Application starts in JAVA_HOME folder when running using the Tomcat plugin

Application starts in JAVA_HOME folder when running using the Tomcat plugin. Is there a way to specify the base folder for the application?

Here the default startup script:

/Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk/Contents/Home/bin/java -Dcatalina.base=/Users/***/Library/Caches/IntelliJIdea2016.3/tomcat/bundled_-_run_(without_unit_tests)_(1)_cbms-boot_2 -Dcatalina.home=/Users/***/devroot/apache-tomcat-8.0.35 -Djava.io.tmpdir=/Users/***/devroot/apache-tomcat-8.0.35/temp -Dcom.sun.management.jmxremote= -Dcom.sun.management.jmxremote.port=1199 -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false -Djava.rmi.server.hostname=127.0.0.1 -cp /Users/***/devroot/apache-tomcat-8.0.35/bin/bootstrap.jar:/Users/***/devroot/apache-tomcat-8.0.35/bin/tomcat-juli.jar org.apache.catalina.startup.Bootstrap start

OS: OSX