Personally I'd prefer installing the package's patterns to /usr/share/l7-protocols. Patterns installed from source could go to /usr/local/share/l7-protocols. Patterns created by the sysadmin could be stored in /etc/l7-protocols/patterns.d (or similar) and the package shouldn't store any symlinks there. That might require getting some patches upstream though. The loading order would be /usr/share /usr/local /etc so that the sysadmin dirs override the package.
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