wiki: fix median contamination statistics
wiki: update COMEBin benchmarks (all 9 HQ bins) + fix image format
benchmarks: COMEBin best 3 runs (8.3 HQ mean, range 8-9)
benchmarks: HQ-only tables, trim COMEBin to top 3, remove deconvolution and dataset sections
benchmarks: add SemiBin2, remove DAS Tool; add per-bin table for SemiBin2
benchmarks: simplify comparison table to winning AMBER config only
benchmarks: update COMEBin to 9/8/8 (top 3 of 5 single-BAM reruns, mean 8.3)
docs: add COMEBin benchmark results, remove chimera subcommand
production-ready repo: README, wiki, cmake refactor, CPU build path
- CMakeLists.txt: rename target amber_gpu→amber, AMBER_USE_TORCH default OFF,
split CORE vs TORCH sources, git version detection, install target, CTest
- cmake/version.h.in: git-based version header
- include/amber/config.hpp: VERSION from generated version.h
- src/bin2/encoder/damage_aware_infonce.h: move DamageProfile/DamageAccumulator
outside #ifdef USE_LIBTORCH (pure C++ structs, no LibTorch dependency)
- src/cli/cmd_bin_stub.cpp: amber bin error with CPU/GPU build instructions
- src/algorithms/damage_extraction_stub.cpp: amber damage stub when TORCH=OFF
- README.md: comprehensive with math overview, install paths, benchmarks, citation
- wiki/: Home, Methods-and-Model, aDNA-Features, Command-Reference,
Output-Formats, Quick-Start-Tutorial, Benchmarks, _Sidebar
- .github/workflows/ci.yml + release.yml: CI and tag-triggered releases
- conda_recipe/meta.yaml: Bioconda recipe skeleton
- environment.yml: dev environment
- .gitignore: fix 'amber' → '/amber' (was excluding include/amber/ directory)
- polish.cpp, strain_deconvolution.h: --write-modern-bam + deconv stats
- Snakefile: assemble_s17_modern rule, deconvolve modern_bam output