Api version incremented for consistency, even though there was
no change in between v2.3 and v2.4

Fix #296.

Fix restart bug in EDS code, …

While doing plumedcheck, verify that autoconf has been applied correctly

@carlocamilloni \plumedfile only works for input files.

hopefully the last time..

I left it in as a comment so that we do not forget how to add it.