I forgot to mention the C++ packages, the complete list of external code
in Sage (AFAIK):
src/sage/graphs/planarity_c/
https://code.google.com/p/planarity/
src/sage/graphs/graph_decompositions/rankwidth_c
http://pholia.tdi.informatik.uni-frankfurt.de/~philipp/software/rw.shtml
src/sage/schemes/hyperelliptic_curves/hypellfrob
http://web.maths.unsw.edu.au/~davidharvey/code/hypellfrob/
src/sage/rings/bernmm/
http://web.maths.unsw.edu.au/~davidharvey/code/bernmm/
And then there are these, which seem to be external packages, but I
couldn't find a corresponding upstream:
src/sage/modular/arithgroup/*.cpp
src/sage/stats/distributions/*.c
src/sage/combinat/partitions_c.cc
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