Integrated ClassDiscovery2 into the main project. Needs testing however.
Fixed a bug in the CheckOverrides class. It builds now, and all unit tests pass.
Server starts up without error now, however, extensions aren't being loaded.

The startup time is still very slow however, so I'm going to continue to investigate to see if this can be improved at all. Changing over to not using ZipReader (in favor of the ZipIterator class) has exponentially increased the startup speed (from "unusably slow" to "noticeably slow"). Extensions aren't loading, but that's due to no classloaders being installed yet. I'll have to engineer a way for the extension manager to add classloaders to the ClassDiscovery class, like it was doing before, after I speed up the general class loading. I have temporarily disabled CheckOverrides and minimizeJar (in the shade plugin) to make builds faster, as they take several minutes to build currently, which is making testing very hard. The AbstractEnumVerification thread is not wired in appropriately to use the correct class addressing format apparently, as it is throwing an error too, but that is less important than the current issues.
Hooked the ExtensionManager into the DynamicClassLoader and ClassDiscovery classes.
Line endings
The server now starts up, with extensions working too. Things are still too slow though.
Added a class discovery cache mechanism.

The CH jar is automatically scanned at build time, so that step can be skipped for the CH jar at least, and I will get it so that caching only has to happen once per version of an external jar.
Caching is now used, if available. The changes to ClassDiscovery should be complete now.

The only thing remaining is to make caches for each of the jars scanned be persistent, so
that the startup time will go much faster. The startup was nearly halved for the CH jar, so
I anticipate similar gains for the other jars, hopefully reducing the startup time (on my slow
computer) to < 10 seconds, down from the 20-30 seconds I was seeing.
Added ClassDiscoveryCache, which manages writing out the cache files to disk.

It doesn't appear to work, but the bulk of the code is there, and should be down to
just a bug fix or two.
Tied the caching into cmdline mode, and fixed a bug with the ClassDiscoveryCache.

Barring final testing, this *should* be fully working now, and nearly ready to be
merged into master.
Fixed small error with messaging.
Merged in from master
If extensions weren't present, apparently the main functions wouldn't load. Anyways, fixed.