Is there any way to customise what's printed in the server/Eclipse console?

 

Like instead of displaying this:

[sTDOUT]: [apocalypse.fandomcraft.structures.DungeonDekuTree:generateSurface:1088]: Successfully built a forest dungeon at (291, 75, 529)

 

...have it display as this?:

[FandomCraft]: Successfully built a forest dungeon at (291, 75, 529)

 

I've tried looking through the Vanilla/Forge classes but can't find where they do it.

Use a Logger, e.g.

public static final Logger logger = LogManager.getLogger(your_mod_id);

// somewhere in your code:
logger.info("Here's a message");

// prints:
[13:27:48] [server thread/INFO] [your_mod_id] Here's a message

It is possible to further format / customize the output, but that is more work than it's worth, in my opinion.

Quick interjection:

 

The FMLinit events give you a logger. 

event.getModLog()

if I recall correctly.  Just save a reference to that in your main class.