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JAL-3474 removed all .cvsignore files stored in the repo

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JAL-3003 help page mention EPS doesn't support transparency

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JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this in to eclipse classpath generation

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    ./exportseqreport.html
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    ./fileformats.html
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    ./tcoffeescores.html
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