Fixes CmdStan's printing elapsed time to file twice (and none to std::cout)

#### Summary:

CmdStan currently writes the elapsed time to the file twice. See stan-dev/cmdstan#21.

#### Intended Effect:

CmdStan will now write elapsed time to the output file once and to the output stream once.

#### How to Verify:

Run a CmdStan model after the merge. I am creating a pull request with automated tests checking for the correct behavior in CmdStan.

#### Side Effects:

None -- command.hpp is really a CmdStan thing now, but we're leaving it here for reference.

#### Documentation:

The behavior should now match documentation.

#### Reviewer Suggestions:

@betanalpha: you were spot on.