Eliminates the global test filesystem and global test packages directory, in favor of local versions. This guarantees that each test runs with a clean filesystem state, rather than relying on cleanup. It also simplifies understanding the tests, since everything is done via params and return values instead of needing to know about the magic global variables and which methods mutate them.
- Replaces most explicit use of `fileSystem` with path construction using the `child*` utility methods
- Removes explicit passing of a filesystem to the commands; we're already passing a `Directory` for the
root where the tool operates, and we should never be using a different filesystem than that directory's
filesystem, so passing it was both redundant, and a potential source of test bugs.
