In Maven land, provided and system-scope dependencies are very similar,
the latter being an special kind that allows you to specify the path to
the artifact rather than using the repository to locate it.

Prior to this commit, the repackage goal of the maven plugin was
inconsistent as it would repackage provided-scope dependencies but would
ignore the system-scoped ones.

This commit adds an extra boolean flag, `includeSystemScope` to control
this behaviour. For backward compatibility reasons, its default value is
`false`.

Closes gh-2224