Bootstrap Rminibwa as a GPL (>= 2) R package wrapping pinned upstream lh3/minibwa C sources.
Add native bindings for index build/load, raw-vector query mapping, native external-pointer alignment batches, ALTREP column views, and packed CIGAR accessors.
Install inst/include/Rminibwa.h and register C-callable accessors so downstream packages can consume alignment batches directly from C.
Add staged KSW SIMD dispatch following the RsimdDispatch pattern: portable scalar/SIMDe fallback, SSE4, and AVX2 backends are compiled as separate objects and selected at runtime without global ISA compiler flags.
Add AVX2 dual-gap extd2 support from the minibwa binding work and keep it as an optional runtime-dispatched backend.
Vendor minibwa at commit f0fd108456d459e5da3755f29c8700dc7f6fe0df with a patch queue and provenance metadata.
Add Rtinycc inline downstream-C examples in the README, vignette, and tests.
Build and install a package-provided minibwa executable from vendored sources; CLI wrappers now use it by default.
Add developer-only benchmarks comparing internal staged backends and optional external Python/Rust bindings from an explicit local checkout.
Add make asm / tools/check-assembly.R to audit generated SIMD instruction families in staged objects and shared libraries.
Add pkgdown configuration and GitHub Actions workflows for standard R CMD check, Fedora/R-devel CRAN-style check, and GitHub Pages deployment.