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Modifying the ant run target in Linux.
According to a comment at http://code.google.com/p/arduino/issues/detail?id=352 this helps ant find the executable. It still doesn't work for me, but maybe it will for you.
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@ -315,7 +315,7 @@
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<target name="linux-run" depends="linux-build"
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description="Run Linux version">
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<exec executable="linux/work/arduino" dir="linux/work" spawn="false"/>
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<exec executable="./arduino" dir="linux/work" spawn="false"/>
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</target>
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<target name="linux-dist" depends="linux-build"
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