check-style uses "git status" to see changed ya.make files.
However it seems that that the sources was cloned some ancient git
version, likely <2.8, since there was a bug, that has been fixed in 2.8
[1]:
" * A partial rewrite of "git submodule" in the 2.7 timeframe changed
the way the gitdir: pointer in the submodules point at the real
repository location to use absolute paths by accident. This has
been corrected."
[1]: cf11a67975/Documentation/RelNotes/2.8.3.txt (L33-L36)