readProjectFromPaths has weird semantics

[patrickt]

This function, as @robrix pointed out, is a little weird: its second parameter can be a file path rather than a directory, in which case the resulting project’s root is the parent directory of the provided file—and all files, not just the provided file, will be slurped into the resulting project. This is unintuitive behavior that we preserved because we were afraid to change the CLI interface, and we should just kill the CLI vagaries that allow for this behavior.