When I type "make clean", the first thing that happens is that gnulib gets built. This seems to be caused by commit 49501a8888003350 "Add default to generate prerequisistes for any rule", which always build libgl, even if the target is "clean". I don't understand the goal of that commit; the commit message isn't clear to me.
Also, the commit message and the makefile misspell "prerequisites". Maybe the goal is to build the BUILT_SOURCES and libgl.la even when some more specific target is provided to "make". I don't think that's possible without this kind of problem cropping up.