This removes direct file access from within flutter_tools
in favor of using `package:file` via a `FileSystem` that's
accessed via the `ApplicationContext`.
This lays the groundwork for us to be able to easily swap
out the underlying file system when running Flutter tools,
which will be used to provide a record/replay file system,
analogous to what we have for process invocations.
Without this, an FLX with no assets may be completely empty in AOT mode.
This will result in a warning when the engine's unzip library tries to
parse the FLX.
Fixes https://github.com/flutter/flutter/issues/7060
