Level files are referenced by game.xml in the assets folder to be assigned to checkpoints.
The order of checkpoints in the game is determined by the game.xml file in the assets folder. Upon opening the file in your text editor, it should look something like this:
<game>
<levels>
<level name="basic"/>
<level name="night"/>
<level name="holodeck"/>
<level name="cave"/>
<level name="canyon"/>
<level name="ocean"/>
<level name="cave2"/>
<level name="river"/>
<level name="brownie"/>
<level name="phosphor"/>
<level name="hyperspace"/>
<level name="city"/>
<level name="endless"/>
<level name="endless"/>
<level name="endless"/>
</levels>
</game>
You can add, delete and change the entries to shift around the order of checkpoints in the game. Note that adding more entries will not produce more menu segments, checkpoint buttons, new save data, etc. without patching the game's binary.