Elytron will replace most of the functionalities currently provided by PicketBox. However, the JAAS integration is being preserved for a while at and won't be removed right off the bat. The plan is to have a realm that will be compatible with the PicketBox login modules but on the long run this realm will probably be deprecated in favor of other realms, which should give developers time to get used to Elytron and to migrate their apps to the new realms.
This is an ongoing work, so the details are still getting sorted out but you can surely expect extensive documentation on Elytron and on the PicketBox features (aka JAAS) that will be supported in Elytron. We already have some pieces in place and as the integration progresses we will be publishing blog posts, articles, etc, with preliminary information on how to migrate to Elytron while still using JAAS. We understand this is a feature that affects many current users so the sooner we can start giving information out the better.