clippy_dev: Parsing revamp part 3/N

[Jarcho]

Not parsing changes, but a cleanup to make future changes easier. This makes uplifting a lint it's own command rather than being part of rename_lint. Uplifting and deprecation now also share code for filesystem changes.

The deprecate command has a slight regression in that no longer removes the lint from the lint pass declaration. This will be fixed in a later PR where those are parsed and formatted.

changelog: none

[rustbot]

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