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As for SOPC: I have never used it, so I don't know which files I should pick...I'll just leave it open for now.
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All you really need is the .v file for the system, the .sopc file and the .ptf file. All of these will have the same prefix. For example if your system is named "my_sopc", you would need:
my_sopc.v
my_sopc.sopc (7.1 and later)
my_sopc.ptf (not required after 7.1 but recommended)
All other files can be generated from these files.
In addition, you would need to store the source files for any custom components and user libraries that the SOPC system depends on.
Jake