How to avoid navigation popup large size?

To the best of my knowledge, the width of the popup is not configurable. It looks like it adjusts the width as the file path gets longer to accommodate that length, maximizing it to the monitor's width. So in your case, that is problematic with the Windows task bar on the side. I recommend you open a bug report on the issue. This only seems to be an issue with the Navigate to File (Ctrl+Shift+N) action. The Navigate to Class (Ctrl+N), Navigate to Action (Ctrl+Shift+Alt+N) and the Search Everywhere (Hit Shift twice) action all seem to have better behaved dialogs since they do not display the absolute path of the items being found. That means they do not need to grow so large.

Out of curiosity, is there a reason you are searching for a class via the Navigate to File (Ctrl+Shift+N) action rather than the Navigate to Class (Ctrl+N) action? Is it just a convenience so you can search for anything, class or say a properties file, from a common action that you are using Navigate to File (Ctrl+Shift+N) rather than   Navigate to Class (Ctrl+N) ? If it is a case that you need the full path to the class, there is a workaround until the issue is fixed.

1. Use the Navigate to Class (Ctrl+N) to find the class, then open it.
   
   • If the sources are attached, it will open the source file. If they are not attached, IDEA will decompile the class.
     
2. Once you are in the source, use Alt+F1 > Project View (or from the menu Navigate > Select In > Project) to select it in the project view.
   • You can just select "Project View" from the "select in" popup. You do not need to expand the side menu.
3. Once selected, use Ctrl+Shift+C (or open the context menu (context menu key or right click) and select "Copy Path") to Copy the path.

For step #2, you could also use the navigation bar (Alt+Home). The one caveat is that if you have the sources attached, it will copy the path to the source JAR. So you will need to to remove the "-sources" from the copied value if you want to path to the actual class.

If  you need to do this for a file, rather than a class, inside a library JAR, such as the"validation-mapping-1.1.xsd" inside the Hibernate-Validation library, you can do the above, but use Search Everywhere (hit the shift key twice) in step 1.