Added MW cite and docs
Fixed make install with static
Added "has" tools

Added more ways to check if tools are installed. Now also
plumed --has-matheval
is allowed
Improved conditional execution of regtests
Added regtest for MATHEVAL

regtest is executed only if plumed --has-matheval
--has-almost option flag in driver
CS2BACKBONE first regtest (scalar)
CS2BACKBONE AVERAGING test
data folder for CS2BACKBONE
updated regtest gitignore
Fixed permissions upon install

Permissions of installed files were not correct. Now after
install all permissions are reset so that "group" and "others"
can read and execute everything
Fixes (cppcheck)
Fixes #2

(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.
Typo
Fixed opening of Files

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().
Fixed bug in ABMD

When MIN keyword was not used, an array was set as empty and later
accessed.
Changed open() to auto backup version
PLUMED_MAXBACKUP environment variable

Allows to switch off auto backup or to change the maximum number of 
backups
Added fixes to checkpoint writing in analysis

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
Fixed small things in analysis

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.