After further investigation, this is a SWIG 1.3.37 bug. According to
the documentation [1], "the default output directory for these
language specific files is the same directory as the generated C/C++
file" ... which is clearly being violated since the .py file is being
written to the directory where the .i file is located while the .cc
file is being written to ".". I will submit a bug fix to the SWIG
folks, since there doesn't seem to be one yet; I think I've figured
out how to patch their code to correct this issue.
[1] http://www.swig.org/Doc1.3/SWIGDocumentation.html#output
That said: The state of use of SWIGPYTHONFLAGS in individual
components varies significantly (some do not even us it, instead just
recreating those flags in the local Makefile.am) and should probably
be cleaned up.
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