fix(lint): resolve E320, E331, E410, E415, E505, E510 across multiple packages
E505: add missing .mli files for merlint/lib/sexp, monopam-info, and
monopam/lib/{add,clean,ctx,diff,init,pull,push,remove}.
E510: add log source to ca-certs/test/tests.ml.
E410: fix doc ending period in kdf/scrypt.
E415: add pp to ocaml-agent config and runtime_config.
E331: remove redundant get_/make_/find_/create_ prefixes.
E320: remove redundant module prefixes (Diff.diff→compute,
Pull.pull→run, Push.push→run, Remove.remove→run, etc).