The patch utility typically prompts for a path if you're not in the directly relative to the file that needs to be patched.
I'm not sure what you mean by a "patch manager", something FreeBSD wrapped around an already simple task no doubt.
Are you sure you have the source code for mesa on your system? that is a prerequisite for patching.. you also need to build the source after doing that as well.
Have you considered upgrading FreeBSD? the inclusion of that change is likely in a later release.
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