Added comparator package. This needs to be refactored at least for a better package name.
Added CDKMoleculeBuilder and HMTLTagResolver to temporary place. These classes should be inspected later to decide what to do with them.
Refactors comparator package in mdk-tool-compare
Adds google refine's Keyers for name comparisons.
Removes FingerprintKeyer and derived classes, moves classes using these to the FingerprintEncoder and related classes.
Adds additional comparators. Some of these should be replaced by using John's molecule hash coding classes.
Merge branch 'develop' into feature/chemet-db-deps
Adds Brenda parser and PseudoFingerprintChemicalNames
Moved Brenda parser.
Adds molecule connectivity service in lucene, according to the new MDK structure.
Adds connective component and largest connective component finder functionalities.
Adds ChEBI secondary to primary component resolver.
Adds io/text/sdf package with classes to deal at a txt level with cross-references in SDF files.
Adds connectivity search and service interfaces, as well as ChEBI and PubChem Compound Connectivity loaders at the apps level (apps service).
Merge branch 'develop' into feature/chemet-db-deps
Merge branch 'develop' into feature/chemet-db-deps
Merge branch 'develop' into feature/chemet-db-deps

Conflicts:
	service/lucene/src/main/java/uk/ac/ebi/mdk/service/index/other/MoleculeCollectionConnectivityIndex.java
	service/lucene/src/main/java/uk/ac/ebi/mdk/service/query/secondaryresolver/ChEBISecondaryToPrimaryIDQuery.java
	tool/compare/src/main/java/uk/ac/ebi/mdk/tool/comparator/AbstractLinkedComparator.java
	tool/compare/src/main/java/uk/ac/ebi/mdk/tool/comparator/AtomCountComparator.java
	tool/compare/src/main/java/uk/ac/ebi/mdk/tool/comparator/HeavyAtomCountComparator.java
	tool/compare/src/main/java/uk/ac/ebi/mdk/tool/comparator/HeavyAtomElementCountChecker.java
	tool/compare/src/main/java/uk/ac/ebi/mdk/tool/comparator/MetaboliteMassComparator.java
	tool/compare/src/main/java/uk/ac/ebi/mdk/tool/comparator/MetaboliteNameComparator.java
	tool/compare/src/main/java/uk/ac/ebi/mdk/tool/comparator/SimpleStereoUpDownBondCountChecker.java
	tool/compare/src/main/java/uk/ac/ebi/mdk/tool/molstandarization/ConnectiveComponents.java
	tool/domain/src/main/java/uk/ac/ebi/mdk/tool/domain/CDKMoleculeBuilder.java
Merge branch 'develop' into feature/chemet-db-deps
Merge branch 'develop' into feature/chemet-db-deps
Adds checkers GenericStructureParticipants and MissingStructureParticipants for MetabolicReactions