​Change set for a pure Python bundle upgraded from old layout to new layout.

​Change set for a bundle with C++ code upgraded from old layout to new layout. Ignore the changes in apps, which is a one-time change for all bundles.

Conrad: Working my way down. Updated and tested bundles are in black and crossed out. Updated but untested are in blue. Skipped (too scary) are in red. Not updated are in black.

Bundles needing upgrade:

• add_missing_atoms (TomG)
• align_algs (Eric)
• alignments (Eric)
• blastprotein (Conrad)
• bogus (Conrad)
• cage_builder (TomG)
• cellpack (TomG)
• chem_group (Eric) [not updated, sel amide crashes]
• cmd_line (Eric)
• color_globe (TomG)
• contacts (TomG)
• crosslinks (TomG) [updated but untested]
• cytoscape (Scooter)
• exp_cmd (Conrad)
• file_history (TomG)
• hbonds (Eric) [not a bundle]
• help_viewer (Greg)
• ihm (TomG)
• label (TomG)
• list_info (Conrad)
• log (Eric)
• map_series_gui (TomG)
• match_maker (Eric)
• mav (Eric)
• md_crds (Eric)
• mlp (TomG)
• mmtf (Greg)
• model_panel (Eric)
• model_series (TomG) [updated but untested]
• mol2 (Eric) [updated but save test.mol2 crashes]
• morph (TomG) [not updated, tried updating but failed in python setup.py test]
• mouse_modes (TomG)
• movie (TomG) [updated but untested]
• oculus (TomG)
• remote_control (TomG) [updated but untested, this is the XMLRPC part of remotecontrol]
• residue_fit (TomG) [updated but untested]
• rest_server (Conrad)
• shell (Eric)
• shortcuts (TomG)
• sideview (Greg) [updated but does not run python setup.py test because library path is only setup for ChimeraX, not python]
• sim_matrices (Eric) [updated but untested]
• smooth_lines (TomG) [updated but untested]
• spacenavigator (TomG)
• stl (Greg)
• storm (TomG) [updated but untested]
• stringdb (Scooter)
• struts (TomG) [updated but untested]
• test (TomG)
• toolshed (Conrad)
• tug (TomG)
• vive (TomG)
• volume_viewer (TomG)
• vtk (TomG)