Derive `settings_path` from `--filename`

Fixes #1989

`--filename` is a shortcut setting used only in the stdin case to set
the `settings_path`.
Generally, `--settings-path=<file_path>` == `--filename=<filename>`
should hold.

This functionality was removed in 09734212 (Reuse config when items
passed in through stdin as used when items passed in explicitly).