Make multithreaded tasks use all cores by default

Switch multithreaded sections of deenurp to use all available cores by default, as detected by
```{python}
multiprocessing.cpu_count()
```
The old defaults varied by command.

@nhoffman, @crosenth: I also switched the default number of cores for cmalign to 1; the default was varying by command.
If you're interested in adding something more powerful, that would be great.