From IRC:
andypugh: He opines that: “The debian/configure scripts checks presence of libxenomai-dev installation and ask to enable deb-src repositories for compiling."
[10:08pm] jepler: yes that's correct
[10:08pm] andypugh: OK, I will reply that this is expected
[10:09pm] jepler: if there is a libxenomai-dev binary package known to apt-cache search, THEN debian/configure has to find its associated source package
[10:10pm] jepler: .. in order to know the correct list of Debian architectures where libxenomai-dev will be available
[10:10pm] jepler: if your /etc/apt/source.list configuration has libxenomai-dev as a BINARY PACKAGE but cannot find its ASSOCIATED SOURCE PACKAGE then your debian is misconfigured
[10:11pm] jepler: hoever, this seems to happen in practice in the jessie -> stretch update, because you might have leftover information about the jessie version of libxenomai-dev, but no information about the source package because libxenomai-dev is NOT IN debian stretch
[10:11pm] jepler: or you might have it because your distro is just misconfigured to begin with, by not having deb-src lines
