[yabridgectl] Make syncing much more resiliant

This commit does a couple of things since the refactoring made it
difficult to split these things up:

- The counts for managed and new plugins are now always correct, even
  when plugin directory A contains a symlink to plugin directory B.
- Orphan files will now be pruned from managed VST3 directories, making
  switching between different architectures easier. (the previous
  approach involved nuking the entire bundle, which of course has a
  bunch of downsides)

CHANGELOG.md

@@ -88,11 +88,14 @@ Versioning](https://semver.org/spec/v2.0.0.html).
   in an `00cc:err:process:exec_process` error when running `yabridgectl sync`
   because yabridgectl would try to run the 64-bit `yabridge-host.exe` in that
   prefix.
-- Merged VST3 bundles set up in `~/.vst3/yabridge` are now always cleared before
-  yabridgectl adds new files to them. This makes it easier to switch from the
-  64-bit version of a plugin to the 32-bit version, or from a 64-bit version of
-  yabridge to the 32-bit version. I don't know why you would want to do either
-  of those things, but now you can!
+- Fixed incorrect new and total plugin counts. These counts are now always
+  correct, even when using multiple versions of the same VST3 plugin or when a
+  plugin directory contains a symlink to another plugin directory.
+- Aside from pruning only unmanaged VST3 bundles in `~/.vst3/yabridge`, yabridge
+  will now also prompt you to prune unmanaged files within a VST3 bundle. This
+  makes it easy to switch from the 64-bit version of a plugin to the 32-bit
+  version, or from a 64-bit version of yabridge to the 32-bit version. I don't
+  know why you would want to do either of those things, but now you can!
 - Copies of `libyabridge-vst2.so` and `libyabridge-vst3.so` are now reflinked
   when supported by the file system. This speeds up the file coyping process
   while also reducing the amount of disk space used for yabridge when using