In idutils's own top_srcdir, observe this:

$ mkid -m libidu/id-lang.map -p build-aux/snippet
mkid: can't open language map file `libidu/id-lang.map': No such file or directory

The file libidu/id-lang.map is actually present.

The error does not happen for a simpler --prune argument, e.g.

$ mkid -m libidu/id-lang.map -p build-aux

According to a superficial strace inpection, this happens because the processing of the -p option appears to have modified the CWD, so it looks for build-aux/libidu/id-lang.map.

Workaround: pass the -m file name as an absolute pathname.