The startcmd batch script was added to the DITA Open Toolkit as a way to simplify the complex process of building DITA content. Over time it became the most common way to use the toolkit (outside of an editor or content management system). Plans to remove this batch script in one of the 2.X releases have understandably raised concerns, but changes within the toolkit itself really mean that startcmd is no longer needed.
Some longtime toolkit users have expressed concerns about migrating from DITA-OT 1.X to DITA-OT 2.X, because they've heard that it introduces backwards incompatible changes. For many, the fear begins with the "deprecated" message from startcmd, the most familiar entry point to processing. There are good reasons for the backwards incompatible changes - very good reasons, deserving of their own article - but I won't go into those here. Instead, I'll argue that deprecating startcmd is something different - and something better.
Those new to the toolkit and those who never heard of the start command file shouldn't read any further; instead, read the documentation at http://www.dita-ot.org for details about running the toolkit using the dita command.