Add top-level Makefile wrapper around CMake build

.gitignore

@@ -32,7 +32,7 @@ data/*
 CMakeCache.txt
 CMakeFiles/
 cmake_install.cmake
-Makefile
+build*/Makefile
 
 # OS-specific files
 .DS_Store

Makefile

@@ -0,0 +1,25 @@
+# Top-level make wrapper for projects/tooling that expect a Makefile in the
+# repository root. The actual build system is CMake; this just shells out to
+# cmake + make and flattens the resulting binaries into bin/ for consumers
+# that want a single output directory.
+#
+# Typical usage:
+#   make           # build all tools, flatten binaries into bin/
+#   make clean     # remove build/ and bin/
+#
+# This wrapper coexists with compile_wasm.sh and the CMake/Bioconda/Docker
+# flows; none of them depend on this Makefile.
+
+BUILD_DIR := build
+OUT_DIR   := bin
+CMAKE     ?= cmake
+
+all:
+	mkdir -p $(BUILD_DIR) $(OUT_DIR)
+	cd $(BUILD_DIR) && $(CMAKE) -DPYTHON_BINDINGS=OFF .. && $(MAKE)
+	find $(BUILD_DIR)/src -maxdepth 2 -type f -perm -u+x ! -path "*/CMakeFiles/*" -exec cp {} $(OUT_DIR)/ \;
+
+clean:
+	rm -rf $(BUILD_DIR) $(OUT_DIR)
+
+.PHONY: all clean