Currently these resources are sub-directories in data
so should then be in each respective resource
<directory>data/phylotree</directory><directory>data/weights</directory><directory>data/annotation</directory>
Also there should be a targetPath entry as when you run the jar file it can't find the resources files within the jar file. So the lines should be included in each respective resource
<targetPath>phylotree</targetPath><targetPath>weights</targetPath><targetPath>annotation</targetPath>
Currently these resources are sub-directories in data
so should then be in each respective resource
<directory>data/phylotree</directory><directory>data/weights</directory><directory>data/annotation</directory>Also there should be a targetPath entry as when you run the jar file it can't find the resources files within the jar file. So the lines should be included in each respective resource
<targetPath>phylotree</targetPath><targetPath>weights</targetPath><targetPath>annotation</targetPath>Once I made these changes.. all good!