Fix erroneous file change detection Issue #2759

This should fix the erroneous file change detection that was noted by several users in issue #2759. 

It now only scans files which are part of the sketch for changes. 

There is still a possibilitiy for erroneous "file changed" messages if a file that is not part of the sketch is edited with gedit (this is the lesser of 2 evils, the other being a file edited with gedit wouldn't get reloaded)