Analogously to the old UNIX /usr/local directory (which has been perverted from its original intention, but no matter), the newest FAF distribution includes a directory called "local", which mirrors the directory structure of the distribution itself.
As a user, if you want to change something in the code, the new suggested way is to copy the file to its corresponding location under "local", and modify it there. Thus, any time a FAF upgrade is released, it becomes trivial for you to upgrade. Even if you modify some files heavily, merging updates into them will still be a much simpler job this way. In effect, this separates OUR code from YOUR code, and gives easy accountability.
For example, if you wanted to modify the login or wrapper HTML to better suit your page layout, you would copy templates/prom/htmlbegincompact.html to local/templates/prom/htmlbegincompact.html, and you could freely modify it. To change a languag file, you might copy minibb/lang/eng.php to local/minibb/lang/eng.php. Or you could download a language pack and put it there. Want to manually disable something in military.php? Just copy military.php to local/military.php and edit it. Et Voila! (Guide entries can be easily modified in a similar fashion, under local/guide.) Then when we release a huge update, you just unzip it and with a minimum of fuss are happily running the latest version.
As I usually say: all users are encouraged to upgrade! Actually, we will be testing this for a few days, and only then putting it on SourceForge.
~Beatles
[edit] For reference, here is the FAF readme: http://faf.staronesw.com/README
New Upgrade Mechanism
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