I have found here at stackoveflow some codes on how to ZIP a specific file, but how about a specific folder?
Folder/
index.html
picture.jpg
important.tx
Why not Try EFS PhP-ZiP MultiVolume Script ... I zipped and transferred hundreds of gigs and millions of files ... ssh is needed to effectively create archives.
But i belive that resulting files can be used with exec directly from php:
exec('zip -r backup-2013-03-30_0 . -i@backup-2013-03-30_0.txt');
I do not know if it works. I have not tried ...
"the secret" is that the execution time for archiving should not exceed the time allowed for execution of PHP code.