java.lang.ClassNotFoundException in matlabR2014a
See this answer: Why/How is IntelliJ causing debug output in Netbeans?
This is not related to any setup you've done within MATLAB -- it's apparently something that IntelliJ, WebStorm, or PyCharm has put into the clipboard. It goes away if you don't have one of those programs running at the same time.
This error indicates that MATLAB is not able to locate or read your MATLAB preferences directory. This could be due to a setting or variable on your system which is causing MATLAB to look for your preferences in a location where you do not have read access.
Typically this happens due to running a configuration script for MATLAB such as 'config_matlab.sh' which attempts to set your preferences directory to a non-default location where you do not have read or write access. You should start by removing the portion of the script which sets your environment variable.
You should choose a directory where you have both read and write access. The default location is in your home folder.