I **try** to stick to just editing the *.loc file in tool-data for those tools that do not have a data manager. This way I can also track them in my local git branch. But I do agree that it can be complicated to figure out which files to edit for which tool (bwa/bwamem...) and add the correct entry and in the right format.

The data managers make it on the one hand easier, but harder to tell if I was adding entries by hand or through a data manager - especially when not being consistent..

Part of this could be mitigated if the admin web interface would allow for editing these "Tool Data Table Entries" and not just view them -> https://github.com/galaxyproject/galaxy/issues/6819

Cheers,

Jelle