From my understanding, you are allowed to decompile and inspect the released binaries, as well as intercept and analyze all inbound/outbound data, as long as you aren't modifying the running binary in any fashion. Things like debuggers are commonly used for this goal, as are tools like wireshark for analyzing the traffic. Once you create a specification based on your analysis, someone can create a clean-room implementation from that spec.
Yes it is, but thats where other solutions need to be met.... say a script that de-obfuscates a vanilla binary package so the output is created on the users machine vs being distributed as such. You can distribute the script and leave compliance to the end user.
Yes, copyright law is complicated. You need to make sure the script used to create a deobfuscated binary isn't a derived work from the original binary, whatever that means (that's where consulting with a lawyer can help).
Is a patch a derived work from the file it applies to ? It is impossible to produce the patch without using the original file, yet intuitively, I would say no.
