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...
missing regtest
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)
Removed numerical derivatives from regtest
Merge branch 'v2.0' into fast-weighted-msd
Merge tag 'v2.0.1' into fast-weighted-msd
Merge branch 'fast-weighted-msd'
Changelog

closes #6