Yes, I read the documentation on how to make them play nice, and to me it is unacceptable to change suhosin settings intended to protect my users and my site from a malicious user so that I can use a web app that is not open to the public.
No idea what the problems are (couldn't find a list of what the problems are) but
Can you change the suhosin settings with a .htaccess? With the apache htpasswd protection it should be ok to disable some stuff for a particular directory.
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