I've been working on improving the open source Google Protobuf filters for 
Doxygen. The filter converts the protobuf message to a C++ struct and writes 
that to stdout. This worked (well) in 1.8.7. After upgrading, none of the 
messages appear in the documentation. By writing filenames to stderr from the 
script, I also see that the #include statements in the original output 
(translated from protobuf import) are being ignored. However, the script is 
getting called on each file.

I don't believe the failure arises from more careful checking of the script output, which is not 
legal C code. (The buffers' "optional" and "required" qualifiers are left in, 
and are printed by Doxygen in a useful way.) I say this because if I run the script on the .proto 
file manually and redirect stdout to a cpp file, that file will be parsed with correct 
documentation produced.
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