We happen to use the protobuf-dt <https://code.google.com/p/protobuf-dt/> 
plugin for Eclipse. The project (open-source) is owned by two Google 
engineers, but it hasn't been updated in a while - it *really* needs to be 
updated. It can be configured to compile your .proto files (using 
protoc.exe) and place the generated files in a location of your choosing. 
It also supports editing and syntax highlighting of .proto files, which is 
really nice. 
- You can seek additional help at the protobuf-dt google group 
<https://groups.google.com/forum/#!forum/protobuf-dt>.

You can always compile your .proto files manually outside of Eclipse too, 
or write a script for it.

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