This isn't really a bug report, just some UX feedback. If you create a new project and select ConfigTools | Clocks (for example) from the menu bar, it complains that no MCU is selected and gives you no option to select an MCU, or indeed any information about what's going on at all.
The correct answer (covered in the instruction manual, which is why this isn't a bug report) is to right-click on the project in the project explorer and open ConfigTools from there the first time.
This seems pointlessly confusing. There are at least two other ways to get to the configuration perspectives, both of which are visible without clicking on anything and would seem to be the more obvious ways to get there. They should either launch the first-time setup like the right-click menu does, or they should at least be hidden or disabled until the configuration is created.