Regarding your first question, I suggest you checkout my general suggestions on resolving issues with Run External Command @ http://www.tersus.com/#Id=1039.
Regarding your second question, I'm not sure I follow, but if the question is what is the base path to which relative paths "relate", the answer depends on the application's deployment configuration.In general it is the working directory of the executable (studio/eclipse or tomcat). You can use the following model to find out what it is:
This will work on Linux (and Windows+Cygwin).
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