Steps to reproduce:
1) wget http://downloads.xiph.org/releases/theora/libtheora-1.2.0alpha1.tar.gz
2) tar zxf libtheora-1.2.0alpha1.tar.gz
3) cd libtheora-1.2.0alpha1
4) ./configure && make && make clean

Expected results:
4) no files that were part of the original distribution tarball are modified

Actual results:
4) The file

doc/spec/Theora.pdf

is modified.

More info:
1) This causes trouble for packaging.
2) If the PDF is generated on build, maybe it should not be part of the distribution tarball? Or maybe --disable-spec should be default since very few people need to rebuild the PDF if it is included already...