[Soot-list] Bug when -oaat is used with -outjar

[Saswat Anand]

When -oaat and -outjar are used together, the output jar file remains empty.

That is because, even with -oaat flag, PackManager:writeOutput is called
from soot.Main at line 199. I dont think there is no need for that call
because with -oaat flag, the classes have already been output at that point.

The fix is to move that call to writeOutput from Soot.Main to inside the
else branch in PackManager.runPacks() method.

Saswat
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