Organisation of subprojects

tl;dr: I'm calling for a moratorium on copying third-party code into the repo, and I'm proposing that we move a few dirs around.

We all hate code duplication. So why is it okay for us to needlessly copy entire codebases?
snip (Cut out a bunch of back-and-forth here since I feel none of you need to be convinced this is a good idea, only that it's worth the effort to do it. edit: Apparently natt did need convincing. Scroll down for arguments.)

So let's assess the damage (I think this is up-to-date as of 2.10; checkboxes are for arbitrary threshold of 50 kLOC):

• /ExternalCoreProjects/Virtu, Virtu core, < 11 kLOC, upstream is https://github.com/digital-jellyfish/Virtu/tree/master/Virtu
• /ExternalProjects/NLua, Lua host, < 10 kLOC, upstream is https://github.com/NLua/NLua
• /ExternalProjects/iso-parser, disc system, < 2 kLOC, upstream was on Google Code
• /blip_buf, multiple cores, < 2 kLOC, upstream was on Google Code
• /libmupen64plus, Mupen64Plus and plugins, < 340 kLOC, upstreams are under https://github.com/mupen64plus
  • resolved by #4117
• /lynx, Handy core, < 12 kLOC, upstream is in tarball (or https://github.com/TASEmulators/mednafen/tree/master/src/lynx)
• /psx, Octoshock core, < 68 kLOC, upstream is in tarball (or https://github.com/TASEmulators/mednafen/tree/master/src/psx)
  • resolved by #4180
• /quicknes replaced with submodule
• /waterbox/ares64/ares, Ares64 core, < 55 kLOC, upstream is https://github.com/ares-emulator/ares
• /waterbox/bsnescore/bsnes, (new) BSNES core, < 67 kLOC, upstream is https://github.com/bsnes-emu/bsnes
  • moved from my personal notes #11
• /waterbox/gpgx replaced with submodule
• /waterbox/libsnes, (old) BSNES core, < 63 kLOC, upstream is https://github.com/bsnes-emu/bsnes
  • resolved by #4183
• /waterbox/nyma/zlib, zlib for Nyma cores, < 19 kLOC, upstream is https://github.com/madler/zlib
• /waterbox/picodrive, PicoDrive core, < 79 kLOC, upstream is https://github.com/notaz/picodrive
• /waterbox/tic80, TIC-80 core, < 17 kLOC, upstream is https://github.com/nesbox/TIC-80
• /waterbox/uzem, Uzem core, < 5 kLOC, upstream is https://github.com/Uzebox/uzebox/tree/master/tools/uzem
• /waterbox/virtualjaguar/src, Virtual Jaguar core, < 52 kLOC, upstream was on a self-hosted Git server
• /wonderswan, Cygne core, < 8 kLOC, upstream is in tarball (or https://github.com/TASEmulators/mednafen/tree/master/src/wswan)

In total, the upper bound is 917 kLOC of source code, severed from its trunks and waiting to bitrot. (For reference, just the BizHawk solution is ~450 kLOC, and Mesen is ~325 kLOC.)
Not listed are several binaries in /Assets/dll which are rundeps for unmanaged cores. I'll be looking at these as part of my Nix experiments. I also discounted dependencies of these projects whenever I noticed e.g. .../vendor near the bottom of the filesize list—but they are nonetheless checked-in to this repo.

I propose that from today we only use Git submodules for this purpose:

• if possible, pulling in the upstream and only checking-in build scripts and patches, or else having a mirror/fork in the TASEmulators org (TODO copy and expand https://github.com/TASEmulators/BizHawk/commit/2af6bf3c34f8a31690fe7e9d8500e54bd01c671d#commitcomment-140199736); and
• placing submodules in /submodules, and supplemental files like Makefiles or shell scripts in one of /ExternalProjects, /ExternalCoreProjects, or /waterbox when those are necessary.

I also propose we migrate all subprojects, starting with those listed above, to the same scheme.
Adding a submodule and removing the checked-in copy can be squished into a single commit.

Moved here from my personal notes #118; see also #2423 and #2312.

Review the listed third-party directories, the proposed /submodules layout, and related issues #2423 and #2312. Begin by identifying one subproject with a defined upstream and checking its existing build scripts and patches. Done means the checked-in copy is replaced by a submodule and the project still builds with any required supplemental files in the proposed locations.