Fix `dir` of stream cleanup and do cleanup for other commands. (#178)

Address the failure when `stream cleanup` is used after `clone follow`
caused by `dir` is passed as `NULL` to `copydb_init_workdir`, which leads
`copydb_prepare_filepaths` to set `topdir` to an undesired location.

Includes cleanup of commands that do not require working directory, by
removing `copydb_init_workdir`. And, sets `dir` to appropriate value that
do requires working directory.