To add internal customers to JIRA Service Desk 2, is there anyway to do this on mass through LDAP or other authentication method that uses their existing organisational accounts as I don't want to have to get internal users to sign up to use the service desk.
As Timothy mentioned you can use REST to add each customer to your Service Desk. If you have an LDAP server, you can also use JIRA's LDAP integration to add these users to the system (https://confluence.atlassian.com/display/JIRA/Configuring+User+Directories).
However, at this point in time, there is not a way to make these users agents in an automated manner.
My apologies, unfortunately LDAP integration is only available on the Server version of JIRA, not on On Demand (https://confluence.atlassian.com/display/AOD/Restricted+Functions+in+Atlassian+OnDemand). I did find this page which details other options for importing users onto On Demand (https://confluence.atlassian.com/display/AOD/Importing+Users).
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