Fix 3798: Unable to use more than 50% of machine memory for server

JVM settings were used by scripts when checking the validity of the instance.
This modification removes the use of the JVM setting during the bootstrapping phase.
This fixes the following issues:

   * if JVM is configured for the server instance suspends on start up
     for debugging, the server suspends during the bootstrapping phase
     rather than when the real server instance has started. (remaining
     issue related to issue 3711)
   * if the JVM is configured to use more than around 45% of the
     machine's memory, we run out of memory (issue 3798)