​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.

Bundles needing upgrade:

• add_missing_atoms (TomG)
• align_algs (Eric)
• alignments (Eric)
• blastprotein (Conrad)
• bogus (Conrad)
• cage_builder (TomG)
• cellpack (TomG)
• chem_group (Eric)
• cmd_line (Eric)
• color_globe (TomG)
• contacts (TomG)
• crosslinks (TomG) [updated but untested]
• cytoscape (Scooter)
• exp_cmd (Conrad)
• file_history (TomG)
• hbonds (Eric)
• 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)
• 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)