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The configure file is not supplied and has to be generated with ./autogen.sh. This issue goes back to charybdis-ircd and possibly ircd-ratbox where the build system originates. I believe the downside is that autotools has to be installed by the user (builder) rather than just by the developer (packager), but this hasn't been a problem with the popularization of package management systems in the early-2000's. In the mid-2000's with the popularization of version control like cvs/svn/git there might be some benefit to not checking-in the 30,000 line configure script but that's up for debate.
In any case, you are probably looking to build from https://github.com/jevolk/charybdis right now, and I have to find some time to merge upstream back to matrix-construct/construct. With growing debt like authenticated-media and protocol format changes causing new error messages even in the aforementioned fork-branch it's becoming increasingly difficult to make a release here, however a couple weeks of worth of work at this point could make it possible.
The build instructions suggest to supply the configure script with some prefixes, but there's no such file on the main branch.