You've found a bug there. It is only supposed to show it if the README.TXT is in the top level directory. We'll hopefully have it fixed for the next patch to 6.1. Unfortunately you can't work around it in current versions without changing the name of your files.
When a plugin is installed a 'plugin notes' window is sometimes shown. It seems like Geneious searches through the plugin directory structure until it finds a README.TXT file and displays the first one it finds. Is there any way to change this behavior or override it? The species model files included with Augustus all have README.TXT files included with them that I would like to show to the user (thus I can't remove them) and Geneious is picking one of these and displaying it.
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