Symptoms 

The error "User already exists in directory" is thrown when you attempt to migrate users from JIRA Directory to a Delegated Directory.

The following error appears in the atlassian-jira.log:

2014-09-23 15:10:34,770 http-bio-8080-exec-14 ERROR admin 910x1748x1 lx1zni 0:0:0:0:0:0:0:1 /plugins/servlet/embedded-crowd/directories/migrate/ [embedded.admin.directory.MigrateDirectoryUsersController] User migration failed
java.lang.RuntimeException: com.atlassian.crowd.exception.UserAlreadyExistsException: User already exists in directory [10002] with name [jira1]

Causes

There is an existing user in the directory. If you check the error message below, jira1 user is exist in Directory ID = 10002.

User already exists in directory [10002] with name [jira1]

Diagnosis

If you would like to know which users are not migrated to the Directory, you can run the following SQL query and check the returned results:

select directory_id, lower_user_name, active from cwd_user where directory_id = '<directory_id>' AND lower_user_name not in (select lower_user_name from cwd_user where directory_id = '<destination>');

 Replace <directory_id> and <destination> accordingly.

Resolution

If the user does not exist in the directory, you can refer the following resolution steps:

1. Disable the current failing delegated ldap directory.
2. Create a new Internal With LDAP Authentication directory and leave the option Copy User on Login disabled for the moment. If needed you can go back and re-enable the copy option once this is complete.
3. Move the newly created directory to the top of the directory list.
4. Complete your migration.