I've run into a similar issue, Lukas, and found out that MATLAB has its own, special version of protobuf3 with no documentation and no (useful) version info. This special version conflicts with the standard version we're running and MATLAB just errors out if we try to call one of the standard protobuf3 methods. It's possible the method doesn't even exist in their special version. The only workaround we've come up with so far is to comment out the line with protobuf3 on it in classpath.txt, e.g.:
.
.
.
$matlabroot/java/jarext/lucene-queries.jar
$matlabroot/java/jarext/lucene-core.jar
$matlabroot/java/jar/ja_JP/mw_java_help_ui_res.jar
# $matlabroot/java/jarext/protobuf3.jar
$matlabroot/java/jar/toolbox/compiler_mdwas.jar
$matlabroot/java/jar/path_api.jar
$matlabroot/java/jarext/lucene-highlighter.jar
.
.
.
and then restart MATLAB and load our standard version as part of a JAR-with-dependencies. You can find your classpath.txt by running:
which classpath.txt
It's a pretty terrible solution, especially if you're going to deploy your code to someone else's computer, but it seems to be all Mathworks has left us with. Good luck!
