Added notes on file backup/restart/suffix
gmx5 patch fix: Plumed.h was included incorrectly, thanks Luca for spotting it
Fixed portability of Stopwatch

I fixed some probability issue in Stopwatch.
Before this fix, the macro used to check the presence of
clock_gettime was not properly recognized. Additionally,
gettimeofday was considered as compulsory, causing problems
on bgxlc (as pointed out by Teodoro Laino).

After this fix, both gettimeofday and clock_gettime
are searched and considered as optional. If present,
clock_gettime is used. Otherwise gettimeofday is used.
If none is present, time is just not measured.
changelog
configure: added the test for bz2 that is optional in almost and so
should be checked before almost in order to link it correctly.
configure: link almost to plumed
updated CHANGES
doc: install with almost update
Merge remote-tracking branch 'origin/v2.1'