Clean the patches to InnoDB for submission upstream

We've patched InnoDB already in several places. Some of them were for build warnings. Some have been for name or path changes. In one place already we actually introduced a wrapper struct. Some of these changes can be submitted as it (with a formatting change or two I'm sure) Others will likely need ifdefs of some sort, or reworking so that they might live in the InnoDB tree and work with both Drizzle and MySQL.