My opinion is here: https://intfiction.org/t/mercurial-and-command-line-tools/3883/1
If you’re going to share the code with others then I think you definitely need uuid.txt and the .plist files. If you might be transferring between computers then you should too. If you’re just using it to track changes on a single computer then I guess you could leave them out, but I see no reason to either.
Now I hadn’t thought of there possibly being problems with non-existent directories. Does I7 not like that? If so then I guess the directories should be put in the vcs, but not their contents.