Control:
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amule-control: Scripts to ease preview and managing amule, amuled, amuleweb and amulegui.
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web-gmui: a remote web interface for MLdonkey, aMule, rTorrent, Transmission and giFT.
emulecollection:
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amule-emc: A command line link extractor
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WOA: emulecollection files on osx
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Kollection: A KDE service menu to open emulecollection files with support for aMule and mldonkey. Allows selection of files.
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amuleKollection for KDE4: A KDE4 port of Kollection
Do you know more tools? Please post them here!