I'm somewhat at a loss about how to actually use a long-running Session in practice.

The problem is with Exceptions: I have no idea how to deal with them without compromising the application's modularity.
The normal approach would be: rollback, close Session, create a new Session.
Trouble is: Any module in the application might have now-detached objects lying around. They need to be reattached, usually through a merge() in a newly opened Session.

But how do I find out which POJOs are actually entities and need to get merged?

Approach 1: For each object that needs to be merged, have a piece of code that does that.
Approach 2: Subclass Session and keep a list of all managed entities.
Approach 3: Use an Interceptor and keep a list of all managed entities.
Approach 4: Cast Session to SessionImpl and dig through the data structures until you find the first-level object cache. That's the entities that need to be reattached.

None of the above approaches are satisfactory.
#1 is inherently unmodular. It's also error-prone since programmers tend to neglect/overlook the exceptional case (I know I do, particularly under deadline pressure).
#2 is hard to get right. For example, delete() makes an entity detached, but after rollback, it should be merged anyway because the record has reappeared in the database; the next complication is cascading persists and deletes. Also, duplicating work that Hibernate already does for its internal object cache is disgusting.
#3 has essentially the same problems as #2.
#4 avoids duplication of work and would probably be easier to get right, but it's prone to breakage as Hibernate evolves.

Does this mean that long-running sessions are a hopeless case?
Or did I overlook an approach?

*bump*

Sorry, but I need to know...

Okay, seeing that I haven't gotten an answer in almost a month now, I guess that there is either no answer, or nobody knowledgeable is willing to answer on that (which is almost as bad).

I do hope somebody does have a good answer.
This is my last attempt at getting a useful answer out of this. I have already spent two years of my professional life, constantly under the impression that I'm fighting an uphill battle against the tool.
I feel myself forced to the conclusion that Hibernate's design around sessions is fundamentally broken by design. Please prove me wrong.