fix(document): avoid premature partial search on missing RPC responses

.aegir.js

@@ -2,7 +2,16 @@
 import * as findUp from "find-up";
 import path from "path";
 
-const root = path.dirname(await findUp.findUp(".git", { type: "directory" }));
+// In git worktrees, `.git` is a *file* (not a directory), so don't constrain the type.
+// Fall back to workspace markers for non-git environments.
+const rootMarker =
+	(await findUp.findUp(".git")) ??
+	(await findUp.findUp("pnpm-workspace.yaml")) ??
+	(await findUp.findUp("package.json"));
+if (!rootMarker) {
+	throw new Error("Unable to locate repo root (no .git/workspace marker found)");
+}
+const root = path.dirname(rootMarker);
 
 export default {
 	// global options

debugging-plan.md

@@ -0,0 +1,12 @@
+# Findings (2026-02-06)
+- `queryAll` uses RPC default timeout of 10s; search/iterate does not override this even when `remote.wait.timeout` is much longer. Under churn, RPC requests can time out before `waitForResolved` deadlines, leading to missing responses that are silently swallowed unless `throwOnMissing` is set. This can cause partial results to be treated as complete. (see `packages/programs/rpc/src/controller.ts` and `packages/programs/data/document/document/src/search.ts`)
+- `MissingResponsesError` is caught in `queryCommence` and only logged unless `remote.throwOnMissing` is set, so caller has no signal to keep iterator open or requery missing peers.
+
+# Changes Applied
+- `queryCommence` now aligns RPC timeout with `remote.wait.timeout` when provided, reducing premature MissingResponsesError during churn.
+- `MissingResponsesError` now carries `missingGroups` metadata and `queryCommence` exposes this via an `onMissingResponses` callback.
+- `iterate` marks the initial fetch as incomplete when missing responses are detected to avoid prematurely closing the iterator.
+
+# Tests
+- Attempted: `node ./node_modules/aegir/src/index.js run test --roots ./packages/programs/rpc -- -t node --grep "queryAll"`
+- Result: failed (missing local dependency `node_modules/aegir`)

packages/clients/peerbit/.aegir.js

@@ -4,7 +4,16 @@ import fs from "fs";
 import { createRequire } from "module";
 import path from "path";
 
-const root = path.dirname(await findUp.findUp(".git", { type: "directory" }));
+// In git worktrees, `.git` is a *file* (not a directory), so don't constrain the type.
+// Fall back to workspace markers for non-git environments.
+const rootMarker =
+	(await findUp.findUp(".git")) ??
+	(await findUp.findUp("pnpm-workspace.yaml")) ??
+	(await findUp.findUp("package.json"));
+if (!rootMarker) {
+	throw new Error("Unable to locate repo root (no .git/workspace marker found)");
+}
+const root = path.dirname(rootMarker);
 const resolverFromRoot = createRequire(path.join(root, "package.json"));
 const resolverFromLocal = createRequire(import.meta.url);
 

packages/programs/data/document/document/src/search.ts

@@ -289,6 +289,7 @@ type QueryDetailedOptions<
 		response: types.AbstractSearchResult,
 		from: PublicSignKey,
 	) => void | Promise<void>;
+	onMissingResponses?: (error: MissingResponsesError) => void | Promise<void>;
 	remote?: {
 		from?: string[]; // if specified, only query these peers
 	};
@@ -2237,6 +2238,15 @@ export class DocumentIndex<
 			// this will lead to bad UX as you usually want to list/expore whats going on before doing any replication work
 			remote.priority = 2;
 		}
+		if (remote && remote.timeout == null && options?.remote) {
+			const waitPolicy =
+				typeof options.remote === "object" ? options.remote.wait : undefined;
+			const waitTimeout =
+				typeof waitPolicy === "object" ? waitPolicy.timeout : undefined;
+			if (waitTimeout != null) {
+				remote.timeout = waitTimeout;
+			}
+		}
 
 		if (!local && !remote) {
 			throw new Error(
@@ -2403,6 +2413,9 @@ export class DocumentIndex<
 				} catch (error) {
 					if (error instanceof MissingResponsesError) {
 						warn("Did not reciveve responses from all shard");
+						if (options?.onMissingResponses) {
+							await options.onMissingResponses(error);
+						}
 						if (remote?.throwOnMissing) {
 							throw error;
 						}
@@ -2961,6 +2974,7 @@ export class DocumentIndex<
 		): Promise<boolean> => {
 			await warmupPromise;
 			let hasMore = false;
+			let missingResponses = false;
 			const discoverTargets =
 				typeof options?.remote === "object"
 					? options.remote.reach?.discover
@@ -3096,10 +3110,17 @@ export class DocumentIndex<
 							);
 						}
 					},
+					onMissingResponses: () => {
+						missingResponses = true;
+					},
 				},
 				fetchOptions?.fetchedFirstForRemote,
 			);
 
+			if (missingResponses) {
+				hasMore = true;
+				unsetDone();
+			}
 			if (!hasMore) {
 				maybeSetDone();
 			}

packages/programs/rpc/src/utils.ts

@@ -13,8 +13,10 @@ import type {
 } from "./io.js";
 
 export class MissingResponsesError extends Error {
-	constructor(message: string) {
+	missingGroups: string[][];
+	constructor(message: string, missingGroups: string[][] = []) {
 		super(message);
+		this.missingGroups = missingGroups;
 	}
 }
 export type RPCRequestAllOptions<_Q, R> = RPCRequestResponseOptions<R> &
@@ -84,6 +86,7 @@ export const queryAll = async <Q, R>(
 		throw new MissingResponsesError(
 			"Did not receive responses from all shards: " +
 				JSON.stringify(missingReponses),
+			missingReponses,
 		);
 	}
 };

packages/programs/rpc/test/index.spec.ts

@@ -11,6 +11,7 @@ import { TestSession } from "@peerbit/test-utils";
 import { AbortError, delay, waitFor, waitForResolved } from "@peerbit/time";
 import { expect } from "chai";
 import {
+	MissingResponsesError,
 	RPC,
 	type RPCResponse,
 	type RequestEvent,
@@ -734,4 +735,24 @@ describe("queryAll", () => {
 		await expect(promise).rejectedWith("TestAborted");
 		expect(+new Date() - t1).lessThan(1000);
 	});
+
+	it("reports missing groups on timeout", async () => {
+		clients[1].delay = 200;
+		const missingGroup = [[clients[1].node.identity.publicKey.hashcode()]];
+		try {
+			await queryAll(
+				clients[0].query,
+				missingGroup,
+				new Body({ arr: new Uint8Array([1]) }),
+				() => {},
+				{ timeout: 50 },
+			);
+			expect.fail("Expected MissingResponsesError");
+		} catch (error) {
+			expect(error).to.be.instanceOf(MissingResponsesError);
+			expect((error as MissingResponsesError).missingGroups).to.deep.equal(
+				missingGroup,
+			);
+		}
+	});
 });

packages/utils/any-store/any-store/.aegir.js

@@ -4,7 +4,16 @@ import fs from "fs";
 import { createRequire } from "module";
 import path from "path";
 
-const root = path.dirname(await findUp.findUp(".git", { type: "directory" }));
+// In git worktrees, `.git` is a *file* (not a directory), so don't constrain the type.
+// Fall back to workspace markers for non-git environments.
+const rootMarker =
+	(await findUp.findUp(".git")) ??
+	(await findUp.findUp("pnpm-workspace.yaml")) ??
+	(await findUp.findUp("package.json"));
+if (!rootMarker) {
+	throw new Error("Unable to locate repo root (no .git/workspace marker found)");
+}
+const root = path.dirname(rootMarker);
 const resolverFromRoot = createRequire(path.join(root, "package.json"));
 const resolverFromLocal = createRequire(import.meta.url);
 

packages/utils/indexer/sqlite3/.aegir.js

@@ -2,7 +2,16 @@ import * as findUp from "find-up";
 import fs from "fs";
 import path from "path";
 
-const root = path.dirname(await findUp.findUp(".git", { type: "directory" }));
+// In git worktrees, `.git` is a *file* (not a directory), so don't constrain the type.
+// Fall back to workspace markers for non-git environments.
+const rootMarker =
+	(await findUp.findUp(".git")) ??
+	(await findUp.findUp("pnpm-workspace.yaml")) ??
+	(await findUp.findUp("package.json"));
+if (!rootMarker) {
+	throw new Error("Unable to locate repo root (no .git/workspace marker found)");
+}
+const root = path.dirname(rootMarker);
 
 export default {
 	// test cmd options