[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.

== 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)
 * add_missing_atoms (TomG)
 * cage_builder (TomG)
 * cellpack (TomG)
 * cmd_line (Eric)
 * color_globe (TomG)
 * contacts (TomG)
 * crosslinks (TomG)
 * cytoscape (Scooter)
 * exp_cmd (Conrad)
 * file_history (TomG)
 * help_viewer (Greg)
 * ihm (TomG)
 * label (TomG)
 * list_info (Conrad)
 * log (Eric)
 * map_series_gui (TomG)
 * match_maker (Eric)
 * 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)
 * stl (Greg)
 * storm (TomG)
 * stringdb (Scooter)
 * struts (TomG)
 * test (TomG)
 * ~~toolshed (Conrad) [no longer used]
 * tug (TomG)
 * vive (TomG)
 * volume_viewer (TomG)
 * vtk (TomG)

== Trendsetters ==
(bundle_info.xml)
 * [[span(style=color: #FF0000, alignments (Eric) -- ~~**custom init now needed in bundle info**)]]
 * blastprotein (Conrad)
 * bogus (Conrad)
 * bundle_builder (Conrad) -- Does not use **bundle_info.xml** since it **must** use setup.py.in because the {{{ dev }}} command depends on this bundle
 * [[span(style=color: #0000FF, hbonds (Eric) -- ~~**bundle testing procedure needs improvement**)]]
 * rest_server (Conrad)
 * spacenavigator (TomG)