Refactor commonly-used classes to importable modules (issue #1018)

Move classes from command files to dedicated modules for cleaner imports:

- ReadIdStore, CoordMapper, CoordMapper2Seqs, CoordMapperError -> core/misc.py
- TaxonomyDb, TaxIdError, and helper functions -> classify/taxonomy.py (new)
- IlluminaDirectory, RunInfo, SampleSheet, SampleSheetError -> core/illumina_utils.py (new)

Original files re-export classes via top-level imports for backwards compatibility.
Also fixes QCError import path in taxon_filter.py.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: dpark01

src/viral_ngs/classify/__init__.py

@@ -8,3 +8,4 @@
 from . import kraken2
 from . import krona
 from . import last
+from . import taxonomy