While regular mods for Bethesda games are installed into the data folder, there are some additional tools that belong into the root folder. These are not automatically moved by Wabbajack. Instructions for them are included in the Installation setup, this page merely serves as an overview over the files in question and their purpose.
WTP does not use the Stock Game Folder system and likely never will.
The Fallout 4 Script Extender (F4SE) is essential to modding Fallout 4 and required by many mods. Its executable and DLLs have to be inside the root folder.
The xSE Plugin Preloader F4 is required for Buffout.
Buffout 4 requires the TBB library, a small plugin that needs to be placed in the root folder.
The ENBSeries for Fallout 4 binaries, required for ENB presets to work.
My personal enblocal.ini with customised hotkeys.
The FallOpt ENB preset.