Lets say you have found a bug, such as with objects placed into the scene ending up partially below the terrain.
objects on the scene partly come under the landscape.
You can easily debug and fix this issue by using Visual Studio 2008 or 2010's best of breed debugging tools and Edit-and-Continue support.
In this case, you could put a breakpoint in Scene.DropObjects.cs and add a command to the alignment of object. (Though this is not the best solution to an issue like this, it is provided as an example of a quick fix or workaround you could make.  The same concept can be applied to editing your not just your own C# entity, ability, action and other classes, but also the many classes provided to users for all Visual3D licenses, such as AvatarBase, and can be used for debugging and customizing the core rendering engine and toolset even for those with Studio Source or Enterprise Source licenses.

This example is covered at time 9:07-10:05 in the Build a Game tutorial video shown below.