THRIFT-417. rb: BufferedTransport can enter an infinite loop
Switch native proto implementations to use read_all instead of read. Add a bunch of tests to verify.
Also:
- removed some commented code in binary_protocol_accelerated.c
- struct.c was missing one of the possible native method calls
- updates gem manifest (included files that didn't exist)
- fixed svn:ignores of test/rb/gen-rb and lib/java/gen-java
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