I copied the whole mysql directory, manually. A practice i used for years, because mysqldump is very lunatic.
lunatic? what is wrong with it?
Copying the directory manually (with a running server) isn't something what people should do. Of course InnoDB may refuse to start, as you're having inconsistent snapshot.
After a system crash I recovered the old Wiki but not the new one. That is very bad, how could I be aware of this innodb things ?
Have you ever tried what happens when you shoot a bullet into your head? :) To some people that also turns out to be bad.