I haven't split up the headers and sources...?
I wouldn't split my headers from my cpp files
I've edited the directory structure. All program and tool sources come into the same src-directory (with subdirectory). The src-directory might also have lib*-subdirs, which include the source files of project specific libraries. Such a library might be used for reading and writing custom file formats (e.g. level files), which might be used by both the final game and the level editor (a tool).
In addition the tree now have a certain place where to put the distributable files (in general copies of the bin and share folders, packed in archives, installers, etc.).