[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 [[span(style=color: #0000FF, blue)]].  Skipped (too scary) are in [[span(style=color: #FF0000, red)]].  Not updated are in black.

== Old School ==
(no src subdir)
 * [[span(style=color: #FF0000, align_algs (Eric))]]
 * [[span(style=color: #FF0000, chem_group (Eric))]] ~~**[not updated, `sel amide` crashes]**
 * [[span(style=color: #FF0000, md_crds (Eric))]]
 * ~~oculus (TomG) [not part of distribution]

== Slightly Behind the Times ==
(src subdir, no bundle_info.xml)
 * ~~cytoscape (Scooter) [no longer in distribution]
 * mav (Eric)
 * mlp (TomG)
 * mmtf (Greg)
 * mmtf-python (Greg)
 * model_panel (Eric)
 * model_series (TomG)
 * [[span(style=color: #0000FF, mol2 (Eric) ~~**[updated but `save test.mol2` crashes]**)]]
 * morph (TomG)
 * mouse_modes (TomG)
 * movie (TomG)
 * remote_control (TomG)~~ [no XMLRPC test case for `remotecontrol`]
 * residue_fit (TomG)
 * shell (Eric)
 * shortcuts (TomG)
 * sideview (Greg)
 * sim_matrices (Eric)
 * smooth_lines (TomG)
 * ~~stringdb (Scooter) [no longer in distribution]
 * ~~toolshed (Conrad) [no longer used]
 * tug (TomG)
 * vive (TomG)
 * volume_viewer (TomG)
 * vtk (TomG)

== Trendsetters ==
(bundle_info.xml)
 * add_missing_atoms (TomG)
 * [[span(style=color: #FF0000, alignments (Eric) -- ~~**custom init now needed in bundle info**)]]
 * blastprotein (Conrad)
 * bogus (Conrad)
 * bundle_builder (Conrad) -- must use **setup.py.in** because the {{{ dev }}} command depends on this bundle
 * cage_builder (TomG)
 * cellpack (TomG)
 * cmd_line (Eric)
 * color_globe (TomG)
 * contacts (TomG)
 * crosslinks (TomG)
 * exp_cmd (Conrad)
 * file_history (TomG)
 * [[span(style=color: #0000FF, 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)
 * rest_server (Conrad)
 * spacenavigator (TomG)
 * stl (Greg)
 * storm (TomG)
 * struts (TomG)
 * test (TomG)