​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) -- bundle installation procedure needs improvement
• 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)
• cytoscape (Scooter)
• exp_cmd (Conrad)
• file_history (TomG)
• hbonds (Eric) -- bundle testing procedure needs improvement
• 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) [updated but save test.mol2 crashes]
• morph (TomG)
• mouse_modes (TomG)
• movie (TomG)
• oculus (TomG) [not part of distribution]
• remote_control (TomG) [no XMLRPC test case for remotecontrol]
• 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)