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I know, this has already been asked a few times, but it doesn't seem to cover my case yet.

I'm trying to package a Mono-application to run from /opt.

First, I tried these guides:

But they don't seem to do the job.

The problem I see is that dh_make doesn't seem to like building packages that are installed in /opt. It always applies its own prefix to the path (/usr/) and puts the files in the usual directorys (bin/share/lib). But what I want is a flat layout just as I have it usually when building directly with MonoDevelop.

How can I do that with dh_make? do I have to create the debian/rules file manually to force installation to /opt?

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The packaging produced by dh_make should just be considered a starting point. In all but the most straight forward cases, you'll need to edit some of the files. In order to install to /opt, you'll need to set an install prefix. Assuming that you are using an autotools build system, your debian/rules file might look like:

#!/usr/bin/make -f

%:
    dh $@ --with cli

override_dh_auto_configure:
    dh_auto_configure -- --prefix=/opt/my_program
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