Perhaps something along the lines of data in the "root" directory, with DLLs in a "lib" directory and various executables in a "bin" directory, along with a "doc" directory for locating the documentation, and a "src" directory for the project source codes?
Or have I missed your point completely?
I tend to put the source code files in the "root" directory of a project with auxiliary directories under that for various things like data, documentation, etc.
My finished projects are installed into the standard directories: executables in one of the $PATH "bin"s (usually /usr/local/bin), shared libs in one of the standard "lib" directories (mainly /usr/lib). The data gets put into a dedicated directory: somewhere in /home if it's data that is short-term or it gets put somewhere on the "archive" filesystem if it's stuff that's "write once and keep for ever".