[https://www.cgl.ucsf.edu/trac/ChimeraX/changeset/3ec87b83d5971f83a1f53bd0d309cb5e6dfaad54/ Change set] for a pure Python bundle upgraded from old layout to new layout.

[https://www.cgl.ucsf.edu/trac/ChimeraX/changeset/47a758ab16089fe4bc0e72ab9d928d155745e6f5/ 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)
 * ~~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)