Update linters and fixers to apply command formatting more

[w0rp]

Now that #2556 has been implemented, it's important that linters and fixers generally use %s and %t formatting with filename-modifiers like %s:h for a file's directory name, and so on. The more linters use this kind of formatting, the more they will be capable of running in Docker, in virtual machines, or on other computers. We should go over all of the existing linters and fixers and update them to work this way.

[w0rp]

I've applied the formatting wherever I safely could to existing linters now. There are quite a few linters that will require some careful adjustments if we want to support running them with some other file system, but we can handle those some other day.