Refactor + display changes

[lukekarrys]

A mix of refactoring that fell out from the new display changes and some additional behavior.

This PR is separated into commits that are smaller logical chunks of work. I'll call out the most important changes here:

CLI

• Created lib/cli/ dir for files that are CLI specific. This should have more files added to it in the future as we separate CLI behavior from new Npm() behavior.
  • Moved some behavior to CLI files such as update-notifier, nonDashArgs, and graceful-fs
  • Also moved some things out of exit-handler such as logging about the log file error and timing file. These required getting a bunch of state from npm that can now be kept internal
• npm.load() has the ability to exit early, this is only used for npm --version right now but this speeds up the command from having to create logfiles and caches it will never use
• Make some properties of npm, timers, logfile private since they are no longer needed outside of themselves

File structure

• Made lib/utils/ completely flat and moved some lib/workspaces into lib/utils/
• Renamed base-command to base-cmd to match other commands

Display

• Use proc-log.META for forcing logs and flushing output
• Make display responsible for creating chalk instances
• Don't hide all output on silent. This uses a hack to hide spawn banner output to match previous behavior now
• Remove a bunch of timers and logs that were superflous

Log file

• Don't write timing logs to debug log file unless --timing is set

[wraithgar]

Just one "are we sure we need this?" question on a test, not a show stopper.