Comment #6 on issue 2418 by [email protected]: Patch: Don't copy GNUmakefile and *.make from within builddir to builddir
http://code.google.com/p/lilypond/issues/detail?id=2418
As I said: lilypond uses _wildcards_ for finding things in its source directory. Which is what caused this issue in the first place. If you copy a whole build structure into a directory inside of the source directory, you can't expect the build system to magically not see anything you put inside of that build directory while it notices everything put in the source directory that it should see.
The build system could ask git whether a given file is known, but then it would become impossible to build LilyPond from a tarball instead of a git checkout.
Anyway, this patch fixes one problem in connection with your favorite directory arrangement, so it seems strange that you complain.
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