cask: Add TODOs to deprecate integrated cask commands

[whoiswillma]

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Move deprecation from cask cmds and into cmd.rb.

When deprecating the run method of each command, tests had to be rewritten to avoid calling the run method since otherwise a deprecation exception was thrown. By deprecating at the Cask::Cmd level, all cask cmd tests continue to pass.

[MikeMcQuaid]

Nice cleanup, thanks again @whoiswillma!