Change how CheckParseTrees receives NodeLocConverters

[jonmeow]

This is really a set of closely related changes:

1. We really shouldn't be creating a Check::Unit for Lower. This fixes that by storing the diagnostic converter for reuse.
2. Rather than passing in node converters to Check as their own array, pass diagnostic converters as part of Check::Unit.
3. To support creating the converters early, pass SemIR::File pre-constructed.
4. Since SemIR::File construction was used to track "checked", add is_checked for that.
5. Clarifies a subtle edge case around input_filename_ use with -.

Note the key consequence of this change, where I actually started, is that Check only has one array of Check::Unit instead of receiving NodeLocConverter as a separate array.