Previously repackaging of an archive was performed in three steps:

1. Write the manifest
2. Write entries from the source archive into the destination
3. Write any libraries into the destination if they’re not already there

This worked fine for jar files, but not for war files. In the war file
case the libraries are already in the source archive’s WEB-INF/lib
directory so they’re copied into the destination in step 2. This means
that step 3 largely becomes a no-op and, crucially, the UNPACK comment
is not applied to any libraries that require it.

This commit reorders steps 2 and 3 so that the libraries are copied into
the destination first (allowing the UNPACK comment to be written, if
required) and then any entries in the source are written into the
destination if they’re not already there.

Fixes gh-2588