candidate.handle.close().catch(() => { });
+    }
+    const recoveryGate = await tryAcquireMutationLockRecoveryGate(lockPath, ops);
+    if (recoveryGate === undefined) {
+        return false;
+    }
+    try {
+        const observed = await observeMutationLock(lockPath, ops);
+        if (observed === undefined) {
+            return false;
+        }
+        try {
+            if (!isRecoverableStaleMutationLock(observed)) {
+                return false;
+            }
+            await beforeStaleRemoval?.();
+            if (!await canRecoverStale()) {
+                return false;
+            }
+            return await removeMutationLockIfCurrent(lockPath, observed.fingerprint, ops);
+        }
+        finally {
+            await observed.handle.close().catch(() => { });
+        }
+    }
+    finally {
+        await removeMutationLockIfCurrent(`${lockPath}${CONTEXT_BUILDER_MUTATION_LOCK_RECOVERY_SUFFIX}`, recoveryGate.fingerprint, ops);
+        await recoveryGate.handle.close().catch(() => { });
+    }
+}
+async function tryAcquireMutationLockRecoveryGate(lockPath, ops) {
+    const gatePath = `${lockPath}${CONTEXT_BUILDER_MUTATION_LOCK_RECOVERY_SUFFIX}`;
+    const open = ops.open ?? fsOpen;
+    let handle;
+    try {
+        handle = await open(gatePath, "wx", 0o600);
+    }
+    catch (error) {
+        if (isNodeError(error) && error.code === "EEXIST") {
+            return undefined;
+        }
+        throw error;
+    }
+    try {
+        await writeMutationLockMetadata(handle, undefined);
+        return {
+            handle,
+            fingerprint: await fingerprintOpenHandle(handle),
+        };
+    }
+    catch (error) {
+        const fingerprint = await fingerprintOpenHandle(handle).catch(() => undefined);
+        if (fingerprint !== undefined) {
+            await removeMutationLockIfCurrent(gatePath, fingerprint, ops);
+        }
+        await handle.close().catch(() => { });
+        throw error;
+    }
+}
+async function observeMutationLock(lockPath, ops) {
+    const lstat = ops.lstat ?? fsLstat;
+    const open = ops.open ?? fsOpen;
+    let handle;
+    try {
+        const pathStats = await lstat(lockPath, { bigint: true });
+        if (!pathStats.isFile()) {
+            return undefined;
+        }
+        handle = await open(lockPath, "r");
+        const before = await handle.stat({ bigint: true });
+        if (!before.isFile()
+            || before.nlink === 0n
+            || !sameMutationLockIncarnation(fingerprintFromStats(pathStats), fingerprintFromStats(before))) {
+            return undefined;
+        }
+        const raw = await handle.readFile({ encoding: "utf8" });
+        const after = await handle.stat({ bigint: true });
+        const beforeFingerprint = fingerprintFromStats(before);
+        const afterFingerprint = fingerprintFromStats(after);
+        if (after.nlink === 0n
+            || !mutationLockFingerprintsEqual(beforeFingerprint, afterFingerprint)) {
+            return undefined;
+        }
+        const observed = {
+            handle,
+            fingerprint: afterFingerprint,
+            metadata: parseMutationLockMetadata(raw),
+        };
+        handle = undefined;
+        return observed;
+    }
+    catch {
+        return undefined;
+    }
+    finally {
+        await handle?.close().catch(() => { });
+    }
+}
+function isRecoverableStaleMutationLock(observed) {
+    const mtimeMs = Number(observed.fingerprint.mtimeNs / 1000000n);
+    if (Date.now() - mtimeMs < CONTEXT_BUILDER_STALE_MUTATION_LOCK_MS) {
+        return false;
+    }
+    return observed.metadata === "invalid"
+        || isStaleMutationLockMetadata(observed.metadata);
+}
+async function fingerprintOpenHandle(handle) {
+    return fingerprintFromStats(await handle.stat({ bigint: true }));
+}
+async function removeMutationLockIfCurrent(lockPath, expected, ops) {
+    // Node has no portable conditional-unlink primitive. Keeping the admitted
+    // descriptor open prevents inode reuse while this fingerprint recheck rejects
+    // replacements visible before unlink. Ordinary owner and recovery-gate release
+    // are safe under cooperative ownership. Stale main-lock removal holds the
+    // per-run recovery gate across this boundary; that gate is never stale-recovered.
+    const lstat = ops.lstat ?? fsLstat;
+    const rm = ops.rm ?? fsRm;
+    let current;
+    try {
+        current = await lstat(lockPath, { bigint: true });
+    }
+    catch {
+        return false;
+    }
+    if (!current.isFile()
+        || !mutationLockFingerprintsEqual(fingerprintFromStats(current), expected)) {
+        return false;
+    }
+    try {
+        await rm(lockPath, { force: true });
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+function parseMutationLockMetadata(raw) {
+    let parsed;
+    try {
+        parsed = JSON.parse(raw);
+    }
+    catch {
+        return "invalid";
+    }
+    if (parsed === null || typeof parsed !== "object") {
+        return "invalid";
+    }
+    const metadata = parsed;
+    if (typeof metadata.pid !== "number"
+        || !Number.isInteger(metadata.pid)
+        || typeof metadata.hostname !== "string"
+        || typeof metadata.created_at !== "string") {
+        return "invalid";
+    }
+    if (metadata.owner_nonce !== undefined
+        && typeof metadata.owner_nonce !== "string") {
+        return "invalid";
+    }
+    return {
+        pid: metadata.pid,
+        hostname: metadata.hostname,
+        created_at: metadata.created_at,
+        ...(metadata.owner_nonce === undefined
+            ? {}
+            : { owner_nonce: metadata.owner_nonce }),
+    };
+}
+function fingerprintFromStats(stats) {
+    return {
+        dev: stats.dev,
+        ino: stats.ino,
+        mtimeNs: stats.mtimeNs,
+        ctimeNs: stats.ctimeNs,
+        size: stats.size,
+        nlink: stats.nlink,
+    };
+}
+function sameMutationLockIncarnation(left, right) {
+    return left.dev === right.dev && left.ino === right.ino;
+}
+function mutationLockFingerprintsEqual(left, right) {
+    return sameMutationLockIncarnation(left, right)
+        && left.mtimeNs === right.mtimeNs
+        && left.ctimeNs === right.ctimeNs
+        && left.size === right.size
+        && left.nlink === right.nlink;
+}
+function isStaleMutationLockMetadata(metadata) {
+    const createdAtMs = Date.parse(metadata.created_at);
+    if (!Number.isFinite(createdAtMs)
+        || Date.now() - createdAtMs < CONTEXT_BUILDER_STALE_MUTATION_LOCK_MS) {
+        return false;
+    }
+    if (metadata.hostname !== hostname()) {
+        return false;
+    }
+    return !isProcessAlive(metadata.pid);
+}
+function isProcessAlive(pid) {
+    if (pid <= 0) {
+        return false;
+    }
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (error) {
+        return !(isNodeError(error) && error.code === "ESRCH");
+    }
+}
+function isNodeError(error) {
+    return error instanceof Error && "code" in error;
+}
+async function delay(ms) {
+    await new Promise((resolveDelay) => setTimeout(resolveDelay, ms));
+}
+function isPathInsideDirectory(candidate, directory) {
+    const relation = relative(directory, candidate);
+    return relation !== "" && !relation.startsWith("..") && !isAbsolute(relation);
+}
+//# sourceMappingURL=mutation-lock.js.map

package/dist/context-builder/mutation-lock.js.map

@@ -0,0 +1 @@
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package/dist/context-builder/path-signals.js

@@ -3,12 +3,16 @@
 // helpers previously had divergent copies in both modules; unify here so the
 // two can never silently re-diverge.
 export function isTestPath(relativePath) {
-    return (relativePath.startsWith("test/") ||
-        relativePath.startsWith("tests/") ||
-        relativePath.startsWith("frontend/tests/") ||
-        relativePath.startsWith("backend/tests/") ||
-        relativePath.includes("/__tests__/") ||
+    return (
+    // A `test/` or `tests/` path SEGMENT anywhere (leading or nested) — e.g.
+    // `tests/foo`, `pkg/test/bar`, `<anyrepo>/tests/baz`. Repo-agnostic: no
+    // hardcoded top-level prefixes tied to a particular project layout.
+    /(?:^|\/)tests?\//.test(relativePath) ||
+        // A `__tests__/` directory segment anywhere (leading or nested).
+        /(?:^|\/)__tests__\//.test(relativePath) ||
+        // `.test.`/`.spec.` JS/TS filename suffix.
         /\.(?:test|spec)\.[cm]?[jt]sx?$/.test(relativePath) ||
+        // Python `test_*.py` filename.
         /(?:^|\/)test_[^/]+\.py$/.test(relativePath));
 }
 export function isGenericConfigPath(relativePath) {

package/dist/context-builder/path-signals.js.map

@@ -1 +1 @@
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package/dist/context-builder/progress.d.ts

@@ -1,4 +1,5 @@
 import type { Server } from "@modelcontextprotocol/sdk/server/index.js";
+import type { ContextBuilderLifecycleObserver } from "./lifecycle-observer.js";
 export type ContextBuilderProgressStage = "validating" | "scanning" | "searching" | "selecting" | "curating" | "finalizing" | "writing" | "complete";
 export type ContextBuilderProgressTarget = {
     server: Server;
@@ -9,7 +10,8 @@ export declare class ContextBuilderProgressReporter {
     private highestEmitted;
     private chain;
     constructor(target: ContextBuilderProgressTarget);
-    emit(stage: ContextBuilderProgressStage): Promise<void>;
+    observe: ContextBuilderLifecycleObserver;
+    private emit;
     private emitNow;
 }
 export declare function createContextBuilderProgressReporter(target: ContextBuilderProgressTarget | undefined): ContextBuilderProgressReporter | undefined;