A friend of mine added a few "search for the libs" entries in "configure.in", as well as removed the library inclusion strings of "/lib/include/ffmpeg/" (obsolete).
Here's a link to the unified patch file:
shotdetect-1.0.86-1.0.87.patch.bz2
Here's a quick summary of how to get it working:
1) Download the tar.gz of shotdetect v1.0.86
2) Unzip it:
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tar -xzf latest.tar.gz
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patch -p 0 < shotdetect-1.0.86-1.0.87.patch
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cd shotdetect-1.0.86
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./configure --prefix=/usr/local
make
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sudo checkinstall --pkgname=shotdetect -pkgversion="`date +%Y%m%d%H%M`-1.0.87" --backup=no --default