Poor indication of launch on incompatible file type
Launching a tool on an incompatible file type (e.g. launch IGV on a .xgmml file) indicates the incompatibility with a red X icon. That red X is very similar to the red X used to remove the file from the launch list. And you have to know to hover over the correct point in the screen to see the relevant tool tip.
Can the indication be made more visible? IMO put the text from the tool tip right at the bottom of the file list dialog, always visible when there is an incompatible file in the list.