Something I noticed in the new nightlies just the other day, when creating a new project, C::B now automatically creates a new folder. And configures everything to run out of this one folder. This made making projects for me harder.
The old method used to just save a project file in the folder you specified, and I could use my own setup which was:
Project Folder (contained the .exe and only other files to be used by the program)
/src (subfolder with all the source code and project files)
src/obj
I would create the folders first, and then just save my project file in the src folder.
I now have to clear out all the files, and reconfigure everything from scratch when I make a new project. Before, I just needed to change the .exe to output into the base folder.