GH-2710 module structure reorganization

[abrokenjester]

GitHub issue resolved: #2710

Briefly describe the changes proposed in this PR:

• rdf4j-util split into several smaller 'common' modules to allow smaller footprint of individual dependencies and easier modular boundaries
• removed some obsolete code (OpenRDFException, OpenRDFUtil) and migrated some other classes to different packages (RDF4JException, IsolationLevel)
• added upgrade pointers to release notes

This is quite a large refactor, but it gives us greater flexibility, cleans up a few old things, and sets us up to make followups like #1494 (each package in a single module) easier to achieve.

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[abrokenjester]

Looks like our use of multithreading for the maven build does not agree with the new modular structure. Verified locally that a single-threaded build succeeds. Possibly caused by my relying on transitive dependencies for including libraries like commons-annotations in some places (via rdf4j-model). I'll see if more explicit dependencies can fix this, otherwise may temporarily disable multithreaded builds in our Github actions.

[abrokenjester]

• update BOM and rdf4j-client pom
• verify rdf4j-util is no longer referenced

[hmottestad]

It's a bit big for me to review.

Does this affect any of the ShaclSail code in any way?

Could you confirm that this builds with the following method?

1. mvn clean
2. Delete the org/eclipse/rdf4j folder within your .m2 folder (so that you don't have any cached versions of RDF4J)
3. Disconnect from the internet
4. mvn install -DskipTests

[barthanssens]

Good idea to move IsolationLevel and RDF4JException to common

[barthanssens]

Perhaps the method could be removed altogether, instead of just being deprecated ?

[abrokenjester]

It probably could, but I didn't want to make that decision in this PR.

[abrokenjester]

It's a bit big for me to review.

Yeah, I'd be happy with just checking out the branch and giving it a quick smoke test, eyeballing a few specific changes. I'd like this merged in soon so that we can shake out any problems as we go.

Does this affect any of the ShaclSail code in any way?

A little. There's some refactoring with the exception classes.

Could you confirm that this builds with the following method?

1. mvn clean

2. Delete the org/eclipse/rdf4j folder within your .m2 folder (so that you don't have any cached versions of RDF4J)

3. Disconnect from the internet

4. mvn install -DskipTests

I just ran that (except I used mvn -o rather than physically disconnecting), and it fails, but funnily enough not because of this refactor, but because it can't find the serql parser (obviously have a few dangling dependencies somewhere).

I'll fix those in a separate PR, then rebase this one and try again.

[abrokenjester]

Ran the offline build test again with the dependency fixes merged in, all green.

[abrokenjester]

Unless there are major objections I'll merge this tomorrow morning - I'd like to get this in as soon as possible to minimize the risk of merge conflicts. Of course, I'll be on hand to help out on any other PRs that get conflicts because of this.