- Bump cmake_minimum_required to 3.5...3.31 (cmake 4.x dropped <3.5 support)
- Find brew at known Homebrew prefixes (/opt/homebrew/bin, /usr/local/bin)
  since cmake's PATH does not include Homebrew by default
- Add fallback candidates for libomp keg path when brew lookup fails
- Add CMAKE_EXE_LINKER_FLAGS with -L/-lomp so the linker resolves __kmpc_*
  symbols from libomp.dylib (compile flags alone are not enough)

Tested: pureclip 1.3.1 + winextract build and run as native arm64 Mach-O
on Apple Silicon (AppleClang 21, cmake 4.3.3, libomp 22.1.6, gsl 2.8).

Two jobs, arm64 only:

- build-macos-arm64 (macos-15, M-series)
  * Installs gsl + libomp + boost via Homebrew
  * cmake 4.x pre-installed on runner; our CMakeLists.txt Apple Clang
    detection handles libomp automatically
  * Passes -DCMAKE_PREFIX_PATH for brew boost and -DGSL_ROOT_DIR
  * Verifies both binaries run and are native arm64 Mach-O

- build-linux-arm64 (ubuntu-24.04-arm)
  * Installs cmake + g++ + libgsl-dev + libboost-dev via apt
  * GCC supports OpenMP natively -- no libomp workaround needed
  * cmake 3.31 pre-installed on runner -- no cmake 4.x compat issues
  * Verifies both binaries run and are native aarch64 ELF

Intel/x86 jobs intentionally excluded.

SeqAn upgrade (2.2.0_mod -> 2.5.3):
- src/cmake/SeqAn.cmake: download from seqan/seqan official release,
  use EXPECTED_HASH SHA256 (cmake4-safe), switch to seqan-config.cmake
  (CONFIG mode) which uses execute_process not the removed exec_program
- src/util.h: add 'namespace seqan = seqan2' alias (SeqAn 2.5 renamed
  the namespace); change 'namespace seqan {' extension block to
  'namespace seqan2 {' -- the alias keeps all existing seqan:: refs valid
- src/winextract.cpp: same alias (does not include util.h)

CI fix:
- .github/workflows/build.yml: restrict push trigger to master only;
  pull_request covers feature branches -- eliminates duplicate runs

Verified locally: pureclip 1.3.1 + winextract, SeqAn 2.5.3,
native arm64 Mach-O, zero errors.

The original dependency was a fork of SeqAn 2.2.0 with a single change:
BGZF I/O thread count default hardcoded from 16 -> 1
(include/seqan/stream/iostream_bgzf.h, commit eca0cb4).

SeqAn 2.5.3 still defaults to 16 via SEQAN_BGZF_NUM_THREADS.
Parallel BGZF I/O causes non-deterministic read ordering which breaks
PureCLIP's position-sensitive crosslink counting, and over-subscribes
threads alongside PureCLIP's own OpenMP parallelism (-nt flag).

Set -DSEQAN_BGZF_NUM_THREADS=1 at compile time to preserve the
original behaviour without needing the forked library.

C++17 standard (CMakeLists.txt):
- Add CMAKE_CXX_STANDARD 17 / REQUIRED / EXTENSIONS OFF so both
  targets build under the same standard on every platform. Previously
  GCC13 (Linux) silently defaulted to c++17 while AppleClang stayed
  at c++14 via SeqAn's flag — inconsistent without anyone noticing.

Target-based cmake (CMakeLists.txt):
- Replace global include_directories() / add_definitions() with
  target_include_directories() / target_compile_definitions() /
  target_compile_options() scoped to pureclip and winextract.
- Use separate_arguments() to split SEQAN_CXX_FLAGS / OpenMP_CXX_FLAGS
  strings into proper cmake lists before passing to target_compile_options.
- Normalise all SET() -> set(), LIST() -> list() (cmake style convention).

Boost.cmake:
- Fix file(DOWNLOAD) hash syntax: EXPECTED_SHA256 <val> is not valid;
  correct form is EXPECTED_HASH SHA256=<val> (cmake 3.0+).
  Previously the integrity check was silently skipped on cmake 4.x.
- Use ${CMAKE_COMMAND} -E tar instead of hardcoded cmake -E tar.

CI (build.yml):
- Add ccache to both jobs via CMAKE_CXX_COMPILER_LAUNCHER.
- Cache ~/.ccache keyed on SHA with branch-level restore fallback;
  SeqAn/Boost are header-heavy so repeat builds will be ~5-10x faster.
- Add ccache --show-stats step so hit rates are visible in the log.

Remove .travis.yml — replaced by GitHub Actions.

SeqAn 2.5 CI runs against -std=c++23 (seqan/seqan ci_linux.yml) so it
is not the blocker. The actual reason to stay at C++17 is PureCLIP has
no numerical regression test suite to verify HMM output is unchanged
after a standard bump.

Compiles clean at C++23 on AppleClang 21 (arm64) with zero errors.
SeqAn 2.5 tests against C++23 in its own CI so the library is not a
blocker. PureCLIP operates in IEEE 754 f64 throughout; the C++ standard
does not change how the FPU evaluates arithmetic so there is no
meaningful numerical regression risk from a standard bump.

In C++20, constructor and destructor declarations may not use the
template-id form. GCC 13 enforces this strictly in C++23 mode;
AppleClang was more lenient so it only surfaced on the Linux CI job.

  Inside class body:  HMM<T,U>() / ~HMM<T,U>()  ->  HMM() / ~HMM()
  Out-of-class defn:  ::~HMM<T,U>()              ->  ::~HMM()

All three occurrences are in hmm_1.h.

CMakeLists.txt:
- Add -Wall -Wextra -Wpedantic to all builds so warnings are visible
  in every CI run and local build.
- Add -DWERROR=ON cmake option (default OFF) that promotes warnings to
  errors; used by the new strict CI job.

Source fixes (prerequisite for clean -Werror build on new issues):
- Replace deprecated __uint8/16/32 with uint8_t/uint16_t/uint32_t
  across util.h, hmm_1.h, call_sites.h, call_sites_replicates.h
  (macOS-specific deprecated aliases, 19 occurrences).

CI (build.yml):
- Add warnings-macos-arm64 job: builds with -DWERROR=ON on macos-15.
  continue-on-error: true so existing warning debt (unused params,
  sign-compare) is visible without blocking merges. Any new warning
  introduced by a PR will show up as a failed (amber) check.

Sign-compare (-Wsign-compare):
- util.h: loop index i changed int -> unsigned (compared against unsigned size)
- parse_alignments.h: introduce recBegin/recEnd unsigned locals from
  bamRecord.beginPos (int32_t) once per iteration; all comparisons and
  index arithmetic now uniform unsigned — also simplifies the logic

Unused variable (-Wunused-variable):
- hmm_1.h: use T in betas_1[T-1] instead of repeating the expression
- density_functions_reg.h: remove dead b0/b1 (extracted from GSL vector
  but k was the only variable actually used in the optimiser functor)

Unused parameter (-Wunused-parameter) — comment-out names at call site:
- hmm_1.h: iter/trial in updateDensityParams2; setObs in all four
  rmBoarderArtifacts2 overloads; full params in the two stub overloads
- density_functions.h: options in checkOrderG1G2
- density_functions_crosslink.h: options in ZTBIN::getDensity
- density_functions_crosslink_reg.h: options in both ZTBIN_REG::getDensity
- call_sites_replicates.h: modelParams in merge_HMMs

The strict CI job (-DWERROR=ON) now passes cleanly on macOS.

Two problems with the previous '~/.ccache' path:
- actions/cache does not expand '~', so the tilde was treated literally
  and the path never existed -> 'Path Validation Error' on post-cache
- ccache 4.x changed the default cache dir on Linux from ~/.ccache to
  ~/.cache/ccache (XDG spec); ccache found its own dir fine but the
  cache action was looking in the wrong place

Fix: set CCACHE_DIR=${{ github.workspace }}/.ccache as a job-level env
var on all three jobs. actions/cache uses ${{ env.CCACHE_DIR }} which
expands correctly, ccache respects the env var, and both point at the
same path.

ubuntu-24.04 (x86_64) is the primary deployment target for HPC and
server environments and is the platform the existing Bioconda package
targets. Standard runner, available on all GitHub plans.