Major overhaul: C++ backend, R6 architecture, 9 immune modules, pkgdown site

[ncborcherding]

• C++ backend via RcppArmadillo: BLAS-optimized bulk affinity/distance matrices, clonal selection, network suppression, SHM (5 methods), idiotypic dynamics, kmeans++ initialization, and gradient refinement, replacing per-element R loops
• R6 class architecture with composable module injection (AINet, ImmuneRepertoire, ImmuneAlgorithm) alongside the existing functional API (bHIVE(), honeycombHIVE(), swarmbHIVE())
• 9 new biologically-inspired modules: SHMEngine (5 mutation strategies including adaptive/Adam), IdiotypicNetwork (Ab-Ab dynamics replacing epsilon suppression), GerminalCenter (Tfh selection), Microenvironment (density-dependent zones), VDJLibrary (combinatorial initialization), ActivationGate (two-signal filtering), MemoryPool, ClassSwitcher, ConvergentSelector
• Full documentation refresh: rewritten README, 3 new pkgdown articles (immune modules, advanced workflows, algorithm foundations), GitHub Actions pkgdown deployment
• BiocCheck compliance: vapply/seq_len throughout, R6 roxygen fixes, removed LazyData, updated R version and biocViews, vignettes restructured for BiocStyle + pkgdown dual rendering