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 706007ead9 we decided that was okay.
When adding a dependency, also add the dependency to the metadata hash.
Addresses part 1 of #3591. Prior to this fix, the regnerator only paid attention the mtime of the first dependency it checked, so for posts/pages with N multiple dependencies (i.e., every layout file used to render them), it continues to regenerate the post/page approximately N times, at which point it's seen all of the dependencies.
To address part of #3591, clear the regenerator's cache every time the
site is processed. This ensures that the regenerator doesn't incorrectly
believe a file hasn't changed based on stale information.