Improve the dependencies of the Maven modules

[egonw]

Goals:

• no circular dependencies
• modularize the dependencies on 3rd party libraries (so users can select which dependencies the need more easily)
• minimize the dependencies on 3rd party libraries
• Java Package match 1-to-1 to Maven modules (better for OSGi)

[egonw]

PRs:

• Removed a module that has been empty for a few years cdk#1087

[egonw]

Work on the valency module, but needs cleaning up: cdk/cdk#1086

[egonw]

This was discussed at the CDK UGM. Goal is a reorganization of this, also supporting OSGi compatibility, and making a new "core" module that supports 80% of the cheminformatics users (similarity search, substructure, basic I/O, etc). This also allows creation of a smaller CDK-JavaScript with the core functionality (in the browser).

[egonw]

We also discussed removing the dependency on the underlying library for coordinates, to be replaced by simple classes by our own, possibly preparing for a new Java feature of records.

[johnmay]

So my thoughts were:

1. replace Point2d/Point3d (I have started playing with this)
2. we merge effectively everything in cdk=base except cdk-reaction (and maybe cdk-dict). (step 1)
3. I rewrite the SMILES to not use beam and bring that in cdk-smiles
4. Bring in cdk-smarts (not the substructure testing is already in there0
5. cdk-fingerprints as well but many of these are already in core
6. cdk-sdg
7. Merge the cdk-qsar stuff into one module (cdk-descriptor?)
8. If we can them lite weight, cdk-ctab (for MOLfile)s and cdk-cml (so we can have a "toolkit format")