Improved StopWatch class

Changed so that start()/stop()/pause() return *this.
This allows things like
sw.start().stop()

Stopwatch can be initialized with the reference to a log. In this
case, it logs itself at destruction, provided the log is open.

Added Stopwatch::Handler class
It allows writing exception safe stopwatches which automatically
stop when an exception is caught.

Removed unnecessary start/stop in PlumedMain constructor.

Simplified interface: Use default arguments instead of multiple functions.