PHPC-1497 for 1.7.0 introduced --with-system-libs but never deprecated the original configure flags for libbson and libmongoc. Since we plan to removed these in 2.0, we should add a comment that they are deprecated.

To future-proof these switches, the new -with-system-libs (default no) will take precedence over the old with-libbson and -with-libmongoc switches. These can be removed in a 2.0 release.

The deprecation was mentioned in the manual build instructions, but it'd be reasonable to completely remove any reference to the old options there since --with-system-libs has been available for a considerable amount of time.