Small fix

There was a problem when running regtests using another plumed
executable (e.g. the one installed). In particular
a wrong warning was shown. This is fixed now.
Fixed github logo in developer manual
Fixed sample file
Extensive README file
Updated version number
Fixed missing include
Merge branch 'v2.0'

Note: better using <cmath> than <math.h>

Conflicts:
	src/tools/Grid.h