(follow-on to #8698)

`all.dart` is no longer needed. Furthermore, it causes tests to
be skipped, or to silently fail to run anything.

Fixes #7941

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.

With this change, they're run via instance methods on an object
obtained through the context. This will allow us to substitute
that object in tests with replay/record versions to allow us to
mock out the os-layer in tests.

This updates the flutter analyze command to use the .analysis_options_flutter_analyze in the repo root when either the --flutter-repo flag is supplied or the sources being analyzed reside in the flutter repo.

And fix a zillion omissions this uncovered.