Fix fd table behaviours

[AsakuraMizu]

Temporarily using my own fork of flatten_objects, blocked by upstream: arceos-org/flatten_objects#2
The upstream has merged the PR but not yet released

Some functions using fd_table.count() have incorrect behaviours: they assume count to be maximum file descriptor.

To fix it, I have added an ids method on upstream FlattenObjects to retrive all open file descriptors to make copy_inner work properly. The other two use cases are redundant since Directory::from_fd already checks the validity of the file descriptor.

[Azure-stars]

Ok, and after the flatten_object release, please remember to update the dependencies.