Command-line options override options in a configuration file. Run fourmolu --help to see all options.

— README.md

See for yourself:

% cabal run fourmolu -- --indentation 4 --newlines-between-decls 2 src/Ormolu.hs
% rm `fourmolu.yaml`
% cabal run fourmolu -- --indentation 4 --newlines-between-decls 2 src/Ormolu.hs

Expected:

In either invocation, there is indentation by 4 spaces and 2 blank lines between top level declarations.

Actual:

In the first invocation, there is indentation by 2 spaces and 1 blank line between top level declarations, as written in fourmolu.yaml — the options set in fourmolu.yaml override command line options, contrary to the documentation.