​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 ChimeraX]
• 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)
• morph (TomG)
• mouse_modes (TomG)
• movie (TomG)
• oculus (TomG)
• remote_control (Conrad)
• residue_fit (TomG)
• rest_server (Conrad)
• shell (Eric)
• shortcuts (TomG)
• sideview (Greg)
• sim_matrices (Eric)
• smooth_lines (TomG)
• spacenavigator (TomG)
• stl (Greg)
• storm (TomG)
• stringdb (Scooter)
• struts (TomG)
• test (TomG)
• toolshed (Conrad)
• tug (TomG)
• vive (TomG)
• volume_viewer (TomG)
• vtk (TomG)