> 3. The htslib*.mk makefile fragments should not be packaged Looking at debian/libhts-dev.links which also appears to have been introduced for bcftools's benefit, it is clear that the whole /usr/lib/htslib directory is for bcftools's benefit and should not be packaged. If that directory layout is desired by bcftools, the problem is that you are configuring bcftools to build against an htslib source tree rather than an htslib installation.
If you are building bcftools against a separate existing htslib installation, you should configure it (bcftools) as such. If there are problems with that, it would be better to solve them on the bcftools side rather than adding confusing extra complexity to your libhts-dev package. [University of Glasgow: The Times Scottish University of the Year 2018]
