Made it so that virtual routine is not called from constructor.  If the calculation
is terminated during the analysis phase then the analysis is now restarted when
the calculation reaches update on the first loop.  I also removed the duplicated
backup code that was in analysis.  Backup is now done by the routines in OFile.
This routine is now a little more flexible in that you can specify the string
in the backup name.

Checkpoint is appended in restart mode and overwritten when opened at
start of calculation with no restart or when analysis is completed.  Most
of this is looked after within OFile now

I used cppcheck --enable=all.

When using IFile or OFile only, it is sufficient to include
one of the two header files.

Also, consistently:
PlumedIFile -> IFile
PlumedOFile -> OFile
PlumedFileBase -> FileBase

The guard "ifndef/define" has been updated so as to also include the
module name. This is important as it will allow files with the same name
to be used in different directories. Modification was done automatically
using header.sh - just run it routinely to keep names consistent