you can update your war from the command line using java commands as mentioned here:
jar -uvf test.war yourclassesdir
Other useful commands:
Command to unzip/explode the war file
jar -xvf test.war
Command to create the war file
jar -cvf test.war yourclassesdir
Eg:
jar -cvf test.war *
jar -cvf test.war WEB-INF META-INF