diff --git a/Makefile.conf b/Makefile.conf
index cdc86c5e6..0d8435c85 100644
--- a/Makefile.conf
+++ b/Makefile.conf
@@ -67,26 +67,6 @@ DEBUG=placeholder
 WARN=placeholder
 
 
-######### MIME #########
-# This is before the C/C++ stuff because pEpMIME runs on a different
-# C++ version than we'd like for the moment and we need to set it conditionally
-
-######### pEp MIME #########
-PEP_MIME=0
-PEP_MIME_SRC=$(HOME)/src/pEpMIME/src
-
-
-######### libetpan #########
-# libetpan library search flag
-#
-ETPAN_LIB=
-#ETPAN_LIB=-L$(HOME)/lib
-
-# libetpan include search flag
-ETPAN_INC=
-#ETPAN_INC=-I$(HOME)/include
-
-
 ######### C and C++ #########
 TARGET_ARCH=
 
@@ -99,22 +79,23 @@ else ifeq ($(BUILD_FOR),Darwin)
     LDFLAGS+=-bind_at_load
 endif
 
+# Are we wiping this on purpose?
 LDLIBS=
 
-
 ######### C #########
 ifeq ($(BUILD_FOR),Linux)
-    CC=gcc -std=c99 -pthread
+    CC=gcc 
 else ifeq ($(BUILD_FOR),Darwin)
-    # clang issues a warning when "-pthread" is used for linking.
-    # So, include it in CFLAGS, and not in CC
-    CC=clang -std=c99
+    CC=clang 
 endif
 
+CFLAGS+=-std=c99 -pthread
+CFLAGS+=-fPIC -fstrict-aliasing
+
 ifeq ($(BUILD_FOR),Linux)
-    CFLAGS+=-fPIC -fstrict-aliasing -fdiagnostics-color=auto
+    CFLAGS+=-fdiagnostics-color=auto
 else ifeq ($(BUILD_FOR),Darwin)
-    CFLAGS+=-pthread -fPIC -fstrict-aliasing -fcolor-diagnostics
+    CFLAGS+=-fcolor-diagnostics
 endif
 
 # The flag -DNDEBUG will always be removed from CFLAGS for compiling tests.
@@ -150,33 +131,26 @@ ifeq ($(BUILD_FOR),Linux)
     # otherwise printed during the compilation of every asn1c-generated C file.
     # It's a glibc specific warning, only present in few versions around ~2.19.
     # See https://lwn.net/Articles/590381/ for a discussion.
-    CFLAGS_GENERATED=-D_DEFAULT_SOURCE
+    CPPFLAGS_GENERATED=-D_DEFAULT_SOURCE
 else ifeq ($(BUILD_FOR),Darwin)
-    CFLAGS_GENERATED=
+    CPPFLAGS_GENERATED=
 endif
 
 
 ######### C++ #########
 ifeq ($(BUILD_FOR),Linux)
-ifndef PEP_MIME
-    CXX=g++ -std=gnu++11 -pthread
-else
-    CXX=g++ -std=gnu++14 -pthread
-endif
+    CXX=g++ 
+    CXXFLAGS+=-std=gnu++11
 else ifeq ($(BUILD_FOR),Darwin)
-ifndef PEP_MIME
-    # clang issues a warning when "-pthread" is used for linking. So, include it in CXXFLAGS, and not in CXX
-    CXX=clang -std=c++11
-else
-    # clang issues a warning when "-pthread" is used for linking. So, include it in CXXFLAGS, and not in CXX
-    CXX=clang -std=c++14
-endif
+    CXX=clang 
+    CXXFLAGS+=-std=c++11
 endif
 
-# The flag -DNDEBUG will always be removed from CXXFLAGS for compiling tests.
+CXXFLAGS+=-pthread
+
+# The flag -DNDEBUG will always be removed from CPPFLAGS for compiling tests.
+#
 # The tests do not work properly, if compiled with -DNDEBUG
-# FIXME: -D flags traditionally go in CPPFLAGS, as they're preprocessor defines. We need to clean
-# this up in the whole build system.
 ifeq ($(BUILD_FOR),Linux)
     CXXFLAGS+=-fdiagnostics-color=auto -I../src -I../asn.1 $(ETPAN_INC)
     ifdef WARN
@@ -187,10 +161,11 @@ ifeq ($(BUILD_FOR),Linux)
     ifdef DEBUG
         CXXFLAGS+= -g -ggdb
     else
-        CXXFLAGS+= -O3 -DNDEBUG
+        CXXFLAGS+= -O3 
+        CPPFLAGS+= -DNDEBUG
     endif
 else ifeq ($(BUILD_FOR),Darwin)
-    CXXFLAGS+=-pthread -fcolor-diagnostics -I../src -I../asn.1 $(ETPAN_INC)
+    CXXFLAGS+=-fcolor-diagnostics -I../src -I../asn.1 $(ETPAN_INC)
     ifdef WARN
         CXXFLAGS+=
     else
@@ -199,13 +174,11 @@ else ifeq ($(BUILD_FOR),Darwin)
     ifdef DEBUG
         CXXFLAGS+= -O0 -g
     else
-        CXXFLAGS+= -O3 -DNDEBUG
+        CXXFLAGS+= -O3 
+        CPPFLAGS+= -DNDEBUG
     endif
 endif
 
-ifdef PEP_MIME
-    CXXFLAGS+=-fPIC -fvisibility=hidden
-endif
 
 ######### C and C++ #########
 ifeq ($(BUILD_FOR),Darwin)
@@ -233,12 +206,36 @@ ASN1C=asn1c
 ASN1C_INC=
 #ASN1C_INC=-I$(HOME)/include
 
+
 ######### sqlite3 #########
 # If empty (or undefined), compile sqlite3 from the sources shipped with the pEp distribution.
 # Otherwise, use an sqlite3 implementation found in the OS's include/library paths.
 SQLITE3_FROM_OS=placeholder
 
 
+######### MIME #########
+
+######### pEp MIME #########
+# Set pEpMIME= anything (there are ifdefs on it) in your local.conf if you want
+# to compile built-in pEpMIME (requires a separate libppEpMIME source repo to be
+# checked out elsewhere on the system - define or redefine these in local.conf
+# if you want to use it; otherwise, we default to etpan. (This will eventually
+# become the default, but not yet.
+#
+PEP_MIME=
+PEP_MIME_SRC=$(HOME)/src/pEpMIME/src
+
+
+######### libetpan #########
+# libetpan library search flag
+#
+ETPAN_LIB=
+#ETPAN_LIB=-L$(HOME)/lib
+
+# libetpan include search flag
+ETPAN_INC=
+#ETPAN_INC=-I$(HOME)/include
+
 ######### OpenPGP #########
 # Selects OpenPGP implementation. must be `SEQUOIA`
 OPENPGP=SEQUOIA
@@ -271,6 +268,10 @@ EXCLUDE=
 
 
 ######### Footer #########
+
+################################
+# Include local.conf for any overrides and additional flags
+################################
 -include $(HERE)/local.conf
 
 ifdef BUILD_CONFIG
@@ -278,10 +279,9 @@ ifdef BUILD_CONFIG
 endif
 
 ######### Post processing assignments ########
-# These variables are ineffective when set anywhere else but here.
-# KB: I have no idea why we do this - it totally defeats the purpose of
-#     local.conf.
-#     For now: set if has no value.
+
+# If sequoia has been set up and the SEQUOIA flags aren't defined, set them up.
+# Otherwise, add them to the CFLAGS/CXXFLAGS/LDFLAGS and library/include variables
 ifeq ($(OPENPGP),SEQUOIA)
 ifeq ($(SEQUOIA_CFLAGS),)
     SEQUOIA_CFLAGS+=$(shell pkg-config --cflags-only-other sequoia-openpgp)
@@ -296,12 +296,18 @@ ifeq ($(SEQUOIA_INC),)
     SEQUOIA_INC=$(shell pkg-config --cflags-only-I sequoia-openpgp)
 endif
     CFLAGS+= $(SEQUOIA_CFLAGS)
+    CXXFLAGS+= $(SEQUOIA_CFLAGS)
     LD_FLAGS+= $(SEQUOIA_LDFLAGS)
 endif
 
 # YML_PATH is needed in the environment of every call to a program of the YML2 distribution
 export YML_PATH=$(YML2_PATH)
 
+# Postprocess for pEpMIME
+ifdef PEP_MIME
+    # Replace c++11 with c++14 for now (limiting the subst to the ++11 means it doesn't matter if gnu or not)
+    CXXFLAGS:=$(subst ++11,++14,$(CXXFLAGS)) -fPIC -fvisibility=hidden
+endif
 ifdef PEP_MIME
 ifndef PEP_MIME_SRC
     $(error "Compiling with the PEP_MIME option set requires the value of PEP_MIME_SRC to be set to the source directory for libpEpMIME")
diff --git a/asn.1/Makefile b/asn.1/Makefile
index 483a020e7..a1fe1cc75 100644
--- a/asn.1/Makefile
+++ b/asn.1/Makefile
@@ -5,7 +5,7 @@ include ../Makefile.conf
 
 ALL_SOURCE=$(subst $(NO_SOURCE),,$(wildcard *.c))
 ALL_OBJECTS=$(subst .c,.o,$(ALL_SOURCE))
-CPPFLAGS+=$(CFLAGS_GENERATED)
+CPPFLAGS+=$(CPPFLAGS_GENERATED)
 ASN1C_INC+= -I.
 
 .PHONY: all clean install uninstall
diff --git a/pEpMIME/Makefile b/pEpMIME/Makefile
index 100977775..1b4bd5616 100644
--- a/pEpMIME/Makefile
+++ b/pEpMIME/Makefile
@@ -37,17 +37,29 @@ else
     SED=sed -i	
 endif
 
+######################################################################
+#
+# libpEpMIME can be built as a separate library in its own repository.
+#
+# However, it is dependent on the engine, which obviously does not
+# work within the engine, as the engine is dependent upon IT.
+# Because header files within the engine are local and not defined
+# to exist in some installed library under pEp/header_file.h, we simply
+# copy them into this directory and build/modify them as needed.
+#
+######################################################################
+# Repo source
 PEPMIME_SRC_FILES:= $(wildcard $(PEP_MIME_SRC)/*.cc) $(wildcard $(PEP_MIME_SRC)/*.hh) $(wildcard $(PEP_MIME_SRC)/*.hxx)
+# Stripped filenames
 LOCAL_PEPMIME_SRC:= $(subst $(PEP_MIME_SRC)/,,$(PEPMIME_SRC_FILES))
 
-#$(error $(PEP_MIME_SRC) BOB $(PEPMIME_SRC_FILES) ********************   $(LOCAL_PEPMIME_SRC))
-
 all: lib
 
 lib: mimesrc libpEpMIME.a
 
 mimesrc: ${LOCAL_PEPMIME_SRC}
 
+# Copy the files to the local directory and change their engine header references to quoted references
 %.hh : $(PEP_MIME_SRC)/%.hh
 	cp -p $< $@
 	$(SED) 's/#include <pEp\/\(.*\)>/#include "..\/src\/\1"/g' $@
diff --git a/src/Makefile b/src/Makefile
index db3155ef0..16d78d4ab 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -31,14 +31,14 @@ LDLIBS+= -lc -lasn1
 
 ifeq ($(BUILD_ON),Darwin)
     ifeq ($(BUILD_FOR),Darwin)
-        CFLAGS+= -DSQLITE_THREADSAFE=1
+        CPPFLAGS+= -DSQLITE_THREADSAFE=1
         LDLIBS+= -lz -liconv -mmacosx-version-min=10.10
     else
         $(error I do not know how to make for $(BUILD_FOR) on $(BUILD_ON))
     endif
 else ifeq ($(BUILD_ON),Linux)
     ifeq ($(BUILD_FOR),Linux)
-        CFLAGS+= -DSQLITE_THREADSAFE=1 -D_GNU_SOURCE
+        CPPFLAGS+= -DSQLITE_THREADSAFE=1 -D_GNU_SOURCE
         LDLIBS+= -ldl -luuid
     else
         $(error I do not know how to make for $(BUILD_FOR) on $(BUILD_ON))
@@ -49,12 +49,13 @@ endif
 
 ifdef SQLITE3_FROM_OS
     NO_SOURCE+= sqlite3.c
-    CFLAGS+= -DSQLITE3_FROM_OS
+    CPPFLAGS+= -DSQLITE3_FROM_OS
     LDLIBS+= -lsqlite3
 endif
 
 ifeq ($(OPENPGP),SEQUOIA)
-    CFLAGS+= -DUSE_SEQUOIA $(SEQUOIA_CFLAGS) $(SEQUOIA_INC)
+    CPPFLAGS+= -DUSE_SEQUOIA
+    CFLAGS+= $(SEQUOIA_CFLAGS) $(SEQUOIA_INC)
     LDFLAGS+= $(SEQUOIA_LDFLAGS)
     LDLIBS+= $(SEQUOIA_LIB)
 else
@@ -81,7 +82,7 @@ ifneq ($(MAKECMDGOALS),clean)
 endif
 
 $(TARGET): libpEpEngine.a
-	$(CC) $(CFLAGS) $(ALL_OBJECTS) $(LDFLAGS) $(LDLIBS) -o $@
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(ALL_OBJECTS) $(LDFLAGS) $(LDLIBS) -o $@
 
 .PHONY: objects clean install_headers install uninstall beinstall
 
@@ -96,7 +97,7 @@ clean:
 	rm -f KeySync_fsm.* Sync_actions.c Sync_event.* Sync_func.* Sync_impl.* sync_codec.* distribution_codec.*
 
 # CAVEAT:
-# install_headers is needed for building pEp MIME
+# install_headers is needed for building *STANDALONE* pEp MIME - it is NOT used for built-in functionality!!!
 
 install_headers: $(TARGET)
 	mkdir -p $(PREFIX)/include/pEp
@@ -107,6 +108,7 @@ install_headers: $(TARGET)
 	   status_to_string.h aux_mime_msg.h keyreset_command.h platform.h platform_unix.h ../asn.1/*.h \
  	   $(PREFIX)/include/pEp/
 
+# FIXME: Does anyone but Roker use install_headers? Otherwise, remove the dependency.
 install: $(TARGET) install_headers
 	mkdir -p "$(PREFIX)/lib/"
 	cp -v $< $(PREFIX)/lib/
diff --git a/test/Makefile b/test/Makefile
index 02cf21596..45ed5ec48 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -26,7 +26,7 @@ ifeq ($(shell grep -c $(GTEST_SUITE_SYM) $(GTEST_SRC_DIR)/src/gtest.cc),0)
     GTEST_SUITE_SYM=test_case_name
 endif
 
-CXXFLAGS+= -DGTEST_SUITE_SYM=$(GTEST_SUITE_SYM)
+CPPFLAGS+= -DGTEST_SUITE_SYM=$(GTEST_SUITE_SYM)
 
 ifeq ($(OPENPGP),GPG)
     LDFLAGS+= $(GPGME_LIB)
@@ -49,7 +49,8 @@ endif
 ifeq ($(OPENPGP),SEQUOIA)
     LDFLAGS+= $(SEQUOIA_LDFLAGS)
     LDLIBS+= $(SEQUOIA_LIB)
-    CXXFLAGS+= $(SEQUOIA_CFLAGS) -DUSE_SEQUOIA
+    CXXFLAGS+= $(SEQUOIA_CFLAGS) 
+    CPPFLAGS+= -DUSE_SEQUOIA
     INC_FLAGS+= $(SEQUOIA_INC)
 endif
 
@@ -57,26 +58,12 @@ ifdef SQLITE3_FROM_OS
     LDLIBS+= -lsqlite3
 endif
 
-ifeq ($(OPENPGP),GPG)
-    #LDLIBS+= -lgpgme
-else ifeq ($(OPENPGP),NETPGP)
-    LDLIBS+= -lnetpgp
-    ifeq ($(BUILD_FOR),Linux)
-        LDLIBS+= -ltre
-    endif
-endif
-
 CXXFLAGS:=-I$(GTEST_INC_DIR) $(filter-out -DNDEBUG,$(CXXFLAGS))
+CPPFLAGS:=$(filter-out -DNDEBUG,$(CPPFLAGS))
 
 # FIXME Possibly missing incdirs: ASN1C_INC
 CXXFLAGS+= -I./src -I../src -I ../asn.1 -I../sync $(INC_FLAGS) -Wno-deprecated -Wno-unused-variable
 
-ifeq ($(OPENPGP),GPG)
-    CXXFLAGS+= -DUSE_GPG $(GPGME_INC)
-else ifeq ($(OPENPGP),NETPGP)
-    CXXFLAGS+= -DUSE_NETPGP $(NETPGP_INC)
-endif
-
 EXTRA_LIB_PATHS=.:../src:
 ifndef PEP_MIME
 ifdef ETPAN_LIB
@@ -84,13 +71,6 @@ ifdef ETPAN_LIB
 endif
 endif
 
-ifdef GPGME_LIB
-    EXTRA_LIB_PATHS:=$(EXTRA_LIB_PATHS)$(patsubst -L%,%,$(GPGME_LIB)):
-endif
-ifdef NETPGP_LIB
-    EXTRA_LIB_PATHS:=$(EXTRA_LIB_PATHS)$(patsubst -L%,%,$(NETPGP_LIB)):
-endif
-
 # Remove trailing ':'
 EXTRA_LIB_PATHS:=$(EXTRA_LIB_PATHS::=)
 
@@ -114,7 +94,7 @@ all:
 	$(CXX) -MM $(CPPFLAGS) $(CXXFLAGS) $< | sed -e 's,\($*\)\.o[ :]*,\1.o $@: ,g' > $@
 
 $(TARGET): $(OBJS)
-	${CXX} ${LDFLAGS} -L${PREFIX}/lib -o $@ $^ -lpEpEngine -lgtest -lgtest_main -lsequoia_openpgp_ffi $(LDLIBS)
+	${CXX} ${CPPFLAGS} ${LDFLAGS} -L${PREFIX}/lib -o $@ $^ -lpEpEngine -lgtest -lgtest_main -lsequoia_openpgp_ffi $(LDLIBS)
 
 
 test: all