You can encrypt them back into an installable format(*.app, *.h3 files) using nuspacker http://gbatemp.net/threads/nuspacker-pack-files-into-installable-packages.447689/
You will need to be in CFW to launch anything installed using this method since it won't be signed. Not sure if this is what you are looking for but hopefully it helps.
Similar threads
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FlareReZ:
@JuanMena, Thanks for the info on this dude. I could tell that there was definitely something wrong with him at first, but I hope he can change his ways. -
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FlareReZ:
@Xdqwerty65, That's quite harsh to say, not 'dead' but away so to speak. He's currently dealing with his mental health state.
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FlareReZ:
I hope he can come back with a positive note, because last time he was here, used to go on about his ongoing situation with Chary.
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FlareReZ:
Would just constantly make these threads until the mods locked them, before he got banned.
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