Allow working directory reuse

Jobs should be able to reuse working directories with intermediate files. If the job's output file already exists in the working directory and is more recent than its input, it should simply skip.

This will make the pipeline more efficient w.r.t. spot preemption. If a step completed previously, no need to repeat it.

This will also make debugging easier, if we populate a working directory with intermediate files, we can effectively start the pipeline where we like.