Repository issues: The Custom Application

After a project meeting today, it was suggested that I keep a note of all of the "interesting" issues that I encounter with the various data repositories I encounter on the project. So, here's the first of them.
At least two of our repositories consist of custom-built applications. One of them is a fairly large piece of PHP, backed by a MySQL database. The PHP for this repository is complex, and only understood by one person. The database schema is also fairly cryptic, and almost entirely undocumented. To make matters worse, the web user interface implemented by the PHP is actually a GUI, developed with (I think) Google Gears. The only way of querying this data store through an alternative interface is to access the database directly1.
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