diff --git a/.dev/utils/DEBUGGING_FLAGS.patch b/.dev/utils/DEBUGGING_FLAGS.patch
deleted file mode 100644
index e02c6f5..0000000
--- a/.dev/utils/DEBUGGING_FLAGS.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-diff --git a/config/compiler.gfortran.mk b/config/compiler.gfortran.mk
-index 007a335..3fdf8e4 100644
---- a/config/compiler.gfortran.mk
-+++ b/config/compiler.gfortran.mk
-@@ -24,7 +24,7 @@ endif
- 
- FMAKEDEP = $(SCRIPTS_DIR)/sfmakedepend
- CPPFLAGS += -DCOMPILER_G95
--FFLAGS = -g -cpp -fconvert=big-endian -O2 -fno-range-check -fallow-argument-mismatch
-+FFLAGS = -g -cpp -fconvert=big-endian -O0 -Wall -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion -fbacktrace -fallow-argument-mismatch
- F90FLAGS = $(FFLAGS) -ffree-line-length-none
- LFLAGS =
- ifeq ($(MP),YES)
-diff --git a/config/compiler.intel.mk b/config/compiler.intel.mk
-index a73a4fe..68839af 100644
---- a/config/compiler.intel.mk
-+++ b/config/compiler.intel.mk
-@@ -4,9 +4,9 @@ IFORT_RELEASE := $(shell ifort --version | perl -e \
-   'while(<>){ if(/ifort.* (\d+\.\d+)/) { print "$$1"; } }')
- FMAKEDEP = $(SCRIPTS_DIR)/sfmakedepend
- CMP_MOD = $(SCRIPTS_DIR)/compare_module_file.pl -compiler INTEL-ifort-9-0-on-LINUX
--FFLAGS = -fpp -O2 -ftz -convert big_endian
-+FFLAGS = -fpp -O0 -warn all -check bounds -check uninit -check pointers -traceback -assume byterecl -ftz -convert big_endian
- F90FLAGS = $(FFLAGS) -free
--LFLAGS = -O2 -ftz
-+LFLAGS = -O0 -ftz
- CPPFLAGS += -DCOMPILER_Intel8 -DCONVERT_BIGENDIAN
- F90_VERSION = $(shell $(F90) --version 2>&1)
- ifeq ($(MP),YES)
-diff --git a/config/rules.mk b/config/rules.mk
-index d981c80..87ef4f2 100644
---- a/config/rules.mk
-+++ b/config/rules.mk
-@@ -62,7 +62,7 @@ I = I
- # by default assume that fortran compiler can do cpp
- EXTERNAL_CPP = NO
- # assume that C compiler understands basic gcc flags
--CFLAGS = -O2
-+CFLAGS = -O0
- # check if ABI was specified
- ifneq ($(ABI),)
-   CFLAGS += -m$(ABI)
-@@ -430,7 +430,7 @@ endif
- 	 $(CPP) $(CPPFLAGS) $< > $@
- 
- %.o: %.c
--	$(CC) -c -O2 -m64 $<
-+	$(CC) -c -O0 -Wall -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion -g -fbacktrace -fallow-argument-mismatch -m64 $<
- 
- %.f: %.m4f
- 	-rm -f $@
-diff --git a/decks/Makefile b/decks/Makefile
-index 4d2791a..c167dc6 100644
---- a/decks/Makefile
-+++ b/decks/Makefile
-@@ -140,7 +140,7 @@ ifeq ($(GC),YES)
- 		-DCMAKE_Fortran_COMPILER="$(F90)" \
- 		-DCMAKE_Fortran_FLAGS="$(F90FLAGS)" \
- 		-DCMAKE_EXE_LINKER_FLAGS="$(CTM_LFLAGS)"
--	cd $(GC_BUILD_DIR) && make -j install
-+	cd $(GC_BUILD_DIR) && make VERBOSE=1 -j install
- 	cp $(GC_BUILD_DIR)/mod/*.mod $(MODEL_DIR)/mod/
- 	cp $(GC_BUILD_DIR)/src/HEMCO/mod/*.mod $(MODEL_DIR)/mod/
- 	cp $(GC_BUILD_DIR)/src/Cloud-J/mod/*.mod $(MODEL_DIR)/mod/
-diff --git a/modele-control.pyar b/modele-control.pyar
-index cf10239..1d78b27 100644
---- a/modele-control.pyar
-+++ b/modele-control.pyar
-@@ -3447,7 +3447,7 @@ macro(modele_set_flags)
-     add_definitions(-DCOMPILER_G95)
-     # This breaks if you try to wrap the long line in the obvious way.
-     set (CMAKE_Fortran_FLAGS_RELEASE "${CPPFLAGS} -O2 -g -fconvert=big-endian -fno-range-check -ffree-line-length-none")
--    set (CMAKE_Fortran_FLAGS_DEBUG "${CPPFLAGS} -O -g -fbacktrace -fconvert=big-endian -fno-range-check -ffree-line-length-none -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion")
-+    set (CMAKE_Fortran_FLAGS_DEBUG "${CPPFLAGS} -O0 -g -fbacktrace -fconvert=big-endian -fno-range-check -ffree-line-length-none -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion")
- 
- 
-     if (CMAKE_BUILD_TYPE MATCHES Release)
diff --git a/.dev/utils/build.sh b/.dev/utils/build.sh
index fa095be..21b0bff 100755
--- a/.dev/utils/build.sh
+++ b/.dev/utils/build.sh
@@ -9,18 +9,20 @@ set -e
 FRESH=false
 OPENMP=false
 GISS_ONLY=false
+MECH=fullchem
 DEBUG=false
 
 # Function to display help text
 show_help() {
-  echo "Usage: $0 [MP=YES|NO] [--openmp] [--giss-only] [-f] [--debug]"
+  echo "Usage: $0 [MECH=fullchem|carbon|Hg|custom] [--openmp] [--giss-only] [-f] [--debug]"
   echo
   echo "Options:"
-  echo "  --help      Show this help message and exit."
-  echo "  --openmp    Compile with OpenMP enabled."
-  echo "  --giss-only Build without GEOS-Chem coupling."
-  echo "  -f          Fresh rebuild of the model."
-  echo "  --debug     Run with debugging turned on."
+  echo "  MECH=<mechanism>  Set the chemical mechanism (defaults to fullchem)."
+  echo "  --openmp          Compile with OpenMP enabled."
+  echo "  --giss-only       Build without GEOS-Chem coupling."
+  echo "  --debug           Run with debugging turned on."
+  echo "  -f                Fresh rebuild of the model."
+  echo "  --help            Show this help message and exit."
 }
 
 # Check for --help option
@@ -32,8 +34,8 @@ fi
 # Parse arguments
 for arg in "$@"; do
   case $arg in
-  NP=*)
-    NP="${arg#*=}"
+  MECH=*)
+    MECH="${arg#*=}"
     ;;
   --openmp)
     OPENMP=true
@@ -68,7 +70,7 @@ else
 fi
 
 # Print the values for verification
-echo "NP=${NP}"
+echo "MECH=${MECH}"
 echo "OPENMP=${OPENMP}"
 echo "GC=${GC}"
 echo "FRESH=${FRESH}"
@@ -85,13 +87,11 @@ fi
 if [ "${DEBUG}" = true ]; then
   ln -s -f ${GISS_HOME}/.github/rundecks/${RUNID}.R $(pwd)/${RUNID}_DEBUG.R
   RUNID="${RUNID}_DEBUG"
-  git apply ${GISS_HOME}/.dev/utils/DEBUGGING_FLAGS.patch
-  make -j setup RUN=${RUNID} F90=mpif90 GC=${GC} MP=${OPENMP} MPI=YES MECH=carbon \
+  make -j setup RUN=${RUNID} F90=mpif90 GC=${GC} MP=${OPENMP} MPI=YES MECH=${MECH} \
     TYPE=Debug DEBUG=YES COMPILE_WITH_TRAPS=YES TRACEBACK=YES OVERWRITE=YES
-  git apply -R ${GISS_HOME}/.dev/utils/DEBUGGING_FLAGS.patch
 else
   ln -s -f ${GISS_HOME}/.github/rundecks/${RUNID}.R $(pwd)/${RUNID}.R
-  make -j setup RUN=${RUNID} F90=mpif90 GC=${GC} MP=${OPENMP} MPI=YES MECH=carbon \
+  make -j setup RUN=${RUNID} F90=mpif90 GC=${GC} MP=${OPENMP} MPI=YES MECH=${MECH} \
     TYPE=Release OVERWRITE=YES
 fi
 
diff --git a/config/compiler.gfortran.mk b/config/compiler.gfortran.mk
index 007a335..d471069 100644
--- a/config/compiler.gfortran.mk
+++ b/config/compiler.gfortran.mk
@@ -24,7 +24,11 @@ endif
 
 FMAKEDEP = $(SCRIPTS_DIR)/sfmakedepend
 CPPFLAGS += -DCOMPILER_G95
+ifeq ($(TYPE),Debug)
+FFLAGS = -g -cpp -fconvert=big-endian -O0 -Wall -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion -fbacktrace -fallow-argument-mismatch
+else
 FFLAGS = -g -cpp -fconvert=big-endian -O2 -fno-range-check -fallow-argument-mismatch
+endif
 F90FLAGS = $(FFLAGS) -ffree-line-length-none
 LFLAGS =
 ifeq ($(MP),YES)
@@ -34,7 +38,7 @@ LFLAGS += -fopenmp
 endif
 CTM_LFLAGS = $(LFLAGS)
 ifeq ($(GC),YES)
-CTM_LFLAGS += -nostartfiles -Wno-main
+CTM_LFLAGS += -nostartfiles
 endif
 
 F90_VERSION = $(shell $(F90) --version | head -1)
diff --git a/config/compiler.intel.mk b/config/compiler.intel.mk
index a73a4fe..f92b644 100644
--- a/config/compiler.intel.mk
+++ b/config/compiler.intel.mk
@@ -4,9 +4,14 @@ IFORT_RELEASE := $(shell ifort --version | perl -e \
   'while(<>){ if(/ifort.* (\d+\.\d+)/) { print "$$1"; } }')
 FMAKEDEP = $(SCRIPTS_DIR)/sfmakedepend
 CMP_MOD = $(SCRIPTS_DIR)/compare_module_file.pl -compiler INTEL-ifort-9-0-on-LINUX
+ifeq ($(TYPE),Debug)
+FFLAGS = -fpp -O0 -warn all -check bounds -check uninit -check pointers -traceback -assume byterecl -ftz -convert big_endian
+LFLAGS = -O0 -ftz
+else
 FFLAGS = -fpp -O2 -ftz -convert big_endian
-F90FLAGS = $(FFLAGS) -free
 LFLAGS = -O2 -ftz
+endif
+F90FLAGS = $(FFLAGS) -free
 CPPFLAGS += -DCOMPILER_Intel8 -DCONVERT_BIGENDIAN
 F90_VERSION = $(shell $(F90) --version 2>&1)
 ifeq ($(MP),YES)
@@ -16,7 +21,7 @@ LFLAGS += -qopenmp
 endif
 CTM_LFLAGS = $(LFLAGS)
 ifeq ($(GC),YES)
-CTM_LFLAGS += -nostartfiles -nofor-main
+CTM_LFLAGS += -nostartfiles
 endif
 R8 = -r8
 EXTENDED_SOURCE = -extend_source
diff --git a/config/rules.mk b/config/rules.mk
index d981c80..b9855f1 100644
--- a/config/rules.mk
+++ b/config/rules.mk
@@ -62,7 +62,11 @@ I = I
 # by default assume that fortran compiler can do cpp
 EXTERNAL_CPP = NO
 # assume that C compiler understands basic gcc flags
+ifeq ($(TYPE),Debug)
+CFLAGS = -O0
+else
 CFLAGS = -O2
+endif
 # check if ABI was specified
 ifneq ($(ABI),)
   CFLAGS += -m$(ABI)
@@ -430,7 +434,7 @@ endif
 	 $(CPP) $(CPPFLAGS) $< > $@
 
 %.o: %.c
-	$(CC) -c -O2 -m64 $<
+	$(CC) -c $(CFLAGS) -m64 $<
 
 %.f: %.m4f
 	-rm -f $@
diff --git a/decks/Makefile b/decks/Makefile
index 4d2791a..ba8ef06 100644
--- a/decks/Makefile
+++ b/decks/Makefile
@@ -123,6 +123,11 @@ $(MODEL_DIR)/Makefile: $(MODEL_E_ROOT)/model/Makefile
 	cp $(MODEL_E_ROOT)/model/Makefile $(MODEL_DIR)/Makefile
 endif
 
+ifeq ($(TYPE),Debug)
+	DEBUG=1
+else
+	DEBUG=0
+endif
 
 gcm $(BIN_DIR)/$(RUN).exe: $(RUN).mk $(BIN_DIR) depend check_vars
 ifeq ($(GC),YES)
@@ -135,12 +140,10 @@ ifeq ($(GC),YES)
 	# If MECH is not specified, it defaults to "fullchem". May also be "carbon".
 	cd $(GC_BUILD_DIR) && cmake ../ -DINSTALLCOPY=.. \
 		-DCMAKE_BUILD_TYPE="$(TYPE)" -DOMP="$(MP)" -DMECH="$(MECH)" \
-		-DCMAKE_C_COMPILER="$(CC)" \
-		-DCMAKE_CXX_COMPILER="$(CXX)" \
 		-DCMAKE_Fortran_COMPILER="$(F90)" \
 		-DCMAKE_Fortran_FLAGS="$(F90FLAGS)" \
 		-DCMAKE_EXE_LINKER_FLAGS="$(CTM_LFLAGS)"
-	cd $(GC_BUILD_DIR) && make -j install
+	cd $(GC_BUILD_DIR) && make VERBOSE=$(DEBUG) -j install
 	cp $(GC_BUILD_DIR)/mod/*.mod $(MODEL_DIR)/mod/
 	cp $(GC_BUILD_DIR)/src/HEMCO/mod/*.mod $(MODEL_DIR)/mod/
 	cp $(GC_BUILD_DIR)/src/Cloud-J/mod/*.mod $(MODEL_DIR)/mod/
diff --git a/modele-control.pyar b/modele-control.pyar
index cf10239..1d78b27 100644
--- a/modele-control.pyar
+++ b/modele-control.pyar
@@ -3447,7 +3447,7 @@ macro(modele_set_flags)
     add_definitions(-DCOMPILER_G95)
     # This breaks if you try to wrap the long line in the obvious way.
     set (CMAKE_Fortran_FLAGS_RELEASE "${CPPFLAGS} -O2 -g -fconvert=big-endian -fno-range-check -ffree-line-length-none")
-    set (CMAKE_Fortran_FLAGS_DEBUG "${CPPFLAGS} -O -g -fbacktrace -fconvert=big-endian -fno-range-check -ffree-line-length-none -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion")
+    set (CMAKE_Fortran_FLAGS_DEBUG "${CPPFLAGS} -O0 -g -fbacktrace -fconvert=big-endian -fno-range-check -ffree-line-length-none -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion")
 
 
     if (CMAKE_BUILD_TYPE MATCHES Release)