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It seems to me that the ideal would be to have symbols that get defined in multiple libraries be listed in a Versions file only once in one place. That is, one library would be the "ABI definer" (let's say libc is) and other libraries overriding those symbols would be bound by the same version crapola as the ABI definer. Off hand, I think the simplest way to do this would be to just throw all the symbols into a single version script without regard to library and essentially use the one version script for all libraries. That should work because excess symbols in a version script file are just ignored by ld -shared. However, it is probably fraught with subtle perils. Another approach would be more magic crunching to apply the version-reassigned symbols from one map to all the others.
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