config: create dirs relative to process.work_dir

The current working directory of a tarantool process is changed during
startup to `process.work_dir`.

The mkdir applier works before and after this point, so it should take
into account both situations.

Before first box.cfg() call (in the box_cfg applier) it should prepend
directories with `process.work_dir`. However, it shouldn't do that after
the current wordking directory change.

Part of #8862

NO_DOC=It is bugfix.