diff --git a/src/__tests__/extension.spec.ts b/src/__tests__/extension.spec.ts
index bb72d567dd..c6485f4abe 100644
--- a/src/__tests__/extension.spec.ts
+++ b/src/__tests__/extension.spec.ts
@@ -139,8 +139,8 @@ vi.mock("../services/mcp/McpServerManager", () => ({
 	},
 }))
 
-vi.mock("../services/code-index/manager", () => ({
-	CodeIndexManager: {
+vi.mock("../services/code-index/code-index-manager-registry", () => ({
+	CodeIndexManagerRegistry: {
 		getInstance: vi.fn().mockReturnValue(null),
 	},
 }))
diff --git a/src/activate/__tests__/registerCommands.spec.ts b/src/activate/__tests__/registerCommands.spec.ts
index 67a2b935ec..88e96f80be 100644
--- a/src/activate/__tests__/registerCommands.spec.ts
+++ b/src/activate/__tests__/registerCommands.spec.ts
@@ -67,8 +67,8 @@ vi.mock("../../core/config/importExport", () => ({
 	importSettingsWithFeedback: vi.fn(),
 }))
 
-vi.mock("../../services/code-index/manager", () => ({
-	CodeIndexManager: {
+vi.mock("../../services/code-index/code-index-manager-registry", () => ({
+	CodeIndexManagerRegistry: {
 		getInstance: vi.fn(),
 	},
 }))
diff --git a/src/activate/registerCommands.ts b/src/activate/registerCommands.ts
index 692aabfd68..f062b56eab 100644
--- a/src/activate/registerCommands.ts
+++ b/src/activate/registerCommands.ts
@@ -10,7 +10,7 @@ import { ClineProvider } from "../core/webview/ClineProvider"
 import { ContextProxy } from "../core/config/ContextProxy"
 import { focusPanel } from "../utils/focusPanel"
 import { handleNewTask } from "./handleTask"
-import { CodeIndexManager } from "../services/code-index/manager"
+import { CodeIndexManagerRegistry } from "../services/code-index/code-index-manager-registry"
 import { importSettingsWithFeedback } from "../core/config/importExport"
 import { MdmService } from "../services/mdm/MdmService"
 import { registerRipgrepDiagnosticCommand } from "../services/ripgrep/diagnostic"
@@ -227,7 +227,7 @@ export const openClineInNewTab = async ({ context, outputChannel }: Omit<Registe
 	// don't need to use that event).
 	// https://github.com/microsoft/vscode-extension-samples/blob/main/webview-sample/src/extension.ts
 	const contextProxy = await ContextProxy.getInstance(context)
-	const codeIndexManager = CodeIndexManager.getInstance(context)
+	const codeIndexManager = CodeIndexManagerRegistry.getInstance(context)
 
 	// Get the existing MDM service instance to ensure consistent policy enforcement
 	let mdmService: MdmService | undefined
diff --git a/src/core/prompts/system.ts b/src/core/prompts/system.ts
index 93f4a52846..fe5db965e9 100644
--- a/src/core/prompts/system.ts
+++ b/src/core/prompts/system.ts
@@ -8,7 +8,7 @@ import { formatLanguage } from "../../shared/language"
 import { isEmpty } from "../../utils/object"
 
 import { McpHub } from "../../services/mcp/McpHub"
-import { CodeIndexManager } from "../../services/code-index/manager"
+import { CodeIndexManagerRegistry } from "../../services/code-index/code-index-manager-registry"
 import { SkillsManager } from "../../services/skills/SkillsManager"
 
 import type { SystemPromptSettings } from "./types"
@@ -79,7 +79,7 @@ async function generatePrompt(
 	}
 	const shouldIncludeMcp = hasMcpGroup && hasMcpServers
 
-	const codeIndexManager = CodeIndexManager.getInstance(context, cwd)
+	const codeIndexManager = CodeIndexManagerRegistry.getInstance(context, cwd)
 
 	// Tool calling is native-only.
 	const effectiveProtocol = "native"
diff --git a/src/core/prompts/tools/__tests__/codebase-search-readiness.spec.ts b/src/core/prompts/tools/__tests__/codebase-search-readiness.spec.ts
new file mode 100644
index 0000000000..2da17edc6d
--- /dev/null
+++ b/src/core/prompts/tools/__tests__/codebase-search-readiness.spec.ts
@@ -0,0 +1,89 @@
+import type OpenAI from "openai"
+import type { ModeConfig } from "@roo-code/types"
+import type { CodeIndexManager } from "../../../../services/code-index/manager"
+import { filterNativeToolsForMode, getAvailableToolsInGroup, isToolAllowedInMode } from "../filter-tools-for-mode"
+
+type Readiness = Pick<CodeIndexManager, "isFeatureEnabled" | "isFeatureConfigured" | "isInitialized">
+
+function makeManager(flags: Readiness): CodeIndexManager {
+	// These filters only read the three public readiness getters; no manager services are needed.
+	return flags as CodeIndexManager
+}
+
+const ready = { isFeatureEnabled: true, isFeatureConfigured: true, isInitialized: true }
+const nativeTools: OpenAI.Chat.ChatCompletionTool[] = [
+	"codebase_search",
+	"read_file",
+	"list_files",
+	"search_files",
+].map((name) => ({ type: "function", function: { name, parameters: { type: "object", properties: {} } } }))
+const noReadMode: ModeConfig = { slug: "no-read", name: "No read", roleDefinition: "No reading", groups: ["command"] }
+
+function checkAvailability(
+	manager: CodeIndexManager | undefined,
+	expected: boolean,
+	mode = "code",
+	settings: { disabledTools?: string[] } = {},
+) {
+	const names = filterNativeToolsForMode(nativeTools, mode, [noReadMode], {}, manager, settings).flatMap((tool) =>
+		"function" in tool ? [tool.function.name] : [],
+	)
+	const group = getAvailableToolsInGroup("read", mode, [noReadMode], {}, manager, settings)
+	expect(names.includes("codebase_search")).toBe(expected)
+	expect(isToolAllowedInMode("codebase_search", mode, [noReadMode], {}, manager, settings)).toBe(expected)
+	expect(group.includes("codebase_search")).toBe(expected)
+	for (const tool of ["read_file", "list_files", "search_files"] as const) {
+		expect(names.includes(tool)).toBe(mode === "code")
+		expect(isToolAllowedInMode(tool, mode, [noReadMode], {}, manager, settings)).toBe(mode === "code")
+		expect(group.includes(tool)).toBe(mode === "code")
+	}
+}
+
+describe("codebase_search readiness across mode filtering APIs", () => {
+	it("excludes search without a manager while retaining ordinary read tools", () => {
+		checkAvailability(undefined, false)
+	})
+
+	for (const isFeatureEnabled of [false, true]) {
+		for (const isFeatureConfigured of [false, true]) {
+			for (const isInitialized of [false, true]) {
+				it(`agrees for enabled=${isFeatureEnabled}, configured=${isFeatureConfigured}, initialized=${isInitialized}`, () => {
+					checkAvailability(
+						makeManager({ isFeatureEnabled, isFeatureConfigured, isInitialized }),
+						isFeatureEnabled && isFeatureConfigured && isInitialized,
+					)
+				})
+			}
+		}
+	}
+
+	it.each(["isFeatureEnabled", "isFeatureConfigured", "isInitialized"] as const)(
+		"rereads live %s changes",
+		(flag) => {
+			const flags = { ...ready }
+			const manager = makeManager(flags)
+			checkAvailability(manager, true)
+			flags[flag] = false
+			checkAvailability(manager, false)
+			flags[flag] = true
+			checkAvailability(manager, true)
+		},
+	)
+
+	it("keeps alternating managers isolated", () => {
+		const enabled = makeManager({ ...ready })
+		const disabled = makeManager({ ...ready, isFeatureEnabled: false })
+		checkAvailability(enabled, true)
+		checkAvailability(disabled, false)
+		checkAvailability(undefined, false)
+		checkAvailability(enabled, true)
+	})
+
+	it("does not bypass a mode without the read group", () => {
+		checkAvailability(makeManager({ ...ready }), false, "no-read")
+	})
+
+	it("does not bypass disabledTools with a ready manager", () => {
+		checkAvailability(makeManager({ ...ready }), false, "code", { disabledTools: ["codebase_search"] })
+	})
+})
diff --git a/src/core/prompts/tools/filter-tools-for-mode.ts b/src/core/prompts/tools/filter-tools-for-mode.ts
index 2b31714a4c..828f9b877a 100644
--- a/src/core/prompts/tools/filter-tools-for-mode.ts
+++ b/src/core/prompts/tools/filter-tools-for-mode.ts
@@ -376,17 +376,22 @@ export function isToolAllowedInMode(
 ): boolean {
 	const modeSlug = mode ?? defaultModeSlug
 
+	// codebase_search belongs to the read group, not ALWAYS_AVAILABLE_TOOLS.
+	// Readiness can deny access, but must not bypass mode or disabled-tool restrictions.
+	if (
+		toolName === "codebase_search" &&
+		(!codeIndexManager ||
+			!codeIndexManager.isFeatureEnabled ||
+			!codeIndexManager.isFeatureConfigured ||
+			!codeIndexManager.isInitialized ||
+			settings?.disabledTools?.includes(toolName))
+	) {
+		return false
+	}
+
 	// Check if it's an always-available tool
 	if (ALWAYS_AVAILABLE_TOOLS.includes(toolName)) {
 		// But still check for conditional exclusions
-		if (toolName === "codebase_search") {
-			return !!(
-				codeIndexManager &&
-				codeIndexManager.isFeatureEnabled &&
-				codeIndexManager.isFeatureConfigured &&
-				codeIndexManager.isInitialized
-			)
-		}
 		if (toolName === "update_todo_list") {
 			return settings?.todoListEnabled !== false
 		}
diff --git a/src/core/task/__tests__/Task.spec.ts b/src/core/task/__tests__/Task.spec.ts
index 1bcacd459c..dfe410bdb6 100644
--- a/src/core/task/__tests__/Task.spec.ts
+++ b/src/core/task/__tests__/Task.spec.ts
@@ -131,6 +131,13 @@ vi.mock("p-wait-for", () => ({
 	default: vi.fn().mockImplementation(async () => Promise.resolve()),
 }))
 
+// Task tests do not exercise indexing; keep workspace resolution and its cache out of this suite.
+vi.mock("../../../services/code-index/code-index-manager-registry", () => ({
+	CodeIndexManagerRegistry: {
+		getInstance: vi.fn().mockReturnValue(undefined),
+	},
+}))
+
 vi.mock("vscode", () => {
 	const mockDisposable = { dispose: vi.fn() }
 	const mockEventEmitter = { event: vi.fn(), fire: vi.fn() }
diff --git a/src/core/task/__tests__/build-tools-readiness.integration.spec.ts b/src/core/task/__tests__/build-tools-readiness.integration.spec.ts
new file mode 100644
index 0000000000..32ad7c02ed
--- /dev/null
+++ b/src/core/task/__tests__/build-tools-readiness.integration.spec.ts
@@ -0,0 +1,74 @@
+import type OpenAI from "openai"
+import type { CodeIndexManager } from "../../../services/code-index/manager"
+import { CodeIndexManagerRegistry } from "../../../services/code-index/code-index-manager-registry"
+import { makeExtensionContext } from "../../../test-utils/vscode"
+import type { ClineProvider } from "../../webview/ClineProvider"
+import { buildNativeToolsArrayWithRestrictions } from "../build-tools"
+
+vi.mock("../../../services/code-index/code-index-manager-registry", () => ({
+	CodeIndexManagerRegistry: { getInstance: vi.fn() },
+}))
+
+function toolNames(tools: OpenAI.Chat.ChatCompletionTool[]) {
+	return tools.flatMap((tool) => ("function" in tool ? [tool.function.name] : []))
+}
+
+describe("task tool building with real readiness filtering", () => {
+	beforeEach(() => vi.clearAllMocks())
+
+	it.each([false, true])("uses task cwd/context and live manager readiness (restrictions=%s)", async (restricted) => {
+		const context = makeExtensionContext()
+		// The builder only consumes context and getMcpHub; avoid constructing the webview provider.
+		const provider = { context, getMcpHub: () => undefined } as ClineProvider
+		const flags = { isFeatureEnabled: true, isFeatureConfigured: true, isInitialized: true }
+		// Only the public readiness getters are consumed by the real filter.
+		const readyManager = flags as CodeIndexManager
+		const unreadyManager = { ...flags, isInitialized: false } as CodeIndexManager
+		const managers = new Map([
+			["/tasks/ready", readyManager],
+			["/tasks/unready", unreadyManager],
+		])
+		vi.mocked(CodeIndexManagerRegistry.getInstance).mockImplementation((receivedContext, cwd) => {
+			expect(receivedContext).toBe(context)
+			return managers.get(cwd ?? "")
+		})
+
+		async function check(cwd: string, expected: boolean, mode = "code", disabledTools: string[] = []) {
+			const result = await buildNativeToolsArrayWithRestrictions({
+				provider,
+				cwd,
+				mode,
+				customModes: [{ slug: "no-read", name: "No read", roleDefinition: "No reading", groups: ["command"] }],
+				experiments: {},
+				apiConfiguration: {},
+				disabledTools,
+				includeAllToolsWithRestrictions: restricted,
+			})
+			expect(CodeIndexManagerRegistry.getInstance).toHaveBeenLastCalledWith(context, cwd)
+			const definitions = toolNames(result.tools)
+			const callable = restricted ? result.allowedFunctionNames : definitions
+			expect(callable).toBeDefined()
+			expect(callable?.includes("codebase_search")).toBe(expected)
+			expect(callable?.includes("read_file")).toBe(mode === "code")
+			if (restricted) {
+				// Historical definitions remain present; only allowedFunctionNames controls calls.
+				expect(definitions).toContain("codebase_search")
+			} else {
+				expect(result.allowedFunctionNames).toBeUndefined()
+			}
+		}
+
+		await check("/tasks/ready", true)
+		await check("/tasks/unready", false)
+		await check("/tasks/missing", false)
+		await check("/tasks/ready", true)
+		for (const flag of ["isFeatureEnabled", "isFeatureConfigured", "isInitialized"] as const) {
+			flags[flag] = false
+			await check("/tasks/ready", false)
+			flags[flag] = true
+			await check("/tasks/ready", true)
+		}
+		await check("/tasks/ready", false, "no-read")
+		await check("/tasks/ready", false, "code", ["codebase_search"])
+	})
+})
diff --git a/src/core/task/build-tools.ts b/src/core/task/build-tools.ts
index ebbdc050dc..998e14de97 100644
--- a/src/core/task/build-tools.ts
+++ b/src/core/task/build-tools.ts
@@ -96,8 +96,8 @@ export async function buildNativeToolsArrayWithRestrictions(options: BuildToolsO
 	const mcpHub = provider.getMcpHub()
 
 	// Get CodeIndexManager for feature checking.
-	const { CodeIndexManager } = await import("../../services/code-index/manager")
-	const codeIndexManager = CodeIndexManager.getInstance(provider.context, cwd)
+	const { CodeIndexManagerRegistry } = await import("../../services/code-index/code-index-manager-registry")
+	const codeIndexManager = CodeIndexManagerRegistry.getInstance(provider.context, cwd)
 
 	// Build settings object for tool filtering.
 	const filterSettings = {
diff --git a/src/core/tools/CodebaseSearchTool.ts b/src/core/tools/CodebaseSearchTool.ts
index f0d906fabd..afc5ee0dd0 100644
--- a/src/core/tools/CodebaseSearchTool.ts
+++ b/src/core/tools/CodebaseSearchTool.ts
@@ -2,7 +2,7 @@ import * as vscode from "vscode"
 import path from "path"
 
 import { Task } from "../task/Task"
-import { CodeIndexManager } from "../../services/code-index/manager"
+import { CodeIndexManagerRegistry } from "../../services/code-index/code-index-manager-registry"
 import { getWorkspacePath } from "../../utils/path"
 import { formatResponse } from "../prompts/responses"
 import { VectorStoreSearchResult } from "../../services/code-index/interfaces"
@@ -57,7 +57,7 @@ export class CodebaseSearchTool extends BaseTool<"codebase_search"> {
 				throw new Error("Extension context is not available.")
 			}
 
-			const manager = CodeIndexManager.getInstance(context)
+			const manager = CodeIndexManagerRegistry.getInstance(context)
 
 			if (!manager) {
 				throw new Error("CodeIndexManager is not available.")
diff --git a/src/core/webview/ClineProvider.ts b/src/core/webview/ClineProvider.ts
index 495fe454b7..854c02899d 100644
--- a/src/core/webview/ClineProvider.ts
+++ b/src/core/webview/ClineProvider.ts
@@ -91,6 +91,7 @@ import { McpServerManager } from "../../services/mcp/McpServerManager"
 import { MarketplaceManager } from "../../services/marketplace"
 import { ShadowCheckpointService } from "../../services/checkpoints/ShadowCheckpointService"
 import { CodeIndexManager } from "../../services/code-index/manager"
+import { CodeIndexManagerRegistry } from "../../services/code-index/code-index-manager-registry"
 import type { IndexProgressUpdate } from "../../services/code-index/interfaces/manager"
 import { MdmService } from "../../services/mdm/MdmService"
 import { SkillsManager } from "../../services/skills/SkillsManager"
@@ -3307,7 +3308,7 @@ export class ClineProvider
 	 * @returns CodeIndexManager instance for the current workspace or the default one
 	 */
 	public getCurrentWorkspaceCodeIndexManager(): CodeIndexManager | undefined {
-		return CodeIndexManager.getInstance(this.context)
+		return CodeIndexManagerRegistry.getInstance(this.context)
 	}
 
 	/**
diff --git a/src/core/webview/__tests__/ClineProvider.spec.ts b/src/core/webview/__tests__/ClineProvider.spec.ts
index bfd4706dcc..97c4dd877e 100644
--- a/src/core/webview/__tests__/ClineProvider.spec.ts
+++ b/src/core/webview/__tests__/ClineProvider.spec.ts
@@ -3225,7 +3225,7 @@ describe("webviewMessageHandler no-floating-promises coverage", () => {
 	})
 
 	it("catches auto-enabled indexing failures and posts the resulting status", async () => {
-		const { CodeIndexManager } = await import("../../../services/code-index/manager")
+		const { CodeIndexManagerRegistry } = await import("../../../services/code-index/code-index-manager-registry")
 		let workspaceEnabled = false
 		const manager = createIndexManager({
 			setAutoEnableDefault: vi.fn().mockImplementation(async () => {
@@ -3235,8 +3235,8 @@ describe("webviewMessageHandler no-floating-promises coverage", () => {
 		})
 		Object.defineProperty(manager, "isWorkspaceEnabled", { get: () => workspaceEnabled })
 		const getAllInstances = vi
-			.spyOn(CodeIndexManager, "getAllInstances")
-			.mockReturnValue([manager] as unknown as ReturnType<typeof CodeIndexManager.getAllInstances>)
+			.spyOn(CodeIndexManagerRegistry, "getAllInstances")
+			.mockReturnValue([manager] as unknown as ReturnType<typeof CodeIndexManagerRegistry.getAllInstances>)
 		const provider = createProvider({
 			getCurrentWorkspaceCodeIndexManager: vi.fn().mockReturnValue(manager),
 		})
diff --git a/src/core/webview/webviewMessageHandler.ts b/src/core/webview/webviewMessageHandler.ts
index 0dad65a480..34a35ea3ca 100644
--- a/src/core/webview/webviewMessageHandler.ts
+++ b/src/core/webview/webviewMessageHandler.ts
@@ -62,7 +62,7 @@ import { Package } from "../../shared/package"
 import { type RouterName, toRouterName } from "../../shared/api"
 import { MessageEnhancer } from "./messageEnhancer"
 
-import { CodeIndexManager } from "../../services/code-index/manager"
+import { CodeIndexManagerRegistry } from "../../services/code-index/code-index-manager-registry"
 import { checkExistKey } from "../../shared/checkExistApiConfig"
 import { getRouterRemovalMessage, getRouterUnavailableSignInMessage } from "../config/routerRemoval"
 import { experimentDefault } from "../../shared/experiments"
@@ -3311,7 +3311,7 @@ export const webviewMessageHandler = async (
 					return
 				}
 				// Capture prior state for every manager before persisting the global change
-				const allManagers = CodeIndexManager.getAllInstances()
+				const allManagers = CodeIndexManagerRegistry.getAllInstances()
 				const priorStates = new Map(allManagers.map((m) => [m, m.isWorkspaceEnabled]))
 				await manager.setAutoEnableDefault(message.bool ?? true)
 				// Apply stop/start to every affected manager
diff --git a/src/eslint-suppressions.json b/src/eslint-suppressions.json
index d90272962b..0e5207046c 100644
--- a/src/eslint-suppressions.json
+++ b/src/eslint-suppressions.json
@@ -1301,7 +1301,7 @@
 	},
 	"services/code-index/__tests__/manager.spec.ts": {
 		"@typescript-eslint/no-explicit-any": {
-			"count": 89
+			"count": 87
 		}
 	},
 	"services/code-index/__tests__/orchestrator.spec.ts": {
diff --git a/src/extension.ts b/src/extension.ts
index 0a78cd32ba..13bcf61666 100644
--- a/src/extension.ts
+++ b/src/extension.ts
@@ -35,6 +35,7 @@ import { openAiCodexOAuthManager } from "./integrations/openai-codex/oauth"
 import { kimiCodeOAuthManager } from "./integrations/kimi-code/oauth"
 import { McpServerManager } from "./services/mcp/McpServerManager"
 import { CodeIndexManager } from "./services/code-index/manager"
+import { CodeIndexManagerRegistry } from "./services/code-index/code-index-manager-registry"
 import { MdmService } from "./services/mdm/MdmService"
 import { migrateSettings } from "./utils/migrateSettings"
 import { autoImportSettings } from "./utils/autoImportSettings"
@@ -200,7 +201,7 @@ export async function activate(context: vscode.ExtensionContext) {
 
 	if (vscode.workspace.workspaceFolders) {
 		for (const folder of vscode.workspace.workspaceFolders) {
-			const manager = CodeIndexManager.getInstance(context, folder.uri.fsPath)
+			const manager = CodeIndexManagerRegistry.getInstance(context, folder.uri.fsPath)
 
 			if (manager) {
 				codeIndexManagers.push(manager)
diff --git a/src/services/code-index/__tests__/code-index-manager-registry.spec.ts b/src/services/code-index/__tests__/code-index-manager-registry.spec.ts
new file mode 100644
index 0000000000..fd5547f61c
--- /dev/null
+++ b/src/services/code-index/__tests__/code-index-manager-registry.spec.ts
@@ -0,0 +1,120 @@
+import * as vscode from "vscode"
+import { makeExtensionContext, makeTextDocument, makeTextEditor, makeUri } from "../../../test-utils/vscode"
+import { CodeIndexManager } from "../manager"
+import { CodeIndexManagerRegistry } from "../code-index-manager-registry"
+
+vi.mock("vscode", () => ({
+	workspace: { workspaceFolders: undefined, getWorkspaceFolder: vi.fn() },
+	window: { activeTextEditor: undefined },
+	Uri: { file: vi.fn() },
+}))
+
+vi.mock("../manager", () => ({
+	CodeIndexManager: vi.fn().mockImplementation(function () {
+		return { dispose: vi.fn() }
+	}),
+}))
+
+describe("CodeIndexManagerRegistry", () => {
+	let context: vscode.ExtensionContext
+	let first: vscode.WorkspaceFolder
+	let second: vscode.WorkspaceFolder
+
+	beforeEach(() => {
+		vi.clearAllMocks()
+		context = makeExtensionContext()
+		first = { uri: makeUri("/first"), name: "first", index: 0 }
+		second = { uri: makeUri("/second"), name: "second", index: 1 }
+		Object.defineProperty(vscode.workspace, "workspaceFolders", { configurable: true, value: [first, second] })
+		Object.defineProperty(vscode.window, "activeTextEditor", { configurable: true, value: undefined })
+		vi.mocked(vscode.workspace.getWorkspaceFolder).mockReturnValue(undefined)
+		vi.mocked(vscode.Uri.file).mockImplementation((value) => makeUri(value))
+	})
+
+	afterEach(() => {
+		CodeIndexManagerRegistry.disposeAll()
+		vi.restoreAllMocks()
+	})
+
+	it.each([{ folders: undefined }, { folders: [] }])("returns no manager with folders=$folders", ({ folders }) => {
+		Object.defineProperty(vscode.workspace, "workspaceFolders", { configurable: true, value: folders })
+		expect(CodeIndexManagerRegistry.getInstance(context)).toBeUndefined()
+		expect(CodeIndexManager).not.toHaveBeenCalled()
+	})
+
+	it("uses the first workspace when there is no active editor", () => {
+		CodeIndexManagerRegistry.getInstance(context)
+		expect(CodeIndexManager).toHaveBeenCalledWith("/first", first.uri, context)
+	})
+
+	it("prefers the active editor's workspace", () => {
+		const editor = makeTextEditor({ document: makeTextDocument({ uri: makeUri("/second/file.ts") }) })
+		Object.defineProperty(vscode.window, "activeTextEditor", { configurable: true, value: editor })
+		vi.mocked(vscode.workspace.getWorkspaceFolder).mockReturnValue(second)
+		CodeIndexManagerRegistry.getInstance(context)
+		expect(vscode.workspace.getWorkspaceFolder).toHaveBeenCalledWith(editor.document.uri)
+		expect(CodeIndexManager).toHaveBeenCalledWith("/second", second.uri, context)
+	})
+
+	it("falls back to the first workspace for an editor outside all folders", () => {
+		Object.defineProperty(vscode.window, "activeTextEditor", { configurable: true, value: makeTextEditor() })
+		CodeIndexManagerRegistry.getInstance(context)
+		expect(CodeIndexManager).toHaveBeenCalledWith("/first", first.uri, context)
+	})
+
+	it("gives an explicit path priority over the active editor", () => {
+		Object.defineProperty(vscode.window, "activeTextEditor", { configurable: true, value: makeTextEditor() })
+		vi.mocked(vscode.workspace.getWorkspaceFolder).mockReturnValue(first)
+		CodeIndexManagerRegistry.getInstance(context, "/second")
+		expect(CodeIndexManager).toHaveBeenCalledWith("/second", second.uri, context)
+		expect(vscode.workspace.getWorkspaceFolder).not.toHaveBeenCalled()
+	})
+
+	it("preserves the actual remote workspace URI", () => {
+		const uri = makeUri("/remote", { scheme: "vscode-remote", authority: "ssh-remote+host" })
+		Object.defineProperty(vscode.workspace, "workspaceFolders", {
+			configurable: true,
+			value: [{ uri, name: "remote", index: 0 }],
+		})
+		CodeIndexManagerRegistry.getInstance(context, "/remote")
+		expect(CodeIndexManager).toHaveBeenCalledWith("/remote", uri, context)
+		expect(vi.mocked(CodeIndexManager).mock.calls[0][1]).toBe(uri)
+		expect(vscode.Uri.file).not.toHaveBeenCalled()
+	})
+
+	it("constructs a file URI for an explicit path without open workspaces", () => {
+		Object.defineProperty(vscode.workspace, "workspaceFolders", { configurable: true, value: undefined })
+		const uri = makeUri("/outside folder/#name")
+		vi.mocked(vscode.Uri.file).mockReturnValue(uri)
+		CodeIndexManagerRegistry.getInstance(context, uri.fsPath)
+		expect(vscode.Uri.file).toHaveBeenCalledWith(uri.fsPath)
+		expect(CodeIndexManager).toHaveBeenCalledWith(uri.fsPath, uri, context)
+	})
+
+	it("reuses the same path and keeps different paths isolated", () => {
+		const a = CodeIndexManagerRegistry.getInstance(context, "/first")
+		expect(CodeIndexManagerRegistry.getInstance(makeExtensionContext(), "/first")).toBe(a)
+		const b = CodeIndexManagerRegistry.getInstance(context, "/second")
+		expect(b).not.toBe(a)
+		expect(CodeIndexManager).toHaveBeenCalledTimes(2)
+		expect(CodeIndexManagerRegistry.getAllInstances()).toEqual([a, b])
+	})
+
+	it("returns a snapshot that cannot mutate the cache", () => {
+		expect(CodeIndexManagerRegistry.getAllInstances()).toEqual([])
+		const manager = CodeIndexManagerRegistry.getInstance(context)
+		CodeIndexManagerRegistry.getAllInstances().pop()
+		expect(CodeIndexManagerRegistry.getAllInstances()).toEqual([manager])
+	})
+
+	it("disposes every manager, supports repeated cleanup and recreates instances", () => {
+		const a = CodeIndexManagerRegistry.getInstance(context, "/first")!
+		const b = CodeIndexManagerRegistry.getInstance(context, "/second")!
+		CodeIndexManagerRegistry.disposeAll()
+		CodeIndexManagerRegistry.disposeAll()
+		expect(a.dispose).toHaveBeenCalledTimes(1)
+		expect(b.dispose).toHaveBeenCalledTimes(1)
+		expect(CodeIndexManagerRegistry.getAllInstances()).toEqual([])
+		expect(CodeIndexManagerRegistry.getInstance(context, "/first")).not.toBe(a)
+	})
+})
diff --git a/src/services/code-index/__tests__/manager.spec.ts b/src/services/code-index/__tests__/manager.spec.ts
index ce52593ed5..33ba6b0cd1 100644
--- a/src/services/code-index/__tests__/manager.spec.ts
+++ b/src/services/code-index/__tests__/manager.spec.ts
@@ -1,4 +1,5 @@
 import { CodeIndexManager } from "../manager"
+import { CodeIndexManagerRegistry } from "../code-index-manager-registry"
 import { CodeIndexServiceFactory } from "../service-factory"
 import type { MockedClass } from "vitest"
 import * as path from "path"
@@ -126,7 +127,7 @@ describe("CodeIndexManager - handleSettingsChange regression", () => {
 
 	beforeEach(() => {
 		// Clear all instances before each test
-		CodeIndexManager.disposeAll()
+		CodeIndexManagerRegistry.disposeAll()
 
 		const workspaceStateStore: Record<string, any> = {}
 		const globalStateStore: Record<string, any> = {}
@@ -160,11 +161,11 @@ describe("CodeIndexManager - handleSettingsChange regression", () => {
 			languageModelAccessInformation: {} as any,
 		}
 
-		manager = CodeIndexManager.getInstance(mockContext)!
+		manager = CodeIndexManagerRegistry.getInstance(mockContext)!
 	})
 
 	afterEach(() => {
-		CodeIndexManager.disposeAll()
+		CodeIndexManagerRegistry.disposeAll()
 	})
 
 	describe("handleSettingsChange", () => {
@@ -733,7 +734,7 @@ describe("CodeIndexManager - handleSettingsChange regression", () => {
 		})
 
 		it("should store enablement per folder URI, not per window", async () => {
-			CodeIndexManager.disposeAll()
+			CodeIndexManagerRegistry.disposeAll()
 
 			const vscode = await import("vscode")
 
@@ -764,8 +765,8 @@ describe("CodeIndexManager - handleSettingsChange regression", () => {
 				{ uri: folderBUri, name: "folderB", index: 1 },
 			]
 
-			const managerA = CodeIndexManager.getInstance(sharedContext as any, folderAPath)!
-			const managerB = CodeIndexManager.getInstance(sharedContext as any, folderBPath)!
+			const managerA = CodeIndexManagerRegistry.getInstance(sharedContext, folderAPath)!
+			const managerB = CodeIndexManagerRegistry.getInstance(sharedContext, folderBPath)!
 
 			// Both start disabled (autoEnableDefault is false via globalState mock)
 			expect(managerA.isWorkspaceEnabled).toBe(false)
@@ -784,7 +785,7 @@ describe("CodeIndexManager - handleSettingsChange regression", () => {
 			expect(managerA.isWorkspaceEnabled).toBe(false)
 			expect(managerB.isWorkspaceEnabled).toBe(true)
 
-			CodeIndexManager.disposeAll()
+			CodeIndexManagerRegistry.disposeAll()
 		})
 	})
 
diff --git a/src/services/code-index/code-index-manager-registry.ts b/src/services/code-index/code-index-manager-registry.ts
new file mode 100644
index 0000000000..4610bd5d36
--- /dev/null
+++ b/src/services/code-index/code-index-manager-registry.ts
@@ -0,0 +1,53 @@
+import * as vscode from "vscode"
+import { CodeIndexManager } from "./manager"
+
+/** Resolves workspaces and owns their cached CodeIndexManager instances. */
+export class CodeIndexManagerRegistry {
+	private static instances = new Map<string, CodeIndexManager>()
+
+	public static getInstance(context: vscode.ExtensionContext, workspacePath?: string): CodeIndexManager | undefined {
+		const folder = this.resolveWorkspaceFolder(workspacePath)
+		const resolvedPath = workspacePath || folder?.uri.fsPath
+		if (!resolvedPath) {
+			return undefined
+		}
+
+		const existing = this.instances.get(resolvedPath)
+		if (existing) {
+			return existing
+		}
+
+		// Preserve real workspace URIs, including remote schemes and authorities.
+		const folderUri = folder?.uri ?? vscode.Uri.file(resolvedPath)
+		const manager = new CodeIndexManager(resolvedPath, folderUri, context)
+		this.instances.set(resolvedPath, manager)
+		return manager
+	}
+
+	public static getAllInstances(): CodeIndexManager[] {
+		return Array.from(this.instances.values())
+	}
+
+	public static disposeAll(): void {
+		for (const instance of this.instances.values()) {
+			instance.dispose()
+		}
+		this.instances.clear()
+	}
+
+	private static resolveWorkspaceFolder(workspacePath?: string): vscode.WorkspaceFolder | undefined {
+		if (workspacePath) {
+			return vscode.workspace.workspaceFolders?.find((folder) => folder.uri.fsPath === workspacePath)
+		}
+
+		const activeEditor = vscode.window.activeTextEditor
+		if (activeEditor) {
+			const folder = vscode.workspace.getWorkspaceFolder(activeEditor.document.uri)
+			if (folder) {
+				return folder
+			}
+		}
+
+		return vscode.workspace.workspaceFolders?.[0]
+	}
+}
diff --git a/src/services/code-index/manager.ts b/src/services/code-index/manager.ts
index dd36a32d88..967bb855b3 100644
--- a/src/services/code-index/manager.ts
+++ b/src/services/code-index/manager.ts
@@ -18,9 +18,6 @@ import { TelemetryService } from "@roo-code/telemetry"
 import { TelemetryEventName } from "@roo-code/types"
 
 export class CodeIndexManager {
-	// --- Singleton Implementation ---
-	private static instances = new Map<string, CodeIndexManager>() // Map workspace path to instance
-
 	// Specialized class instances
 	private _configManager: CodeIndexConfigManager | undefined
 	private readonly _stateManager: CodeIndexStateManager
@@ -33,61 +30,11 @@ export class CodeIndexManager {
 	// Flag to prevent race conditions during error recovery
 	private _isRecoveringFromError = false
 
-	public static getInstance(context: vscode.ExtensionContext, workspacePath?: string): CodeIndexManager | undefined {
-		// Resolve the workspace folder to get both fsPath and the real URI
-		let folder: vscode.WorkspaceFolder | undefined
-
-		if (workspacePath) {
-			folder = vscode.workspace.workspaceFolders?.find((f) => f.uri.fsPath === workspacePath)
-		} else {
-			const activeEditor = vscode.window.activeTextEditor
-			if (activeEditor) {
-				folder = vscode.workspace.getWorkspaceFolder(activeEditor.document.uri)
-			}
-			if (!folder) {
-				const workspaceFolders = vscode.workspace.workspaceFolders
-				if (!workspaceFolders || workspaceFolders.length === 0) {
-					return undefined
-				}
-				folder = workspaceFolders[0]
-			}
-			workspacePath = folder.uri.fsPath
-		}
-
-		if (!CodeIndexManager.instances.has(workspacePath)) {
-			// folder may be undefined when workspacePath was provided but doesn't match
-			// any workspace folder (e.g. cwd passed from a tool). Fall back to file:// URI.
-			const folderUri =
-				folder?.uri ??
-				({
-					fsPath: workspacePath,
-					scheme: "file",
-					authority: "",
-					path: workspacePath,
-					toString: () => `file://${workspacePath}`,
-				} as unknown as vscode.Uri)
-			CodeIndexManager.instances.set(workspacePath, new CodeIndexManager(workspacePath, folderUri, context))
-		}
-		return CodeIndexManager.instances.get(workspacePath)!
-	}
-
-	public static getAllInstances(): CodeIndexManager[] {
-		return Array.from(CodeIndexManager.instances.values())
-	}
-
-	public static disposeAll(): void {
-		for (const instance of CodeIndexManager.instances.values()) {
-			instance.dispose()
-		}
-		CodeIndexManager.instances.clear()
-	}
-
 	private readonly workspacePath: string
 	private readonly _folderUri: vscode.Uri
 	private readonly context: vscode.ExtensionContext
 
-	// Private constructor for singleton pattern
-	private constructor(workspacePath: string, folderUri: vscode.Uri, context: vscode.ExtensionContext) {
+	public constructor(workspacePath: string, folderUri: vscode.Uri, context: vscode.ExtensionContext) {
 		this.workspacePath = workspacePath
 		this._folderUri = folderUri
 		this.context = context