Addresses the third point of jekyll#3591, in which the incremental regenerator doesn't notice that destination files have gone missing.

Use easier-to-follow checks for missing-destinations in the regenerator.

Clean up the destination modified check in `source_modified_or_dest_missing?` to be easier to read. Note that it can now return `nil` instead of `false` for an unmodified `source_path` and a `nil` `dest_path`, but in a discussion on 706007e we decided that was okay.