irmin-pack: implement `fresh` for lower layer

[metanivek]

A low priority leftover task from #2182.

Currently the code does not properly support using the fresh configuration flag when using a lower layer. It simply prints a message telling the user to remove the data in the lower layer path provided. To properly support this flag, we should recursively delete the data in the provided path.

irmin/src/irmin-pack/unix/file_manager.ml

Lines 470 to 475 in 03ad27f

	(* TODO: implement recursive delete for lower root *)
	failwith
	(Fmt.str
	"Lower root already exists but fresh = true in configuration. \
	Please manually remove %s."
	path)