first try with regexp for arguments
Added documentation on use of regex

Here you can use regex to refer to argument in a list
For example in
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1.[xy]|t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f
Fix (wrapatoms uninitialized)

This is a quick fix to avoid regtest failures. The real bug
is the fact that wrapatoms is not read on input in simplemd,
and should be fixed (see #30)
Fixed bug

There was a potential bug when stripping blanks from short strings (1 char)
Fixes #30

I also changed a regtest as a check
Added other shortcuts for cross-compilation

Now all the scripts in /scripts are mapped to executable scripts
in the form "plumed-xxx" (similarly to "plumed-patch"). Allows to use
those shell tools in a cross-compile environment (e.g.
to use plumed-mklib on the login node when plumed is compiled
for compute node)
Plumed now crashes when there is an error parsing matheval expression
Fixed cross-compiled tools

The note "shell only version ..." now goes to
stderr instead of stdout. This is better, because some tool
might produce a meaningful stdout and that should be the
same when using "plumed xxx" and "plumed-xxx"
Slight optimization in rational switching functions

* Better algorithm for int powers
* Simplification when 2*N=M (which is the usual case)
Modified the way groups are read in in multicolvar

You can now read in groups with names other than GROUPA, GROUPB and
GROUPC.  Also output of the atoms in groups is neater.  Lastly I realized that I
had accidentally added some crap to regtest/multicovar/rt45 - I have
now deleted this.
Added BRIDGE colvar, which is equivalent to PLUMED1 waterbridge
Replica echange + neighbor lists do not work

I added a check that disables this combination which can
be problematic. I had to also update a regtest
Added regtest. Compile with -D__PLUMED_HAS_CREGEX
Clarified usage of dot in regexp
regtest consistency
Merge branch 'args-with-regex' into v2.0
Fixed regest (directives were erroneously commented)
forgot files in last commit sorry
Optimized OFile

Removed many scans of the output buffer by keeping trace of buffer length.
Time needed to write a long line with a sequence of file.printf() is
now linear with line length. Before it was quatradic, causing problems
especially when logging huge atom lists at startup.
Fix

cmd("useNaturalUnits") was erroneously crashing