This prevents multiple simultaneous runs of the analyzer from stomping
over each other (e.g. multiple runs of 'update-packages'). Certain
long-lived commands (like analyze, run, logs) are exempted once they've
done enough work to be safe from most stomping action.

This still doesn't make us entirely safe from craziness, e.g. if you're
half way through an 'update-packages' run and you call 'git pull', who
knows what state you'll end up in. But there's only so much one can do.

Fixes https://github.com/flutter/flutter/issues/2762

* 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

* send ext.flutter.exit

* listen for help restart, quit

* refactor into a separate class

* rework flutter run

* fix npe with --debug-port

* connect to obs and exit when that conneciton closes

* update todos

rename to printTrace(), printStatus(), and printError()

Also fix a bug where the trace command may capture the wrong file
if multiple trace file paths are in the Android log buffer.

Previously we found a lower bound timestamp for the trace path log
by running the date command on the device and parsing the result on
the host.  This could yield an inaccurate result if the device and
host are using different time zones.

The command will now obtain the most recent timestamp in the device's
time format by running logcat.

remove device type specific checks

@chinmaygarde

1) Moved basic utility code into base/ directory to make it clear which code
   doesn't depend on Flutter-specific knowldge.
2) Move the CommandRunner subclasses into a runner/ directory because these
   aren't commands themselves.

remove an unused import

review comments

rename st --> stack

This patch makes `flutter start` work without a clone of the engine git
repository. Making this work pulled a relatively large refactor of how the
commands interact with application packages and devices. Now commands that want
to interact with application packages or devices inherit from a common base
class that holds stores of those objects as members.

In production, the commands download and connect to devices based on the build
configuration stored on the FlutterCommandRunner. In testing, these fields are
used to mock out the real application package and devices.

Also fixes some minor bugs with iOS and Android interactions.

I'm trying to get a feel for the code by writing some simple cleanup patches.