What exactly do you want to do?
I use 7zip to manage my Gerber files in a ZIP file. While I need to create the first one manually, after that I use a batch file with a 7zip command (see below) to automatically update the zip file whenever I make changes. I simply drag and drop the ZIP file onto a shortcut to the batch file and any files that need updating get updated. Note that this only works when you drag and drop to a shortcut to the batch file; this doesn't work in Windows if you drag and drop to the batch file directly.
7z u -ur0 %1
rem DON'T run the .BAT file directly from windows
rem run the shortcut from windows
rem also, you must run this batch file in the directory with the gerber files.
rem otherwise it will report no changes when changes may be present.
we have a simmilar batch for generating a ZIP file. But we would like to generate the gerber files also in batch mode.