diff --git a/rollup.config.js b/rollup.config.js
index 8c69a5d..e21b160 100644
--- a/rollup.config.js
+++ b/rollup.config.js
@@ -14,7 +14,7 @@ if you want to view the source visit the plugins github repository
 */
 `
 
-const production = false//!process.env.ROLLUP_WATCH
+const production = !process.env.ROLLUP_WATCH
 
 export default {
   input: './src/main.ts',
diff --git a/src/__tests__/event-bus-tests.ts b/src/__tests__/event-bus-tests.ts
index 3da3d6f..f59a14b 100644
--- a/src/__tests__/event-bus-tests.ts
+++ b/src/__tests__/event-bus-tests.ts
@@ -1,4 +1,4 @@
-import { EventBus } from '../event-bus'
+import { EventBus } from '../tools/event-bus'
 
 describe('EventBus', () => {
   it('should refuse the registering of invalid ctx/event names', () => {
diff --git a/src/__tests__/query-tests.ts b/src/__tests__/query-tests.ts
index 49c98bd..36bdc6a 100644
--- a/src/__tests__/query-tests.ts
+++ b/src/__tests__/query-tests.ts
@@ -1,4 +1,4 @@
-import { Query } from '../query'
+import { Query } from '../search/query'
 
 describe('The Query class', () => {
   const stringQuery =
diff --git a/src/__tests__/utils-tests.ts b/src/__tests__/utils-tests.ts
index 986b458..043466d 100644
--- a/src/__tests__/utils-tests.ts
+++ b/src/__tests__/utils-tests.ts
@@ -1,5 +1,5 @@
 import type { CachedMetadata } from 'obsidian'
-import { getAliasesFromMetadata } from '../utils'
+import { getAliasesFromMetadata } from '../tools/utils'
 
 describe('Utils', () => {
   describe('getAliasesFromMetadata', () => {
diff --git a/src/cache-manager.ts b/src/cache-manager.ts
index 54d4740..96a629e 100644
--- a/src/cache-manager.ts
+++ b/src/cache-manager.ts
@@ -1,120 +1,50 @@
-import { throttle } from 'lodash-es'
-import type MiniSearch from 'minisearch'
 import type { TFile } from 'obsidian'
-import { deflate, inflate } from 'pako'
-import {
-  notesCacheFilePath,
-  minisearchCacheFilePath,
-  type IndexedDocument,
-} from './globals'
-import { settings } from './settings'
+import type { IndexedDocument } from './globals'
 
 class CacheManager {
-  notesCache: Record<string, IndexedDocument> = {}
-  compress = true
-  writeInterval = 5_000 // In milliseconds
+  private documentsCache: Map<string, IndexedDocument> = new Map()
+  private writeInterval = 10_000 // In milliseconds
 
-  //#region Minisearch
-
-  /**
-   * Serializes and writes the Minisearch index on the disk
-   */
-  public writeMinisearchIndex = throttle(
-    this._writeMinisearchIndex,
-    this.writeInterval,
-    {
-      leading: true,
-      trailing: true,
-    }
-  )
-  private async _writeMinisearchIndex(minisearch: MiniSearch): Promise<void> {
-    if (!settings.persistCache) {
-      return
-    }
-    const json = JSON.stringify(minisearch)
-    const data = this.compress ? deflate(json) : json
-    await app.vault.adapter.writeBinary(minisearchCacheFilePath, data as any)
-    console.log('Omnisearch - Minisearch index saved on disk')
+  public async updateDocument(path: string, note: IndexedDocument) {
+    this.documentsCache.set(path, note)
   }
 
-  public async readMinisearchIndex(): Promise<string | null> {
-    if (!settings.persistCache) {
-      return null
-    }
-    if (await app.vault.adapter.exists(minisearchCacheFilePath)) {
-      try {
-        const data = await app.vault.adapter.readBinary(minisearchCacheFilePath)
-        return (
-          this.compress ? new TextDecoder('utf8').decode(inflate(data)) : data
-        ) as any
-      } catch (e) {
-        console.trace(
-          'Omnisearch - Could not load MiniSearch index from the file:'
-        )
-        console.warn(e)
-        app.vault.adapter.remove(minisearchCacheFilePath)
-      }
-    }
-    return null
+  public deleteDocument(key: string): void {
+    this.documentsCache.delete(key)
   }
 
-  //#endregion Minisearch
-
-  public async loadNotesCache() {
-    if (!settings.persistCache) {
-      return null
-    }
-    if (await app.vault.adapter.exists(notesCacheFilePath)) {
-      try {
-        const data = await app.vault.adapter.readBinary(notesCacheFilePath)
-        const json = (
-          this.compress ? new TextDecoder('utf8').decode(inflate(data)) : data
-        ) as any
-        this.notesCache = JSON.parse(json)
-      } catch (e) {
-        console.trace('Omnisearch - Could not load notes cache:')
-        console.warn(e)
-        app.vault.adapter.remove(notesCacheFilePath)
-      }
-    }
-    return null
-  }
-
-  public saveNotesCache = throttle(this._saveNotesCache, this.writeInterval, {
-    leading: true,
-    trailing: true,
-  })
-  private async _saveNotesCache() {
-    if (!settings.persistCache) {
-      return
-    }
-    const json = JSON.stringify(this.notesCache)
-    const data = this.compress ? deflate(json) : json
-    await app.vault.adapter.writeBinary(notesCacheFilePath, data as any)
-    console.log('Omnisearch - Notes cache saved on disk')
-  }
-
-  public addNoteToMemCache(path: string, note: IndexedDocument) {
-    this.notesCache[path] = note
-    this.saveNotesCache()
-  }
-
-  public removeNoteFromMemCache(key: string): void {
-    delete this.notesCache[key]
-  }
-
-  public getNoteFromMemCache(key: string): IndexedDocument | undefined {
-    return this.notesCache[key]
+  public getDocument(key: string): IndexedDocument | undefined {
+    return this.documentsCache.get(key)
   }
 
   public getNonExistingNotesFromMemCache(): IndexedDocument[] {
-    return Object.values(this.notesCache).filter(note => note.doesNotExist)
+    return Object.values(this.documentsCache).filter(note => note.doesNotExist)
   }
 
-  public isNoteInMemCacheOutdated(file: TFile): boolean {
-    const indexedNote = this.getNoteFromMemCache(file.path)
+  public isDocumentOutdated(file: TFile): boolean {
+    const indexedNote = this.getDocument(file.path)
     return !indexedNote || indexedNote.mtime !== file.stat.mtime
   }
+
+  // private async _writeMinisearchIndex(minisearch: MiniSearch): Promise<void> {
+  //   if (!settings.persistCache) {
+  //     return
+  //   }
+  //   const json = JSON.stringify(minisearch)
+  //   const data = deflate(json)
+  //   await app.vault.adapter.writeBinary(minisearchCacheFilePath, data as any)
+  //   console.log('Omnisearch - Minisearch index saved on disk')
+  // }
+  //
+  // private async _saveNotesCache() {
+  //   if (!settings.persistCache) {
+  //     return
+  //   }
+  //   const json = JSON.stringify(Array.from(this.documentsCache.entries()))
+  //   const data = deflate(json)
+  //   await app.vault.adapter.writeBinary(notesCacheFilePath, data as any)
+  //   console.log('Omnisearch - Notes cache saved on disk')
+  // }
 }
 
 export const cacheManager = new CacheManager()
diff --git a/src/components/ModalInFile.svelte b/src/components/ModalInFile.svelte
index 3012a59..93d3d59 100644
--- a/src/components/ModalInFile.svelte
+++ b/src/components/ModalInFile.svelte
@@ -10,16 +10,16 @@
     type ResultNote,
     type SearchMatch,
   } from 'src/globals'
-  import { loopIndex } from 'src/utils'
+  import { loopIndex } from 'src/tools/utils'
   import { onDestroy, onMount, tick } from 'svelte'
   import { MarkdownView } from 'obsidian'
-  import * as Search from 'src/search'
+  import * as Search from 'src/search/search'
   import ModalContainer from './ModalContainer.svelte'
-  import { OmnisearchInFileModal, OmnisearchVaultModal } from 'src/modals'
+  import { OmnisearchInFileModal, OmnisearchVaultModal } from 'src/components/modals'
   import ResultItemInFile from './ResultItemInFile.svelte'
-  import { Query } from 'src/query'
-  import { openNote } from 'src/notes'
-  import { saveSearchHistory } from '../search-history'
+  import { Query } from 'src/search/query'
+  import { openNote } from 'src/tools/notes'
+  import { saveSearchHistory } from '../search/search-history'
 
   export let modal: OmnisearchInFileModal
   export let parent: OmnisearchVaultModal | null = null
diff --git a/src/components/ModalVault.svelte b/src/components/ModalVault.svelte
index 353a827..792f0ce 100644
--- a/src/components/ModalVault.svelte
+++ b/src/components/ModalVault.svelte
@@ -4,13 +4,13 @@
   import InputSearch from './InputSearch.svelte'
   import ModalContainer from './ModalContainer.svelte'
   import { eventBus, type ResultNote } from 'src/globals'
-  import { createNote, openNote } from 'src/notes'
-  import * as Search from 'src/search'
-  import { getCtrlKeyLabel, getExtension, loopIndex } from 'src/utils'
-  import { OmnisearchInFileModal, type OmnisearchVaultModal } from 'src/modals'
+  import { createNote, openNote } from 'src/tools/notes'
+  import * as Search from 'src/search/search'
+  import { getCtrlKeyLabel, getExtension, loopIndex } from 'src/tools/utils'
+  import { OmnisearchInFileModal, type OmnisearchVaultModal } from 'src/components/modals'
   import ResultItemVault from './ResultItemVault.svelte'
-  import { Query } from 'src/query'
-  import { saveSearchHistory, searchHistory } from 'src/search-history'
+  import { Query } from 'src/search/query'
+  import { saveSearchHistory, searchHistory } from 'src/search/search-history'
   import { settings } from '../settings'
   import * as NotesIndex from '../notes-index'
 
diff --git a/src/components/ResultItemInFile.svelte b/src/components/ResultItemInFile.svelte
index b4221e5..3f35c51 100644
--- a/src/components/ResultItemInFile.svelte
+++ b/src/components/ResultItemInFile.svelte
@@ -1,6 +1,6 @@
 <script lang="ts">
   import type { ResultNote } from '../globals'
-  import { highlighter, makeExcerpt, stringsToRegex } from '../utils'
+  import { highlighter, makeExcerpt, stringsToRegex } from '../tools/utils'
   import ResultItemContainer from './ResultItemContainer.svelte'
 
   export let offset: number
diff --git a/src/components/ResultItemVault.svelte b/src/components/ResultItemVault.svelte
index 22e3136..e4230c3 100644
--- a/src/components/ResultItemVault.svelte
+++ b/src/components/ResultItemVault.svelte
@@ -2,7 +2,7 @@
   import { cacheManager } from 'src/cache-manager'
   import { settings, showExcerpt } from 'src/settings'
   import type { ResultNote } from '../globals'
-  import { highlighter, makeExcerpt, stringsToRegex } from '../utils'
+  import { highlighter, makeExcerpt, stringsToRegex } from '../tools/utils'
   import ResultItemContainer from './ResultItemContainer.svelte'
 
   export let selected = false
@@ -10,7 +10,7 @@
 
   $: reg = stringsToRegex(note.foundWords)
   $: cleanedContent = makeExcerpt(note.content, note.matches[0]?.offset ?? -1)
-  $: glyph = cacheManager.getNoteFromMemCache(note.path)?.doesNotExist
+  $: glyph = cacheManager.getDocument(note.path)?.doesNotExist
   $: title = settings.showShortName ? note.basename : note.path
 </script>
 
diff --git a/src/modals.ts b/src/components/modals.ts
similarity index 94%
rename from src/modals.ts
rename to src/components/modals.ts
index b74a709..508ccd3 100644
--- a/src/modals.ts
+++ b/src/components/modals.ts
@@ -1,8 +1,8 @@
 import { App, Modal, TFile } from 'obsidian'
-import ModalVault from './components/ModalVault.svelte'
-import ModalInFile from './components/ModalInFile.svelte'
-import {eventBus, EventNames, isInputComposition} from './globals'
-import { settings } from './settings'
+import ModalVault from './ModalVault.svelte'
+import ModalInFile from './ModalInFile.svelte'
+import {eventBus, EventNames, isInputComposition} from '../globals'
+import { settings } from '../settings'
 
 abstract class OmnisearchModal extends Modal {
   protected constructor(app: App) {
diff --git a/src/database.ts b/src/database.ts
index 97cd728..5565aac 100644
--- a/src/database.ts
+++ b/src/database.ts
@@ -1,15 +1,23 @@
 import Dexie from 'dexie'
+import type { IndexedDocument } from './globals'
 
 class OmnisearchCache extends Dexie {
   pdf!: Dexie.Table<
     { path: string; hash: string; size: number; text: string },
     string
   >
+  documents!: Dexie.Table<
+    { document: IndexedDocument; path: string; mtime: number },
+    string
+  >
+  minisearch!: Dexie.Table<string>
 
   constructor() {
     super(app.appId + '_omnisearch')
-    this.version(1).stores({
+    this.version(2).stores({
       pdf: 'path, hash, size, text',
+      documents: 'path, mtime, document',
+      minisearch: 'data',
     })
   }
 }
diff --git a/src/file-loader.ts b/src/file-loader.ts
new file mode 100644
index 0000000..667f997
--- /dev/null
+++ b/src/file-loader.ts
@@ -0,0 +1,92 @@
+import { cacheManager } from './cache-manager'
+import {
+  extractHeadingsFromCache,
+  getAliasesFromMetadata,
+  getTagsFromMetadata,
+  isFilePlaintext,
+  removeDiacritics,
+} from './tools/utils'
+import * as NotesIndex from './notes-index'
+import type { TFile } from 'obsidian'
+import type { IndexedDocument } from './globals'
+import { pdfManager } from './pdf/pdf-manager'
+import { getNonExistingNotes } from './tools/notes'
+
+/**
+ * Return all plaintext files as IndexedDocuments
+ */
+export async function getPlainTextFiles(): Promise<IndexedDocument[]> {
+  const allFiles = app.vault.getFiles().filter(f => isFilePlaintext(f.path))
+  const data: IndexedDocument[] = []
+  for (const file of allFiles) {
+    const doc = await fileToIndexedDocument(file)
+    data.push(doc)
+    await cacheManager.updateDocument(file.path, doc)
+  }
+  return data
+}
+
+/**
+ * Return all PDF files as IndexedDocuments.
+ * If a PDF isn't cached, it will be read from the disk and added to the IndexedDB
+ */
+export async function getPDFFiles(): Promise<IndexedDocument[]> {
+  const allFiles = app.vault.getFiles().filter(f => f.path.endsWith('.pdf'))
+  const data: IndexedDocument[] = []
+
+  const input = []
+  for (const file of allFiles) {
+    input.push(
+      NotesIndex.processQueue(async () => {
+        const doc = await fileToIndexedDocument(file)
+        cacheManager.updateDocument(file.path, doc)
+        data.push(doc)
+      })
+    )
+  }
+  await Promise.all(input)
+  return data
+}
+
+/**
+ * Convert a file into an IndexedDocument.
+ * Will use the cache if possible.
+ * @param file
+ */
+export async function fileToIndexedDocument(
+  file: TFile
+): Promise<IndexedDocument> {
+  let content: string
+  if (isFilePlaintext(file.path)) {
+    content = removeDiacritics(await app.vault.cachedRead(file))
+  } else if (file.path.endsWith('.pdf')) {
+    content = removeDiacritics(await pdfManager.getPdfText(file))
+  } else {
+    throw new Error('Invalid file: ' + file.path)
+  }
+
+  content = removeDiacritics(content)
+  const metadata = app.metadataCache.getFileCache(file)
+
+  // Look for links that lead to non-existing files,
+  // and add them to the index.
+  if (metadata) {
+    const nonExisting = getNonExistingNotes(file, metadata)
+    for (const name of nonExisting.filter(o => !cacheManager.getDocument(o))) {
+      NotesIndex.addNonExistingToIndex(name, file.path)
+    }
+  }
+
+  return {
+    basename: removeDiacritics(file.basename),
+    content,
+    path: file.path,
+    mtime: file.stat.mtime,
+
+    tags: getTagsFromMetadata(metadata),
+    aliases: getAliasesFromMetadata(metadata).join(''),
+    headings1: metadata ? extractHeadingsFromCache(metadata, 1).join(' ') : '',
+    headings2: metadata ? extractHeadingsFromCache(metadata, 2).join(' ') : '',
+    headings3: metadata ? extractHeadingsFromCache(metadata, 3).join(' ') : '',
+  }
+}
diff --git a/src/globals.ts b/src/globals.ts
index 6f46587..48e01b3 100644
--- a/src/globals.ts
+++ b/src/globals.ts
@@ -1,6 +1,4 @@
-import pLimit from 'p-limit'
-import { EventBus } from './event-bus'
-import { settings } from './settings'
+import { EventBus } from './tools/event-bus'
 
 export const regexLineSplit = /\r?\n|\r|((\.|\?|!)( |\r?\n|\r))/g
 export const regexYaml = /^---\s*\n(.*?)\n?^---\s?/ms
@@ -14,8 +12,6 @@ export const highlightClass = 'suggestion-highlight omnisearch-highlight'
 
 export const eventBus = new EventBus()
 
-export const minisearchCacheFilePath = `${app.vault.configDir}/plugins/omnisearch/searchIndex.data`
-export const notesCacheFilePath = `${app.vault.configDir}/plugins/omnisearch/notesCache.data`
 export const historyFilePath = `${app.vault.configDir}/plugins/omnisearch/historyCache.json`
 
 export const EventNames = {
diff --git a/src/main.ts b/src/main.ts
index e2db52c..2108b2c 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -1,29 +1,26 @@
 import { Notice, Plugin, TFile } from 'obsidian'
-import * as Search from './search'
-import { OmnisearchInFileModal, OmnisearchVaultModal } from './modals'
+import * as Search from './search/search'
+import {
+  OmnisearchInFileModal,
+  OmnisearchVaultModal,
+} from './components/modals'
 import { loadSettings, settings, SettingsTab, showExcerpt } from './settings'
 import { eventBus, EventNames } from './globals'
 import { registerAPI } from '@vanakat/plugin-api'
-import api from './api'
-import { loadSearchHistory } from './search-history'
-import { isFilePlaintext } from './utils'
+import api from './tools/api'
+import { loadSearchHistory } from './search/search-history'
+import { isFilePlaintext } from './tools/utils'
 import * as NotesIndex from './notes-index'
-import { cacheManager } from './cache-manager'
-
-function _registerAPI(plugin: OmnisearchPlugin): void {
-  registerAPI('omnisearch', api, plugin as any)
-  ;(app as any).plugins.plugins.omnisearch.api = api
-  plugin.register(() => {
-    delete (app as any).plugins.plugins.omnisearch.api
-  })
-}
+import * as FileLoader from './file-loader'
 
 export default class OmnisearchPlugin extends Plugin {
   async onload(): Promise<void> {
     await cleanOldCacheFiles()
     await loadSettings(this)
     await loadSearchHistory()
-    await cacheManager.loadNotesCache()
+
+    // Initialize minisearch
+    await Search.initSearchEngine()
 
     _registerAPI(this)
 
@@ -69,7 +66,7 @@ export default class OmnisearchPlugin extends Plugin {
       )
       this.registerEvent(
         this.app.vault.on('modify', async file => {
-          NotesIndex.addNoteToReindex(file)
+          NotesIndex.markNoteForReindex(file)
         })
       )
       this.registerEvent(
@@ -81,7 +78,7 @@ export default class OmnisearchPlugin extends Plugin {
         })
       )
 
-      await Search.initGlobalSearchIndex()
+      await populateIndex()
     })
 
     // showWelcomeNotice(this)
@@ -99,11 +96,36 @@ export default class OmnisearchPlugin extends Plugin {
   }
 }
 
+/**
+ * Read the files and feed them to Minisearch
+ */
+async function populateIndex(): Promise<void> {
+  // Load plain text files
+  console.time('Omnisearch - Timing')
+  const files = await FileLoader.getPlainTextFiles()
+  // Index them
+  await Search.addAllToMinisearch(files)
+  console.log(`Omnisearch - Indexed ${files.length} notes`)
+  console.timeEnd('Omnisearch - Timing')
+
+  // Load PDFs
+  if (settings.PDFIndexing) {
+    console.time('Omnisearch - Timing')
+    const pdfs = await FileLoader.getPDFFiles()
+    // Index them
+    await Search.addAllToMinisearch(pdfs)
+    console.log(`Omnisearch - Indexed ${pdfs.length} PDFs`)
+    console.timeEnd('Omnisearch - Timing')
+  }
+}
+
 async function cleanOldCacheFiles() {
   const toDelete = [
     `${app.vault.configDir}/plugins/omnisearch/searchIndex.json`,
     `${app.vault.configDir}/plugins/omnisearch/notesCache.json`,
-    `${app.vault.configDir}/plugins/omnisearch/pdfCache.data`
+    `${app.vault.configDir}/plugins/omnisearch/notesCache.data`,
+    `${app.vault.configDir}/plugins/omnisearch/searchIndex.data`,
+    `${app.vault.configDir}/plugins/omnisearch/pdfCache.data`,
   ]
   for (const item of toDelete) {
     if (await app.vault.adapter.exists(item)) {
@@ -130,3 +152,11 @@ New beta feature: PDF search 🔎📄
 
   plugin.saveData(settings)
 }
+
+function _registerAPI(plugin: OmnisearchPlugin): void {
+  registerAPI('omnisearch', api, plugin as any)
+  ;(app as any).plugins.plugins.omnisearch.api = api
+  plugin.register(() => {
+    delete (app as any).plugins.plugins.omnisearch.api
+  })
+}
diff --git a/src/notes-index.ts b/src/notes-index.ts
index 48aada4..31ba5c1 100644
--- a/src/notes-index.ts
+++ b/src/notes-index.ts
@@ -1,20 +1,12 @@
 import { Notice, TAbstractFile, TFile } from 'obsidian'
-import {
-  extractHeadingsFromCache,
-  getAliasesFromMetadata,
-  getTagsFromMetadata,
-  isFileIndexable,
-  removeDiacritics,
-  wait,
-} from './utils'
-import { getNonExistingNotes, removeAnchors } from './notes'
-import { pdfManager } from './pdf-manager'
+import { isFileIndexable, wait } from './tools/utils'
+import { removeAnchors } from './tools/notes'
 import { settings } from './settings'
-import * as Search from './search'
-// import PQueue from 'p-queue-compat'
+import * as Search from './search/search'
 import { cacheManager } from './cache-manager'
 import pLimit from 'p-limit'
 import type { IndexedDocument } from './globals'
+import { fileToIndexedDocument } from './file-loader'
 
 /**
  * Use this processing queue to handle all heavy work
@@ -33,59 +25,21 @@ export async function addToIndexAndMemCache(
     return
   }
 
-  // Check if the file was already indexed as non-existent,
-  // and if so, remove it from the index (before adding it again)
-  if (cacheManager.getNoteFromMemCache(file.path)?.doesNotExist) {
+  // Check if the file was already indexed as non-existent.
+  // If so, remove it from the index, and add it again as a real note.
+  if (cacheManager.getDocument(file.path)?.doesNotExist) {
     removeFromIndex(file.path)
   }
 
   try {
-    // Look for links that lead to non-existing files,
-    // and index them as well
-    const metadata = app.metadataCache.getFileCache(file)
-    if (metadata) {
-      const nonExisting = getNonExistingNotes(file, metadata)
-      for (const name of nonExisting.filter(
-        o => !cacheManager.getNoteFromMemCache(o)
-      )) {
-        addNonExistingToIndex(name, file.path)
-      }
-    }
-
-    if (cacheManager.getNoteFromMemCache(file.path)) {
+    if (cacheManager.getDocument(file.path)) {
       throw new Error(`${file.basename} is already indexed`)
     }
 
-    let content
-    if (file.path.endsWith('.pdf')) {
-      content = removeDiacritics(await pdfManager.getPdfText(file as TFile))
-    } else {
-      // Fetch content from the cache to index it as-is
-      content = removeDiacritics(await app.vault.cachedRead(file))
-    }
-
     // Make the document and index it
-    const note: IndexedDocument = {
-      basename: removeDiacritics(file.basename),
-      content,
-      path: file.path,
-      mtime: file.stat.mtime,
-
-      tags: getTagsFromMetadata(metadata),
-      aliases: getAliasesFromMetadata(metadata).join(''),
-      headings1: metadata
-        ? extractHeadingsFromCache(metadata, 1).join(' ')
-        : '',
-      headings2: metadata
-        ? extractHeadingsFromCache(metadata, 2).join(' ')
-        : '',
-      headings3: metadata
-        ? extractHeadingsFromCache(metadata, 3).join(' ')
-        : '',
-    }
-
-    Search.minisearchInstance.add(note)
-    cacheManager.addNoteToMemCache(note.path, note)
+    const note = await fileToIndexedDocument(file)
+    Search.addSingleToMinisearch(note)
+    await cacheManager.updateDocument(note.path, note)
   } catch (e) {
     // console.trace('Error while indexing ' + file.basename)
     console.error(e)
@@ -101,7 +55,7 @@ export async function addToIndexAndMemCache(
 export function addNonExistingToIndex(name: string, parent: string): void {
   name = removeAnchors(name)
   const filename = name + (name.endsWith('.md') ? '' : '.md')
-  if (cacheManager.getNoteFromMemCache(filename)) return
+  if (cacheManager.getDocument(filename)) return
 
   const note: IndexedDocument = {
     path: filename,
@@ -118,29 +72,30 @@ export function addNonExistingToIndex(name: string, parent: string): void {
     doesNotExist: true,
     parent,
   }
-  Search.minisearchInstance.add(note)
-  cacheManager.addNoteToMemCache(filename, note)
+  Search.addSingleToMinisearch(note)
+  cacheManager.updateDocument(filename, note)
 }
 
 /**
- * Removes a file from the index, by its path
- * @param path
+ * Removes a file from the index, by its path.
  */
 export function removeFromIndex(path: string): void {
   if (!isFileIndexable(path)) {
     console.info(`"${path}" is not an indexable file`)
     return
   }
-  const note = cacheManager.getNoteFromMemCache(path)
+  const note = cacheManager.getDocument(path)
   if (note) {
-    Search.minisearchInstance.remove(note)
-    cacheManager.removeNoteFromMemCache(path)
-    cacheManager
-      .getNonExistingNotesFromMemCache()
-      .filter(n => n.parent === path)
-      .forEach(n => {
-        removeFromIndex(n.path)
-      })
+    Search.removeFromMinisearch(note)
+    cacheManager.deleteDocument(path)
+
+    // FIXME: only remove non-existing notes if they don't have another parent
+    // cacheManager
+    //   .getNonExistingNotesFromMemCache()
+    //   .filter(n => n.parent === path)
+    //   .forEach(n => {
+    //     removeFromIndex(n.path)
+    //   })
   } else {
     console.warn(`Omnisearch - Note not found under path ${path}`)
   }
@@ -148,7 +103,11 @@ export function removeFromIndex(path: string): void {
 
 const notesToReindex = new Set<TAbstractFile>()
 
-export function addNoteToReindex(note: TAbstractFile): void {
+/**
+ * Updated notes are not reindexed immediately for performance reasons.
+ * They're added to a list, and reindex is done the next time we open Omnisearch.
+ */
+export function markNoteForReindex(note: TAbstractFile): void {
   notesToReindex.add(note)
 }
 
@@ -163,35 +122,5 @@ export async function refreshIndex(): Promise<void> {
       await wait(0)
     }
     notesToReindex.clear()
-    await cacheManager.writeMinisearchIndex(Search.minisearchInstance)
-  }
-}
-
-export async function indexPDFs() {
-  if (settings.PDFIndexing) {
-    const files = app.vault.getFiles().filter(f => f.path.endsWith('.pdf'))
-    console.time('PDF Indexing')
-    console.log(`Omnisearch - Indexing ${files.length} PDFs`)
-    const input = []
-    for (const file of files) {
-      if (cacheManager.getNoteFromMemCache(file.path)) {
-        removeFromIndex(file.path)
-      }
-      input.push(
-        processQueue(async () => {
-          await addToIndexAndMemCache(file)
-          await cacheManager.writeMinisearchIndex(Search.minisearchInstance)
-        })
-      )
-    }
-    await Promise.all(input)
-    // await pdfQueue.onEmpty()
-    console.timeEnd('PDF Indexing')
-
-    if (settings.showIndexingNotices) {
-      new Notice(`Omnisearch - Indexed ${files.length} PDFs`)
-    }
-
-    await pdfManager.cleanCache()
   }
 }
diff --git a/src/pdf-manager.ts b/src/pdf/pdf-manager.ts
similarity index 97%
rename from src/pdf-manager.ts
rename to src/pdf/pdf-manager.ts
index 0fa1348..aebd726 100644
--- a/src/pdf-manager.ts
+++ b/src/pdf/pdf-manager.ts
@@ -1,7 +1,7 @@
 import type { TFile } from 'obsidian'
 import WebWorker from 'web-worker:./pdf-worker.ts'
-import { makeMD5 } from './utils'
-import { database } from './database'
+import { makeMD5 } from '../tools/utils'
+import { database } from '../database'
 
 const workerTimeout = 120_000
 
diff --git a/src/pdf-worker.ts b/src/pdf/pdf-worker.ts
similarity index 84%
rename from src/pdf-worker.ts
rename to src/pdf/pdf-worker.ts
index 6be1289..828d521 100644
--- a/src/pdf-worker.ts
+++ b/src/pdf/pdf-worker.ts
@@ -1,5 +1,5 @@
-import rustPlugin from '../pkg/obsidian_search_bg.wasm'
-import * as plugin from '../pkg/obsidian_search'
+import rustPlugin from '../../pkg/obsidian_search_bg.wasm'
+import * as plugin from '../../pkg'
 
 const decodedPlugin = decodeBase64(rustPlugin as any)
 
diff --git a/src/query.ts b/src/search/query.ts
similarity index 87%
rename from src/query.ts
rename to src/search/query.ts
index 1bb8d2a..389436d 100644
--- a/src/query.ts
+++ b/src/search/query.ts
@@ -1,6 +1,6 @@
-import { settings } from './settings'
-import { removeDiacritics, stripSurroundingQuotes } from './utils'
-import { parseQuery } from './vendor/parse-query'
+import { settings } from '../settings'
+import { removeDiacritics, stripSurroundingQuotes } from '../tools/utils'
+import { parseQuery } from '../vendor/parse-query'
 
 type QueryToken = {
   /**
diff --git a/src/search-history.ts b/src/search/search-history.ts
similarity index 93%
rename from src/search-history.ts
rename to src/search/search-history.ts
index 4a0b5e5..6c3b2d1 100644
--- a/src/search-history.ts
+++ b/src/search/search-history.ts
@@ -1,4 +1,4 @@
-import { historyFilePath } from './globals'
+import { historyFilePath } from '../globals'
 
 export let searchHistory: string[] = []
 
diff --git a/src/search.ts b/src/search/search.ts
similarity index 63%
rename from src/search.ts
rename to src/search/search.ts
index 0782d2f..b399011 100644
--- a/src/search.ts
+++ b/src/search/search.ts
@@ -1,25 +1,25 @@
-import { Notice } from 'obsidian'
-import MiniSearch, { type Options, type SearchResult } from 'minisearch'
+import MiniSearch, {
+  type AsPlainObject,
+  type Options,
+  type SearchResult,
+} from 'minisearch'
 import {
   chsRegex,
   type IndexedDocument,
   type ResultNote,
-  minisearchCacheFilePath,
   type SearchMatch,
   SPACE_OR_PUNCTUATION,
-} from './globals'
+} from '../globals'
 import {
-  isFilePlaintext,
   removeDiacritics,
   stringsToRegex,
   stripMarkdownCharacters,
-} from './utils'
+} from '../tools/utils'
 import type { Query } from './query'
-import { settings } from './settings'
-import * as NotesIndex from './notes-index'
-import { cacheManager } from './cache-manager'
+import { settings } from '../settings'
+import { cacheManager } from '../cache-manager'
 
-export let minisearchInstance: MiniSearch<IndexedDocument>
+let minisearchInstance: MiniSearch<IndexedDocument>
 
 const tokenize = (text: string): string[] => {
   const tokens = text.split(SPACE_OR_PUNCTUATION)
@@ -32,98 +32,38 @@ const tokenize = (text: string): string[] => {
   } else return tokens
 }
 
+const minisearchOptions: Options<IndexedDocument> = {
+  tokenize,
+  processTerm: (term: string) =>
+    (settings.ignoreDiacritics ? removeDiacritics(term) : term).toLowerCase(),
+  idField: 'path',
+  fields: [
+    'basename',
+    'aliases',
+    'content',
+    'headings1',
+    'headings2',
+    'headings3',
+  ],
+  storeFields: ['tags'],
+}
+
 /**
  * Initializes the MiniSearch instance,
  * and adds all the notes to the index
  */
-export async function initGlobalSearchIndex(): Promise<void> {
-  const options: Options<IndexedDocument> = {
-    tokenize,
-    processTerm: (term: string) =>
-      (settings.ignoreDiacritics ? removeDiacritics(term) : term).toLowerCase(),
-    idField: 'path',
-    fields: [
-      'basename',
-      'aliases',
-      'content',
-      'headings1',
-      'headings2',
-      'headings3',
-    ],
-    storeFields: ['tags'],
-  }
-
+export async function initSearchEngine(): Promise<void> {
   // Default instance
-  minisearchInstance = new MiniSearch(options)
+  minisearchInstance = new MiniSearch(minisearchOptions)
+}
 
-  // Load Minisearch cache, if it exists
-  if (await app.vault.adapter.exists(minisearchCacheFilePath)) {
-    try {
-      const json = await cacheManager.readMinisearchIndex()
-      if (json) {
-        // If we have cache data, reload it
-        minisearchInstance = MiniSearch.loadJSON(json, options)
-      }
-      console.log('Omnisearch - MiniSearch index loaded from the file')
-    } catch (e) {
-      console.trace(
-        'Omnisearch - Could not load MiniSearch index from the file'
-      )
-      console.error(e)
-    }
-  }
-
-  // if (!minisearchInstance) {
-  //   resetNotesCache()
-  // }
-
-  // Index files that are already present
-  const start = new Date().getTime()
-
-  const allFiles = app.vault.getFiles().filter(f => isFilePlaintext(f.path))
-
-  let files
-  let notesSuffix
-  if (settings.persistCache) {
-    files = allFiles.filter(file => cacheManager.isNoteInMemCacheOutdated(file))
-    notesSuffix = 'modified notes'
-  } else {
-    files = allFiles
-    notesSuffix = 'notes'
-  }
-
-  if (files.length > 0) {
-    console.log(`Omnisearch - Indexing ${files.length} ${notesSuffix}`)
-  }
-
-  // Read and index all the files into the search engine
-  const input = []
-  for (const file of files) {
-    if (cacheManager.getNoteFromMemCache(file.path)) {
-      NotesIndex.removeFromIndex(file.path)
-    }
-    input.push(
-      NotesIndex.processQueue(() => NotesIndex.addToIndexAndMemCache(file))
-    )
-  }
-
-  await Promise.all(input)
-
-  if (files.length > 0) {
-    const message = `Omnisearch - Indexed ${files.length} ${notesSuffix} in ${
-      new Date().getTime() - start
-    }ms`
-
-    console.log(message)
-
-    if (settings.showIndexingNotices) {
-      new Notice(message)
-    }
-
-    await cacheManager.writeMinisearchIndex(minisearchInstance)
-
-    // PDFs are indexed later, since they're heavier
-    await NotesIndex.indexPDFs()
+export async function initSearchEngineFromData(json: string): Promise<void> {
+  try {
+    minisearchInstance = MiniSearch.loadJSON(json, minisearchOptions)
+    console.log('Omnisearch - MiniSearch index loaded from the file')
+  } catch (e) {
+    console.error('Omnisearch - Could not load MiniSearch index from json')
+    console.error(e)
   }
 }
 
@@ -165,10 +105,9 @@ async function search(query: Query): Promise<SearchResult[]> {
   const exactTerms = query.getExactTerms()
   if (exactTerms.length) {
     results = results.filter(r => {
-      const title =
-        cacheManager.getNoteFromMemCache(r.id)?.path.toLowerCase() ?? ''
+      const title = cacheManager.getDocument(r.id)?.path.toLowerCase() ?? ''
       const content = stripMarkdownCharacters(
-        cacheManager.getNoteFromMemCache(r.id)?.content ?? ''
+        cacheManager.getDocument(r.id)?.content ?? ''
       ).toLowerCase()
       return exactTerms.every(q => content.includes(q) || title.includes(q))
     })
@@ -179,7 +118,7 @@ async function search(query: Query): Promise<SearchResult[]> {
   if (exclusions.length) {
     results = results.filter(r => {
       const content = stripMarkdownCharacters(
-        cacheManager.getNoteFromMemCache(r.id)?.content ?? ''
+        cacheManager.getDocument(r.id)?.content ?? ''
       ).toLowerCase()
       return exclusions.every(q => !content.includes(q.value))
     })
@@ -247,7 +186,7 @@ export async function getSuggestions(
 
   // Map the raw results to get usable suggestions
   return results.map(result => {
-    const note = cacheManager.getNoteFromMemCache(result.id)
+    const note = cacheManager.getDocument(result.id)
     if (!note) {
       throw new Error(`Note "${result.id}" not indexed`)
     }
@@ -286,3 +225,25 @@ export async function getSuggestions(
     return resultNote
   })
 }
+
+// #region Read/write minisearch index
+
+export function getMinisearchIndexJSON(): AsPlainObject {
+  return minisearchInstance.toJSON()
+}
+
+export async function addAllToMinisearch(
+  documents: IndexedDocument[]
+): Promise<void> {
+  await minisearchInstance.addAllAsync(documents)
+}
+
+export function addSingleToMinisearch(document: IndexedDocument): void {
+  minisearchInstance.add(document)
+}
+
+export function removeFromMinisearch(document: IndexedDocument): void {
+  minisearchInstance.remove(document)
+}
+
+// #endregion
\ No newline at end of file
diff --git a/src/settings.ts b/src/settings.ts
index 93e8d1b..62389f6 100644
--- a/src/settings.ts
+++ b/src/settings.ts
@@ -6,7 +6,6 @@ import {
   SliderComponent,
 } from 'obsidian'
 import { writable } from 'svelte/store'
-import { notesCacheFilePath, minisearchCacheFilePath } from './globals'
 import type OmnisearchPlugin from './main'
 
 interface WeightingSettings {
@@ -28,7 +27,7 @@ export interface OmnisearchSettings extends WeightingSettings {
   /** Max number of spawned processes for background tasks, such as extracting text from PDFs */
   backgroundProcesses: number
   /** Write cache files on disk (unrelated to PDFs) */
-  persistCache: boolean
+  // persistCache: boolean
   /** Display Omnisearch popup notices over Obsidian */
   showIndexingNotices: boolean
   /** Activate the small 🔍 button on Obsidian's ribbon */
@@ -141,37 +140,27 @@ export class SettingsTab extends PluginSettingTab {
     //       })
     //   })
 
-    // Store index
-    const serializedIndexDesc = new DocumentFragment()
-    serializedIndexDesc.createSpan({}, span => {
-      span.innerHTML = `This will speedup startup times after the initial indexing. Do not activate it unless indexing is too slow on your device:
-        <ul>
-          <li>PDF indexing is not affected by this setting</li>
-          <li>⚠️ The index can become corrupted - if you notice any issue, disable and re-enable this option to clear the cache.</li>
-          <li>⚠️ Cache files in <code>.obsidian/plugins/omnisearch/*.data</code> must not be synchronized between your devices.</li>
-        </ul>
-        <strong style="color: var(--text-accent)">Needs a restart to fully take effect.</strong>
-        `
-    })
-    new Setting(containerEl)
-      .setName('Persist cache on disk')
-      .setDesc(serializedIndexDesc)
-      .addToggle(toggle =>
-        toggle.setValue(settings.persistCache).onChange(async v => {
-          try {
-            await app.vault.adapter.remove(notesCacheFilePath)
-          } catch (e) {
-            console.warn(e)
-          }
-          try {
-            await app.vault.adapter.remove(minisearchCacheFilePath)
-          } catch (e) {
-            console.warn(e)
-          }
-          settings.persistCache = v
-          await saveSettings(this.plugin)
-        })
-      )
+    // // Store index
+    // const serializedIndexDesc = new DocumentFragment()
+    // serializedIndexDesc.createSpan({}, span => {
+    //   span.innerHTML = `This will speedup startup times after the initial indexing. Do not activate it unless indexing is too slow on your device:
+    //     <ul>
+    //       <li>PDF indexing is not affected by this setting</li>
+    //       <li>⚠️ The index can become corrupted - if you notice any issue, disable and re-enable this option to clear the cache.</li>
+    //       <li>⚠️ Cache files in <code>.obsidian/plugins/omnisearch/*.data</code> must not be synchronized between your devices.</li>
+    //     </ul>
+    //     <strong style="color: var(--text-accent)">Needs a restart to fully take effect.</strong>
+    //     `
+    // })
+    // new Setting(containerEl)
+    //   .setName('Persist cache on disk')
+    //   .setDesc(serializedIndexDesc)
+    //   .addToggle(toggle =>
+    //     toggle.setValue(settings.persistCache).onChange(async v => {
+    //       settings.persistCache = v
+    //       await saveSettings(this.plugin)
+    //     })
+    //   )
 
     // PDF Indexing
     const indexPDFsDesc = new DocumentFragment()
@@ -363,7 +352,7 @@ export const DEFAULT_SETTINGS: OmnisearchSettings = {
   CtrlJK: false,
   CtrlNP: false,
 
-  persistCache: false,
+  // persistCache: false,
 
   welcomeMessage: '',
 } as const
diff --git a/src/api.ts b/src/tools/api.ts
similarity index 83%
rename from src/api.ts
rename to src/tools/api.ts
index 663af82..2e5523d 100644
--- a/src/api.ts
+++ b/src/tools/api.ts
@@ -1,6 +1,6 @@
-import type { ResultNote, SearchMatch } from './globals'
-import { Query } from './query'
-import * as Search from './search'
+import type { ResultNote, SearchMatch } from '../globals'
+import { Query } from '../search/query'
+import * as Search from '../search/search'
 
 type ResultNoteApi = {
   score: number
diff --git a/src/event-bus.ts b/src/tools/event-bus.ts
similarity index 100%
rename from src/event-bus.ts
rename to src/tools/event-bus.ts
diff --git a/src/notes.ts b/src/tools/notes.ts
similarity index 98%
rename from src/notes.ts
rename to src/tools/notes.ts
index 97323ce..3c02ed4 100644
--- a/src/notes.ts
+++ b/src/tools/notes.ts
@@ -1,6 +1,6 @@
 import { type CachedMetadata, MarkdownView, TFile } from 'obsidian'
 import { stringsToRegex } from './utils'
-import type { ResultNote } from './globals'
+import type { ResultNote } from '../globals'
 
 export async function openNote(
   item: ResultNote,
diff --git a/src/utils.ts b/src/tools/utils.ts
similarity index 95%
rename from src/utils.ts
rename to src/tools/utils.ts
index 6ae1658..f051a33 100644
--- a/src/utils.ts
+++ b/src/tools/utils.ts
@@ -1,5 +1,5 @@
-import { type CachedMetadata, Notice, Platform, Plugin } from 'obsidian'
-import type { SearchMatch } from './globals'
+import { type CachedMetadata, Platform } from 'obsidian'
+import type { SearchMatch } from '../globals'
 import {
   excerptAfter,
   excerptBefore,
@@ -8,9 +8,9 @@ import {
   regexLineSplit,
   regexStripQuotes,
   regexYaml,
-} from './globals'
-import { settings } from './settings'
-import { createHash, type BinaryLike } from 'crypto'
+} from '../globals'
+import { settings } from '../settings'
+import { type BinaryLike, createHash } from 'crypto'
 import { md5 } from 'pure-md5'
 
 export function highlighter(str: string): string {