[richard-burhans]

Two make/shell variable bugs in build_c, the same class as #46 — an expression that looks like shell but is resolved (or not resolved) by make.

1. The arm64 branch is unreachable

if [ ARCH = "arm64" ]; then \
	CFLAGS="... -arch arm64"; \

ARCH here is a bare word, not $(ARCH) or $$ARCH, so [ compares the literal string ARCH against arm64. That is always false, the else branch always runs, and -arch arm64 is never passed — including on Apple Silicon, where ARCH=$(shell uname -m) really does evaluate to arm64.

2. CFLAGS is empty for both shared libraries

CFLAGS is assigned in the first recipe line. The two gcc calls for chain_coords_converter_slib.so and chain_bst_lib.so are separate recipe lines, and make runs each recipe line in its own shell, so $$CFLAGS is unset there. Both shared libraries are compiled with no -O2, no -std=c99, no warnings — silently, since gcc is happy to compile without them.

Only chain_filter_by_id gets the flags, because it is on the same continued line as the assignment.

Measured

With a stub gcc that echoes its arguments:

# before — identical for ARCH=x86_64 and ARCH=arm64
GCC-ARGS: -Wall -Wextra -O2 -g -std=c99 -o bin/chain_filter_by_id src/c/chain_filter_by_id.c
GCC-ARGS: -fPIC -shared -o src/python/modules/chain_coords_converter_slib.so ...
GCC-ARGS: -fPIC -shared -o src/python/modules/chain_bst_lib.so ...

# after, ARCH=arm64
GCC-ARGS: -Wall -Wextra -O2 -g -std=c99 -arch arm64 -o bin/chain_filter_by_id ...
GCC-ARGS: -Wall -Wextra -O2 -g -std=c99 -arch arm64 -fPIC -shared -o .../chain_coords_converter_slib.so ...
GCC-ARGS: -Wall -Wextra -O2 -g -std=c99 -arch arm64 -fPIC -shared -o .../chain_bst_lib.so ...

The fix

Hoist the flags into a make variable with an ifeq on $(ARCH). That fixes both problems at once and removes the shell conditional entirely. The variable is named TOGA_CFLAGS rather than CFLAGS so it is not exported into the CESAR2.0 sub-make, which has its own build.

make build_c compiles cleanly and produces all three artifacts.