The way to do this is somewhat undocumented. The client has no GUI option for this, but after digging in logs and source code I discovered that it looks in ~/.csync/csync_exclude.conf for an exclusion list. A example is installed by the .deb package into /usr/etc/. This is an unused directory on Ubuntu; even the ownCloud client ignores it. I copied it to ~/.csync. Here is what mine looks like:
*.filepart
*~
*.bak
*.part
*.unison*
*csync_timedif.ctmp*
.*.sw?
.*.*sw?
.DS_Store
.ds_store
desktop.ini
Thumbs.db
*~
*.bak
*.part
*.unison*
*csync_timedif.ctmp*
.*.sw?
.*.*sw?
.DS_Store
.ds_store
desktop.ini
Thumbs.db
Also note that the .DB file in the ~/.csync folder is a list of files synced. If your rebuilding a synced folder and ot’s empty on you computer, normally the cloud version WILL BE DELETED if you start OwnCloud Agent. Remove the DB and your client will download the files and not tell the server to delete them !!!