Could you clarify the Linux distribution (e.g. Ubuntu 12.04, Ubuntu 14.04, CentOS 5.x, CentOS 6.x, etc)?
Could you attach or provide links for the output of the spoon.sh command and screenshots?
To clarify, the perspective showed up after the initial install, but disappeared after adding/removing plugins and JAR files? Could you elaborate on what these files were, and how they were added/removed?
This information will help in allowing us to reproduce the issue on an environment where we can better investigate the cause, so we can get it fixed. If needed, you might reach out to the Pentaho Community for help on how to gather this information.