Previously, the Repackager would write entries in the following
order:

- Libraries that require unpacking
- Existing entries
    - Application classes
    - WEB-INF/lib jars in a war
- Libraries that do not require unpacking
- Loader classes

Libraries that require unpacking were written before existing entries
so that, when repackaging a war, an entry in WEB-INF/lib would not
get in first and prevent a library with same location from being
unpacked. However, this had the unwanted side-effect of changing
the classpath order when an entry requires unpacking.

This commit reworks the handling of existing entries and libraries
that require unpacking so that existing entries can be written first
while also marking any that match a library that requires unpacking
as requiring unpacking.

Additionally, loader classes are now written first. They are the
first classes in the jar that will be used so it seems to make sense
for them to appear first. This aligns Maven-based repackaging
with the Gradle plugin's behaviour and with the structure documented
in the reference documentation's "The Executable Jar Format" appendix.

The net result of the changes described above is that entries are
now written in the following order:

- Loader classes
- Existing entries
    - Application classes
    - WEB-INF/lib jars in a war marked for unpacking if needed
- Libraries

Closes gh-11695
Closes gh-11696