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Project files structure refers to Flash builder, for example, all source files are under one folder such as folder src. Binary file is under another directory such as Debug.
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lua needs be installed because this program is writteny by lua. Of course you can port it in other language.
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Decompress binary file before doing proguard
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lua proguard.lua -i INPUTDIR -b INPUTBIN -o OUTNAME -n WORDLEN
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Compress OUTNAME into new binary output
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Check if new binary works or not (YOUR new binary may NOT work, considering you replace something which should NOT be replaced!). If it doesn't work, goto step 2 and change input paramters