How can I encourage my advisor to adopt better work practices? I'm a second year PhD student.  In general I love my advisor, but recently we've run into some small bumps in the road while working on a paper together.  He's controlling the "master" copy and I send most of my contributions and comments through email for him to incorporate.  

A few days into the process, we had a conversation that went something like this...


  Me: "Hey, so I cited a few papers you might not have seen.  How do you
  keep track of your references?  I use JabRef to keep up with BibTex
  entries, but I can export those citations to a bunch of different
  formats..."
  
  Advisor: "What are you talking about?" 
  
  Me: "Like, when you need to
  make your references section... how do you keep track of all the
  papers you've cited in the text? Refworks? Endnote? Zotero?" 
  
  Advisor: "What?  ...I use
  the 'copy/paste' method."


I was baffled by that answer.  I know he's been doing this for a long time with good success, but I cannot fathom someone who has been collaborating with so many people for so many years is still at the level of manually formatting each entry in a Microsoft Word document and then copying/pasting over whenever that reference is needed elsewhere.

Any suggestions on how I can help bring this faculty member into the 21st century without seeming presumptuous?
Turn the tables.  For your next paper, you maintain the master copy.  Make sure all the infrastructure is in place, including a fairly solid draft of the paper, before you involve your advisor in the writing process at all.  Use whatever version control and reference system you find most useful.

Your advisor may simply refuse to use your tools; fine, you can still incorporate their emailed inputs.  Or they may just need someone else to figure out the infrastructure and teach them how to use the tools, instead of figuring it out themselves from the manuals.  Either way, you'll have some extra work to bring your inexperienced (and possibly resistant) coauthor up to speed, but that's a standard part of the student-advisor relationship.

In the worst case, your advisor may simply refuse to give up control of the master copy.  (Never mind that it's already too late.)  In that case, you may need to encourage them to look for another student.