Implemented fast weighted alignment with align!=displace

In this version the fast routine is hard-coded. I do not compute explicitly the derivatives of the rotational matrix.
Instead, I assume them to be zero and at the end add a contribution which resets total "force" and "torque" (i.e.
I enforce translational and rotational invariance of the RMSD). In test rt47/check one can appreciate that
numerical derivatives come out correct. I do not know exactly why...
Added internal lapack/blas

Adapted from GROMACS
missing regtest
libmolfile plugin in driver
test for molfile_plugin
added rt2
Missing malloc. Thanks to Toni
Merge branch 'v2.0' into internal-lapack
Merge branch 'v2.0' into internal-lapack
Fixed configuration file)
(suggested by Toni Giorgino)
Merge branch 'v2.0' into internal-lapack
Improved RMSD with align!=displace

I did it in the boring way - full derivatives of rotation matrix.
It seems to work now, but still breaks some test. It is probably
some numerical issue, I will investigate before merging.

It is slower than the align==displace version (~ a factor 1.5),
but I think it is more than acceptable.
Merge branch 'v2.0' into fast-weighted-msd-derivs

(also moved rt47)

Conflicts:
	src/tools/RMSD.cpp
Fixed regtest

There was some small error in a regtest for forces when passing
to the fast RMSD version. I checked that the numerical error
on new derivatives same order as the one with the old (slow)
derivatives. Since that comes out ok, I just reset the regtest here
Clean up

class OptimalAlignment is not used anymore in RMSD
Slighlty optimized MSD

Reference coordinates are saved already shifted to their average.
Weights are stored already normalized.

A regtest has been fixed (it contains numerical derivatives which
slighlty changed with this commit)
Configuration with autoconf

One can now produce a Makefile.conf and a sourceme.sh
using autoconf. Just type:

./configure

Or maybe

./configure CXX=icpc

In case you want to use mpi, just use:

./configure CXX=mpic++

Everything should be smooth. I took care that the generated Makefile.conf
is compatible with those stored in configurations/. In this way,
one can always resort to a saved configuration file. Moreover,
jumping between git branches (without need of reconfiguring) will be
easier.

More info on the manual page (no need to use autoconf to compile
the manual and see that page)

Closes #46
Fix

autoconf places a lot of " in the define string. this is to properly
escape them
Fixed conditional compilation with exceptions

Two fixes:
1. with autoconf, the proper macro for exceptions is __PLUMED_HAS_EXCEPTIONS
I fix it (breaking the compatibility with existing Makefile.conf)
because I think this is not used by anyone actually
2. uses macro __PLUMED_HAS_EXECINFO to decide whether execinfo.h should
be included or not
Removed numerical derivatives from regtest