So if I wanted to exclude the start of a path, how can I accomplish that without excluding a different path that just happens to include the start of the path? 

For example, I want to exclude anything that starts with "Done", so Done\2015-2016, Done\2016-2017. But there exists a folder called Scheduling\Done (no sub-folders within Done) that I don't want to exclude. If I do a "Does not contain" condition with "\Done\" will that exclude everything in the above example (including Scheduling\Done), or just the items where folders are nested under a "Done" folder (e.g. Done\2015-2016)?

Let me see if I get this right. You have a folder structure in the repository like this:

RepoRoot

--Done

----2015-2016

----etc

--Scheduling

----Done

And you want to exclude everything under "\Done" but not under "\Scheduling\Done"?

In this case, "Path starts with \Done" only applies to the folders under "Done" off the root of the repository. Folder paths under \Scheduling wouldn't qualify because the path is the entire set of folders that take you from the repository root to the current folder.