In analysis runs results from previous analysis are saved as
analysis.0.<filename>, analysis.1.<filename> etc.  If the calculation
is NOT restarted and there are files with these names hanging about they are
renamed bck.0.analysis.0.<filename> bck.0.analysis.1.<filename> etc.

OptimalAlignment::weightedAlignment crashed with intel c++ -O3.
I was not able to find why (gdb and valgrind did not help).
With this workaround, that function only is optimized at -O2 anyway.

Fixes #7

Having the backup string specified in OFile::open leads to clashes
with the routine that sets open using w+, w, rw etc.  It is thus changed
so that you can set the backup string to use with a separate method in the class

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

Allows to switch off auto backup or to change the maximum number of 
backups

When MIN keyword was not used, an array was set as empty and later
accessed.

Removed explicit open mode, so that auto backup/auto restart is used also
for DUMPPROJECTIONS, DUMPDERIVATIVES and DUMPFORCES. Regtests has been added
with backup files.

I also removed some unnecessary c_str().

(I refer to issue number 2 in github to test if it
gets closed).

Now replica exchange can be used with plumed even if plumed
does not do anything at the exchange step.

Permissions of installed files were not correct. Now after
install all permissions are reset so that "group" and "others"
can read and execute everything

regtest is executed only if plumed --has-matheval

Added more ways to check if tools are installed. Now also
plumed --has-matheval
is allowed

I adapted the debug replica exchange stuff. Since running on multiple
trajectory could be useful, I leave --multi as a non-hidden option.

I slightly changed behavior of the hidden flag --debug-grex (now one sets the exchange stride, not the number of replicas - the latter is set with --multi). Thus, a couple of retests had to be updated

At variance with EXTERNAL,
this bias is used when calculating the WT hills height

Now getReducedList can be called more than once returning the same list
I also updated a regtest.
The previous test was only testing stride=2 (or, equivalently,
stride=20 into a trajectory with stride 10).

- solved a bug with averaging over parallelized replicas
- more documentation