Granular handling for flycheck diagnostics

[Strackeror]

This is my proposed solution for #18283

This implements 2 things:

• A generation counter for flycheck diagnostics, which allows for progressively replacing previous diagnostics file by file instead of erasing every previous diagnostic as soon as you get the first new one.
• Handling for when the check command is done with a crate to clear all relevant files of outdated diagnostics.

This meant adding some facilities to find a crate by name and iterate over its files, which are the parts I'm the least confident about. This is my first PR for this project, so I'm ready for extensive feedback if need be :)