Flipped EGit to manifest-first maven-3/tycho build

Flipped EGit to manifest-first maven-3/tycho build

New org.sonatype.tycho groupId https://issues.sonatype.org/browse/TYCHO-312
Workaround for https://issues.sonatype.org/browse/TYCHO-168

Removed checkNotNested. Conventional maven project layout results in the following
repository nesting

parallelip-egit <= egit source tree root
  /.git
  /org.eclipse.egit.core.test
    /target
      /work
        /data <= test workspace
          /.git
          /.metadata
          /Project-1

Disable checkNotNested as a short term solution, but in the long term we need to
reintroduce this check with mechanisms like Git's GIT_CEILING_DIRECTORIES to make
sure it does not produce false positive during maven build.

Change-Id: Idec24de111aa21a022654c443376e42ae6caa7cc
Signed-off-by: Igor Fedorenko <igor@ifedorenko.com>