move inverse_svd_threshold to libAtoms/linearalgebra.f95, and
get rid of calls to matrix_inverse (just use overridden name inverse)
increase min verbosity level for inverse_svd_threshold print statements
Add git_pull_all target for top level Makefile
Fix definition of minimum step in msd.py, and add msd_relative_to_mean.py
update  stderr printing of progress
fix typo in msd_relative_to_mean_pos
Add numpy import to msd.py, and print all singular values if verbose for svn in linearalgebra.f95
Added "rename" argument to AtomsReader, AtomsList and qlab.view()

Allows properties and params to be renamed when loading configurations.
Useful for e.g. visualising time-averaged atomic positions with:

   view('traj.nc', rename=[('avgpos', 'pos')])
NEB bug fix to energy of first and last image for integrate_forces=True
added C/fortran wrappers for writing/appending a line to a file, appending a file to another and removing a file
added QW wrapper to QUIP_Utils

Conflicts:
	Tools/quippy/setup.py
Remove debug print
Slightly more robust merge_cp2k_traj.py
More options for binning of bond angle distributions in structure_analysis_traj.f95
Add distribution target to top level Makefile
some permissions changes
various permissions changes
more permissions changes
Add hcp_ortho structure
replaced args_str with args_str=args_str