Separated cdk-pdbcml from cdk-libiocml and created module suite for cdk-test-pdbcml.

Conflicts:
	src/main/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java
Moving tests for MDCustomizer from libiocml to the existing MDMoleculeTest.
Separating out cdk-extra from the cdk-io modules
Separated test-libiocml's dependance on test-qsar* by creating 'test-qsarcml' - this now tests the preexisting module 'qsarcml'
Mocking unit tests for 'cdk-diff'

Conflicts:
	src/META-INF/test-diff.devellibdepends
Removed 'cdk-data' from 'cdk-diff' dependencies requiring that two tests are ignored. Both of these tests were testing the serialisation of the domain object (e.g. data.Atom) opposed to the actual class under test.
Replacing MoleculeFactory with TestMoleculeFactory and removing dependence on 'cdk-extra'.
Removing unnecessary dependence on 'cdk-sdg'.
Move AbstractFingerprinterTest from 'cdk-test-standard' to 'cdk-test'
Removing structure diagram generation from SmilesParser test. This code was likely included for debugging.
Removing unused dependencies from smiles module tests.
Remove structure diagram generation from unit test. The test assets the chiral smiles are correctly created and are not different. It should depend on diagram generation.
Correcting reference comparisons in tests.
Inlining of hydrogen addition, to remove use of hydrogen placer.
Recoordinated coordinates and add hydrogens without hydrogen placer. The coordinates were changed as hydrogens were being adding with Double.NaN coordinates. This test still passes however the cis/trans ring configuration is not valid smiles, and incorrect. One can see that two down bonds (hatch) are written as 'trans' configuration. The reason is the previous code had an inverted bond (fat end of wedge/hatch pointing towards chiral centre). Due the numerous issues, the functionality will likely be removed in future.
Removing redundant hydrogen, these are not needed for the tests to be correct. Even without hydrogens the chiral smiles should be different and they are.
Removed 'test-smiles' dependence on 'sdg'.
Removing non-tests.
Removing 'cdk-formula' dependence on 'cdk-smiles' - required changing a single unit test. The test in questions was checking that when isotope information has not been configured the correct mass is returned (i.e. auto-configured).