revisit `best-practices.md`

[a-frantz]

It needs to have a new entry for cleaning up created files not output by the task. It also might be beneficial to add justifications for some of the less obvious entries.

I'd also like to split the document in two, one for rules that apply to just "any WDL" being written regardless of project, and then a second doc for rules specific to this repo. Currently there are both in the same document and those concerns should be separated.