Everything works fine when I use the @Table annotation like this: @Table(name="`user`"). But when the user table is in the user schema and I try to use the annotion in this way: @Table(name="`user`.`user`") — everything falls apart.
A quick look into the code showed that it checks if the table name starts with `, and if it does, it sets the quoted parameter to true and removes the ` characters on the both sides. So, if I quote the both words like @Table(name="`user`.`user`"), the table name becomes "user`.`user" and it, of course, fails. If I quote it just like @Table(name="`user.user`"), the table name becomes "user.user", which fails too.
If Doctrine allows to escape the reserved words, it should take into account this kind of usage as well.