I am an applied mathematician and I have recently joined a project that involves the development of production code for our scientific application. The code base is not small and it's deployed as part of a web application.
When I joined, the code was miraculously maintained without a revision control system. There was a central folder in a server and researchers would copy from it when they needed to work with the code. Inside this root directory there was a set of directories with different versions of the code, so people would start working on the latest version they found and create a new one with their modifications.
I created a Mercurial repository, added all code versions to it and convinced everyone to use it. However, since moving to Mercurial, we have felt little if any need to upgrade version numbers, even tough using hg copy allows us to keep revision history.
Here's where I need your advice on best practices of maintaining this code base. Does it make sense under a RCS to keep folders with different versions in a repo? If we keep a single copy of our code in the repo, what's the most common way to track versions? The README files? Should we keep snapshots of the code outside the repo specifying versions? Does it make sense to keep things as they are? What strategies do you use?
Our team is a bunch of scientists and no one has experience on how to maintain such a repo, so I'm interested in what is commonly done.
If you are going to use a version control system, forget about those version folders. Completly. Mercurial will do that for you, the repository is a complete history of all files of the project.
A common way to track version numbers is with tags. You assign a tag with the version number to a changeset.
To help you, as a "getting started guide" in version control, I suggest this book: Version Control By Example. It's free, and it starts from the beginning, it talks about CVCS, DVCS, fundamentals, what a repository is, basic commands, etc. It has also some interesting analogies, like the 3D file system: Directories x Files x Time. The book is fun and easy to understand, I highly recommend it.
I also recommend some GUI software like TortoiseHg. In daily usage, I spend most of the time in the console, but the GUI is very handy specially in the beginning when you still don't know all the commands. And the best part is the graph, you have a visual feedback of what is going on.