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
Merge branch 'master' into autoconf

Conflicts:
	CHANGES/v2.1.txt
Fixed a few macro names
Couple of fixes to 'plumed mklib'
Merge branch 'master' into autoconf
configure: added a test for the existence of the sourceme/makefile file
to not return an error in case of ./configure --help
Merge commit 'f3082' into autoconf

Conflicts:
	CHANGES/v2.1.txt
Merge branch 'master' into autoconf

Conflicts:
	CHANGES/Unreleased.txt
	user-doc/Installation.txt
Added search for molfile
Added search for lapack/blas
CHANGELOG
Flag to disable external lapack/blas

mostly for testing
Added flags to switch off library search (on by default)

All libraries can be switched off with
./configure --disable-name

This allows testing or removing libraries that are
known to be buggy or problematic.

Notice that when lapack/blas are off, internal versions
are used (plumed does not work without them).

Also notice that when mpi search is on standard mpi compilers
are searched for before non-mpi ones.
Thus, to configure with mpi just type:

./configure

To configure without mpi use:

./configure --disable-mpi

I made this change since mpi is commonly needed and there is no
expected drawback from using mpi.
Improved doc
Merge branch 'autoconf'