added new "ide" profile

Created a new profile and moved the lifecycle-mapping,
maven-dependency-plugin, and maven-clean-plugin to the profile.  Running
this profile is only necessary if a developer is setting up the Eclipse
development environment to work with Protege source code (Eclipse PDE +
m2e +OSGI Framework Launcher mode).  Not desirable to use these plugins
during a normal command line build.

Upgraded to newer version of maven-bundle-plugin.  Added missing groupID
for maven-eclipse-plugin.
updated maven-dependency-plugin to version 2.8
added new "ide" profile

Profile will copy dependency JARs to root of project.  Necessary for
setting up Eclipse in a way that OSGI Framework Launcher will find JARs
in the expected place for runtime classpath.  Updated versions for
various plugins.