diff --git a/docs/mongo-index-retirement.md b/docs/mongo-index-retirement.md
new file mode 100644
index 0000000..e7ff8c6
--- /dev/null
+++ b/docs/mongo-index-retirement.md
@@ -0,0 +1,40 @@
+# Retire redundant file indexes
+
+The November 11 audit found no query use of `path_1`, `path_1_repoId_1`, or
+`repoIDAndPath` since the Mongo restart on November 8. Together they occupied
+3.17 GiB. This observation is a retirement candidate list, not proof that every
+infrequent workload is covered.
+
+Deploy the updated application first so Mongoose no longer recreates the old
+path indexes. The existing additive index migration does not drop indexes.
+Then run these commands in the application environment:
+
+```sh
+node build/scripts/retire-file-indexes.js status
+node build/scripts/retire-file-indexes.js hide
+```
+
+Observe at least one full traffic/maintenance cycle, including ZIP reads,
+legacy snapshots, path searches, tree cleanup and refreshes. Compare slow-query
+plans and latency with the pre-hide baseline. Hidden indexes still consume
+storage and incur write maintenance; hiding alone does not reclaim space.
+
+If queries regress, restore visibility immediately:
+
+```sh
+node build/scripts/retire-file-indexes.js restore
+```
+
+Only after the observation period is satisfactory, reclaim the storage:
+
+```sh
+node build/scripts/retire-file-indexes.js drop
+```
+
+The script accepts only the three audited index definitions, rejects unique,
+TTL, partial, sparse or collated variants, requires the generation/path index
+to be visible and ready, and refuses to drop candidates that are not hidden.
+It never removes the unique or TTL indexes used by other collections. A dropped
+index cannot be restored with `restore`; it must be rebuilt from its original
+key definition. Keep the pre-hide baseline and observation results with the
+operator's deployment record.
diff --git a/src/core/Repository.ts b/src/core/Repository.ts
index 8835774..e7aa8a5 100644
--- a/src/core/Repository.ts
+++ b/src/core/Repository.ts
@@ -1,3 +1,4 @@
+import { REPOSITORY_ID_COLLATION } from "./repository-id";
 import { allowance, reserveRepository } from "./billing/quotas";
 import { FILE_TREE_BATCH_SIZE, FILE_LISTING_LIMIT, deleteRowsInBatches } from "./file-tree";
 import { SourceBase, sourceStorageSize } from "./source/Source";
@@ -422,7 +423,7 @@ export default class Repository {
 
   /** Indexed row markers also discover inserts that finish after a build lease is retired. */
   static async cleanupStagedFileTree(repoId: string, generation: string, now = new Date()) {
-    let current = await AnonymizedRepositoryModel.findOne({ repoId }).exec();
+    let current = await AnonymizedRepositoryModel.findOne({ repoId }, null, { collation: REPOSITORY_ID_COLLATION }).exec();
     if (current && current.treeGeneration !== generation &&
       current.stagedFileTrees?.some(stage => stage.generation === generation && stage.until > now)) return;
     if (current) {
diff --git a/src/core/billing/quotas.ts b/src/core/billing/quotas.ts
index c483c2f..8cb22dd 100644
--- a/src/core/billing/quotas.ts
+++ b/src/core/billing/quotas.ts
@@ -1,3 +1,4 @@
+import { REPOSITORY_ID_COLLATION } from "../repository-id";
 import { randomUUID } from "crypto";
 import ConferenceModel from "../model/conference/conferences.model";
 import config from "../../config";
@@ -30,7 +31,8 @@ export async function reserveRepository(owner: string, repoId: string, bytes: nu
   // count toward the owner's capacity when creating new work.
   if (!await BillingQuota.exists({ _id: limits.scope })) {
     const existing = await RepositoryModel.find(limits.scope.startsWith("user:") ? { owner, status: { $nin: ["removed", "expired"] } }
-      : limits.scope.startsWith("conference:") ? { conference, status: { $nin: ["removed", "expired"] } } : { repoId, status: { $nin: ["removed", "expired"] } })
+      : limits.scope.startsWith("conference:") ? { conference, status: { $nin: ["removed", "expired"] } } : { repoId, status: { $nin: ["removed", "expired"] } }, null,
+      limits.scope.startsWith("repo:") ? { collation: REPOSITORY_ID_COLLATION } : {})
       .select("repoId size owner conference").lean();
     const funded = [];
     for (const repository of existing) {
@@ -42,7 +44,7 @@ export async function reserveRepository(owner: string, repoId: string, bytes: nu
   // Only confirmed terminal repositories release capacity. Unknown reservations
   // remain until reconciled by an operator, so a crash cannot oversell capacity.
   const ledger = await BillingQuota.findById(limits.scope).lean();
-  const terminal = await RepositoryModel.find({ repoId: { $in: ledger?.allocations.map(a => a.repoId) || [] }, status: "removed" }).select("repoId").lean();
+  const terminal = await RepositoryModel.find({ repoId: { $in: ledger?.allocations.map(a => a.repoId) || [] }, status: "removed" }, null, { collation: REPOSITORY_ID_COLLATION }).select("repoId").lean();
   if (terminal.length) await BillingQuota.updateOne({ _id: limits.scope }, { $pull: { allocations: { $or: terminal.map(r => ({
     repoId: r.repoId, reservationId: ledger?.allocations.find(a => a.repoId === r.repoId)?.reservationId || { $exists: false },
   })) } } });
@@ -81,7 +83,7 @@ export async function assertConferenceAdmission(owner: string, repoId: string, c
 export async function reserveFileExpansion(repoId: string, key: string, extraBytes: number) {
   if (!config.BILLING_ENABLED) return;
   if (!Number.isSafeInteger(extraBytes) || extraBytes < 0) throw billingError("billing_invalid_repository_size");
-  const repo = await RepositoryModel.findOne({ repoId }).select("owner conference billingManaged").lean();
+  const repo = await RepositoryModel.findOne({ repoId }, null, { collation: REPOSITORY_ID_COLLATION }).select("owner conference billingManaged").lean();
   if (!repo?.billingManaged) return;
   await reserveRepository(String(repo.owner), repoId, 0, repo.conference, { key, bytes: extraBytes });
 }
diff --git a/src/core/folder-counts.ts b/src/core/folder-counts.ts
index fd5d4c0..ee62754 100644
--- a/src/core/folder-counts.ts
+++ b/src/core/folder-counts.ts
@@ -22,7 +22,7 @@ export async function folderCounts(repo: Repository, requestedPath: unknown): Pr
   const prefix = originalPath ? originalPath + "/" : "";
   const escapedPrefix = prefix.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
   const childDepth = originalPath ? originalPath.split("/").length : 0;
-  const rows = await FileModel.aggregate<{ _id: string; count: number }>([
+  const aggregate = () => FileModel.aggregate<{ _id: string; count: number }>([
     { $match: {
       repoId: repo.repoId,
       treeGeneration: repo.model.treeGeneration || { $exists: false },
@@ -35,7 +35,19 @@ export async function folderCounts(repo: Repository, requestedPath: unknown): Pr
       { $arrayElemAt: [{ $split: ["$path", "/"] }, childDepth] },
     ] } : { $arrayElemAt: [{ $split: ["$path", "/"] }, 0] }, count: { $sum: 1 } } },
     { $limit: FILE_LISTING_LIMIT + 1 },
-  ]).option({ maxTimeMS: 2000, allowDiskUse: true }).exec();
+  ]).option({ maxTimeMS: 2000, allowDiskUse: true });
+  let rows: { _id: string; count: number }[];
+  try {
+    // The short planner trial can favor the size-first index despite its
+    // document fetches. Legacy snapshots still use the default planner.
+    rows = await aggregate().option(repo.model.treeGeneration ? { hint: "file_counts_covering" } : {}).exec();
+  } catch (error) {
+    // During an additive rollout the index may not be ready yet. Retry only
+    // the missing-hint planning error, never timeouts or execution failures.
+    if (!repo.model.treeGeneration || !(error instanceof Error) || !("code" in error) || error.code !== 2 ||
+        !/hint provided does not correspond to an existing index/.test(error.message || "")) throw error;
+    rows = await aggregate().exec();
+  }
   if (rows.length > FILE_LISTING_LIMIT) throw new AnonymousError("file_listing_too_large", { httpStatus: 413 });
   const counts: Record<string, number> = Object.create(null);
   const compiled = compileTerms(repo.options.terms || []);
diff --git a/src/core/model/anonymizedRepositories/anonymizedRepositories.schema.ts b/src/core/model/anonymizedRepositories/anonymizedRepositories.schema.ts
index c552c00..cb17663 100644
--- a/src/core/model/anonymizedRepositories/anonymizedRepositories.schema.ts
+++ b/src/core/model/anonymizedRepositories/anonymizedRepositories.schema.ts
@@ -110,6 +110,10 @@ const AnonymizedRepositorySchema = new Schema({
   },
 });
 
+AnonymizedRepositorySchema.index({ billingNeverExpiresUntil: 1, status: 1 }, {
+  name: "billing_never_expiration",
+  partialFilterExpression: { "options.expirationMode": "never", billingNeverExpiresUntil: { $exists: true } },
+});
 AnonymizedRepositorySchema.index({ "source.repositoryName": 1 });
 AnonymizedRepositorySchema.index({ "coauthors.githubId": 1 });
 AnonymizedRepositorySchema.index({ retiredTreeGenerations: 1 }, { sparse: true });
diff --git a/src/core/model/files/files.schema.ts b/src/core/model/files/files.schema.ts
index 2c2a01b..9979e52 100644
--- a/src/core/model/files/files.schema.ts
+++ b/src/core/model/files/files.schema.ts
@@ -4,7 +4,7 @@ export const UpstreamFileSchema = new Schema({ organization: String, repoName: S
 
 const FileSchema = new Schema({
   name: { type: String, index: true },
-  path: { type: String, index: true },
+  path: { type: String },
   repoId: { type: String, index: true },
   treeGeneration: String,
   treeStaged: Boolean,
@@ -19,7 +19,6 @@ const FileSchema = new Schema({
   },
 });
 
-FileSchema.index({ path: 1, repoId: 1 });
 FileSchema.index({ metadataPending: 1, repoId: 1, treeGeneration: 1 },
   { partialFilterExpression: { metadataPending: true } });
 FileSchema.index({ treeStaged: 1, repoId: 1, treeGeneration: 1 },
diff --git a/src/core/repository-id.ts b/src/core/repository-id.ts
new file mode 100644
index 0000000..233125b
--- /dev/null
+++ b/src/core/repository-id.ts
@@ -0,0 +1,2 @@
+/** Repository URLs and their unique Mongo index use case-insensitive IDs. */
+export const REPOSITORY_ID_COLLATION = { locale: "en", strength: 2 };
diff --git a/src/core/source/GitHubStream.ts b/src/core/source/GitHubStream.ts
index d7cc447..303e276 100644
--- a/src/core/source/GitHubStream.ts
+++ b/src/core/source/GitHubStream.ts
@@ -1,3 +1,4 @@
+import { REPOSITORY_ID_COLLATION } from "../repository-id";
 import { reserveFileExpansion } from "../billing/quotas";
 import { withOwnerAccessRecovery } from "../owner-notifications";
 import { ExpiringMap } from "../expiring-map";
@@ -362,7 +363,7 @@ export default class GitHubStream extends GitHubBase {
       // Retirement markers live inside the storage root and disappear when
       // expiration removes it. The persisted lifecycle also fences late fills.
       if (isConnected) {
-        const current = await AnonymizedRepositoryModel.findOne({ repoId })
+        const current = await AnonymizedRepositoryModel.findOne({ repoId }, null, { collation: REPOSITORY_ID_COLLATION })
           .select("status treeGeneration anonymizeDate contentCacheRevision").lean().exec();
         if (!current || !current.status || [RepositoryStatus.EXPIRING, RepositoryStatus.EXPIRED,
           RepositoryStatus.REMOVING, RepositoryStatus.REMOVED, RepositoryStatus.ARCHIVED].includes(current.status)
@@ -641,7 +642,7 @@ export default class GitHubStream extends GitHubBase {
   private async confirmOwnerAccess<T>(repoId: string, work: () => Promise<T>, confirmed?: (result: T) => boolean): Promise<T> {
     let repository;
     try {
-      repository = isConnected ? await AnonymizedRepositoryModel.findOne({ repoId })
+      repository = isConnected ? await AnonymizedRepositoryModel.findOne({ repoId }, null, { collation: REPOSITORY_ID_COLLATION })
         .select("owner source githubAccess").lean().exec() : null;
     } catch {
       // Email recovery bookkeeping must not prevent the upstream read.
diff --git a/src/core/transformed-cache.ts b/src/core/transformed-cache.ts
index 8f78469..473fa72 100644
--- a/src/core/transformed-cache.ts
+++ b/src/core/transformed-cache.ts
@@ -1,3 +1,4 @@
+import { REPOSITORY_ID_COLLATION } from "./repository-id";
 import { observeCache } from "./cache-observability";
 import { promises as fs } from "fs";
 import { join } from "path";
@@ -18,7 +19,7 @@ interface CacheScope { repoId: string; generation?: string; revision?: string }
 
 async function scopeActive(scope?: CacheScope) {
   if (!scope || !isConnected) return true;
-  const current = await RepositoryModel.findOne({ repoId: scope.repoId })
+  const current = await RepositoryModel.findOne({ repoId: scope.repoId }, null, { collation: REPOSITORY_ID_COLLATION })
     .select("status treeGeneration anonymizeDate contentCacheRevision").lean().exec();
   return !!current?.status && ![RepositoryStatus.EXPIRING, RepositoryStatus.EXPIRED,
     RepositoryStatus.REMOVING, RepositoryStatus.REMOVED, RepositoryStatus.ARCHIVED].includes(current.status)
diff --git a/src/scripts/create-performance-indexes.ts b/src/scripts/create-performance-indexes.ts
index 3a577b2..8ad5c3f 100644
--- a/src/scripts/create-performance-indexes.ts
+++ b/src/scripts/create-performance-indexes.ts
@@ -11,6 +11,10 @@ import Name from "../core/model/dashboard-name";
 async function main() {
   const uri = config.MONGODB_URI || `mongodb://${config.DB_USERNAME}:${config.DB_PASSWORD}@${config.DB_HOSTNAME}:27017/production`;
   await mongoose.connect(uri, { autoIndex: false, ...(config.MONGODB_URI ? {} : { authSource: "admin" }) });
+  await Repository.collection.createIndex({ billingNeverExpiresUntil: 1, status: 1 }, {
+    name: "billing_never_expiration",
+    partialFilterExpression: { "options.expirationMode": "never", billingNeverExpiresUntil: { $exists: true } },
+  });
   // Additive only. Never use syncIndexes here, which can drop deployed indexes.
   await Repository.collection.createIndex({ "coauthors.githubId": 1 });
   await File.collection.createIndex({ repoId: 1, treeGeneration: 1, path: 1, name: 1 });
diff --git a/src/scripts/retire-file-indexes.ts b/src/scripts/retire-file-indexes.ts
new file mode 100644
index 0000000..fdb247f
--- /dev/null
+++ b/src/scripts/retire-file-indexes.ts
@@ -0,0 +1,51 @@
+import "dotenv/config";
+import mongoose, { mongo } from "mongoose";
+import config from "../config";
+
+const candidates = [
+  { name: "path_1", key: { path: 1 } },
+  { name: "path_1_repoId_1", key: { path: 1, repoId: 1 } },
+  { name: "repoIDAndPath", key: { repoId: 1, path: 1 } },
+];
+const replacementKey = { repoId: 1, treeGeneration: 1, path: 1, name: 1 };
+
+/** Operator-controlled retirement: hide first, observe traffic, then drop. */
+export async function retireFileIndexes(db: mongo.Db, action: string) {
+  if (!["status", "hide", "restore", "drop"].includes(action)) throw Error("Use status, hide, restore or drop");
+  const collection = db.collection("files");
+  const indexes = await collection.listIndexes().toArray();
+  const selected = candidates.flatMap(candidate => {
+    const index = indexes.find(index => index.name === candidate.name);
+    if (!index) return [];
+    if (JSON.stringify(index.key) !== JSON.stringify(candidate.key) || index.unique || index.sparse ||
+        index.partialFilterExpression || index.collation || index.expireAfterSeconds !== undefined) {
+      throw Error(`Unexpected definition for ${candidate.name}; refusing retirement`);
+    }
+    return [index];
+  });
+  if (action === "hide" || action === "drop") {
+    if (!indexes.some(index => JSON.stringify(index.key) === JSON.stringify(replacementKey) && !index.hidden &&
+        !index.partialFilterExpression && !index.sparse && !index.collation && !index.buildUUID)) {
+      throw Error("The generation/path replacement index must be ready and visible");
+    }
+  }
+  // Validate every candidate before changing any of them.
+  if (action === "drop" && selected.some(index => !index.hidden)) throw Error("Hide all candidate indexes and observe traffic before dropping them");
+  for (const index of selected) {
+    if (action === "drop") await collection.dropIndex(index.name!);
+    else if (action === "hide" || action === "restore") {
+      await db.command({ collMod: "files", index: { name: index.name, hidden: action === "hide" } });
+    }
+  }
+  return selected.map(index => ({ name: index.name, action, previouslyHidden: !!index.hidden }));
+}
+
+async function main() {
+  const uri = config.MONGODB_URI || `mongodb://${encodeURIComponent(config.DB_USERNAME)}:${encodeURIComponent(config.DB_PASSWORD)}@${config.DB_HOSTNAME}:27017/production`;
+  await mongoose.connect(uri, { autoIndex: false, ...(config.MONGODB_URI ? {} : { authSource: "admin" }) });
+  console.log(await retireFileIndexes(mongoose.connection.db!, process.argv[2] || "status"));
+}
+if (require.main === module) {
+  main().catch(error => { console.error(error instanceof Error ? error.message : "Index retirement failed"); process.exitCode = 1; })
+    .finally(() => mongoose.disconnect());
+}
diff --git a/src/server/routes/github-app.ts b/src/server/routes/github-app.ts
index 4c0a623..4bbd40c 100644
--- a/src/server/routes/github-app.ts
+++ b/src/server/routes/github-app.ts
@@ -1,3 +1,4 @@
+import { REPOSITORY_ID_COLLATION } from "../../core/repository-id";
 import { notificationEmail, normalizeEmail, resetOwnerAccessAlerts } from "../../core/owner-notifications";
 import { saveRegistrationEmail } from "../../core/registration-email";
 import * as express from "express";
@@ -230,7 +231,7 @@ router.post("/connections/migrate", async (req, res) => {
     if (typeof id !== "string" || !["repository", "pull-request"].includes(type) || !["oauth", "github-app"].includes(connection)) throw appError("invalid_connection", 400);
     if (connection === "github-app" && (!config.GITHUB_APP_ENABLED || !config.GITHUB_APP_NEW_CONNECTIONS)) throw appError("github_app_disabled", 503);
     const isRepo = type === "repository";
-    const model = isRepo ? await RepositoryModel.findOne({ repoId: id, owner: user.id }) : await PullRequestModel.findOne({ pullRequestId: id, owner: user.id });
+    const model = isRepo ? await RepositoryModel.findOne({ repoId: id, owner: user.id }, null, { collation: REPOSITORY_ID_COLLATION }) : await PullRequestModel.findOne({ pullRequestId: id, owner: user.id });
     if (!model || ["removed", "archived"].includes(model.status || "")) throw appError("repo_not_found", 404);
     const stalePullRequest = !isRepo && model.status === "download" &&
       (!model.statusDate || model.statusDate.getTime() <= Date.now() - 5 * 60 * 1000);
diff --git a/src/server/schedule.ts b/src/server/schedule.ts
index af1f04d..6f77f86 100644
--- a/src/server/schedule.ts
+++ b/src/server/schedule.ts
@@ -1,3 +1,4 @@
+import { REPOSITORY_ID_COLLATION } from "../core/repository-id";
 import { reconcileNeverExpiration } from "../core/billing/expiration";
 import { Model, Document } from "mongoose";
 import * as schedule from "node-schedule";
@@ -185,7 +186,7 @@ export async function runRepositoryStatusCheck(now = new Date()) {
   for await (const file of pendingCursor) {
     batch.push((async () => {
       try {
-        const data = await AnonymizedRepositoryModel.findOne({ repoId: file.repoId }).exec();
+        const data = await AnonymizedRepositoryModel.findOne({ repoId: file.repoId }, null, { collation: REPOSITORY_ID_COLLATION }).exec();
         if (!data || data.treeGeneration !== file.treeGeneration ||
           (data.status && [RepositoryStatus.EXPIRING, RepositoryStatus.EXPIRED, RepositoryStatus.REMOVING, RepositoryStatus.REMOVED].includes(data.status))) {
           await FileModel.deleteOne({ _id: file._id, metadataPending: true }).exec();
diff --git a/test/billing-integration.test.js b/test/billing-integration.test.js
index 96d6253..1bbae59 100644
--- a/test/billing-integration.test.js
+++ b/test/billing-integration.test.js
@@ -30,6 +30,23 @@ async function rejects(promise, message) {
     await BillingAccount.create({ _id: owner, customerId: "cus_owner" });
   });
   after(async () => { Object.assign(config, original); await mongoose.disconnect(); });
+  it("indexes terminal quota lookups by repository ID rather than scanning removed repositories", async () => {
+    await Repo.insertMany(Array.from({ length: 1000 }, (_, i) => ({ repoId: `removed-${i}`, owner, status: "removed" })));
+    await BillingQuota.create({ _id: `user:${owner}`, allocations: [{ repoId: "removed-999", reservationId: "old", bytes: 90 }] });
+    const find = Repo.find; let terminalQuery;
+    Repo.find = function (...args) {
+      const query = find.apply(this, args);
+      if (args[0]?.repoId?.$in) terminalQuery = query;
+      return query;
+    };
+    try {
+      await reserveRepository(owner, "new", 100);
+      expect((await BillingQuota.findById(`user:${owner}`)).allocations.map(a => a.repoId)).to.deep.equal(["new"]);
+      const plan = await terminalQuery.clone().explain("executionStats");
+      expect(plan.executionStats.totalDocsExamined).to.equal(1);
+      expect(plan.executionStats.totalKeysExamined).to.equal(1);
+    } finally { Repo.find = find; }
+  });
   it("atomically admits only three concurrent repositories", async () => {
     const results = await Promise.allSettled(Array.from({ length: 12 }, (_, i) => reserveRepository(owner, `repo-${i}`, 10)));
     expect(results.filter(r => r.status === "fulfilled")).to.have.length(3);
diff --git a/test/folder-counts.test.js b/test/folder-counts.test.js
index 0a1d90d..52a212c 100644
--- a/test/folder-counts.test.js
+++ b/test/folder-counts.test.js
@@ -17,6 +17,22 @@ describe("folder count request validation", () => {
       expect(error.message).to.equal("invalid_path"); expect(error.httpStatus).to.equal(400);
     });
   }
+  for (const error of [Object.assign(Error("operation exceeded time limit"), { code: 50 }),
+    Object.assign(Error("unrelated bad value"), { code: 2 })]) {
+    it(`does not retry ${error.message}`, async () => {
+      const original = File.aggregate; let calls = 0;
+      File.aggregate = () => {
+        calls++;
+        return { option() { return this; }, exec: async () => { throw error; } };
+      };
+      try {
+        const caught = await folderCounts({ repoId: "fixture", model: { treeGeneration: "active" } }, "")
+          .then(() => null, error => error);
+        expect(caught).to.equal(error); expect(calls).to.equal(1);
+      } finally { File.aggregate = original; }
+    });
+  }
+
 });
 
 (uri ? describe : describe.skip)("scoped folder counts with MongoDB", function () {
@@ -50,17 +66,31 @@ describe("folder count request validation", () => {
     await insert(Array.from({ length: 2000 }, (_, i) => ({ name: `file${i}`, path: `src/folder${i % 20}`, size: i % 2 })));
     await insert([{ name: "excluded-directory", path: "" },
       { name: "old", path: "old", size: 1, treeGeneration: "retired" }]);
-    let pipeline;
+    let pipeline, query;
     const aggregate = File.aggregate;
-    File.aggregate = function (stages, ...args) { pipeline = stages; return aggregate.call(this, stages, ...args); };
+    File.aggregate = function (stages, ...args) {
+      pipeline = stages; query = aggregate.call(this, stages, ...args); return query;
+    };
     try { expect(await folderCounts(repo, "")).to.deep.equal({ "": 2000, src: 2000 }); }
     finally { File.aggregate = aggregate; }
-    const explained = await File.aggregate(pipeline).option({ hint: "file_counts_covering" }).explain("executionStats");
+    expect(query.options.hint).to.equal("file_counts_covering");
+    const explained = await File.aggregate(pipeline).option(query.options).explain("executionStats");
     const cursor = explained.stages?.find(stage => stage.$cursor)?.$cursor || explained;
     expect(cursor.executionStats.totalDocsExamined).to.equal(0);
     expect(cursor.executionStats.totalKeysExamined).to.be.at.least(2000);
   });
 
+  it("falls back before the covering index exists and uses it after creation", async () => {
+    await insert([{ name: "one", path: "src", size: 1 }]);
+    await File.collection.dropIndex("file_counts_covering");
+    try {
+      expect(await folderCounts(repo, "")).to.deep.equal({ "": 1, src: 1 });
+    } finally {
+      await File.collection.createIndex({ repoId: 1, treeGeneration: 1, path: 1, size: 1 }, { name: "file_counts_covering" });
+    }
+    expect(await folderCounts(repo, "")).to.deep.equal({ "": 1, src: 1 });
+  });
+
   it("preserves counts for legacy repositories without a generation", async () => {
     repo.model.treeGeneration = undefined; await repo.model.save();
     await File.collection.insertMany([
diff --git a/test/mongo-index-audit.test.js b/test/mongo-index-audit.test.js
new file mode 100644
index 0000000..9cfde81
--- /dev/null
+++ b/test/mongo-index-audit.test.js
@@ -0,0 +1,123 @@
+const { expect } = require("chai");
+require("ts-node/register/transpile-only");
+const mongoose = require("mongoose");
+const config = require("../src/config").default;
+const db = require("../src/server/database");
+const Repo = require("../src/core/model/anonymizedRepositories/anonymizedRepositories.model").default;
+const File = require("../src/core/model/files/files.model").default;
+const { assertTransformScopeActive } = require("../src/core/transformed-cache");
+const GitHubStream = require("../src/core/source/GitHubStream").default;
+const { reconcileNeverExpiration } = require("../src/core/billing/expiration");
+const { retireFileIndexes } = require("../src/scripts/retire-file-indexes");
+const uri = process.env.PERFORMANCE_MONGO_URI;
+const owner = new mongoose.Types.ObjectId();
+const replacement = { repoId: 1, treeGeneration: 1, path: 1, name: 1 };
+
+(uri ? describe : describe.skip)("Mongo index audit regressions", function () {
+  this.timeout(60000);
+  const originalBilling = config.BILLING_ENABLED;
+  before(async () => {
+    if (!/\/perf_test_[A-Za-z0-9_-]+(?:\?|$)/.test(uri)) throw Error("Use an isolated perf_test_ database");
+    await mongoose.connect(uri); db.isConnected = true;
+    await Promise.all([Repo, File].map(m => m.createIndexes()));
+  });
+  after(async () => {
+    config.BILLING_ENABLED = originalBilling; db.isConnected = false;
+    await mongoose.connection.dropDatabase(); await mongoose.disconnect();
+  });
+  beforeEach(async () => { await Repo.deleteMany({}); await File.deleteMany({}); });
+
+  it("uses the case-insensitive index for cache guards without weakening lifecycle or revision checks", async () => {
+    const when = new Date("2026-01-01");
+    const repo = await Repo.create({ repoId: "Mixed-Case", owner, status: "ready", treeGeneration: "generation",
+      anonymizeDate: when, contentCacheRevision: "revision" });
+    const options = { repoId: "mixed-case", cacheGeneration: `generation:${when.toISOString()}`, cacheRevision: "revision" };
+    const find = Repo.findOne; let query;
+    Repo.findOne = function (...args) { query = find.apply(this, args); return query; };
+    try {
+      await assertTransformScopeActive(options);
+      const plan = await query.clone().explain("executionStats");
+      expect(plan.executionStats.totalDocsExamined).to.equal(1);
+      expect(plan.executionStats.totalKeysExamined).to.equal(1);
+    } finally { Repo.findOne = find; }
+    for (const patch of [{ cacheGeneration: "stale" }, { cacheRevision: "stale" }]) {
+      const error = await assertTransformScopeActive({ ...options, ...patch }).catch(e => e);
+      expect(error.message).to.equal("repository_changed");
+    }
+    await Repo.updateOne({ _id: repo._id }, { $set: { status: "archived" } });
+    const error = await assertTransformScopeActive(options).catch(e => e);
+    expect(error.message).to.equal("repository_changed");
+  });
+
+  it("keeps raw-cache generation guards indexed and rejects a stale snapshot before upstream work", async () => {
+    await Repo.create({ repoId: "Mixed-Case", owner, status: "ready", treeGeneration: "new" });
+    const find = Repo.findOne; let query;
+    Repo.findOne = function (...args) { query = find.apply(this, args); return query; };
+    try {
+      const source = new GitHubStream({ cacheGeneration: "old:", getToken: () => { throw Error("unexpected upstream"); } });
+      const error = await source.getFileContentCache("README.md", "mixed-case", () => ({ sha: "a".repeat(40) }), true).catch(e => e);
+      expect(error.message).to.equal("repository_changed");
+      const plan = await query.clone().explain("executionStats");
+      expect(plan.executionStats.totalDocsExamined).to.equal(1);
+      expect(plan.executionStats.totalKeysExamined).to.equal(1);
+    } finally { Repo.findOne = find; }
+  });
+
+  it("uses the partial billing index and excludes legacy never-expiring repositories", async () => {
+    config.BILLING_ENABLED = true;
+    await Repo.insertMany(Array.from({ length: 1000 }, (_, i) => ({ repoId: `legacy-${i}`, owner,
+      status: "ready", options: { expirationMode: "never" } })));
+    await Repo.insertMany(Array.from({ length: 11 }, (_, i) => ({ repoId: `paid-${i}`, owner,
+      status: "ready", options: { expirationMode: "never" }, billingNeverExpiresUntil: new Date("2099-01-01") })));
+    const find = Repo.find; let query;
+    Repo.find = function (...args) { query = find.apply(this, args); return query; };
+    try {
+      await reconcileNeverExpiration(new Date("2026-01-01"), async () => { throw Error("unexpected reconciliation"); });
+      const plan = await query.clone().explain("executionStats");
+      expect(plan.executionStats.nReturned).to.equal(11);
+      expect(plan.executionStats.totalDocsExamined).to.equal(11);
+      expect(JSON.stringify(plan.queryPlanner.winningPlan)).to.include("billing_never_expiration");
+    } finally { Repo.find = find; }
+    expect(await Repo.countDocuments({ billingNeverExpiresUntil: { $exists: false }, "options.expirationMode": "never" })).to.equal(1000);
+  });
+
+  it("hides, restores and only then drops the audited indexes while preserving file reads", async () => {
+    const coll = File.collection;
+    for (const [key, name] of [[{ path: 1 }, "path_1"], [{ path: 1, repoId: 1 }, "path_1_repoId_1"], [{ repoId: 1, path: 1 }, "repoIDAndPath"]]) {
+      await coll.createIndex(key, { name });
+    }
+    await File.insertMany([{ repoId: "fixture", treeGeneration: "active", path: "src", name: "one", size: 1 },
+      { repoId: "fixture", path: "legacy", name: "two", size: 2 }]);
+    const database = mongoose.connection.db;
+    const rejected = await retireFileIndexes(database, "drop").catch(e => e);
+    expect(rejected.message).to.include("Hide all");
+    await retireFileIndexes(database, "hide");
+    expect((await coll.indexes()).find(i => i.name === "path_1").hidden).to.equal(true);
+    for (const filter of [{ repoId: "fixture", treeGeneration: "active", path: "src" },
+      { repoId: "fixture", treeGeneration: { $exists: false }, path: "legacy" }]) {
+      expect(await File.countDocuments(filter)).to.equal(1);
+    }
+    await retireFileIndexes(database, "restore");
+    expect((await coll.indexes()).find(i => i.name === "path_1").hidden).not.to.equal(true);
+    await retireFileIndexes(database, "hide"); await retireFileIndexes(database, "drop");
+    const indexes = await coll.indexes();
+    expect(indexes.some(i => i.name === "path_1")).to.equal(false);
+    expect(indexes.some(i => JSON.stringify(i.key) === JSON.stringify(replacement))).to.equal(true);
+  });
+
+  it("refuses hiding when the replacement index is absent", async () => {
+    await File.collection.dropIndex("repoId_1_treeGeneration_1_path_1_name_1");
+    try {
+      const error = await retireFileIndexes(mongoose.connection.db, "hide").catch(e => e);
+      expect(error.message).to.include("replacement index must be ready");
+    } finally { await File.collection.createIndex(replacement); }
+  });
+
+  it("refuses retirement of an unexpectedly unique candidate", async () => {
+    await File.collection.createIndex({ path: 1 }, { name: "path_1", unique: true });
+    try {
+      const error = await retireFileIndexes(mongoose.connection.db, "hide").catch(e => e);
+      expect(error.message).to.include("Unexpected definition");
+    } finally { await File.collection.dropIndex("path_1"); }
+  });
+});