I've not recompiled this myself yet, but you have to set Eclipse up to use the correct "workspace".
If you don't know how to use Eclipse or compile Java, I recommend getting started on a Java tutorial FIRST,
if you want to run a private server that you can upgrade and update.
Otherwise, if you just want to play an online game, you can find someone else's server like mine,
or, join the Pokemonium server, which has many more bugfixes than I may be able to have by the end of the month.
In short, if you don't want to learn how to use Eclipse, give up running your own server for anyone else to play on.
It sounds harsh, but it's the truth: Other players will just get MAD at you if you try to change things,
but don't have a single clue what you're doing, making them lose data or something.
Not saying "Don't try", but saying "you need this if you plan to try".