feat: add gemini memory embeddings

CHANGELOG.md

@@ -9,22 +9,35 @@ Docs: https://docs.clawd.bot
 - macOS: stop syncing Peekaboo as a git submodule in postinstall.
 - Swabble: use the tagged Commander Swift package release.
 - CLI: add `clawdbot acp client` interactive ACP harness for debugging.
+- Memory: add native Gemini embeddings provider for memory search. (#1151) — thanks @gumadeiras.
 
 ### Fixes
 - Auth profiles: keep auto-pinned preference while allowing rotation on failover; user pins stay locked. (#1138) — thanks @cheeeee.
 - macOS: avoid touching launchd in Remote over SSH so quitting the app no longer disables the remote gateway. (#1105)
+- Memory: index atomically so failed reindex preserves the previous memory database. (#1151) — thanks @gumadeiras.
+
 ## 2026.1.18-3
 
 ### Changes
 - Exec: add host/security/ask routing for gateway + node exec.
+- Exec: add `/exec` directive for per-session exec defaults (host/security/ask/node).
 - macOS: migrate exec approvals to `~/.clawdbot/exec-approvals.json` with per-agent allowlists and skill auto-allow toggle.
 - macOS: add approvals socket UI server + node exec lifecycle events.
-- Plugins: ship Discord/Slack/Telegram/Signal/WhatsApp as bundled channel plugins via the shared SDK (iMessage now bundled + opt-in).
+- Nodes: add headless node host (`clawdbot node start`) for `system.run`/`system.which`.
+- Nodes: add node daemon service install/status/start/stop/restart.
+- Bridge: add `skills.bins` RPC to support node host auto-allow skill bins.
+- Slash commands: replace `/cost` with `/usage off|tokens|full` to control per-response usage footer; `/usage` no longer aliases `/status`. (Supersedes #1140) — thanks @Nachx639.
+- Sessions: add daily reset policy with per-type overrides and idle windows (default 4am local), preserving legacy idle-only configs. (#1146) — thanks @austinm911.
+- Agents: auto-inject local image references for vision models and avoid reloading history images. (#1098) — thanks @tyler6204.
 - Docs: refresh exec/elevated/exec-approvals docs for the new flow. https://docs.clawd.bot/tools/exec-approvals
+- Docs: add node host CLI + update exec approvals/bridge protocol docs. https://docs.clawd.bot/cli/node
+- ACP: add experimental ACP support for IDE integrations (`clawdbot acp`). Thanks @visionik.
 
 ### Fixes
+- Exec approvals: enforce allowlist when ask is off; prefer raw command for node approvals/events.
 - Tools: return a companion-app-required message when node exec is requested with no paired node.
-- Tests: avoid extension imports when wiring plugin registries in unit tests.
+- Streaming: emit assistant deltas for OpenAI-compatible SSE chunks. (#1147) — thanks @alauppe.
+- Model fallback: treat timeout aborts as failover while preserving user aborts. (#1137) — thanks @cheeeee.
 
 ## 2026.1.18-2
 

docs/concepts/memory.md

@@ -89,7 +89,26 @@ OAuth only covers chat/completions and does **not** satisfy embeddings for
 memory search. When using a custom OpenAI-compatible endpoint, set
 `memorySearch.remote.apiKey` (and optional `memorySearch.remote.headers`).
 
-If you want to use a **custom OpenAI-compatible endpoint** (like Gemini, OpenRouter, or a proxy),
+If you want to use **Gemini embeddings** directly, set the provider to `gemini`:
+
+```json5
+agents: {
+  defaults: {
+    memorySearch: {
+      provider: "gemini",
+      model: "gemini-embedding-001", // default
+      remote: {
+        apiKey: "${GEMINI_API_KEY}"
+      }
+    }
+  }
+}
+```
+
+Gemini uses `GEMINI_API_KEY` (or `models.providers.google.apiKey`). Override
+`memorySearch.remote.baseUrl` to point at a custom Gemini-compatible endpoint.
+
+If you want to use a **custom OpenAI-compatible endpoint** (like OpenRouter or a proxy),
 you can use the `remote` configuration:
 
 ```json5
@@ -99,8 +118,8 @@ agents: {
       provider: "openai",
       model: "text-embedding-3-small",
       remote: {
-        baseUrl: "https://generativelanguage.googleapis.com/v1beta/openai/",
+        baseUrl: "https://proxy.example/v1",
-        apiKey: "YOUR_GEMINI_API_KEY",
+        apiKey: "YOUR_PROXY_KEY",
         headers: { "X-Custom-Header": "value" }
       }
     }

docs/gateway/configuration-examples.md

@@ -261,10 +261,9 @@ Save to `~/.clawdbot/clawdbot.json` and you can DM the bot from that number.
         ackMaxChars: 300
       },
       memorySearch: {
-        provider: "openai",
+        provider: "gemini",
-        model: "text-embedding-004",
+        model: "gemini-embedding-001",
         remote: {
-          baseUrl: "https://generativelanguage.googleapis.com/v1beta/openai/",
           apiKey: "${GEMINI_API_KEY}"
         }
       },

src/agents/memory-search.test.ts

@@ -101,6 +101,26 @@ describe("memory search config", () => {
     expect(resolved?.remote).toBeUndefined();
   });
 
+  it("includes remote defaults for gemini without overrides", () => {
+    const cfg = {
+      agents: {
+        defaults: {
+          memorySearch: {
+            provider: "gemini",
+          },
+        },
+      },
+    };
+    const resolved = resolveMemorySearchConfig(cfg, "main");
+    expect(resolved?.remote?.batch).toEqual({
+      enabled: true,
+      wait: true,
+      concurrency: 2,
+      pollIntervalMs: 2000,
+      timeoutMinutes: 60,
+    });
+  });
+
   it("merges remote defaults with agent overrides", () => {
     const cfg = {
       agents: {

src/agents/memory-search.ts

@@ -9,7 +9,7 @@ import { resolveAgentConfig } from "./agent-scope.js";
 export type ResolvedMemorySearchConfig = {
   enabled: boolean;
   sources: Array<"memory" | "sessions">;
-  provider: "openai" | "local";
+  provider: "openai" | "gemini" | "local";
   remote?: {
     baseUrl?: string;
     apiKey?: string;
@@ -66,7 +66,8 @@ export type ResolvedMemorySearchConfig = {
   };
 };
 
-const DEFAULT_MODEL = "text-embedding-3-small";
+const DEFAULT_OPENAI_MODEL = "text-embedding-3-small";
+const DEFAULT_GEMINI_MODEL = "gemini-embedding-001";
 const DEFAULT_CHUNK_TOKENS = 400;
 const DEFAULT_CHUNK_OVERLAP = 80;
 const DEFAULT_WATCH_DEBOUNCE_MS = 1500;
@@ -111,7 +112,7 @@ function mergeConfig(
     overrides?.experimental?.sessionMemory ?? defaults?.experimental?.sessionMemory ?? false;
   const provider = overrides?.provider ?? defaults?.provider ?? "openai";
   const hasRemote = Boolean(defaults?.remote || overrides?.remote);
-  const includeRemote = hasRemote || provider === "openai";
+  const includeRemote = hasRemote || provider === "openai" || provider === "gemini";
   const batch = {
     enabled: overrides?.remote?.batch?.enabled ?? defaults?.remote?.batch?.enabled ?? true,
     wait: overrides?.remote?.batch?.wait ?? defaults?.remote?.batch?.wait ?? true,
@@ -133,7 +134,10 @@ function mergeConfig(
       }
     : undefined;
   const fallback = overrides?.fallback ?? defaults?.fallback ?? "openai";
-  const model = overrides?.model ?? defaults?.model ?? DEFAULT_MODEL;
+  const model =
+    overrides?.model ??
+    defaults?.model ??
+    (provider === "gemini" ? DEFAULT_GEMINI_MODEL : DEFAULT_OPENAI_MODEL);
   const local = {
     modelPath: overrides?.local?.modelPath ?? defaults?.local?.modelPath,
     modelCacheDir: overrides?.local?.modelCacheDir ?? defaults?.local?.modelCacheDir,

src/config/schema.ts

@@ -374,9 +374,9 @@ const FIELD_HELP: Record<string, string> = {
     'Sources to index for memory search (default: ["memory"]; add "sessions" to include session transcripts).',
   "agents.defaults.memorySearch.experimental.sessionMemory":
     "Enable experimental session transcript indexing for memory search (default: false).",
-  "agents.defaults.memorySearch.provider": 'Embedding provider ("openai" or "local").',
+  "agents.defaults.memorySearch.provider": 'Embedding provider ("openai", "gemini", or "local").',
   "agents.defaults.memorySearch.remote.baseUrl":
-    "Custom OpenAI-compatible base URL (e.g. for Gemini/OpenRouter proxies).",
+    "Custom base URL for remote embeddings (OpenAI-compatible proxies or Gemini overrides).",
   "agents.defaults.memorySearch.remote.apiKey": "Custom API key for the remote embedding provider.",
   "agents.defaults.memorySearch.remote.headers":
     "Extra headers for remote embeddings (merged; remote overrides OpenAI headers).",

src/config/types.tools.ts

@@ -170,7 +170,7 @@ export type MemorySearchConfig = {
     sessionMemory?: boolean;
   };
   /** Embedding provider mode. */
-  provider?: "openai" | "local";
+  provider?: "openai" | "gemini" | "local";
   remote?: {
     baseUrl?: string;
     apiKey?: string;

src/config/zod-schema.agent-runtime.ts

@@ -218,7 +218,7 @@ export const MemorySearchSchema = z
         sessionMemory: z.boolean().optional(),
       })
       .optional(),
-    provider: z.union([z.literal("openai"), z.literal("local")]).optional(),
+    provider: z.union([z.literal("openai"), z.literal("gemini"), z.literal("local")]).optional(),
     remote: z
       .object({
         baseUrl: z.string().optional(),

src/memory/embeddings.test.ts

@@ -107,6 +107,39 @@ describe("embedding provider remote overrides", () => {
     const headers = (fetchMock.mock.calls[0]?.[1]?.headers as Record<string, string>) ?? {};
     expect(headers.Authorization).toBe("Bearer provider-key");
   });
+
+  it("uses gemini embedContent endpoint with x-goog-api-key", async () => {
+    const fetchMock = vi.fn(async () => ({
+      ok: true,
+      status: 200,
+      json: async () => ({ embedding: { values: [1, 2, 3] } }),
+    })) as unknown as typeof fetch;
+    vi.stubGlobal("fetch", fetchMock);
+
+    const { createEmbeddingProvider } = await import("./embeddings.js");
+    const authModule = await import("../agents/model-auth.js");
+    vi.mocked(authModule.resolveApiKeyForProvider).mockResolvedValue({
+      apiKey: "gemini-key",
+    });
+
+    const result = await createEmbeddingProvider({
+      config: {} as never,
+      provider: "gemini",
+      remote: {
+        baseUrl: "https://gemini.example/v1beta",
+      },
+      model: "gemini-embedding-001",
+      fallback: "openai",
+    });
+
+    await result.provider.embedQuery("hello");
+
+    const [url, init] = fetchMock.mock.calls[0] ?? [];
+    expect(url).toBe("https://gemini.example/v1beta/models/gemini-embedding-001:embedContent");
+    const headers = (init?.headers ?? {}) as Record<string, string>;
+    expect(headers["x-goog-api-key"]).toBe("gemini-key");
+    expect(headers["Content-Type"]).toBe("application/json");
+  });
 });
 
 describe("embedding provider local fallback", () => {

src/memory/embeddings.ts

@@ -12,10 +12,11 @@ export type EmbeddingProvider = {
 
 export type EmbeddingProviderResult = {
   provider: EmbeddingProvider;
-  requestedProvider: "openai" | "local";
+  requestedProvider: "openai" | "gemini" | "local";
   fallbackFrom?: "local";
   fallbackReason?: string;
   openAi?: OpenAiEmbeddingClient;
+  gemini?: GeminiEmbeddingClient;
 };
 
 export type OpenAiEmbeddingClient = {
@@ -24,10 +25,16 @@ export type OpenAiEmbeddingClient = {
   model: string;
 };
 
+export type GeminiEmbeddingClient = {
+  baseUrl: string;
+  headers: Record<string, string>;
+  model: string;
+};
+
 export type EmbeddingProviderOptions = {
   config: ClawdbotConfig;
   agentDir?: string;
-  provider: "openai" | "local";
+  provider: "openai" | "gemini" | "local";
   remote?: {
     baseUrl?: string;
     apiKey?: string;
@@ -43,6 +50,8 @@ export type EmbeddingProviderOptions = {
 
 const DEFAULT_OPENAI_BASE_URL = "https://api.openai.com/v1";
 const DEFAULT_LOCAL_MODEL = "hf:ggml-org/embeddinggemma-300M-GGUF/embeddinggemma-300M-Q8_0.gguf";
+const DEFAULT_GEMINI_BASE_URL = "https://generativelanguage.googleapis.com/v1beta";
+const DEFAULT_GEMINI_MODEL = "gemini-embedding-001";
 
 function normalizeOpenAiModel(model: string): string {
   const trimmed = model.trim();
@@ -51,6 +60,14 @@ function normalizeOpenAiModel(model: string): string {
   return trimmed;
 }
 
+function normalizeGeminiModel(model: string): string {
+  const trimmed = model.trim();
+  if (!trimmed) return DEFAULT_GEMINI_MODEL;
+  if (trimmed.startsWith("models/")) return trimmed.slice("models/".length);
+  if (trimmed.startsWith("google/")) return trimmed.slice("google/".length);
+  return trimmed;
+}
+
 async function createOpenAiEmbeddingProvider(
   options: EmbeddingProviderOptions,
 ): Promise<{ provider: EmbeddingProvider; client: OpenAiEmbeddingClient }> {
@@ -89,6 +106,83 @@ async function createOpenAiEmbeddingProvider(
   };
 }
 
+function extractGeminiEmbeddingValues(entry: unknown): number[] {
+  if (!entry || typeof entry !== "object") return [];
+  const record = entry as { values?: unknown; embedding?: { values?: unknown } };
+  const values = record.values ?? record.embedding?.values;
+  if (!Array.isArray(values)) return [];
+  return values.filter((value): value is number => typeof value === "number");
+}
+
+function parseGeminiEmbeddings(payload: unknown): number[][] {
+  if (!payload || typeof payload !== "object") return [];
+  const data = payload as { embedding?: unknown; embeddings?: unknown[] };
+  if (Array.isArray(data.embeddings)) {
+    return data.embeddings.map((entry) => extractGeminiEmbeddingValues(entry));
+  }
+  if (data.embedding) {
+    return [extractGeminiEmbeddingValues(data.embedding)];
+  }
+  return [];
+}
+
+async function createGeminiEmbeddingProvider(
+  options: EmbeddingProviderOptions,
+): Promise<{ provider: EmbeddingProvider; client: GeminiEmbeddingClient }> {
+  const client = await resolveGeminiEmbeddingClient(options);
+  const baseUrl = client.baseUrl.replace(/\/$/, "");
+  const model = `models/${client.model}`;
+
+  const embedContent = async (input: string): Promise<number[]> => {
+    const res = await fetch(`${baseUrl}/${model}:embedContent`, {
+      method: "POST",
+      headers: client.headers,
+      body: JSON.stringify({
+        model,
+        content: { parts: [{ text: input }] },
+      }),
+    });
+    if (!res.ok) {
+      const text = await res.text();
+      throw new Error(`gemini embeddings failed: ${res.status} ${text}`);
+    }
+    const payload = await res.json();
+    const embeddings = parseGeminiEmbeddings(payload);
+    return embeddings[0] ?? [];
+  };
+
+  const embedBatch = async (input: string[]): Promise<number[][]> => {
+    if (input.length === 0) return [];
+    const res = await fetch(`${baseUrl}/${model}:batchEmbedContents`, {
+      method: "POST",
+      headers: client.headers,
+      body: JSON.stringify({
+        requests: input.map((text) => ({
+          model,
+          content: { parts: [{ text }] },
+        })),
+      }),
+    });
+    if (!res.ok) {
+      const text = await res.text();
+      throw new Error(`gemini embeddings failed: ${res.status} ${text}`);
+    }
+    const payload = await res.json();
+    const embeddings = parseGeminiEmbeddings(payload);
+    return embeddings;
+  };
+
+  return {
+    provider: {
+      id: "gemini",
+      model: client.model,
+      embedQuery: embedContent,
+      embedBatch,
+    },
+    client,
+  };
+}
+
 async function resolveOpenAiEmbeddingClient(
   options: EmbeddingProviderOptions,
 ): Promise<OpenAiEmbeddingClient> {
@@ -116,6 +210,33 @@ async function resolveOpenAiEmbeddingClient(
   return { baseUrl, headers, model };
 }
 
+async function resolveGeminiEmbeddingClient(
+  options: EmbeddingProviderOptions,
+): Promise<GeminiEmbeddingClient> {
+  const remote = options.remote;
+  const remoteApiKey = remote?.apiKey?.trim();
+  const remoteBaseUrl = remote?.baseUrl?.trim();
+
+  const { apiKey } = remoteApiKey
+    ? { apiKey: remoteApiKey }
+    : await resolveApiKeyForProvider({
+        provider: "google",
+        cfg: options.config,
+        agentDir: options.agentDir,
+      });
+
+  const providerConfig = options.config.models?.providers?.google;
+  const baseUrl = remoteBaseUrl || providerConfig?.baseUrl?.trim() || DEFAULT_GEMINI_BASE_URL;
+  const headerOverrides = Object.assign({}, providerConfig?.headers, remote?.headers);
+  const headers: Record<string, string> = {
+    "Content-Type": "application/json",
+    "x-goog-api-key": apiKey,
+    ...headerOverrides,
+  };
+  const model = normalizeGeminiModel(options.model);
+  return { baseUrl, headers, model };
+}
+
 async function createLocalEmbeddingProvider(
   options: EmbeddingProviderOptions,
 ): Promise<EmbeddingProvider> {
@@ -168,6 +289,10 @@ export async function createEmbeddingProvider(
   options: EmbeddingProviderOptions,
 ): Promise<EmbeddingProviderResult> {
   const requestedProvider = options.provider;
+  if (options.provider === "gemini") {
+    const { provider, client } = await createGeminiEmbeddingProvider(options);
+    return { provider, requestedProvider, gemini: client };
+  }
   if (options.provider === "local") {
     try {
       const provider = await createLocalEmbeddingProvider(options);

src/memory/manager.atomic-reindex.test.ts

@@ -0,0 +1,91 @@
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+import { getMemorySearchManager, type MemoryIndexManager } from "./index.js";
+
+let shouldFail = false;
+
+vi.mock("chokidar", () => ({
+  default: {
+    watch: vi.fn(() => ({
+      on: vi.fn(),
+      close: vi.fn(async () => undefined),
+    })),
+  },
+}));
+
+vi.mock("./embeddings.js", () => {
+  return {
+    createEmbeddingProvider: async () => ({
+      requestedProvider: "openai",
+      provider: {
+        id: "mock",
+        model: "mock-embed",
+        embedQuery: async () => [0.1, 0.2, 0.3],
+        embedBatch: async (texts: string[]) => {
+          if (shouldFail) {
+            throw new Error("embedding failure");
+          }
+          return texts.map((_, index) => [index + 1, 0, 0]);
+        },
+      },
+    }),
+  };
+});
+
+describe("memory manager atomic reindex", () => {
+  let workspaceDir: string;
+  let indexPath: string;
+  let manager: MemoryIndexManager | null = null;
+
+  beforeEach(async () => {
+    shouldFail = false;
+    workspaceDir = await fs.mkdtemp(path.join(os.tmpdir(), "clawdbot-mem-"));
+    indexPath = path.join(workspaceDir, "index.sqlite");
+    await fs.mkdir(path.join(workspaceDir, "memory"));
+    await fs.writeFile(path.join(workspaceDir, "MEMORY.md"), "Hello memory.");
+  });
+
+  afterEach(async () => {
+    if (manager) {
+      await manager.close();
+      manager = null;
+    }
+    await fs.rm(workspaceDir, { recursive: true, force: true });
+  });
+
+  it("keeps the prior index when a full reindex fails", async () => {
+    const cfg = {
+      agents: {
+        defaults: {
+          workspace: workspaceDir,
+          memorySearch: {
+            provider: "openai",
+            model: "mock-embed",
+            store: { path: indexPath },
+            sync: { watch: false, onSessionStart: false, onSearch: false },
+          },
+        },
+        list: [{ id: "main", default: true }],
+      },
+    };
+
+    const result = await getMemorySearchManager({ cfg, agentId: "main" });
+    expect(result.manager).not.toBeNull();
+    if (!result.manager) throw new Error("manager missing");
+    manager = result.manager;
+
+    await manager.sync({ force: true });
+    const before = await manager.search("Hello");
+    expect(before.length).toBeGreaterThan(0);
+
+    shouldFail = true;
+    await expect(manager.sync({ force: true })).rejects.toThrow("embedding failure");
+
+    const after = await manager.search("Hello");
+    expect(after.length).toBeGreaterThan(0);
+  });
+});

src/memory/manager.ts

@@ -16,6 +16,7 @@ import {
   createEmbeddingProvider,
   type EmbeddingProvider,
   type EmbeddingProviderResult,
+  type GeminiEmbeddingClient,
   type OpenAiEmbeddingClient,
 } from "./embeddings.js";
 import {
@@ -104,9 +105,10 @@ export class MemoryIndexManager {
   private readonly workspaceDir: string;
   private readonly settings: ResolvedMemorySearchConfig;
   private readonly provider: EmbeddingProvider;
-  private readonly requestedProvider: "openai" | "local";
+  private readonly requestedProvider: "openai" | "gemini" | "local";
   private readonly fallbackReason?: string;
   private readonly openAi?: OpenAiEmbeddingClient;
+  private readonly gemini?: GeminiEmbeddingClient;
   private readonly batch: {
     enabled: boolean;
     wait: boolean;
@@ -114,7 +116,7 @@ export class MemoryIndexManager {
     pollIntervalMs: number;
     timeoutMs: number;
   };
-  private readonly db: DatabaseSync;
+  private db: DatabaseSync;
   private readonly sources: Set<MemorySource>;
   private readonly providerKey: string;
   private readonly cache: { enabled: boolean; maxEntries?: number };
@@ -142,6 +144,7 @@ export class MemoryIndexManager {
   private sessionsDirtyFiles = new Set<string>();
   private sessionWarm = new Set<string>();
   private syncing: Promise<void> | null = null;
+  private readonly allowAtomicReindex: boolean;
 
   static async get(params: {
     cfg: ClawdbotConfig;
@@ -182,6 +185,7 @@ export class MemoryIndexManager {
     workspaceDir: string;
     settings: ResolvedMemorySearchConfig;
     providerResult: EmbeddingProviderResult;
+    options?: { allowAtomicReindex?: boolean; enableBackgroundSync?: boolean };
   }) {
     this.cacheKey = params.cacheKey;
     this.cfg = params.cfg;
@@ -192,6 +196,8 @@ export class MemoryIndexManager {
     this.requestedProvider = params.providerResult.requestedProvider;
     this.fallbackReason = params.providerResult.fallbackReason;
     this.openAi = params.providerResult.openAi;
+    this.gemini = params.providerResult.gemini;
+    this.allowAtomicReindex = params.options?.allowAtomicReindex ?? true;
     this.sources = new Set(params.settings.sources);
     this.db = this.openDatabase();
     this.providerKey = computeEmbeddingProviderKey({
@@ -200,6 +206,13 @@ export class MemoryIndexManager {
       openAi: this.openAi
         ? { baseUrl: this.openAi.baseUrl, model: this.openAi.model, headers: this.openAi.headers }
         : undefined,
+      gemini: this.gemini
+        ? {
+            baseUrl: this.gemini.baseUrl,
+            model: this.gemini.model,
+            headers: this.gemini.headers,
+          }
+        : undefined,
     });
     this.cache = {
       enabled: params.settings.cache.enabled,
@@ -216,9 +229,12 @@ export class MemoryIndexManager {
     if (meta?.vectorDims) {
       this.vector.dims = meta.vectorDims;
     }
+    const enableBackgroundSync = params.options?.enableBackgroundSync ?? true;
+    if (enableBackgroundSync) {
       this.ensureWatcher();
       this.ensureSessionListener();
       this.ensureIntervalSync();
+    }
     this.dirty = this.sources.has("memory");
     if (this.sources.has("sessions")) {
       this.sessionsDirty = true;
@@ -782,7 +798,7 @@ export class MemoryIndexManager {
     force?: boolean;
     progress?: (update: MemorySyncProgressUpdate) => void;
   }) {
-    const progress = params?.progress ? this.createSyncProgress(params.progress) : undefined;
+    const progressCallback = params?.progress;
     const vectorReady = await this.ensureVectorReady();
     const meta = this.readMeta();
     const needsFullReindex =
@@ -794,6 +810,12 @@ export class MemoryIndexManager {
       meta.chunkTokens !== this.settings.chunking.tokens ||
       meta.chunkOverlap !== this.settings.chunking.overlap ||
       (vectorReady && !meta?.vectorDims);
+    if (needsFullReindex && this.allowAtomicReindex) {
+      await this.runAtomicReindex({ reason: params?.reason, progress: progressCallback });
+      return;
+    }
+
+    const progress = progressCallback ? this.createSyncProgress(progressCallback) : undefined;
     if (needsFullReindex) {
       this.resetIndex();
     }
@@ -833,6 +855,126 @@ export class MemoryIndexManager {
     }
   }
 
+  private createScratchManager(tempPath: string): MemoryIndexManager {
+    const scratchSettings: ResolvedMemorySearchConfig = {
+      ...this.settings,
+      store: {
+        ...this.settings.store,
+        path: tempPath,
+      },
+      sync: {
+        ...this.settings.sync,
+        watch: false,
+        intervalMinutes: 0,
+      },
+    };
+
+    return new MemoryIndexManager({
+      cacheKey: `${this.cacheKey}:scratch:${Date.now()}`,
+      cfg: this.cfg,
+      agentId: this.agentId,
+      workspaceDir: this.workspaceDir,
+      settings: scratchSettings,
+      providerResult: {
+        provider: this.provider,
+        requestedProvider: this.requestedProvider,
+        fallbackReason: this.fallbackReason,
+        openAi: this.openAi,
+        gemini: this.gemini,
+      },
+      options: {
+        allowAtomicReindex: false,
+        enableBackgroundSync: false,
+      },
+    });
+  }
+
+  private buildTempIndexPath(): string {
+    const basePath = resolveUserPath(this.settings.store.path);
+    const dir = path.dirname(basePath);
+    ensureDir(dir);
+    const stamp = `${Date.now()}-${Math.random().toString(16).slice(2, 10)}`;
+    return path.join(dir, `${path.basename(basePath)}.tmp-${stamp}`);
+  }
+
+  private reopenDatabase() {
+    this.db = this.openDatabase();
+    this.fts.available = false;
+    this.fts.loadError = undefined;
+    this.ensureSchema();
+    this.vector.available = null;
+    this.vector.loadError = undefined;
+    this.vectorReady = null;
+    this.vector.dims = undefined;
+    const meta = this.readMeta();
+    if (meta?.vectorDims) {
+      this.vector.dims = meta.vectorDims;
+    }
+  }
+
+  private async swapIndexFile(tempPath: string): Promise<void> {
+    const dbPath = resolveUserPath(this.settings.store.path);
+    const backupPath = `${dbPath}.bak-${Date.now()}`;
+    let hasBackup = false;
+    let shouldReopen = false;
+
+    this.db.close();
+
+    try {
+      try {
+        await fs.rename(dbPath, backupPath);
+        hasBackup = true;
+      } catch (err) {
+        const code = (err as NodeJS.ErrnoException).code;
+        if (code !== "ENOENT") throw err;
+      }
+      await fs.rename(tempPath, dbPath);
+      shouldReopen = true;
+      if (hasBackup) {
+        await fs.rm(backupPath, { force: true });
+      }
+    } catch (err) {
+      if (hasBackup) {
+        try {
+          await fs.rename(backupPath, dbPath);
+          shouldReopen = true;
+        } catch {}
+      }
+      if (!shouldReopen) {
+        try {
+          await fs.access(dbPath);
+          shouldReopen = true;
+        } catch {}
+      }
+      throw err;
+    } finally {
+      await fs.rm(tempPath, { force: true });
+      if (shouldReopen) {
+        this.reopenDatabase();
+      }
+    }
+  }
+
+  private async runAtomicReindex(params: {
+    reason?: string;
+    progress?: (update: MemorySyncProgressUpdate) => void;
+  }) {
+    const tempPath = this.buildTempIndexPath();
+    const scratch = this.createScratchManager(tempPath);
+    try {
+      await scratch.sync({ reason: params.reason, force: true, progress: params.progress });
+    } catch (err) {
+      await fs.rm(tempPath, { force: true });
+      throw err;
+    } finally {
+      await scratch.close().catch(() => undefined);
+    }
+    await this.swapIndexFile(tempPath);
+    this.dirty = false;
+    this.sessionsDirty = false;
+    this.sessionsDirtyFiles.clear();
+  }
+
   private resetIndex() {
     this.db.exec(`DELETE FROM files`);
     this.db.exec(`DELETE FROM chunks`);

src/memory/provider-key.ts

@@ -5,6 +5,7 @@ export function computeEmbeddingProviderKey(params: {
   providerId: string;
   providerModel: string;
   openAi?: { baseUrl: string; model: string; headers: Record<string, string> };
+  gemini?: { baseUrl: string; model: string; headers: Record<string, string> };
 }): string {
   if (params.openAi) {
     const headerNames = fingerprintHeaderNames(params.openAi.headers);
@@ -17,5 +18,16 @@ export function computeEmbeddingProviderKey(params: {
       }),
     );
   }
+  if (params.gemini) {
+    const headerNames = fingerprintHeaderNames(params.gemini.headers);
+    return hashText(
+      JSON.stringify({
+        provider: "gemini",
+        baseUrl: params.gemini.baseUrl,
+        model: params.gemini.model,
+        headerNames,
+      }),
+    );
+  }
   return hashText(JSON.stringify({ provider: params.providerId, model: params.providerModel }));
 }