build: unify static/dynamic linking for conda/package manager compatibility

[KimYannn]

Summary

• Replace platform-specific linking logic (Linux -static vs macOS .a fallback) with a single unified approach
• If .a static archives exist in LIBRARY_DIRS, link statically (unchanged behavior)
• If only shared libs are available, fallback to -l dynamic linking (new)

Motivation

The current Linux Makefile uses -static which requires a static glibc. This breaks builds in package managers like conda/bioconda where only shared system libraries are available (see bioconda/bioconda-recipes#63664).

Behavior

Scenario	Before	After
User builds with .a libs installed	Static link	Static link (unchanged)
make LIBRARY_DIRS=/path/to/static/libs	Static link	Static link (unchanged)
conda/apt (shared libs only)	Fails (-static needs static glibc)	Dynamic link (works)
macOS with Homebrew	Static preferred, fallback dynamic	Same (unchanged)

Test plan

• Build on Linux with static libs installed (same as before)
• Build on macOS (same as before)
• Build in conda environment (now works without LD_FLAGS override)

🤖 Generated with Claude Code

[KimYannn]

@sfchen Hi, this PR is motivated by the bioconda packaging effort for fastp 1.2.0 (see bioconda/bioconda-recipes#63676 and #63664).

Problem

The current Makefile uses -static on Linux, which requires a static glibc — unavailable in conda and most package manager environments. This causes the bioconda build to fail.

What this PR does

1. Unify static/dynamic linking: on Linux, if all .a archives are found, the fully static binary is built as before. If some .a are missing (e.g. conda/apt where only shared libs exist), it gracefully falls back to linking .a where available + -l dynamic for the rest. macOS behavior is unchanged.

2. Auto-detect deps via pkg-config: the Makefile now queries pkg-config for libhwy, libisal, and libdeflate paths. When libraries are installed via conda, brew, or apt, their include/lib paths are picked up automatically — no need to pass INCLUDE_DIRS/LIBRARY_DIRS manually.

3. Remove bundled headers: src/igzip_lib.h and src/libdeflate.h are removed. All three libraries now use standard angle-bracket includes (<isa-l/igzip_lib.h>, <libdeflate.h>, <hwy/...>) resolved via pkg-config or -I flags.

Behavior matrix

Scenario	Before	After
User builds with static libs installed	Static binary ✅	Static binary ✅ (unchanged)
make LIBRARY_DIRS=/path/to/libs	Static binary ✅	Static binary ✅ (unchanged)
conda / apt (shared libs only)	Fails	Dynamic link ✅
macOS + Homebrew	Static preferred	Same (unchanged)
bioconda build.sh	Needs LD_FLAGS override	Just make

With this change, the bioconda recipe simplifies to:

c src/readpool.cpp -o obj/readpool.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/seprocessor.cpp -o obj/seprocessor.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/unittest.cpp -o obj/unittest.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/threadconfig.cpp -o obj/threadconfig.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/umiprocessor.cpp -o obj/umiprocessor.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/stats.cpp -o obj/stats.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/simd.cpp -o obj/simd.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/read.cpp -o obj/read.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/processor.cpp -o obj/processor.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/polyx.cpp -o obj/polyx.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/peprocessor.cpp -o obj/peprocessor.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/overlapanalysis.cpp -o obj/overlapanalysis.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/options.cpp -o obj/options.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/nucleotidetree.cpp -o obj/nucleotidetree.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/main.cpp -o obj/main.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/jsonreporter.cpp -o obj/jsonreporter.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/htmlreporter.cpp -o obj/htmlreporter.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/filterresult.cpp -o obj/filterresult.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/filter.cpp -o obj/filter.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/fastqreader.cpp -o obj/fastqreader.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/evaluator.cpp -o obj/evaluator.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/duplicate.cpp -o obj/duplicate.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/basecorrector.cpp -o obj/basecorrector.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/adaptertrimmer.cpp -o obj/adaptertrimmer.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/writer.cpp -o obj/writer.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
c src/writerthread.cpp -o obj/writerthread.o -std=c++11 -pthread -g -O3 -MD -MP -I. -I./inc -O3 -std=c++14
install fastp /bin/fastp

No vendored sources, no patches, no workarounds.