Currently, it appears that ford ignores an --exclude_dir command-line argument if the excluded directory name appears in a src_dir statement in the project file:
$ cat project.md
project: override-me
src_dir: include-me
src_dir: skip-me
$ ford --exclude_dir skip-me project.md
Reading file include-me/hello.f90
Reading file skip-me/goodbye.f90
It would be nice to be able to override the project-file src_dir statement with at the command line.