[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.

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)
 * [[span(style=color: #FF0000, align_algs (Eric))]]
 * [[span(style=color: #FF0000, 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)
 * [[span(style=color: #0000FF, crosslinks (TomG) **[updated but untested]**)]]
 * ~~cytoscape (Scooter)
 * ~~exp_cmd (Conrad)
 * ~~file_history (TomG)
 * hbonds (Eric) **[not a bundle]**
 * ~~help_viewer (Greg)
 * [[span(style=color: #0000FF, ihm (TomG) **[updated but not tested, does not run `python setup.py test` because library path is only setup for `ChimeraX`, not `python`]**)]]
 * ~~label (TomG)
 * ~~list_info (Conrad)
 * ~~log (Eric)
 * [[span(style=color: #0000FF, map_series_gui (TomG) **[updated but untested]**)]]
 * ~~match_maker (Eric)
 * ~~[[span(style=color: #0000FF, mav (Eric) **[updated but untested]**)]]
 * [[span(style=color: #FF0000, md_crds (Eric))]]
 * ~~mlp (TomG)
 * ~~mmtf (Greg)
 * ~~model_panel (Eric)
 * [[span(style=color: #0000FF, model_series (TomG) **[updated but untested]**)]]
 * [[span(style=color: #0000FF, mol2 (Eric) **[updated but `save test.mol2` crashes]**)]]
 * [[span(style=color: #FF0000, morph (TomG) **[not updated, tried updating but failed in `python setup.py test`])]]
 * ~~mouse_modes (TomG)
 * [[span(style=color: #0000FF, movie (TomG) **[updated but untested]**)]]
 * [[span(style=color: #FF0000, oculus (TomG))]]
 * [[span(style=color: #0000FF, remote_control (TomG) **[updated but untested, this is the XMLRPC part of `remotecontrol`]**)]]
 * [[span(style=color: #0000FF, residue_fit (TomG) **[updated but untested]**)]]
 * ~~rest_server (Conrad)
 * ~~shell (Eric)
 * ~~shortcuts (TomG)
 * ~~[[span(style=color: #0000FF, sideview (Greg) **[updated but does not run `python setup.py test` because library path is only setup for `ChimeraX`, not `python`]**)]]
 * ~~[[span(style=color: #0000FF, sim_matrices (Eric) **[updated but untested]**)]]
 * [[span(style=color: #0000FF, smooth_lines (TomG) **[updated but untested]**)]]
 * [[span(style=color: #FF0000, spacenavigator (TomG))]]
 * ~~stl (Greg)
 * [[span(style=color: #0000FF, storm (TomG) **[updated but untested]**)]]
 * ~~stringdb (Scooter)
 * [[span(style=color: #0000FF, struts (TomG) **[updated but untested]**)]]
 * ~~test (TomG)
 * ~~toolshed (Conrad)
 * [[span(style=color: #0000FF, tug (TomG) **[updated but untested]**)]]
 * [[span(style=color: #FF0000, vive (TomG))]]
 * [[span(style=color: #0000FF, volume_viewer (TomG) **[updated but untested]**)]]
 * [[span(style=color: #0000FF, vtk (TomG) **[updated but untested]**)]]