This code changes are dangerous. For example you changed all "BOOL" to "bool", its useless and broke serialization compatibility with previous version (and without reason changed design of Serialization functions). You replaced MFC "CList" (list-style) with different class "std::set" (array-style), i see no point doing this. So many unneeded changes in code masks real ones and difficult its reviewing.
(I prefer several tiny patches over one massive even in few source files)