sci-chemistry/freeon-1.0.4: Version bump.

I also removed older versions from before the new versioning scheme. This
includes the patches, which are not needed anymore.

Package-Manager: portage-2.2.1
sci-physics/lammps-20130923: Version bump.

I also removed older versions to clean up a bit.

Package-Manager: portage-2.2.1
fix broken patch

Package-Manager: portage-2.2.1
sys-clyster/charm-6.5.1-r1: Fix missing DEPEND.

This addresses bug 486202. The ebuild had a missing DEPEND using the doc USE
flag.

Package-Manager: portage-2.2.1
Merge branch 'master' of github.com:gentoo-science/sci

Conflicts:
	sys-cluster/charm/ChangeLog
sys-cluster/charm-6.5.1-r1: Added another missing DEPEND.

Package-Manager: portage-2.2.1
sys-cluster/charm-6.5.1-r1: doc depends on python-2

Package-Manager: portage-2.2.1
sys-cluster/charm-6.5.1-r1: Added python dependencies

The documentation is built partly with python2.x scripts. I added the
necessary dependencies.

Package-Manager: portage-2.2.1
sci-chemistry/freeon-1.0.5: Version bump.

Package-Manager: portage-2.2.1
sci-chemistry/coot: Adjust pc patch for latest head

Package-Manager: portage-2.2.6
sci-biology/bowtie: Exchange common variables, fix SRC_URI

Package-Manager: portage-2.2.7