If you're sharing classes, assets, images, etc. across domains you could setup a shared folder for each in the user's $home and ssh in and create the relevant directories as symbolic links in the domains you want to have access to the shared content.
in domain1.com create a symbolic link called assets pointing to /home/assets
in domain2.com create a symbolic link called assets to /home/assets, a symbolic link called classes to /home/classes, a symbolic link called images to /home/images, etc.
That way an edit on one file (eg. in the classes folder) will be used by all the domains that symlink to the communal classes folder.
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