diff --git a/services/web/frontend/js/features/file-tree/components/file-tree-context.tsx b/services/web/frontend/js/features/file-tree/components/file-tree-context.tsx
index 95224aeb64..2913c6f9e0 100644
--- a/services/web/frontend/js/features/file-tree/components/file-tree-context.tsx
+++ b/services/web/frontend/js/features/file-tree/components/file-tree-context.tsx
@@ -10,7 +10,6 @@ import { FC } from 'react'
 // FileTreeMutable: provides entities mutation operations
 // FileTreeSelectable: handles selection and multi-selection
 const FileTreeContext: FC<{
-  reindexReferences: () => void
   refProviders: Record<string, boolean>
   setRefProviderEnabled: (provider: string, value: boolean) => void
   setStartedFreeTrial: (value: boolean) => void
@@ -18,7 +17,6 @@ const FileTreeContext: FC<{
   fileTreeContainer?: HTMLDivElement
 }> = ({
   refProviders,
-  reindexReferences,
   setRefProviderEnabled,
   setStartedFreeTrial,
   onSelect,
@@ -30,10 +28,9 @@ const FileTreeContext: FC<{
       refProviders={refProviders}
       setRefProviderEnabled={setRefProviderEnabled}
       setStartedFreeTrial={setStartedFreeTrial}
-      reindexReferences={reindexReferences}
     >
       <FileTreeSelectableProvider onSelect={onSelect}>
-        <FileTreeActionableProvider reindexReferences={reindexReferences}>
+        <FileTreeActionableProvider>
           <FileTreeDraggableProvider fileTreeContainer={fileTreeContainer}>
             {children}
           </FileTreeDraggableProvider>
diff --git a/services/web/frontend/js/features/file-tree/components/file-tree-root.tsx b/services/web/frontend/js/features/file-tree/components/file-tree-root.tsx
index a5a4844bf0..66f547aa5c 100644
--- a/services/web/frontend/js/features/file-tree/components/file-tree-root.tsx
+++ b/services/web/frontend/js/features/file-tree/components/file-tree-root.tsx
@@ -26,11 +26,9 @@ const FileTreeRoot = React.memo<{
   isConnected: boolean
   setRefProviderEnabled: () => void
   setStartedFreeTrial: () => void
-  reindexReferences: () => void
   refProviders: Record<string, boolean>
 }>(function FileTreeRoot({
   refProviders,
-  reindexReferences,
   setRefProviderEnabled,
   setStartedFreeTrial,
   onSelect,
@@ -95,7 +93,6 @@ const FileTreeRoot = React.memo<{
           refProviders={refProviders}
           setRefProviderEnabled={setRefProviderEnabled}
           setStartedFreeTrial={setStartedFreeTrial}
-          reindexReferences={reindexReferences}
           onSelect={onSelect}
           fileTreeContainer={fileTreeContainer}
         >
diff --git a/services/web/frontend/js/features/file-tree/contexts/file-tree-actionable.tsx b/services/web/frontend/js/features/file-tree/contexts/file-tree-actionable.tsx
index c85926b61b..1b0257e5b9 100644
--- a/services/web/frontend/js/features/file-tree/contexts/file-tree-actionable.tsx
+++ b/services/web/frontend/js/features/file-tree/contexts/file-tree-actionable.tsx
@@ -33,6 +33,7 @@ import {
   DuplicateFilenameMoveError,
 } from '../errors'
 import { Folder } from '../../../../../types/folder'
+import { useReferencesContext } from '@/features/ide-react/context/references-context'
 
 type DroppedFile = File & {
   relativePath?: string
@@ -216,11 +217,10 @@ function fileTreeActionableReducer(state: State, action: Action) {
   }
 }
 
-export const FileTreeActionableProvider: FC<{
-  reindexReferences: () => void
-}> = ({ reindexReferences, children }) => {
+export const FileTreeActionableProvider: FC = ({ children }) => {
   const { _id: projectId } = useProjectContext()
   const { permissionsLevel } = useEditorContext()
+  const { indexAllReferences } = useReferencesContext()
 
   const [state, dispatch] = useReducer(
     permissionsLevel === 'readOnly'
@@ -305,7 +305,7 @@ export const FileTreeActionableProvider: FC<{
         // @ts-ignore (TODO: improve mapSeries types)
         .then(() => {
           if (shouldReindexReferences) {
-            reindexReferences()
+            indexAllReferences(true)
           }
           dispatch({ type: ACTION_TYPES.CLEAR })
         })
@@ -314,7 +314,7 @@ export const FileTreeActionableProvider: FC<{
           dispatch({ type: ACTION_TYPES.ERROR, error })
         })
     )
-  }, [fileTreeData, projectId, selectedEntityIds, reindexReferences])
+  }, [fileTreeData, projectId, selectedEntityIds, indexAllReferences])
 
   // moves entities. Tree is updated immediately and data are sync'd after.
   const finishMoving = useCallback(
diff --git a/services/web/frontend/js/features/file-tree/contexts/file-tree-main.tsx b/services/web/frontend/js/features/file-tree/contexts/file-tree-main.tsx
index 33a051a633..85872fe129 100644
--- a/services/web/frontend/js/features/file-tree/contexts/file-tree-main.tsx
+++ b/services/web/frontend/js/features/file-tree/contexts/file-tree-main.tsx
@@ -5,7 +5,6 @@ type ContextMenuCoords = { top: number; left: number }
 const FileTreeMainContext = createContext<
   | {
       refProviders: object
-      reindexReferences: () => void
       setRefProviderEnabled: (provider: string, value: boolean) => void
       setStartedFreeTrial: (value: boolean) => void
       contextMenuCoords: ContextMenuCoords | null
@@ -27,13 +26,11 @@ export function useFileTreeMainContext() {
 }
 
 export const FileTreeMainProvider: FC<{
-  reindexReferences: () => void
   refProviders: object
   setRefProviderEnabled: (provider: string, value: boolean) => void
   setStartedFreeTrial: (value: boolean) => void
 }> = ({
   refProviders,
-  reindexReferences,
   setRefProviderEnabled,
   setStartedFreeTrial,
   children,
@@ -45,7 +42,6 @@ export const FileTreeMainProvider: FC<{
     <FileTreeMainContext.Provider
       value={{
         refProviders,
-        reindexReferences,
         setRefProviderEnabled,
         setStartedFreeTrial,
         contextMenuCoords,
diff --git a/services/web/frontend/js/features/ide-react/components/file-tree.tsx b/services/web/frontend/js/features/ide-react/components/file-tree.tsx
index 26c6e427bc..980c7d9754 100644
--- a/services/web/frontend/js/features/ide-react/components/file-tree.tsx
+++ b/services/web/frontend/js/features/ide-react/components/file-tree.tsx
@@ -1,6 +1,5 @@
 import React, { memo, useCallback, useState } from 'react'
 import { useUserContext } from '@/shared/context/user-context'
-import { useReferencesContext } from '@/features/ide-react/context/references-context'
 import { useIdeReactContext } from '@/features/ide-react/context/ide-react-context'
 import { useConnectionContext } from '@/features/ide-react/context/connection-context'
 import { RefProviders } from '../../../../../types/user'
@@ -9,7 +8,6 @@ import { useFileTreeOpenContext } from '@/features/ide-react/context/file-tree-o
 
 export const FileTree = memo(function FileTree() {
   const user = useUserContext()
-  const { indexAllReferences } = useReferencesContext()
   const { setStartedFreeTrial } = useIdeReactContext()
   const { isConnected, connectionState } = useConnectionContext()
   const { handleFileTreeInit, handleFileTreeSelect, handleFileTreeDelete } =
@@ -19,10 +17,6 @@ export const FileTree = memo(function FileTree() {
     () => user.refProviders || {}
   )
 
-  function reindexReferences() {
-    indexAllReferences(true)
-  }
-
   const setRefProviderEnabled = useCallback(
     (provider: keyof RefProviders, value = true) => {
       setRefProviders(refProviders => ({ ...refProviders, [provider]: value }))
@@ -33,7 +27,6 @@ export const FileTree = memo(function FileTree() {
   return (
     <FileTreeRoot
       refProviders={refProviders}
-      reindexReferences={reindexReferences}
       setRefProviderEnabled={setRefProviderEnabled}
       setStartedFreeTrial={setStartedFreeTrial}
       isConnected={isConnected || connectionState.reconnectAt !== null}
diff --git a/services/web/frontend/js/features/ide-react/context/ide-react-context.tsx b/services/web/frontend/js/features/ide-react/context/ide-react-context.tsx
index 49f19b2f60..a164931cbc 100644
--- a/services/web/frontend/js/features/ide-react/context/ide-react-context.tsx
+++ b/services/web/frontend/js/features/ide-react/context/ide-react-context.tsx
@@ -22,7 +22,6 @@ import { populateEditorScope } from '@/features/ide-react/scope-adapters/editor-
 import { postJSON } from '@/infrastructure/fetch-json'
 import { EventLog } from '@/features/ide-react/editor/event-log'
 import { populateOnlineUsersScope } from '@/features/ide-react/context/online-users-context'
-import { populateReferenceScope } from '@/features/ide-react/context/references-context'
 import { ReactScopeEventEmitter } from '@/features/ide-react/scope-event-emitter/react-scope-event-emitter'
 import getMeta from '@/utils/meta'
 
@@ -77,7 +76,6 @@ export function createReactScopeValueStore(projectId: string) {
   populateProjectScope(scopeStore)
   populatePdfScope(scopeStore)
   populateOnlineUsersScope(scopeStore)
-  populateReferenceScope(scopeStore)
   populateReviewPanelScope(scopeStore)
 
   scopeStore.allowNonExistentPath('hasLintingError')
diff --git a/services/web/frontend/js/features/ide-react/context/references-context.tsx b/services/web/frontend/js/features/ide-react/context/references-context.tsx
index 46d1fe8849..8d929e4a0e 100644
--- a/services/web/frontend/js/features/ide-react/context/references-context.tsx
+++ b/services/web/frontend/js/features/ide-react/context/references-context.tsx
@@ -10,64 +10,32 @@ import {
 } from 'react'
 import { useIdeReactContext } from '@/features/ide-react/context/ide-react-context'
 import { useConnectionContext } from '@/features/ide-react/context/connection-context'
-import _ from 'lodash'
 import { postJSON } from '@/infrastructure/fetch-json'
 import { ShareJsDoc } from '@/features/ide-react/editor/share-js-doc'
-import useScopeValue from '@/shared/hooks/use-scope-value'
-import { ReactScopeValueStore } from '@/features/ide-react/scope-value-store/react-scope-value-store'
 import { useFileTreeData } from '@/shared/context/file-tree-data-context'
 import { findDocEntityById } from '@/features/ide-react/util/find-doc-entity-by-id'
 import { IdeEvents } from '@/features/ide-react/create-ide-event-emitter'
 import { debugConsole } from '@/utils/debugging'
 
-type References = {
-  keys: string[]
-}
-
-type ReferencesContextValue = {
-  indexReferencesIfDocModified: (
-    doc: ShareJsDoc,
-    shouldBroadcast: boolean
-  ) => void
-  indexAllReferences: (shouldBroadcast: boolean) => void
-}
-
-type IndexReferencesResponse = References
-
-const ReferencesContext = createContext<ReferencesContextValue | undefined>(
-  undefined
-)
-
-export function populateReferenceScope(store: ReactScopeValueStore) {
-  store.set('$root._references', { keys: [] })
-}
+export const ReferencesContext = createContext<
+  | {
+      referenceKeys: Set<string>
+      indexAllReferences: (shouldBroadcast: boolean) => void
+    }
+  | undefined
+>(undefined)
 
 export const ReferencesProvider: FC = ({ children }) => {
   const { fileTreeData } = useFileTreeData()
   const { eventEmitter, projectId } = useIdeReactContext()
   const { socket } = useConnectionContext()
 
-  const [references, setReferences] =
-    useScopeValue<References>('$root._references')
+  const [referenceKeys, setReferenceKeys] = useState(new Set<string>())
 
   const [existingIndexHash, setExistingIndexHash] = useState<
     Record<string, { hash: string; timestamp: number }>
   >({})
 
-  const storeReferencesKeys = useCallback(
-    (newKeys: string[], replaceExistingKeys: boolean) => {
-      const oldKeys = references.keys
-      const keys = replaceExistingKeys ? newKeys : _.union(oldKeys, newKeys)
-      window.dispatchEvent(
-        new CustomEvent('project:references', {
-          detail: keys,
-        })
-      )
-      setReferences({ keys })
-    },
-    [references.keys, setReferences]
-  )
-
   const indexAllReferences = useCallback(
     (shouldBroadcast: boolean) => {
       postJSON(`/project/${projectId}/references/indexAll`, {
@@ -75,15 +43,15 @@ export const ReferencesProvider: FC = ({ children }) => {
           shouldBroadcast,
         },
       })
-        .then((response: IndexReferencesResponse) => {
-          storeReferencesKeys(response.keys, true)
+        .then((response: { keys: string[] }) => {
+          setReferenceKeys(new Set(response.keys))
         })
         .catch(error => {
           // allow the request to fail
           debugConsole.error(error)
         })
     },
-    [projectId, storeReferencesKeys]
+    [projectId]
   )
 
   const indexReferencesIfDocModified = useCallback(
@@ -132,25 +100,15 @@ export const ReferencesProvider: FC = ({ children }) => {
     }
   }, [eventEmitter, fileTreeData, indexReferencesIfDocModified])
 
-  useEffect(() => {
-    const handleShouldReindex = () => {
-      indexAllReferences(true)
-    }
-
-    eventEmitter.on('references:should-reindex', handleShouldReindex)
-
-    return () => {
-      eventEmitter.off('references:should-reindex', handleShouldReindex)
-    }
-  }, [eventEmitter, indexAllReferences])
-
   useEffect(() => {
     const handleProjectJoined = () => {
       // We only need to grab the references when the editor first loads,
       // not on every reconnect
-      socket.on('references:keys:updated', (keys, allDocs) =>
-        storeReferencesKeys(keys, allDocs)
-      )
+      socket.on('references:keys:updated', (keys, allDocs) => {
+        setReferenceKeys(oldKeys =>
+          allDocs ? new Set(keys) : new Set([...oldKeys, ...keys])
+        )
+      })
       indexAllReferences(false)
     }
 
@@ -159,14 +117,14 @@ export const ReferencesProvider: FC = ({ children }) => {
     return () => {
       eventEmitter.off('project:joined', handleProjectJoined)
     }
-  }, [eventEmitter, indexAllReferences, socket, storeReferencesKeys])
+  }, [eventEmitter, indexAllReferences, socket])
 
-  const value = useMemo<ReferencesContextValue>(
+  const value = useMemo(
     () => ({
-      indexReferencesIfDocModified,
+      referenceKeys,
       indexAllReferences,
     }),
-    [indexReferencesIfDocModified, indexAllReferences]
+    [indexAllReferences, referenceKeys]
   )
 
   return (
@@ -176,7 +134,7 @@ export const ReferencesProvider: FC = ({ children }) => {
   )
 }
 
-export function useReferencesContext(): ReferencesContextValue {
+export function useReferencesContext() {
   const context = useContext(ReferencesContext)
 
   if (!context) {
diff --git a/services/web/frontend/js/features/ide-react/create-ide-event-emitter.ts b/services/web/frontend/js/features/ide-react/create-ide-event-emitter.ts
index b130090afd..ed20e380c4 100644
--- a/services/web/frontend/js/features/ide-react/create-ide-event-emitter.ts
+++ b/services/web/frontend/js/features/ide-react/create-ide-event-emitter.ts
@@ -20,7 +20,6 @@ export type IdeEvents = {
   'cursor:editor:syncToPdf': []
   'scroll:editor:update': []
   'comment:start_adding': []
-  'references:should-reindex': []
   'history:toggle': []
   'entity:deleted': [entity: FileTreeFindResult]
 }
diff --git a/services/web/frontend/js/features/source-editor/extensions/language.ts b/services/web/frontend/js/features/source-editor/extensions/language.ts
index da61b4c09b..b36c14135c 100644
--- a/services/web/frontend/js/features/source-editor/extensions/language.ts
+++ b/services/web/frontend/js/features/source-editor/extensions/language.ts
@@ -24,7 +24,7 @@ type Metadata = {
   labels: Set<string>
   packageNames: Set<string>
   commands: Command[]
-  references: string[]
+  referenceKeys: Set<string>
   fileTreeData: Folder
 }
 
diff --git a/services/web/frontend/js/features/source-editor/hooks/use-codemirror-scope.ts b/services/web/frontend/js/features/source-editor/hooks/use-codemirror-scope.ts
index 853633916c..c83fe1c617 100644
--- a/services/web/frontend/js/features/source-editor/hooks/use-codemirror-scope.ts
+++ b/services/web/frontend/js/features/source-editor/hooks/use-codemirror-scope.ts
@@ -60,6 +60,7 @@ import { useLayoutContext } from '@/shared/context/layout-context'
 import { debugConsole } from '@/utils/debugging'
 import { useMetadataContext } from '@/features/ide-react/context/metadata-context'
 import { useUserContext } from '@/shared/context/user-context'
+import { useReferencesContext } from '@/features/ide-react/context/references-context'
 
 function useCodeMirrorScope(view: EditorView) {
   const { fileTreeData } = useFileTreeData()
@@ -107,7 +108,7 @@ function useCodeMirrorScope(view: EditorView) {
 
   const [visual] = useScopeValue<boolean>('editor.showVisual')
 
-  const [references] = useScopeValue<{ keys: string[] }>('$root._references')
+  const { referenceKeys } = useReferencesContext()
 
   // build the translation phrases
   const phrases = usePhrases()
@@ -214,7 +215,7 @@ function useCodeMirrorScope(view: EditorView) {
   // TODO: read this data from the scope?
   const metadataRef = useRef({
     ...metadata,
-    references: references.keys,
+    referenceKeys,
     fileTreeData,
   })
 
@@ -226,13 +227,9 @@ function useCodeMirrorScope(view: EditorView) {
 
   // listen to project reference keys updates
   useEffect(() => {
-    const listener = (event: Event) => {
-      metadataRef.current.references = (event as CustomEvent<string[]>).detail
-      view.dispatch(setMetadata(metadataRef.current))
-    }
-    window.addEventListener('project:references', listener)
-    return () => window.removeEventListener('project:references', listener)
-  }, [view])
+    metadataRef.current.referenceKeys = referenceKeys
+    view.dispatch(setMetadata(metadataRef.current))
+  }, [view, referenceKeys])
 
   // listen to project root folder updates
   useEffect(() => {
diff --git a/services/web/frontend/js/features/source-editor/languages/latex/completions/references.ts b/services/web/frontend/js/features/source-editor/languages/latex/completions/references.ts
index 147d3e86b8..1e994481a2 100644
--- a/services/web/frontend/js/features/source-editor/languages/latex/completions/references.ts
+++ b/services/web/frontend/js/features/source-editor/languages/latex/completions/references.ts
@@ -16,10 +16,10 @@ export function buildReferenceCompletions(
     return
   }
 
-  for (const reference of metadata.references) {
+  for (const referenceKey of metadata.referenceKeys) {
     completions.references.push({
       type: 'reference',
-      label: reference,
+      label: referenceKey,
       extend: extendRequiredParameter,
     })
   }
diff --git a/services/web/frontend/stories/decorators/scope.tsx b/services/web/frontend/stories/decorators/scope.tsx
index 5529a762d2..9f8838125b 100644
--- a/services/web/frontend/stories/decorators/scope.tsx
+++ b/services/web/frontend/stories/decorators/scope.tsx
@@ -97,11 +97,6 @@ const initialize = () => {
       //
     },
     $broadcast: () => {},
-    $root: {
-      _references: {
-        keys: ['bibkeyExample'],
-      },
-    },
     ui: {
       chatOpen: true,
       pdfLayout: 'flat',
diff --git a/services/web/frontend/stories/file-tree.stories.jsx b/services/web/frontend/stories/file-tree.stories.jsx
index 1832024e25..51621cb094 100644
--- a/services/web/frontend/stories/file-tree.stories.jsx
+++ b/services/web/frontend/stories/file-tree.stories.jsx
@@ -155,9 +155,6 @@ export default {
       console.log('started free trial')
     },
     refProviders: {},
-    reindexReferences: () => {
-      console.log('reindex references')
-    },
     setRefProviderEnabled: provider => {
       console.log(`ref provider ${provider} enabled`)
     },
diff --git a/services/web/frontend/stories/modals/create-file/create-file-modal-decorator.jsx b/services/web/frontend/stories/modals/create-file/create-file-modal-decorator.jsx
index bb1ea8dc7d..a70a507436 100644
--- a/services/web/frontend/stories/modals/create-file/create-file-modal-decorator.jsx
+++ b/services/web/frontend/stories/modals/create-file/create-file-modal-decorator.jsx
@@ -7,9 +7,6 @@ import PropTypes from 'prop-types'
 
 const defaultFileTreeContextProps = {
   refProviders: { mendeley: false, zotero: false },
-  reindexReferences: () => {
-    console.log('reindex references')
-  },
   setRefProviderEnabled: provider => {
     console.log(`ref provider ${provider} enabled`)
   },
diff --git a/services/web/test/frontend/features/file-tree/components/file-tree-root.spec.tsx b/services/web/test/frontend/features/file-tree/components/file-tree-root.spec.tsx
index fa95db490d..6021f60083 100644
--- a/services/web/test/frontend/features/file-tree/components/file-tree-root.spec.tsx
+++ b/services/web/test/frontend/features/file-tree/components/file-tree-root.spec.tsx
@@ -30,7 +30,6 @@ describe('<FileTreeRoot/>', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -73,7 +72,6 @@ describe('<FileTreeRoot/>', function () {
         >
           <FileTreeRoot
             refProviders={{}}
-            reindexReferences={cy.stub()}
             setRefProviderEnabled={cy.stub()}
             setStartedFreeTrial={cy.stub()}
             onSelect={cy.stub()}
@@ -117,7 +115,6 @@ describe('<FileTreeRoot/>', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -154,7 +151,6 @@ describe('<FileTreeRoot/>', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub().as('onSelect')}
@@ -202,7 +198,6 @@ describe('<FileTreeRoot/>', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -247,7 +242,6 @@ describe('<FileTreeRoot/>', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -318,7 +312,6 @@ describe('<FileTreeRoot/>', function () {
         >
           <FileTreeRoot
             refProviders={{}}
-            reindexReferences={cy.stub()}
             setRefProviderEnabled={cy.stub()}
             setStartedFreeTrial={cy.stub()}
             onSelect={cy.stub()}
diff --git a/services/web/test/frontend/features/file-tree/flows/context-menu.spec.tsx b/services/web/test/frontend/features/file-tree/flows/context-menu.spec.tsx
index 312738b627..11eb1a97b6 100644
--- a/services/web/test/frontend/features/file-tree/flows/context-menu.spec.tsx
+++ b/services/web/test/frontend/features/file-tree/flows/context-menu.spec.tsx
@@ -27,7 +27,6 @@ describe('FileTree Context Menu Flow', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -64,7 +63,6 @@ describe('FileTree Context Menu Flow', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -101,7 +99,6 @@ describe('FileTree Context Menu Flow', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
diff --git a/services/web/test/frontend/features/file-tree/flows/create-folder.spec.tsx b/services/web/test/frontend/features/file-tree/flows/create-folder.spec.tsx
index 1731dd8189..a7ccca400b 100644
--- a/services/web/test/frontend/features/file-tree/flows/create-folder.spec.tsx
+++ b/services/web/test/frontend/features/file-tree/flows/create-folder.spec.tsx
@@ -30,7 +30,6 @@ describe('FileTree Create Folder Flow', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -100,7 +99,6 @@ describe('FileTree Create Folder Flow', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -177,7 +175,6 @@ describe('FileTree Create Folder Flow', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
@@ -244,7 +241,6 @@ describe('FileTree Create Folder Flow', function () {
       >
         <FileTreeRoot
           refProviders={{}}
-          reindexReferences={cy.stub()}
           setRefProviderEnabled={cy.stub()}
           setStartedFreeTrial={cy.stub()}
           onSelect={cy.stub()}
diff --git a/services/web/test/frontend/features/file-tree/flows/delete-entity.spec.tsx b/services/web/test/frontend/features/file-tree/flows/delete-entity.spec.tsx
index 51d0d40a7f..d074476374 100644
--- a/services/web/test/frontend/features/file-tree/flows/delete-entity.spec.tsx
+++ b/services/web/test/frontend/features/file-tree/flows/delete-entity.spec.tsx
@@ -35,7 +35,6 @@ describe('FileTree Delete Entity Flow', function () {
           >
             <FileTreeRoot
               refProviders={{}}
-              reindexReferences={cy.stub().as('reindexReferences')}
               setRefProviderEnabled={cy.stub()}
               setStartedFreeTrial={cy.stub()}
               onSelect={cy.stub()}
@@ -84,7 +83,6 @@ describe('FileTree Delete Entity Flow', function () {
       ).should('not.exist')
 
       cy.get('@deleteDoc.all').should('have.length', 1)
-      cy.get('@reindexReferences').should('not.have.been.called')
     })
 
     it('continues delete on 404s', function () {
@@ -162,7 +160,6 @@ describe('FileTree Delete Entity Flow', function () {
           >
             <FileTreeRoot
               refProviders={{}}
-              reindexReferences={cy.stub().as('reindexReferences')}
               setRefProviderEnabled={cy.stub()}
               setStartedFreeTrial={cy.stub()}
               onSelect={cy.stub()}
@@ -226,7 +223,6 @@ describe('FileTree Delete Entity Flow', function () {
           >
             <FileTreeRoot
               refProviders={{}}
-              reindexReferences={cy.stub().as('reindexReferences')}
               setRefProviderEnabled={cy.stub()}
               setStartedFreeTrial={cy.stub()}
               onSelect={cy.stub()}
@@ -282,7 +278,6 @@ describe('FileTree Delete Entity Flow', function () {
 
       cy.get('@deleteDoc.all').should('have.length', 1)
       cy.get('@deleteFile.all').should('have.length', 1)
-      cy.get('@reindexReferences').should('have.been.calledOnce')
     })
   })
 })
diff --git a/services/web/test/frontend/features/file-tree/flows/rename-entity.spec.tsx b/services/web/test/frontend/features/file-tree/flows/rename-entity.spec.tsx
index b03676621f..f63ae301c2 100644
--- a/services/web/test/frontend/features/file-tree/flows/rename-entity.spec.tsx
+++ b/services/web/test/frontend/features/file-tree/flows/rename-entity.spec.tsx
@@ -42,7 +42,6 @@ describe('FileTree Rename Entity Flow', function () {
         >
           <FileTreeRoot
             refProviders={{}}
-            reindexReferences={cy.stub()}
             setRefProviderEnabled={cy.stub()}
             setStartedFreeTrial={cy.stub()}
             onSelect={cy.stub().as('onSelect')}
diff --git a/services/web/test/frontend/features/file-tree/helpers/file-tree-provider.tsx b/services/web/test/frontend/features/file-tree/helpers/file-tree-provider.tsx
index 1fdcee55f1..714128f946 100644
--- a/services/web/test/frontend/features/file-tree/helpers/file-tree-provider.tsx
+++ b/services/web/test/frontend/features/file-tree/helpers/file-tree-provider.tsx
@@ -12,7 +12,6 @@ export const FileTreeProvider: FC<{
 
   if (propsRef.current === undefined) {
     propsRef.current = {
-      reindexReferences: cy.stub().as('reindexReferences'),
       setRefProviderEnabled: cy.stub().as('setRefProviderEnabled'),
       setStartedFreeTrial: cy.stub().as('setStartedFreeTrial'),
       onSelect: cy.stub(),
diff --git a/services/web/test/frontend/features/source-editor/components/codemirror-editor-autocomplete.spec.tsx b/services/web/test/frontend/features/source-editor/components/codemirror-editor-autocomplete.spec.tsx
index 2350a90a3e..ab05c9958e 100644
--- a/services/web/test/frontend/features/source-editor/components/codemirror-editor-autocomplete.spec.tsx
+++ b/services/web/test/frontend/features/source-editor/components/codemirror-editor-autocomplete.spec.tsx
@@ -8,6 +8,7 @@ import { User, UserId } from '../../../../../types/user'
 import { TestContainer } from '../helpers/test-container'
 import { FC } from 'react'
 import { MetadataContext } from '@/features/ide-react/context/metadata-context'
+import { ReferencesContext } from '@/features/ide-react/context/references-context'
 
 describe('autocomplete', { scrollBehavior: false }, function () {
   beforeEach(function () {
@@ -62,7 +63,6 @@ describe('autocomplete', { scrollBehavior: false }, function () {
     ]
 
     const scope = mockScope()
-    scope.$root._references.keys = ['foo']
     scope.project.rootFolder = rootFolder
 
     cy.mount(
@@ -209,7 +209,6 @@ describe('autocomplete', { scrollBehavior: false }, function () {
     ]
 
     const scope = mockScope()
-    scope.$root._references.keys = ['foo']
 
     cy.mount(
       <TestContainer>
@@ -373,11 +372,27 @@ describe('autocomplete', { scrollBehavior: false }, function () {
     ]
 
     const scope = mockScope()
-    scope.$root._references.keys = ['ref-1', 'ref-2', 'ref-3']
+
+    const ReferencesProvider: FC = ({ children }) => {
+      return (
+        <ReferencesContext.Provider
+          value={{
+            referenceKeys: new Set(['ref-1', 'ref-2', 'ref-3']),
+            indexAllReferences: cy.stub(),
+          }}
+        >
+          {children}
+        </ReferencesContext.Provider>
+      )
+    }
 
     cy.mount(
       <TestContainer>
-        <EditorProviders scope={scope} rootFolder={rootFolder as any}>
+        <EditorProviders
+          scope={scope}
+          providers={{ ReferencesProvider }}
+          rootFolder={rootFolder as any}
+        >
           <CodeMirrorEditor />
         </EditorProviders>
       </TestContainer>
@@ -428,7 +443,6 @@ describe('autocomplete', { scrollBehavior: false }, function () {
     ]
 
     const scope = mockScope()
-    scope.$root._references.keys = ['foo']
     scope.project.rootFolder = rootFolder
 
     cy.mount(
@@ -893,7 +907,6 @@ describe('autocomplete', { scrollBehavior: false }, function () {
     ]
 
     const scope = mockScope()
-    scope.$root._references.keys = ['foo']
     scope.project.rootFolder = rootFolder
 
     cy.mount(
diff --git a/services/web/test/frontend/features/source-editor/helpers/mock-scope.ts b/services/web/test/frontend/features/source-editor/helpers/mock-scope.ts
index 0e91ad952c..0e2b5462ea 100644
--- a/services/web/test/frontend/features/source-editor/helpers/mock-scope.ts
+++ b/services/web/test/frontend/features/source-editor/helpers/mock-scope.ts
@@ -80,10 +80,5 @@ export const mockScope = (content?: string) => {
     $on: cy.stub().log(false),
     $broadcast: cy.stub().log(false),
     $emit: cy.stub().log(false),
-    $root: {
-      _references: {
-        keys: ['foo'],
-      },
-    },
   }
 }