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Get suite running smoothly again (#824)

Am planning on proposing/implementing a new feature, but first I noticed
that there are a number of failing specs on main, so I figured I would
start with that.

As written, this includes four main adjustments, two of which might
actually be bugfixes:
- one spec was hanging indefinitely for me locally on a `Thread.join`
call - explicitly capturing the child threads and joining them directly
fixed it (might be machine dependent?)
- when an encoding is specified, the rails schema up to date hook was
passing arguments incorrectly (kwarg containing `encoding` was being
interpreted as the `length` positional arg) (possible bug)
- many specs were attempting to create file submodules without the
`protocol.file.allow=always` config option causing failure
- alias detection for amendment appeared to be broken, due to regexp
incompatibilities between ruby/git (git wasn't properly parsing `\s` in
the value matcher for `git config --regexp [key] [value]` command), so
moved that matching into ruby (possible bug, also maybe machine/git
build opt dependent)
- dropped ruby 2.6 from the test matrix - it appears that it's far
enough EOL that github has trouble even setting it up. I can attempt to
add it back/get it working, but I figured it might be time to ditch it

*I don't have a windows machine, so I'm not gonna be much help with
those CI builds (should note fails appear unrelated to anything I've
done here).
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