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Can someone tell me if it's possible to change the links in the game so that instead of being directed to the main website they are directed to a seperate site on the same server, I've been looking through the JAR files but can't work out which file they are under
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I'm not sure what URLs you mean specifically, and they may be in different parts of the Stendhal code (client, or server). They may be hard coded or set via a configuration property. The property may be checked at runtime for a server but at compilation time for a client.
So, your best strategy is probably to look at the source code rather than compiled files. Then you can do a text search for the specific URLs (or parts of them) that you are interested in changing. If they look like the original URLS in the code, then you can modify them and rebuild it, to get what you want. If they look like they are set with some variable which is set via a property, you can investigate where that property is set (or you are welcome to ask, if you specify the file you found the variable in and where it is.)
You can get the source code at https://sourceforge.net/projects/arianne/files/stendhal/ then look for the …src.tar.gz file in the version you are interested in.
If you do a search for a URL and can't find anything do let us know and we'll try help.
Here is an example: if you type /atlas then the stendhalgame.org atlas page opens. If you search the source code for the start of the URL that opens, which is http://stendhalgame.org/world/atlas.html you should find this file matches: http://arianne.cvs.sourceforge.net/viewvc/arianne/stendhal/src/games/stendhal/client/actions/AtlasBrowserLaunchCommand.java?revision=1.1&view=markup