Fix at least one of the bugs with getting the logical_path from shadowed root paths.

Added a test case to cover the fix which fails if the fix isn't applied. Without the fix `pathname_plus_shadowed_dir(fixture_path("default-shadowed/application.js")).logical_path` returns `../default-shadowed/application.js`
Removing the known issues comment.

(Unless there are still other known issues the fix in f730ce81 doesn't cover?)