Purpose of custom folder in Open UI

Hi,

Having read all content in Bookshelf about placing all custom javascript files and custom webtemplate files in \\siebelroot\build number\..\custom folder, if we do an new upgrade and build number gets changed, will these custom files copied automatically during upgrade or it will be a manual copy?

If it's a manual process to copy these custom files then would it be a better idea to create a custom folder outside of build number and place files in this folder?

Thanks,

Abhijeet