It's not intended that the functionality they provided be lost in any way. We are just cleaning up the core distribution and hopefully pushing along some development on these modules. HEAD is very unstable at the moment and does not reflect what 2.0 will look like (remember it's at least 8 months away).
Note also that NO data has been (or will be) deleted - all the tables and data for those modules will still be there in upgraded sites even if the code is missing. Adding the code from contrib to your installation will Just Work (tm). We're planning to have notices come up during the upgrade to explain the situation in case anyone gets caught out.
So please don't panic.
More details:
Journal module - works OK and has been maintained with the bare minimum of upgrades, but has been disabled by default since Moodle 1.5 (when all Journals were converted to Online Assignments). If anyone wants to help add an "overview" to Online Assignment (which was the only feature that Journal had that OA doesn't) or to maintain Journal in contrib, please put up your hand! Discussion in Journal forum
Exercise module - was a mistake to be in core in the first place. It was NEVER actually included in core package distributions (it was only in CVS). The idea was good but Ray disappeared soon afterward it got checked in and it was never really maintained. Discussion in Exercise forum
Workshop module - has a lot of fans but it also has a lot of users who can not make any sense of the interface, as well as a lot of programmers who tremble when they look at the spaghetti code. It needs a total overhaul and replacement. The idea was to replace both this and Exercise with one module that can do all peer-evaluated assignments. The best candidate for this is Peerlight, currently, which we'll be looking into more deeply soon. If someone wants to maintain Workshop independently in contrib please put up your hand! Discussion in Workshop forum
LAMS module - was maintained by the LAMS guys but they've dropped support for it. I don't think very many people were using this module at all and it just confuses people. It currently only supports LAMS 1 (and the world seems to be using LAMS 2 now). Again, if someone wants to maintain this in contrib, let's hear from you!