FiberHMM 2.16.3 — README overhaul + docs/reference.md

• README overhaul: rewrote ~1016 → ~456 lines (table of contents, lean Quick start, a single "Choosing a command" table, a Workflows section with all DddA guidance consolidated, one flags-table per tool).
• New docs/reference.md: MA/AQ tag schema, the LLR scoring model, tq/el/er encoding, output modes, circular molecules, and the tag glossary.
• Doc fixes: DddA nucleosome recall is ON by default (was self-contradictory); fiberhmm-apply --msp-min-size default 0 and --min-mapq default 0 (docs were wrong); dropped deprecated --bigbed/--footprint from examples.