If you run your program from IntelliJ then you can set the java.library.path in the VM options input field in the Run/Debug Configurations dialog. Example: -Djava.library.path=”C:\path\to\where\the\jni\lib\is”
Update: Since this answer was first written, a better way to deploy war files to tomcat with zero downtime has emerged. In recent versions of tomcat you can include version numbers in your war filenames. So for example, you can deploy the files ROOT##001.war and ROOT##002.war to the same context simultaneously. Everything after the ## … Read more