Homebrew-installed Clang fails to find headers on Mac OS X - c

Question

So, for no apparent reason (I haven't installed a new version of clang, or changed any compiler configuration), clang suddenly can't find assert.h on my Mac.
In my development VM, running Ubuntu, both gcc and clang compile the project fine; on the host Mac OS X, gcc still compiles it fine, but clang spits out the following:
> make
clang -g -O0 -Wall -Wextra -pedantic -Wshadow -Wstrict-overflow -Wno-missing-field-initializers -std=c99 -m64 -Wno-unused-variable -Wno-unused-parameter -o csim csim.c cachelab.c -lm
csim.c:1:10: fatal error: 'assert.h' file not found
#include <assert.h>
^
1 error generated.
cachelab.c:5:10: fatal error: 'assert.h' file not found
#include <assert.h>
^
1 error generated.
make: *** [csim] Error 1
Here's some further relevant information:
> xcode-select --print-path
/Applications/Xcode-beta.app/Contents/Developer
> gcc -g -O0 -Wall -Wextra -pedantic -Wshadow -Wstrict-overflow -Wno-missing-field-initializers -std=c99 -m64 -Wno-unused-variable -Wno-unused-parameter -o csim csim.c cachelab.c -lm
> clang -std=c99 -o csim csim.c -v
clang version 3.8.1 (tags/RELEASE_381/final)
Target: x86_64-apple-darwin16.0.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
"/usr/local/Cellar/llvm/3.8.1/bin/clang-3.8" -cc1 -triple x86_64-apple-macosx10.12.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name csim.c -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 273 -v -dwarf-column-info -debugger-tuning=lldb -resource-dir /usr/local/Cellar/llvm/3.8.1/bin/../lib/clang/3.8.1 -std=c99 -fdebug-compilation-dir /Users/ec/Dropbox/Documents/Homework/CS351/mps/04 -ferror-limit 19 -fmessage-length 211 -stack-protector 1 -fblocks -fobjc-runtime=macosx-10.12.0 -fencode-extended-block-signature -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -o /var/folders/xt/wm01x2h50nv993t_csb1t5qm0000gn/T/csim-9590db.o -x c csim.c
clang -cc1 version 3.8.1 based upon LLVM 3.8.1 default target x86_64-apple-darwin16.0.0
ignoring nonexistent directory "/usr/include"
#include "..." search starts here:
#include <...> search starts here:
/usr/local/include
/usr/local/Cellar/llvm/3.8.1/bin/../lib/clang/3.8.1/include
/System/Library/Frameworks (framework directory)
/Library/Frameworks (framework directory)
End of search list.
csim.c:1:10: fatal error: 'assert.h' file not found
#include <assert.h>
^
1 error generated.