> Yes, I deleted the build directory before redoing autogen.sh, redid `mkdir > build && cd build` in between autogen.sh and configure
Then you failure is pretty strange. Can you show the output of "build/out/bin/lilypond -V" please? Verbose mode should give some information about load paths. Also, if you were able to build and run master recently, perhaps try pinpointing the problematic commit (cf. "git bisect"). I'm puzzled because I do not see any recent commit that seems like it would have anything to do with this problem.
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