rename most cases of jakarta- to apache-

The Apache Softare Foundation used to maintain an umbrella project named
Jakarta but it was retired on 2011. This name now conflicts with the new
name for Java EE under the Eclipse Foundation.

Rename most of the packages to be more consistent. Some other packages remain
but they will require intervention by their corresponding maintainers.

Approved by: thierry (mentor), makc
Differential Revision: https://reviews.freebsd.org/D21902