This process works on Snow Leopard. Not sure about other OS versions.
1) Download an Ant task specifically built to make Mac apps out of Java code, called JarBundler.
2) Install the bundle somewhere that Ant can use it. On Snow Leopard, this means copying the jarbundler-2.2.0.jar into /usr/share/ant/lib. You probably will need to use sudo to do this:
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sudo cp ~/Downloads/jarbundler-2.2.0/jarbundler-2.2.0.jar /usr/share/ant/lib/
build.xml - A small Ant script to invoke the jarbundler task with MapTool specific information. (This could be easily moved into the main build file, btw.)
maptool.icns - An ICNS version of the MapTool icon.
4) Download a version of MapTool and expand it. I tested this with version 1.3b75, as that is the version required to use the iPad/iPhone client application MaPnakotic. Could be that other versions need some tweaking.
5) Open a Terminal. Move to the directory of the supporting files. Probably something like:
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cd ~/Downloads/bundleMapTool
6) Run the following command:
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ant -Dmaptool.macbundle.source=$SOURCE -Dmaptool.macbundle.version=$VERSION
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ant -Dmaptool.macbundle.source=/Users/yourname/Downloads/maptool-1.3.b75 -Dmaptool.macbundle.version=1.3.b75