I'd need to get the passwords either in md5 hash or in clear.
Storing the password in plain text or as an md5 hash is a security risk. It is very easy to find a password collision (a password with the same hash) once you got its hash.
I checked out the manual [1], password aren't stored as simple MD5 hash, an additional string is added. Is there a way I can convert them into regular hash of the password?
No, that's called security that not everyone who has access to the database can see the user passwords. Therefore a salt is added. If you don't know the password there shouldn't be any ways to get it.