Provide update to user

Provide update to user

I am working in a java application, in which all the users will get
automatic update when the user is connected to internet. I am trying a
simple logic like this:
My application will search for the validity of the user.
If the user is valid a folder will be downloaded from
http://example.com/update/
The downloaded folder will be stored somewhere in disk.
My project folder's dist folder will be replaced with the new downloaded
file.
I am stumbled in the No. 4. OS does not allow me to replace in-use files.
Is there any other solution, so that I can provide updates to my users.?