Delete 29 more orphan files across 10 packages

Removed files with zero external references:
- 4 signature orphans (FixedLabeller, SignatureMatcher, etc.)
- 4 labelling orphans (InChiMoleculeLabeller, SmilesReactionCanoniser, etc.)
- 3 fingerprint orphans (MolFingerprint, IQueryTool, ISPFingerprinter, FingerprintSubset)
- 3 tool orphans (CreateDirectory, LayoutCheck, RXNFileManipulator)
- 2 container orphans (InChIContainer, ReactionDBContainer)
- 2 descriptor orphans (LipinskiRuleOfFive, CXlogP)
- 2 interface orphans (IDataSource, IReactionBuilder)
- 2 utility orphans (EBIArrayList, EBIBitSet, SortMap)
- Plus MDLFileReader, GlobalEntropyCalculator, ReactionFileData

345 → 162 Java files (53% reduction). All 135 tests pass.

Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>

Author: asad