$ cvmfs_server tag test.galaxyproject.org | grep bd3496b
tools-bd3496b                                          │   500839 │ trunk   │ 5 Jun 2019 11:21:08  │        │ Automated tool install for commit bd3496b4c196360a3d93a4410318df0453b64f50

Installed on Test and available immediately upon CVMFS propagation without a restart! Tool panel indexing appears to have worked as well.

It went into the correct section name but the section ID (chip-seq) doesn't match the existing ChIP-seq section (chip_seq). I'm going to fix shed_tool_conf.xml in CVMFS by hand and for the time being, tool installs/updates should use tool_panel_section_id instead of tool_panel_section_label.

Further details on the issue and proposed solutions for usegalaxy.* are in #9.