The two base64.h files are not at all similar, so just referring to the other 
one does not help.
heimdal's just provides two function headers (in a win32-compatible way):
ROKEN_LIB_FUNCTION int base64_encode(const void *, int, char **);
ROKEN_LIB_FUNCTION int base64_decode(const char *, void *);

The ros-ros-comm one provides a whole base64-encode/decode C++ implementation.

I've not looked to see how much commonality there is in the other 101
'base64.h' include files in all the other packages. I do wonder if a
libbase64-dev is what's really needed here.  The file comes from an
embedded xmlrpcpp implementation from Chris Morley which should
probably be packaged separately anyway.
http://sourceforge.net/projects/xmlrpcpp/
Which is seems used to be in debian but was removed in 2008: 
https://tracker.debian.org/pkg/xmlrpc++
That is the same version. Available here: 
http://snapshot.debian.org/package/xmlrpc%2B%2B/0.7%2Bcvs20040713-2.1/
This could be resurrected. I think it has the same base64.h file clash though.

Debian now has this xmplrpc c++ implementation: 
https://tracker.debian.org/pkg/xmlrpc-c
maybe ros-ros-comm could just use that? I've not looked to see how well the 
APIs match up. 

Wookey
-- 
Principal hats:  Linaro, Debian, Wookware, ARM
http://wookware.org/

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