Say you have a project directory like this:
mount/ is a directory added to the maps gameinfo so that hammer mounts the directory to access custom content within it.
You can add a build step to hammer with the following command line options to generate a bspzip filelist from the mount directory:
Then you can run bspzip to pack it.
This is an alternative to VIDE that can be easily automated within your build process. Set it up and it just works!