Better warning message when running Cobrawap from the first stage

[mdenker]

In response to #70, @gulpgiulia made the following suggestion:

I also suggest to consider to send an alert to the user any time (as in this case) when the user's settings have been overwritten, something like: logger.warning(Cobrawap is running from first stage - ‘STAGE_INPUT forced to Nan. Your user settings have been overwritten)