Anything that you do manually leaves the door open for error; this is especially true for your file system. Aside from that, automated processes are usually faster. Magnus Mengelbier has applied this philosophy to providing version control capabilities to SAS data sets, programs and outputs.
"A manual process is most often implemented to retain versions and snapshots of data, programs and deliverables with varying degrees of success," writes Mengelbier writes in his SAS Global Forum 2012 paper. He says that there are many software solutions to provide version control and an audit trail - automatically. In his paper, Mengelbier explains how SAS processses and tools can be integrated for use with Subversion (open source software) for "simple and quick implementations for a SAS analytics environment as well as advanced integration with formal compliance controls."
In addition to version control, Mengelbier says that many providers - including Subversion - provide add-ons such as electronic signatures and business controls.
Mengelbier's macro and templates can be used in any clinical study, but he says "it provides the greatest advantage for a set of clinical studies that have similar design and endpoints."
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This paper is a great introduction to version control concepts and how a tool like Subversion can work. See this post to see how you can use version control (source management) with SAS Enterprise Guide as well.