Add flag to collect MANIFEST sections.

This change adds a flag to the ManifestResourceTransformer that will
make it collect all additional manifest sections (non-main) and add
them to the manifest of the shaded jar.

This is useful if per-jar information is stored in Manifests
(e.g. build information) and should still be present in the resulting
shaded jar.

If a section is present in one or more source jars, they are merged
into a single section (TODO: add code to choose between "replace",
"merge" or "fail").