Upgraded dependencies.

Upgraded to new versions of the OWL Difference Plug-in and OWL
Difference Engine bundles.
Updated support list information.
Updated scm info from our old SVN to GitHub.
Added link to our issue tracker in GitHub.
Removed scm element from submodules.

Source code information is taken from the protege-parent POM file and is
the same for all submodules.
Updated link to autoupdate's central registry file.

Moved the central registry file with the list of plug-in update URLs to
GitHub.
Updated help menu item.

Point to the main page for the plug-in library on the Protege wiki,
instead of a specific page that only lists plug-ins compatible with the
current version of Protege.  The issue is that most plug-in developers
don't keep version information current on the Protege wiki, so the list
of version specific plug-ins is often outdated.
Updated help menu items.

Updated link to release notes page for P5 beta, and updated link to
citing instructions to go to the new website instead of the wiki.
Updated dependencies.

Upgrade to latest version of the protege-owlapi-extensions bundle, which
is compiled against the OWL API v3.5.0.  Upgrade to latest version of
the owlapi-distribution bundle.  Protege now runs with the latest OWL
API.
Removed client server code from the distribution.

Protege staff decided not to release this as part of the initial Protege
5.0 beta build as the original author is no longer at Stanford, and
current staffing levels aren't sufficient to maintain the codebase.
Prevent aggregator POM from being deployed.
Moved maven-deploy-plugin.
Revert "Moved maven-deploy-plugin."

This reverts commit 03713b610f1f14dad7c8d6aad0280fd4f072cccb.
Added scm block and minor micro to version.
Added scm element back to submodules.

Maven release plugin seems unhappy about submodules inheriting scm
information from the parent POM file.
Refactored Maven build file structure.

Used to have a bare bones aggregator at the root, and a parent POM
at the same level as the submodules. This worked fine until trying to use
the Maven Release Plugin to perform a release. The release plugin
wants to include the aggregator in the release process, which doesn't
make sense for us. Refactored to a slightly simplified approach where
the POM in the root acts as both the parent and aggregator. The same
approach is taken by projects like the OWL API.
[maven-release-plugin] prepare release protege-parent-5.0.0-beta-05
[maven-release-plugin] prepare for next development iteration
[maven-release-plugin] rollback the release of protege-parent-5.0.0-beta-05
Relocated contents of profile to pluginManagement.