Citing a paper with multiple versions
In math we have the same issues.  Here is what I do, most of which is standard:


If a paper has been published, always cite the published version.
If you want to point out the chronology, in particular because it is not clear from publication dates, do it in the text.  People understand that publication dates do not align perfectly with when the papers were originally written.  (My papers don't appear in the order I wrote them.)  If you refer to arXiv versions, it is easy to see the chronology, at least up to the level of month/year, from arXiv ids.
If something is accepted to a certain journal/conference proceedings, you can say "Journal XXX, to appear" in the references.  If you want to say something was announced at a certain conference, you can say so in the text.
Make references (e.g., theorem numbers) to the version you cite.  I personally like to include version numbers in arXiv citations for this reason (e.g., arXiv:1601.0000v37).  If you want to refer to something that appeared only in a previous version, I would cite the published paper if published and say in the text something like: This result appeared as Thm A.B.C of an earlier version (arXiv:1601.0000v36) of [citation]" possibly with some remark about why it's not in the current version.  (Hopefully, if you're using it, it hasn't been removed because there was an error in the proof.)  But if the paper has not been published, you can either do a similar thing or just put a citation to the version you want to refer to.  However, it's probably best to point out in such situations that the result doesn't appear in later versions so the reader doesn't accidentally check the wrong version.