EclipseHelper: handle manifest class path entries correctly

Simply specifying the file name does not make a correct URL, of course...
it needs to be relative to the parent URL.

This was not relevant so far because we only looked at manifest class
path entries of .jar files generated by the surefire-maven-plugin. But
in the next commit, we want to be able to index thoroughly, so we need
to be able to handle bare files instead of full URLs in the manifest's
Class-Path: line.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Do not auto-detect Eclipse when calling the EclipseHelper as main class

There needs to be a way to force the EclipseHelper to index all it can,
even when it thinks it is not running inside Eclipse at all.

The best idea is to make this automatic when calling EclipseHelper as a
main class because we *know* that the developer wants to index the
annotations in this case, even if Eclipse Indigo has passed the class path
elements in a semi-random order.

Wished-for by Christian Dietz.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>