Conflicts:

	deployment/linux/create_bundle.py

The issues manifests when importing large "composite" compounds,
e.g. a ligand derived from several amino acids with the atoms not
listed in order of increasing ordinals. This was not a problem up
until now, since the components.cif dictionary was always (as
far as I know) listing the atoms ordered by ordinal.

It is completely sufficient to mark the organizer dirty. Fixes
BZDNG-250.

Added support for Homebrew MacOSX packaging system and for Eigen3 (in Eigen2 compatibility mode)

The cause for this is actually a bug in Boost.Python that triggers when
arg("arg")... is used in the export and the number of arg("") arguments
doesn't match the number of argument of the function. When one then uses
a wrong kwarg, the program crashes. I'll submit a bug report to the
Boost.Python on this issue. I fear that there are many more cases in
the pymod export where we are using arg("") as we did for the query.

Previously we were returning the wrong index for residues
in chains that contained a certain residue number more
than once. We were always returning the index of the first
residue. Among other things, this fixes BZDNG-229.

added blurps about "picking the right branch" and "updating the source code" to installation instructions

Removed some libraries that should not end up in the bundle