Change how temporary files are dealt with

[akhanf]

Depending on how granular we want the PRs to be for v2.0, these could be separate PRs, but I think the main things we could do are:

1. use temp() directive for any files we don't need in the final output
   for files where a config variable is used to decide what is kept, could do something like:
   output:
   myfile=bids(...) if config['keep_foo'] else temp(bids(...))
2. replace the use of the work dir with the regular root and remove the generic rule that copies from work to results
3. harmonize the CLI option names we use and add any additional options (eg to keep warps)