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I think you can go for JDBC Realm...or you can find a way to add data in web.xml file progarmatically when the registration is successful..
It seems very odd to be that application users are defined at the app-server levelThey're not. Their roles are defined. Typically the users and their roles are defined via an LDAP server. The only thing the app server has to know about is the roles.
As per your comment you want to use J2EE/JAAS security for existing user and want sign in feature. You can do it by providing link on log in screen. Please create sign up page and unprotected resource in web.xml. Once user fill sign in details you can store his detail in your authorization repository ( LDAP / Database ) and then either redirect request to login page or submit to your authorization scheme directly.
Current Java EE specification does provide a standard way of manager user/group. For user/group management there are several options.
1. SPML clients.
2. OID/AD/LDAP/ or other LDAP proprietary APIs
3. OPSS's IGF API
4. An IDM Provisioning system (e,g. OIM)