[One (M9) General] Jonny:
Ok thanks to Lee & svadev's tool here we have a full deodexed system.

Some things to note - The system seems to be running a 32/64 bit mix meaning not all apps are 64-bit, there are 236 64-bit applications and 177 32-bit applications. The 32-bit apps don't need to be deodexed but all of the 64 bit ones do (and have).

For reference the list of apps that didn't need to be deodexed:

/system/framework/core-libart.jar
/system/app/AntHalService.apk
/system/app/ANTRadioService.apk
/system/app/BasicDream.apk
/system/app/Books.apk
/system/app/BrowserProviderProxy.apk
/system/app/Calculator.apk
/system/app/CalculatorWidget.apk
/system/app/CaptivePortalLogin.apk
/system/app/CertInstaller.apk
/system/app/Chrome.apk
/system/app/CloudPrint.apk
/system/app/ConfigUpdater.apk
/system/app/DeviceManagement.apk
/system/app/DocumentsUI.apk
/system/app/DownloadProviderUi.apk
/system/app/DriveActivator.apk
/system/app/Ds.apk
/system/app/FaceLock.apk
/system/app/FMRadioService.apk
/system/app/Font_Helvetica.apk
/system/app/Font_XinGothic.apk
/system/app/Font_Yuen.apk
/system/app/Gmail2.apk
/system/app/GoogleCalendarSyncAdapter.apk
/system/app/GoogleContactsSyncAdapter.apk
/system/app/HoloSpiralWallpaper.apk
/system/app/HtcAccessoryService.apk
/system/app/HtcAutoRotateWidget.apk
/system/app/HtcBackgroundDataWidget.apk
/system/app/HTCBackup.apk
/system/app/HtcBackupReset.apk
/system/app/HtcCarGps.apk
/system/app/HtcCompressViewer.apk
/system/app/HtcGpsWidget.apk
/system/app/HtcLogLevel.apk
/system/app/HtcMessageProvider.apk
/system/app/HtcPowerStripWidget.apk
/system/app/HtcProfilesWidget.apk
/system/app/HtcResetNotify.apk
/system/app/HtcRingtoneWidget.apk
/system/app/HtcScreenBrightnessWidget.apk
/system/app/HtcScreenTimeoutWidget.apk
/system/app/HtcSettingsProvider.apk
/system/app/HTCSetupWizard.apk
/system/app/HtcSyncWidget.apk
/system/app/HTMLViewer.apk
/system/app/IMEHWRPenPower.apk
/system/app/IMEMurasuIndic.apk
/system/app/IMEMurasuViet.apk
/system/app/IME_TP_Basic.apk
/system/app/KeyChain.apk
/system/app/KidMode-google.apk
/system/app/LiveWallpapers.apk
/system/app/Maps.apk
/system/app/Music2.apk
/system/app/Newsstand.apk
/system/app/NewsWeather.apk
/system/app/NfcNciNxp.apk
/system/app/NoiseField.apk
/system/app/PackageInstaller.apk
/system/app/PacProcessor.apk
/system/app/PartnerBookmarksProvider.apk
/system/app/PeelSmartRemote.apk
/system/app/PhaseBeam.apk
/system/app/PlayGames.apk
/system/app/PrintSpooler.apk
/system/app/QXDM2SD.apk
/system/app/Settings.apk
/system/app/skype_raider_stub-2.1.431.31.apk
/system/app/SmartcardService.apk
/system/app/Smith.apk
/system/app/Street.apk
/system/app/talkback.apk
/system/app/TimeService.apk
/system/app/Usage.apk
/system/app/UserDictionaryProvider.apk
/system/app/VisualizationWallpapers.apk
/system/app/WebViewGoogle.apk
/system/app/WifiRouter.apk
/system/priv-app/AndroidForWork.apk
/system/priv-app/AndroidHtcSync.apk
/system/priv-app/Automotive_Home.apk
/system/priv-app/BackupRestoreConfirmation.apk
/system/priv-app/CalendarProvider.apk
/system/priv-app/CheckinProvider.apk
/system/priv-app/ContactsProvider.apk
/system/priv-app/CustomizationSettingsProvider.apk
/system/priv-app/CustomizationSetup.apk
/system/priv-app/DefaultContainerService.apk
/system/priv-app/DemoFLOPackageInstaller.apk
/system/priv-app/DownloadProvider.apk
/system/priv-app/DrawingBoard.apk
/system/priv-app/EasyAccessService.apk
/system/priv-app/ExternalStorageProvider.apk
/system/priv-app/Facebook.apk
/system/priv-app/FlexNet.apk
/system/priv-app/FM_Radio.apk
/system/priv-app/Frisbee.apk
/system/priv-app/FusedLocation.apk
/system/priv-app/GmsCore.apk
/system/priv-app/GoogleBackupTransport.apk
/system/priv-app/GoogleFeedback.apk
/system/priv-app/GoogleLoginService.apk
/system/priv-app/GoogleOneTimeInitializer.apk
/system/priv-app/GooglePartnerSetup.apk
/system/priv-app/GooglePlusPlugin.apk
/system/priv-app/GoogleServicesFramework.apk
/system/priv-app/GSD.apk
/system/priv-app/HMS_VideoPlayer.apk
/system/priv-app/HomePersonalize.apk
/system/priv-app/HTCAdvantage.apk
/system/priv-app/HtcBtWidget.apk
/system/priv-app/HtcCalendarWidgets.apk
/system/priv-app/HtcContactsDialer.apk
/system/priv-app/HtcContactsDNATransfer.apk
/system/priv-app/HtcContactWidgets.apk
/system/priv-app/HtcDataRoamingWidget.apk
/system/priv-app/HtcDataStripWidget.apk
/system/priv-app/HtcDotMatrix.apk
/system/priv-app/HtcEPSLauncher.apk
/system/priv-app/HtcFileManager.apk
/system/priv-app/HtcHotspotWidget.apk
/system/priv-app/HtcLockScreen.apk
/system/priv-app/HtcMobileData.apk
/system/priv-app/HtcMobileNetworkWidget.apk
/system/priv-app/HTCMode.apk
/system/priv-app/HtcMusicWidget.apk
/system/priv-app/HTCOOBEAdvantage.apk
/system/priv-app/HtcPowerManager.apk
/system/priv-app/HtcServicePack.apk
/system/priv-app/HtcSimpleLauncher.apk
/system/priv-app/HtcSoundRecorder.apk
/system/priv-app/HtcWeatherClockWidget.apk
/system/priv-app/HtcWiFiWidget.apk
/system/priv-app/HTC_CIR.apk
/system/priv-app/HTC_LocationServicesSetting.apk
/system/priv-app/InCallUI.apk
/system/priv-app/InputDevices.apk
/system/priv-app/Instagram_SN_Plugin.apk
/system/priv-app/KeepAlive.apk
/system/priv-app/LauncherUpdateScreen.apk
/system/priv-app/LinkedIn_Fsplugin.apk
/system/priv-app/LMW.apk
/system/priv-app/ManagedProvisioning.apk
/system/priv-app/MediaProvider.apk
/system/priv-app/MirrorLink_MirrorLinkService.apk
/system/priv-app/MmsService.apk
/system/priv-app/NeroHTCInstaller.apk
/system/priv-app/Phonesky.apk
/system/priv-app/ProxyHandler.apk
/system/priv-app/SettingsProvider.apk
/system/priv-app/SetupWizard.apk
/system/priv-app/SharedStorageBackup.apk
/system/priv-app/Shell.apk
/system/priv-app/SMSBackup.apk
/system/priv-app/SoundPicker.apk
/system/priv-app/Stk.apk
/system/priv-app/SystemUI.apk
/system/priv-app/Tag.apk
/system/priv-app/Telecomm.apk
/system/priv-app/Telephony.apk
/system/priv-app/TelephonyProvider.apk
/system/priv-app/Transfer.apk
/system/priv-app/Twitter.apk
/system/priv-app/UDove.apk
/system/priv-app/UIBC.apk
/system/priv-app/Updater.apk
/system/priv-app/Velvet.apk
/system/priv-app/VoiceDictation.apk
/system/priv-app/VpnDialogs.apk
/system/priv-app/WallpaperCropper.apk
/system/priv-app/Weather.apk
/system/priv-app/WorldClock.apk
/system/app/Maps/Maps.apk
/system/priv-app/GmsCore/GmsCore.apk
/system/priv-app/GmsCore/GmsCore.apk

Again the download link contains only /app, /framework & /priv-app folders.

Download link >>> http://darkforest-roms.co.uk/Firmware/HTC One M9/1.32.401.15/HIMA_1.32.401.15_Deodex_min.zip