chore(fs): remove flaky `emptyDir()` tests
This PR removes flaky emptyDir() and emptyDirSync() tests.
These tests test Deno's permissions system, which is a runtime concern and outside the scope of the Standard Library. These tests were written a while ago in https://github.com/denoland/deno/pull/3501 and the permission system is a lot more robust today. I think it's fine for these tests to be removed.
Note: test coverage is not affected.
What is the source of flakiness?
Most likely, the use of Deno.Command() in parallel.
I'll close this for now until we confirm the cause of the flakes.
Related #4022