Refactor pipeline processing into focused submodules

Split the 678-line src/pipeline/processing.rs into a processing/ directory:
inputs (parse_inputs + input-format resolution) and read_support (per-gene
SNP/MNV cache counting, exact indel counting, supported phased-indel haplotype
emission). The facade keeps the worker state types, the per-contig
orchestration (process_contig), and output emission.

Pure code move with no behaviour change. The worker structs stay in the facade
and the submodules access them by descendant privilege; functions called from
the facade are scoped pub(super). The crate-internal API used by the pipeline
(parse_inputs, resolve_variant_input_format, process_contig, emit_contig_variants,
reclassify_generic_as_validation) is re-exported / unchanged.

All tests (247 lib + 36 integration + 9 doc), clippy -D warnings, and the
36-scenario suite pass unchanged.

Author: Paururo