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.
* refactor the --resident run option into a separate file
* update daemon to run --resident apps
* re-plumbing daemon start
* send app logs
* update tests
* review changes
* fix test runner
* remove PackageMap.createGlobalInstance; rely on the ctor
* review comments
* rename service_protocol.dart to protocol_discovery.dart
* add a wrapper around the obs. protocol
* use json-rpc in run
* consolidate obs. code; implement flutter run --benchmark
* review comments