diff --git a/.travis/travis_build_linux.sh b/.travis/travis_build_linux.sh
index b993e109f7ec82154791414896c6b02e5b7c645c..ff3cdf0987389f4c7ac73b263219cc4c16b99550 100755
--- a/.travis/travis_build_linux.sh
+++ b/.travis/travis_build_linux.sh
@@ -32,8 +32,6 @@ PYTHON3="/usr/bin/python3"
     # Old makefile based flow.
     $PYTHON2 -m compileall -q .
     if type $PYTHON3 > /dev/null; then $PYTHON3 -m compileall -q . ; fi
-    # Traditional make.
-    make 
     ## CMAKE based flow
     mkdir -p _GSL_BUILD && cd _GSL_BUILD && \
         cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 5dda459827e9ab9c719b762b9e19946bd0ab0daf..0000000000000000000000000000000000000000
--- a/Makefile
+++ /dev/null
@@ -1,512 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment,
-#** also known as GENESIS 3 base code.
-#**           copyright (C) 2003- 2006 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-#######################################################################
-# NOTE:
-# This Makefile is compatible with _GNU Make_.
-# This does not work with nmake or borland make.
-# You may have to specify some variables when calling gnu make as
-# described in the comments below. The defaults should work on most
-# Unix clones.
-########################################################################
-
-# Linux compilation:
-# We recommend two levels of compilation: either full debug, with gdb,
-# unit tests and all the rest, or an optimized version for production
-# simulations, without any unit tests or assertions. If you want some
-# intermediate levels, edit the flags.
-######################################################################
-#
-#     ADDITIONAL COMMANDLINE VARIABLES FOR MAKE
-#
-######################################################################
-# The variable BUILD determines if it should be optimized (release)
-# or a debug version (default).
-# make can be run with a command line parameter like below:
-# make clean BUILD=debug
-# make BUILD=debug
-# another option is to define BUILD as an environment variable:
-# export BUILD=debug
-# make clean
-# make
-#
-# There are some more variables which just need to be defined for
-# controlling the compilation and the value does not matter. These are:
-#
-# USE_GSL - use GNU Scientific Library for integration in kinetic simulations
-#
-# USE_READLINE - use the readline library which provides command history and
-# 		better command line editing capabilities
-#
-# GENERATE_WRAPPERS - useful for python interface developers. The binary created
-# 		with this option looks for a directory named 'generated' in the
-# 		working directory and creates a wrapper class ( one .h file
-# 		and a .cpp file ) and partial code for the swig interface file
-# 		(pymoose.i). These files with some modification can be used for
-# 		generating the python interface using swig.
-#
-# USE_MPI - compile with support for parallel computing through MPICH library
-
-
-# Default values for flags. The operator ?= assigns the given value only if the
-# variable is not already defined.
-
-USE_HDF5?=1
-USE_CUDA?=0
-USE_NEUROKIT?=0
-PYTHON?=2
-# BUILD (= debug, release)
-ifndef BUILD
-BUILD=release
-endif
-
-#If using mac uncomment the following lines
-# PLATFORM=mac
-#export PLATFORM
-
-# Get the processor architecture - i686 or x86_64
-# All these should be taken care of in a script, not in the
-# Makefile. But we are
-ifndef MACHINE
-MACHINE=i686
-endif
-# We are assuming all non-win32 systems to be POSIX compliant
-# and thus have the command uname for getting Unix system name
-ifneq ($(OSTYPE),win32)
-MACHINE=$(shell uname -m)
-PLATFORM := $(shell uname -s)
-endif
-
-USE_NUMPY=1
-# Debug mode:
-
-ifeq ($(BUILD),debug)
-CXXFLAGS = -g -O0 -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-# Optimized mode:
-ifeq ($(BUILD),release)
-CXXFLAGS  = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-# Profiling mode:
-ifeq ($(BUILD),profile)
-CXXFLAGS  = -O3 -pg  -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-# Profiling mode with gperftoools
-ifeq ($(BUILD),gperf)
-CXXFLAGS  = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-LDFLAGS += -lprofiler -ltcmalloc
-USE_GSL = true
-endif
-# Threading mode:
-ifeq ($(BUILD),thread)
-CXXFLAGS  = -O3 -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-
-# MPI mode:
-ifeq ($(BUILD),mpi)
-CXXFLAGS = -g -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
-USE_MPI = 1
-USE_GSL = true
-endif
-
-# optimized MPI mode:
-ifeq ($(BUILD),ompi)
-CXXFLAGS  = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-USE_MPI = 1
-USE_GSL = true
-endif
-
-# optimised mode but with unit tests.
-ifeq ($(BUILD),odebug)
-CXXFLAGS = -O3 -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-
-# including SMOLDYN
-ifdef USE_SMOLDYN
-CXXFLAGS = -g -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-
-# Use a strict compilation
-ifeq ($(BUILD),developer)
-    CXXFLAGS=-g \
-	     -Wall -Werror -Wno-unused-variable -Wno-unused-function \
-	     -DDO_UNIT_TESTS -DDEVELOPER -DDEBUG
-    USE_GSL = true
-endif
-##########################################################################
-#
-# MAC OS X compilation, Debug mode:
-ifeq ($(PLATFORM),Darwin)
-CXXFLAGS += -DMACOSX # GCC compiler also sets __APPLE__ for Mac OS X which can be used instead
-CXXFLAGS += -Wno-deprecated -force_cpusubtype_ALL -mmacosx-version-min=10.4
-endif
-# Use the options below for compiling on GCC4.1
-# GNU C++ 4.1 and newer might need -ffriend-injection
-#
-#CXXFLAGS  =	-g -Wall -pedantic -DDO_UNIT_TESTS -ffriend-injection -DUSE_GENESIS_PARSER
-
-# Insert the svn revision no. into the code as a preprocessor macro.
-# Only for release versions we want to pass SVN=0 to make.
-# No more SVN so pass zero
-SVN=0
-ifndef SVN
-SVN?=1
-endif
-empty :=
-space := $(empty) $(empty)
-ifneq ($(SVN),0)
-# Some versions of svnrevision return "Unversioned directory" which causes confusion to gcc
-SVN_REVISION := $(shell svnversion)
-SVN_REVISION := $(subst $(space),_,$(SVN_REVISION))
-# SVN_REVISION := $(subst :,_,$(SVN_REVISION))
-ifneq ($(SVN_REVISION),export)
-CXXFLAGS+=-DSVN_REVISION=\"$(SVN_REVISION)\"
-endif
-endif
-
-
-# Libraries are defined below.
-SUBLIBS =
-# Notice that pthread is no more included
-LIBS =	-L/usr/lib -L/usr/local/lib
-
-#LIBS = 	-lm
-
-# For 64 bit Linux systems add paths to 64 bit libraries
-ifeq ($(PLATFORM),Linux)
-CXXFLAGS += -DLINUX
-ifeq ($(MACHINE),x86_64)
-LIBS+= -L/lib64 -L/usr/lib64
-endif
-endif
-
-##########################################################################
-#
-# Developer options (Don't try these unless you are writing new code!)
-##########################################################################
-# For parallel (MPI) version:
-ifdef USE_MUSIC
-USE_MPI = 1		# Automatically enable MPI if USE_MUSIC is on
-CXXFLAGS += -DUSE_MUSIC
-LIBS += -lmusic
-endif
-
-# The -DMPICH_IGNORE_CXX_SEEK flag is because of a bug in the
-# MPI-2 standard. Enabled by default because it use crops up
-# often enough. You won't need if if you are not using MPICH, or
-# if your version of MPICH has fixed the issue.
-ifdef USE_MPI
-# CXXFLAGS += -DUSE_MPI
-CXXFLAGS += -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK
-endif
-
-#use this for readline library
-#CXXFLAGS = -g -Wall -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER -DUSE_READLINE
-
-
-# To use GSL, pass USE_GSL=true ( anything on the right will do) in make command line
-ifdef USE_GSL
-LIBS+= $(shell gsl-config --libs)
-#LIBS+= -L/usr/lib -Wl,--no-as-needed -lgsl -lgslcblas -lm
-#LIBS+= -L/usr/lib -lgsl -lgslcblas -lm
-CXXFLAGS+= -DUSE_GSL
-else
-LIBS+= -lm
-endif
-
-#Saeed
-# To use CUDA, pass USE_CUDA=1 in make command line
-ifeq ($(USE_CUDA),1)
-LIBS+= -L/usr/local/cuda/lib64 -LhsolveCuda/cudaLibrary  -lcuda -lcudart -lm -lmooseCudaLibrary
-HCUDA_DIR = hsolveCuda
-HCUDA_LIB = hsolveCuda/_hsolveCuda.o
-endif
-
-# To disable numpy pass USE_NUMPY=0
-ifeq ($(USE_NUMPY),1)
-CXXFLAGS+=-DUSE_NUMPY
-endif
-
-# To compile examples, pass EXAMPLES=true ( anything on the right will do) in make command line
-ifdef EXAMPLES
-EXAMPLES_DIR = examples
-EXAMPLES_LIB = examples/_trials.o
-endif
-
-# To use Smoldyn, pass USE_SMOLDYN=true ( anything on the right will do) in make command line
-ifdef USE_SMOLDYN
-#LIBS+= -L/usr/local/lib -lsmoldyn
-CXXFLAGS+= -DUSE_SMOLDYN
-SMOLDYN_DIR = smol
-SMOLDYN_LIB = smol/_smol.o /usr/local/lib/libsmoldyn.a
-LIBS += -lsmoldyn
-endif
-
-# To compile with readline support pass USE_READLINE=true in make command line
-ifdef USE_READLINE
-LIBS+= -lreadline
-CXXFLAGS+= -DUSE_READLINE
-endif
-
-# To compile with curses support (terminal aware printing) pass USE_CURSES=true in make command line
-ifdef USE_CURSES
-LIBS += -lcurses
-CXXFLAGS+= -DUSE_CURSES
-endif
-
-ifdef USE_MUSIC
-	MUSIC_DIR = music
-	MUSIC_LIB = music/music.o
-endif
-
-# Here we automagically change compilers to deal with MPI.
-ifdef USE_MPI
-	CXX = mpicxx
-#	CXX = /usr/local/mvapich2/bin/mpicxx
-#	PARALLEL_DIR = parallel
-#	PARALLEL_LIB = parallel/parallel.o
-else
-	CXX = g++
-#	CXX = CC	# Choose between Solaris CC and g++ on a Solaris machine
-endif
-
-ifeq ($(USE_HDF5),1)
-	CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I/usr/local/hdf5/include -I/usr/include/hdf5/serial
-	LIBS+= -lhdf5 -lhdf5_hl -L/usr/local/hdf5/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial/
-endif
-
-LD = ld
-
-SUBDIR = \
-	basecode \
-	msg \
-	shell \
-	randnum\
-	scheduling\
-	mpi \
-	builtins\
-	utility \
-	external/muparser \
-	biophysics \
-	synapse \
-	intfire \
-	kinetics \
-	ksolve \
-	mesh \
-	hsolve \
-	diffusion \
-	device \
-	signeur \
-	benchmarks \
-	$(SMOLDYN_DIR) \
-	$(SBML_DIR) \
-	$(HCUDA_DIR) \
-	$(EXAMPLES_DIR) \
-
-# Used for 'make clean'
-CLEANSUBDIR = $(SUBDIR) $(PARALLEL_DIR) pymoose
-
-OBJLIBS =	\
-	basecode/_basecode.o \
-	msg/_msg.o \
-	shell/_shell.o \
-	randnum/_randnum.o \
-	scheduling/_scheduling.o \
-	mpi/_mpi.o \
-	builtins/_builtins.o \
-	utility/_utility.o \
-	external/muparser/_muparser.o \
-	biophysics/_biophysics.o \
-	synapse/_synapse.o \
-	intfire/_intfire.o \
-	kinetics/_kinetics.o \
-	ksolve/_ksolve.o \
-	hsolve/_hsolve.o \
-	mesh/_mesh.o \
-	diffusion/_diffusion.o \
-	device/_device.o \
-	signeur/_signeur.o \
-	benchmarks/_benchmarks.o \
-	$(SMOLDYN_LIB) \
-	$(SBML_LIB) \
-	$(HCUDA_LIB) \
-	$(EXAMPLES_LIB) \
-
-
-ifeq ($(USE_NEUROKIT),1)
-	NEUROKIT_COMMAND = cd ./python/moogli; python setup.py build;  cd ../../; cp ./python/moogli/build/*/_moogli.so ./python/moogli/;
-# else
-# 	NEUROKIT_COMMAND = ""
-endif
-
-
-export CXX
-export CXXFLAGS
-export LD
-export LIBS
-export USE_GSL
-#export USE_SBML
-
-all: moose pymoose
-
-neurokit: ./python/moogli/setup.py
-	$(NEUROKIT_COMMAND)
-
-moose: libs $(OBJLIBS) $(PARALLEL_LIB)
-	$(CXX) $(CXXFLAGS) $(OBJLIBS) $(PARALLEL_LIB) $(LIBS) -o moose
-	@echo "Moose compilation finished"
-
-libmoose.so: libs
-	$(CXX) -G $(LIBS) -o libmoose.so
-	@echo "Created dynamic library"
-
-# Get the python version
-ifneq ($(OSTYPE),win32)
-ifeq ($(PYTHON),3)
-PYTHON_VERSION := $(subst ., ,$(lastword $(shell python3 --version 2>&1)))
-PYTHON_CFLAGS := $(shell python3-config --cflags)
-PYTHON_LDFLAGS := $(shell python3-config --ldflags)
-else # Python 2.x
-PYTHON_VERSION := $(subst ., ,$(lastword $(shell python --version 2>&1)))
-ifneq ($(BUILD),debug)
-PYTHON_CFLAGS := $(shell python-config --cflags)
-PYTHON_LDFLAGS := $(shell python-config --ldflags)
-else
-PYTHON_CFLAGS := $(shell python-config --includes) \
-    -fno-strict-aliasing -fwrapv \
-    -Wstrict-prototypes  \
-    -Wformat -Wformat-security -Werror=format-security \
-    -fstack-protector --param=ssp-buffer-size=4
-
-PYTHON_LDFLAGS := -L/usr/lib/$(INSTALLED_PYTHON) \
-    -Xlinker -export-dynamic -Wl,-O0 -Wl,-Bsymbolic-functions
-endif # ifneq ($(BUILD),debug)
-endif # ifeq ($(PYTHON),3)
-PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION})
-PYTHON_VERSION_MINOR := $(word 2,${PYTHON_VERSION})
-INSTALLED_PYTHON := python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-endif
-
-# For developer build and strict checking
-ifeq ($(BUILD),developer)
-    PYTHON_CFLAGS := $(PYTHON_CFLAGS) -Wall -Werror -Wno-unused-function -Wno-unused-variable
-endif  # ifeq(${BUILD},developer)
-
-ifndef PYTHON_CFLAGS
-PYTHON_CFLAGS := -I/usr/include/$(INSTALLED_PYTHON) -fno-strict-aliasing \
-    -fwrapv \
-     -fstack-protector \
-    #-Wstrict-prototypes \ # This option is obsolete for g++-4.8
-    --param=ssp-buffer-size=4 \
-    -Wformat -Wformat-security -Werror=format-security
-
-PYTHON_LDFLAGS := -L/usr/lib/$(INSTALLED_PYTHON)  -Xlinker -export-dynamic -Wl,-O0 -Wl,-Bsymbolic-functions
-endif
-# There are some unix/gcc specific paths here. Should be cleaned up in future.
-pymoose: python/moose/_moose.so
-pymoose: CXXFLAGS += -DPYMOOSE $(PYTHON_CFLAGS)
-# fix: add include dir for numpy headers required by pymoose/moosemodule.cpp
-pymoose: CXXFLAGS += -I$(shell /usr/bin/python -c 'from numpy import get_include; print get_include()')
-pymoose: OBJLIBS += pymoose/_pymoose.o
-pymoose: LDFLAGS += $(PYTHON_LDFLAGS)
-export CXXFLAGS
-python/moose/_moose.so: libs $(OBJLIBS)
-	$(MAKE) -C pymoose
-	$(CXX) -shared $(LDFLAGS) $(CXXFLAGS) -o $@ $(OBJLIBS) $(LIBS)
-	@echo "pymoose module built."
-
-# This will generate an object file without main
-libs:
-	@for i in $(SUBDIR) $(PARALLEL_DIR); do \
-	    $(MAKE) -C $$i || exit $$?; \
-	done
-	@echo "All Libs compiled"
-
-clean:
-	@(for i in $(CLEANSUBDIR) ; do $(MAKE) -C $$i clean;  done)
-	-rm -rf moose  core.* DOCS/html python/moose/*.so python/moose/*.pyc
-
-############ INSTALL (works for sudo make install and deb packaging using dpkg-buildpackage)
-## get the default python module install location
-## no need to know this, the default for public modules is /usr/share/pyshared
-pydir_cmd := python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())"
-pydistpkg_dir := $(shell $(pydir_cmd))
-## /usr/share/pyshared/ is a directory which is independent of python version,
-## but modules need to be registered with update-python-modules, giving a list of files
-## debhelper (dpkg-buildpackage) will also copy to this location and do the registration.
-## For make install, I stick to the default python .../dist-packages directory.
-pydistpkg_dirB := /usr/share/pyshared/
-
-username=$(shell basename $(HOME))
-
-install_prefix=/usr
-## Note that $(DESTDIR) is provided by dpkg-buildpackage to specify the local install for deb packaging
-## if doing sudo make install, $(DESTDIR) will be undefined and will cause no trouble
-install:
-	## discard symbols from object files
-	strip python/moose/_moose.so
-
-	## delete older .../share/moose, - before rm means ignore errors (eg not found)
-	-rm -rf $(DESTDIR)$(install_prefix)/share/moose
-	## -p creates parent directories also if they don't exist
-	mkdir -p $(DESTDIR)$(install_prefix)/share/moose
-	## copy filtering out the .svn (hidden) files
-	rsync -r --exclude=.svn Demos/* $(DESTDIR)$(install_prefix)/share/moose/Demos
-	rsync -r --exclude=.svn gui/* $(DESTDIR)$(install_prefix)/share/moose/gui
-	test -d $(DESTDIR)$(install_prefix)/share/doc || mkdir -p $(DESTDIR)$(install_prefix)/share/doc
-	rsync -r --exclude=.svn Docs/* $(DESTDIR)$(install_prefix)/share/doc/moose
-	# rsync -r --exclude=.svn Demos/* $(DESTDIR)$(install_prefix)/share/moose/
-	## pymoose module goes to python's dist-packages
-	## delete older .../dist-packages/moose, - before rm means ignore errors (eg not found)
-	-rm -rf $(DESTDIR)$(pydistpkg_dir)/moose
-	-rm -rf $(DESTDIR)$(pydistpkg_dirB)/moose
-	## make directory in case non-existent (needed for deb pkg building)
-	mkdir -p $(DESTDIR)$(pydistpkg_dir)
-	rsync -r --exclude=.svn --exclude=moose_py3k.py python/* $(DESTDIR)$(pydistpkg_dir)/
-
-	## shell command moosegui for the moose GUI.
-	chmod a+x $(DESTDIR)$(install_prefix)/share/moose/gui/MooseGUI.py
-	## -rm instructs make to ignore errors from make eg. file not found
-	-rm -f $(DESTDIR)$(install_prefix)/bin/moosegui
-	mkdir -p $(DESTDIR)$(install_prefix)/bin
-	ln -s $(DESTDIR)$(install_prefix)/share/moose/gui/MooseGUI.py $(DESTDIR)$(install_prefix)/bin/moosegui
-
-	## byte compile the module, gui, Demos (since, later running as user cannot create .pyc in root-owned dirs)
-	python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(pydistpkg_dir)/moose',force=1)"
-	python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(install_prefix)/share/moose/gui',force=1)"
-	python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(install_prefix)/share/moose/Demos',force=1)"
-
-        ## see standards.freedesktop.org for specifications for where to put menu entries and icons
-        ## copy the .desktop files to /usr/share/applications for link to show up in main menu
-	mkdir -p $(DESTDIR)$(install_prefix)/share/applications
-	cp gui/MooseGUI.desktop $(DESTDIR)$(install_prefix)/share/applications/
-	cp gui/MooseSquidAxon.desktop $(DESTDIR)$(install_prefix)/share/applications/
-        ## copy the .desktop files to the desktop too to get icons
-	cp gui/MooseGUI.desktop $$HOME/Desktop/
-	chmod a+x $$HOME/Desktop/MooseGUI.desktop
-	chown $(username) $(HOME)/Desktop/MooseGUI.desktop
-	chgrp $(username) $(HOME)/Desktop/MooseGUI.desktop
-	cp gui/MooseSquidAxon.desktop $$HOME/Desktop/
-	chmod a+x $$HOME/Desktop/MooseSquidAxon.desktop
-	chgrp $(username) $(HOME)/Desktop/MooseSquidAxon.desktop
-	chown $(username) $(HOME)/Desktop/MooseSquidAxon.desktop
-        ## copy icon to /usr/share/icons/hicolor/<size>/apps (hicolor is the fallback theme)
-	mkdir -p $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps
-	cp gui/icons/moose_icon.png $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps/
-	cp gui/icons/squid.png $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps/
-        ## need to update the icon cache to show the icon
-	update-icon-caches $(DESTDIR)$(install_prefix)/share/icons/hicolor/
-
-.PHONY: install
diff --git a/MooseTests.cmake b/MooseTests.cmake
index 58be0f4b931d637b3c4ae6bfa8a4fa15a4e8e79b..38aabc3d7808520ca530d4b32377a35d9d6ba0ae 100644
--- a/MooseTests.cmake
+++ b/MooseTests.cmake
@@ -125,3 +125,11 @@ set_tests_properties(pymoose-test-kkit
     PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/python"
     )
 
+# Test Calcium hsolve support.
+ADD_TEST( NAME pymoose-test-calcium-hsolve 
+    COMMAND ${TEST_COMMAND} 
+    ${PROJECT_SOURCE_DIR}/tests/python/test_hsolve_externalCalcium.py
+    )
+set_tests_properties(pymoose-test-calcium-hsolve
+    PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/python"
+    )
diff --git a/basecode/Makefile b/basecode/Makefile
deleted file mode 100644
index 0639a32c38bce0311fda0e32251dbd5b44eab69a..0000000000000000000000000000000000000000
--- a/basecode/Makefile
+++ /dev/null
@@ -1,99 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment,
-#** also known as GENESIS 3 base code.
-#**           copyright (C) 2004 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-# $Id: $
-#
-# $Log: $
-#
-
-TARGET = _basecode.o
-
-
-#  CXXFLAGS += -I.. -I../kinetics -I../biophysics
-
-OBJ = \
-	consts.o	\
-	Element.o	\
-	DataElement.o	\
-	GlobalDataElement.o	\
-	LocalDataElement.o	\
-	Eref.o	\
-	Finfo.o	\
-	DestFinfo.o	\
-	Cinfo.o	\
-	SrcFinfo.o \
-	ValueFinfo.o \
-	SharedFinfo.o \
-	FieldElementFinfo.o \
-	FieldElement.o \
-	Id.o \
-	ObjId.o \
-	global.o \
-	SetGet.o \
-	OpFuncBase.o \
-	EpFunc.o \
-	HopFunc.o \
-	SparseMatrix.o \
-	doubleEq.o \
-	testAsync.o	\
-	main.o	\
-
-HEADERS = \
-	header.h \
-	Cinfo.h \
-	Conv.h \
-	Dinfo.h \
-	MsgDigest.h \
-	Element.h \
-	DataElement.h \
-	GlobalDataElement.h \
-	LocalDataElement.h \
-	Eref.h \
-	global.h \
-	Finfo.h \
-	DestFinfo.h \
-	Id.h \
-	ObjId.h \
-	../msg/Msg.h \
-	OpFuncBase.h \
-	OpFunc.h \
-	EpFunc.h \
-	HopFunc.h \
-	ProcInfo.h \
-	SrcFinfo.h \
-	ValueFinfo.h \
-	LookupValueFinfo.h \
-	LookupElementValueFinfo.h \
-	SharedFinfo.h \
-	FieldElementFinfo.h \
-	FieldElement.h \
-	MsgFuncBinding.h \
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS) ../shell/Shell.h
-Element.o:	FuncOrder.h
-testAsync.o:	SparseMatrix.h SetGet.h ../scheduling/Clock.h ../biophysics/IntFire.h ../synapse/SynEvent.h ../synapse/SynHandlerBase.h ../synapse/SimpleSynHandler.h ../synapse/Synapse.h ../randnum/RNG.h
-SparseMsg.o:	SparseMatrix.h
-SetGet.o:	SetGet.h ../shell/Neutral.h
-HopFunc.o:	HopFunc.h ../mpi/PostMaster.h
-global.o:       global.h ../randnum/RNG.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) -I../msg -I.. $< -c
-
-.PHONY: pymoose
-
-pymoose: CXXFLAGS += -DPYMOOSE
-
-$(TARGET): $(OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ)
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/benchmarks/Makefile b/benchmarks/Makefile
deleted file mode 100644
index 0eb5aef3628e1e1c1d3186dab04ebbb7b861de48..0000000000000000000000000000000000000000
--- a/benchmarks/Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _benchmarks.o
-
-OBJ = \
-	benchmarks.o	\
-	kineticMarks.o	\
-
-HEADERS = \
-	../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-kineticMarks.o:	../shell/Shell.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/biophysics/Makefile b/biophysics/Makefile
deleted file mode 100644
index 6659630cea1751622c725f27a6a9142bf277384f..0000000000000000000000000000000000000000
--- a/biophysics/Makefile
+++ /dev/null
@@ -1,123 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _biophysics.o
-
-OBJ = \
-	IntFire.o	\
-	SpikeGen.o	\
-	RandSpike.o	\
-	CompartmentDataHolder.o	\
-	CompartmentBase.o	\
-	Compartment.o	\
-	SymCompartment.o	\
-	GapJunction.o	\
-	ChanBase.o	\
-	ChanCommon.o	\
-	HHChannelBase.o	\
-	HHChannel.o	\
-	HHGate.o	\
-	HHGate2D.o	\
-	HHChannel2D.o	\
-	CaConcBase.o	\
-	CaConc.o	\
-	MgBlock.o	\
-	Nernst.o	\
-	Neuron.o	\
-	Spine.o	\
-	ReadCell.o	\
-	SwcSegment.o	\
-	ReadSwc.o	\
-	SynChan.o	\
-	NMDAChan.o	\
-	testBiophysics.o	\
-	IzhikevichNrn.o	\
-	DifShellBase.o \
-	DifShell.o	\
-	DifBufferBase.o	\
-	DifBuffer.o	\
-	Leakage.o	\
-	VectorTable.o	\
-	MarkovRateTable.o	\
-	MarkovChannel.o	\
-	MarkovGslSolver.o	\
-	MatrixOps.o	\
-	MarkovSolverBase.o	\
-	MarkovSolver.o	\
-	VClamp.o	\
-
-
-	# MMpump.o  \
-	# LeakyIaF.o	\
-	# GapJunction.o	\
-	# Nernst.o	\
-	# GHK.o		\
-	# NMDAChan.o	\
-
-# GSL_LIBS = -L/usr/lib -lgsl
-
-HEADERS = \
-	../basecode/header.h \
-	../utility/numutil.h \
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-IntFire.o:	IntFire.h
-SpikeGen.o: SpikeGen.h
-RandSpike.o: RandSpike.h ../randnum/randnum.h
-CompartmentDataHolder.o: CompartmentDataHolder.h
-CompartmentBase.o: CompartmentBase.h CompartmentDataHolder.h
-Compartment.o: CompartmentBase.h Compartment.h
-SymCompartment.o: CompartmentBase.h Compartment.h SymCompartment.h
-ChanBase.o: ChanBase.h
-ChanCommon.o: ChanBase.h ChanCommon.h
-SynChan.o: SynChan.h ChanBase.h ChanCommon.h
-NMDAChan.o: NMDAChan.h SynChan.h ChanBase.h ChanCommon.h
-Leakage.o: Leakage.h ChanBase.h ChanCommon.h
-GapJunction.o: GapJunction.h
-HHChannelBase.o: ChanBase.h HHChannelBase.h HHGate.h
-HHChannel.o: ChanBase.h HHChannel.h HHGate.h
-HHGate.o: HHGate.h
-HHChannel2D.o: ChanBase.h HHChannel2D.h HHGate2D.h
-HHGate2D.o: HHGate2D.h
-CaConcBase.o:	CaConcBase.h
-CaConc.o:	CaConcBase.h CaConc.h
-MgBlock.o:	MgBlock.h ChanBase.h
-Nernst.o:	Nernst.h
-Neuron.o:	Neuron.h SwcSegment.h Spine.h
-Spine.o:	Neuron.h SwcSegment.h Spine.h
-ReadCell.o: CompartmentBase.h Compartment.h SymCompartment.h ReadCell.h ../shell/Shell.h ../utility/utility.h
-SwcSegment.o: SwcSegment.h ../utility/Vec.h
-ReadSwc.o: CompartmentBase.h Compartment.h SymCompartment.h SwcSegment.h ReadSwc.h ../shell/Shell.h ../utility/Vec.h
-IzhikevichNrn.o: IzhikevichNrn.h
-DifShellBase.o: DifShellBase.h
-DifShell.o: DifShellBase.h DifShell.h 
-DifBufferBase.o: DifBufferBase.h
-DifBuffer.o:  DifBufferBase.h DifBuffer.h
-MMPump.o: MMPump.h
-testBiophysics.o: IntFire.h CompartmentBase.h Compartment.h HHChannel.h HHGate.h 
-VectorTable.o : VectorTable.h
-MarkovGslSolver.o : MarkovGslSolver.h 
-MatrixOps.o : MatrixOps.h
-MarkovRateTable.o : VectorTable.h ../builtins/Interpol2D.h MarkovRateTable.h 
-MarkovSolverBase.o : MarkovSolver.h MatrixOps.h MarkovRateTable.h
-MarkovSolver.o : MarkovSolverBase.h MarkovSolver.h
-MarkovChannel.o : VectorTable.h ../builtins/Interpol2D.h MarkovRateTable.h ChanBase.h MarkovChannel.h 
-VClamp.o: VClamp.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../external/muparser/include -I .. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
-	rm -f *.o $(TARGET) core core.*
diff --git a/builtins/Makefile b/builtins/Makefile
deleted file mode 100644
index 7ff1cebed8784468dcd0aec5a15ea65db4f1220f..0000000000000000000000000000000000000000
--- a/builtins/Makefile
+++ /dev/null
@@ -1,68 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _builtins.o
-
-OBJ = \
-      Arith.o	\
-      Group.o	\
-      Mstring.o	\
-      Func.o \
-      Function.o	\
-      Variable.o	\
-      InputVariable.o	\
-      TableBase.o	\
-      Table.o	\
-      Interpol.o	\
-      StimulusTable.o	\
-      TimeTable.o	\
-      Stats.o	\
-      SpikeStats.o	\
-      Interpol2D.o \
-      HDF5WriterBase.o	\
-      HDF5DataWriter.o	\
-      StreamerBase.o \
-      Streamer.o \
-      NSDFWriter.o	\
-      testNSDF.o	\
-      testBuiltins.o	\
-
-HEADERS = \
-	  ../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-Arith.o:	Arith.h
-Group.o:	Group.h
-Mstring.o:		Mstring.h
-Func.o:	Func.h
-Function.o: Function.h
-Variable.o: Variable.h
-TableBase.o:		TableBase.h
-Table.o:		TableBase.h Table.h
-Interpol.o:		TableBase.h Interpol.h
-StimulusTable.o:		TableBase.h StimulusTable.h
-TimeTable.o:	TimeTable.h TableBase.h
-Stats.o:	Stats.h
-SpikeStats.o:	Stats.h SpikeStats.h
-Interpol2D.o:	Interpol2D.h
-HDF5WriterBase.o: HDF5WriterBase.h
-HDF5DataWriter.o: HDF5DataWriter.h HDF5WriterBase.h
-testBuiltins.o:	Group.h Arith.h Stats.h ../msg/DiagonalMsg.h ../basecode/SetGet.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I..  -I../scheduling -I../basecode -I../msg -I../external/muparser/include $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/device/Makefile b/device/Makefile
deleted file mode 100644
index 159d88056dade350936d92f016e3221df7d2e321..0000000000000000000000000000000000000000
--- a/device/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-TARGET = _device.o
-
-OBJ = PulseGen.o	\
-	DiffAmp.o	\
-	PIDController.o	\
-	RC.o	
-
-HEADERS = \
-	../basecode/header.h 	\
-
-default: $(TARGET)
-
-$(OBJ): $(HEADERS)
-PulseGen.o: PulseGen.h
-DiffAmp.o: DiffAmp.h
-PIDController.o: PIDController.h
-RC.o: RC.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
-	rm -f *.o $(TARGET) core core.*
diff --git a/diffusion/Makefile b/diffusion/Makefile
deleted file mode 100644
index 458a5ba9e8026e4675a8e9b2ce525da713047389..0000000000000000000000000000000000000000
--- a/diffusion/Makefile
+++ /dev/null
@@ -1,36 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _diffusion.o
-
-OBJ = \
-	FastMatrixElim.o	\
-	DiffPoolVec.o	\
-	Dsolve.o	\
-	testDiffusion.o	\
-
-HEADERS = \
-	../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-FastMatrixElim.o: ../basecode/SparseMatrix.h FastMatrixElim.h
-Dsolve.o:	../basecode/SparseMatrix.h ../kinetics/PoolBase.h ../kinetics/lookupVolumeFromMesh.h ../mesh/ChemCompt.h ../ksolve/XferInfo.h ../ksolve/ZombiePoolInterface.h 
-DiffPoolVec.o: DiffPoolVec.h ../ksolve/ZombiePoolInterface.h
-testDiffusion.o:	Dsolve.h ../ksolve/ZombiePoolInterface.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(GSL_FLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../ksolve $< -c
-
-$(TARGET):		$(OBJ) $(GSL_OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(GSL_OBJ) $(GSL_LIBS) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/examples/Makefile b/examples/Makefile
deleted file mode 100644
index 1e7f10aba87a81427787ebda1f04f6ab3a10f31b..0000000000000000000000000000000000000000
--- a/examples/Makefile
+++ /dev/null
@@ -1,32 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _trials.o
-
-OBJ = \
-	Example.o	\
-	Ex.o	\
-
-HEADERS = \
-	../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-Example.o: Example.h ../basecode/ElementValueFinfo.h
-Ex.o: Ex.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/external/muparser/Makefile b/external/muparser/Makefile
deleted file mode 100644
index 6b8bb423a78aec4c2840cea4ff9d2181a6bdffb4..0000000000000000000000000000000000000000
--- a/external/muparser/Makefile
+++ /dev/null
@@ -1,42 +0,0 @@
-# Makefile for including muParser into moose.
-# Author: Subhasis Ray
-#
-TARGET = _muparser.o
-
-OBJ = \
-    src/muParserBase.o \
-    src/muParserBytecode.o \
-    src/muParserCallback.o \
-    src/muParser.o  \
-    src/muParserDLL.o \
-    src/muParserError.o \
-    src/muParserInt.o \
-    src/muParserTokenReader.o \
-
-HEADERS = \
-	include/muParser.h	\
-	include/muParserBase.h	\
-	include/muParserBytecode.h	\
-	include/muParserCallback.h	\
-	include/muParserDef.h	\
-	include/muParserError.h	\
-	include/muParserFixes.h	\
-	include/muParserStack.h	\
-	include/muParserToken.h	\
-	include/muParserTokenReader.h		\
-	include/muParserTemplateMagic.h	\
-
-
-default: $(TARGET)
-
-$(OBJ): $(HEADERS)
-
-%.o: %.cpp
-	$(CXX) $(CXXFLAGS) -I. -I../../ -Iinclude $< -c -o $@
-
-$(TARGET):	$(OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ)
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
-
diff --git a/external/tinyxml/Makefile b/external/tinyxml/Makefile
deleted file mode 100644
index 45639837dea61df6d90bf23b3e5a7ee081d3a4d3..0000000000000000000000000000000000000000
--- a/external/tinyxml/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-# Makefile for including muParser into moose.
-# Author: Subhasis Ray
-#
-TARGET = _tinyxml2.o
-
-OBJ = \
-	tinyxml2.o
-
-HEADERS = \
-	tinyxml2.h	\
-
-
-default: $(TARGET)
-
-$(OBJ): $(HEADERS)
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) -I. $< -c
-
-$(TARGET):	$(OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ)
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
-
diff --git a/hsolve/Makefile b/hsolve/Makefile
deleted file mode 100644
index 48ad098f6c7c1e99a9442d35371f90707f6fd933..0000000000000000000000000000000000000000
--- a/hsolve/Makefile
+++ /dev/null
@@ -1,52 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment,
-#** also known as GENESIS 3 base code.
-#**           copyright (C) 2004 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU General Public License version 2
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _hsolve.o
-
-OBJ = \
-	HSolveStruct.o \
-	HinesMatrix.o \
-	HSolvePassive.o \
-	RateLookup.o \
-	HSolveActive.o \
-	HSolveActiveSetup.o \
-	HSolveInterface.o \
-	HSolve.o \
-	HSolveUtils.o \
-	testHSolve.o \
-	ZombieCompartment.o \
-	ZombieCaConc.o \
-	ZombieHHChannel.o \
-
-HEADERS = \
-	../basecode/header.h
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-HSolveStruct.o:	HSolveStruct.h
-HinesMatrix.o:	HinesMatrix.h TestHSolve.h
-HSolvePassive.o:	HSolvePassive.h HinesMatrix.h HSolveStruct.h HSolveUtils.h TestHSolve.h ../biophysics/Compartment.h
-RateLookup.o:	RateLookup.h
-HSolveActive.o:	HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../biophysics/ChanBase.h
-HSolveActiveSetup.o:	HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h HSolveUtils.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHGate.h ../biophysics/CaConc.h
-HSolveInterface.o:	HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h
-HSolve.o:	../biophysics/Compartment.h ZombieCompartment.h ../biophysics/CaConc.h ZombieCaConc.h ../biophysics/HHGate.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ZombieHHChannel.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
-ZombieCompartment.o:	../biophysics/CompartmentBase.h ZombieCompartment.h ../biophysics/Compartment.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
-ZombieCaConc.o:	ZombieCaConc.h ../biophysics/CaConc.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
-ZombieHHChannel.o:	ZombieHHChannel.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHGate.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I.. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
-	rm -f *.o $(TARGET) core core.*
diff --git a/intfire/Makefile b/intfire/Makefile
deleted file mode 100644
index 22261ff9da1a87687e980907a90c5b0172697c0d..0000000000000000000000000000000000000000
--- a/intfire/Makefile
+++ /dev/null
@@ -1,50 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _intfire.o
-
-OBJ = \
-	IntFireBase.o	\
-	LIF.o \
-	QIF.o \
-	ExIF.o \
-	AdExIF.o \
-	AdThreshIF.o \
-	IzhIF.o \
-	testIntFire.o \
-
-# GSL_LIBS = -L/usr/lib -lgsl
-
-HEADERS = \
-	../basecode/header.h \
-	../utility/numutil.h \
-	IntFireBase.h \
-	../biophysics/CompartmentBase.h \
-	../biophysics/Compartment.h
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-LIF.o:	LIF.h
-QIF.o:	QIF.h
-ExIF.o:	ExIF.h
-AdExIF.o:	AdExIF.h
-AdThreshIF.o:	AdThreshIF.h
-IzhIF.o:	IzhIF.h
-testIntFire.o:	LIF.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
-	rm -f *.o $(TARGET) core core.*
diff --git a/kinetics/Makefile b/kinetics/Makefile
deleted file mode 100644
index 9b1f6375d239b8b1ad2ba39eaac061ad0db25d7f..0000000000000000000000000000000000000000
--- a/kinetics/Makefile
+++ /dev/null
@@ -1,58 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _kinetics.o
-
-OBJ = \
-	PoolBase.o	\
-	Pool.o	\
-	BufPool.o	\
-	ReacBase.o	\
-	Reac.o	\
-	EnzBase.o	\
-	CplxEnzBase.o	\
-	Enz.o	\
-	MMenz.o	\
-	Species.o	\
-	ReadKkit.o	\
-	WriteKkit.o	\
-	ReadCspace.o	\
-	lookupVolumeFromMesh.o	\
-	testKinetics.o	\
-
-HEADERS = \
-	../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-Pool.o:	PoolBase.h Pool.h lookupVolumeFromMesh.h
-BufPool.o:	PoolBase.h Pool.h BufPool.h lookupVolumeFromMesh.h
-ReacBase.o:	ReacBase.h lookupVolumeFromMesh.h
-Reac.o:	ReacBase.h Reac.h lookupVolumeFromMesh.h
-EnzBase.o:	EnzBase.h lookupVolumeFromMesh.h
-CplxEnzBase.o:	EnzBase.h CplxEnzBase.h lookupVolumeFromMesh.h
-Enz.o:	EnzBase.h CplxEnzBase.h Enz.h lookupVolumeFromMesh.h
-MMenz.o:	EnzBase.h MMenz.h  lookupVolumeFromMesh.h
-Boundary.o:	Boundary.h
-Species.o:	Species.h
-ReadKkit.o:	lookupVolumeFromMesh.h ReadKkit.h PoolBase.h Pool.h ../shell/Shell.h 
-WriteKkit.o:	lookupVolumeFromMesh.h PoolBase.h
-ReadCspace.o:	lookupVolumeFromMesh.h ReadCspace.h ../shell/Shell.h
-lookupVolumeFromMesh.o: lookupVolumeFromMesh.h
-testKinetics.o:	ReadKkit.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/ksolve/Makefile b/ksolve/Makefile
deleted file mode 100644
index 49b51df4a418ed42d20c7aa9c64bcd06d63c0806..0000000000000000000000000000000000000000
--- a/ksolve/Makefile
+++ /dev/null
@@ -1,100 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _ksolve.o
-
-OBJ = \
-	KinSparseMatrix.o	\
-	ZombiePool.o \
-	ZombieBufPool.o \
-	ZombieReac.o \
-	ZombieEnz.o \
-	ZombieMMenz.o \
-	ZombieFunction.o \
-	VoxelPoolsBase.o \
-	VoxelPools.o \
-	GssaVoxelPools.o \
-	RateTerm.o \
-	FuncTerm.o \
-	Stoich.o \
-	Ksolve.o \
-	SteadyStateGsl.o \
-	Gsolve.o \
-	ZombiePoolInterface.o \
-	testKsolve.o \
-
-HEADERS = \
-	../basecode/header.h \
-	../basecode/SparseMatrix.h \
-	../basecode/ElementValueFinfo.h \
-	RateTerm.h \
-	../external/muparser/include/muParser.h \
-	FuncTerm.h \
-	KinSparseMatrix.h \
-	XferInfo.h \
-	ZombiePoolInterface.h \
-	Stoich.h \
-	../kinetics/Pool.h \
-	../kinetics/lookupVolumeFromMesh.h \
-
-
-# The GSL library (GNU Scientific Library) provides a range of
-# numerical functions, which allow us to use various advanced integration
-# methods. The GslIntegrator accesses these. This library is licenced
-# under the GPL, so only GPL-compliant uses of MOOSE will be able to
-# use it. Should be fine for academic use.
-# Optional: Comment out the following three items if not using GSL
-ifeq ($(USE_GSL),1)
-GSL_OBJ = \
-
-
-GSL_LIBS = -L/usr/lib -lgsl -lgslcblas
-GSL_FLAGS = -DUSE_GSL
-endif
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-KinSparseMatrix.o:	KinSparseMatrix.h ../basecode/SparseMatrix.h
-ZombiePool.o:	../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h ../kinetics/lookupVolumeFromMesh.h
-ZombieBufPool.o:	../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h ZombieBufPool.h ../kinetics/lookupVolumeFromMesh.h
-ZombieBufPool.o:	../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h
-VoxelPoolsBase.o:	VoxelPoolsBase.h ../randnum/RNG.h
-VoxelPools.o:	VoxelPoolsBase.h VoxelPools.h OdeSystem.h RateTerm.h Stoich.h
-GssaVoxelPools.o:	VoxelPoolsBase.h GssaVoxelPools.h ../basecode/SparseMatrix.h \
-    ../randnum/RNG.h KinSparseMatrix.h GssaSystem.h RateTerm.h Stoich.h
-RateTerm.o:		RateTerm.h
-FuncTerm.o:		FuncTerm.h
-Stoich.o:		RateTerm.h FuncTerm.h FuncRateTerm.h Stoich.h ../kinetics/PoolBase.h ../kinetics/ReacBase.h ../kinetics/EnzBase.h ../kinetics/CplxEnzBase.h ../basecode/SparseMatrix.h KinSparseMatrix.h ../scheduling/Clock.h ZombiePoolInterface.h
-ZombieReac.o:		RateTerm.h FuncTerm.h Stoich.h ../kinetics/ReacBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieReac.h
-ZombieEnz.o:		RateTerm.h FuncTerm.h Stoich.h ../kinetics/EnzBase.h ../kinetics/CplxEnzBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieEnz.h
-ZombieMMenz.o:		RateTerm.h FuncTerm.h Stoich.h ../kinetics/EnzBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieMMenz.h
-ZombieFunction.o:		RateTerm.h FuncTerm.h Stoich.h ../builtins/Function.h ZombieFunction.h
-Ksolve.o:		RateTerm.h Stoich.h Ksolve.h VoxelPoolsBase.h VoxelPools.h OdeSystem.h ZombiePoolInterface.h
-SteadyStateGsl.o:	SteadyStateGsl.h ../basecode/SparseMatrix.h KinSparseMatrix.h RateTerm.h FuncTerm.h Stoich.h ../randnum/randnum.h
-Gsolve.o:		RateTerm.h FuncTerm.h FuncRateTerm.h Stoich.h Gsolve.h VoxelPoolsBase.h VoxelPools.h GssaSystem.h ZombiePoolInterface.h ../basecode/SparseMatrix.h KinSparseMatrix.h
-ZombiePoolInterface.o:	VoxelPoolsBase.h ZombiePoolInterface.h ../mesh/VoxelJunction.h Stoich.h ../shell/Shell.h
-testKsolve.o:	../shell/Shell.h
-
-#KineticHub.o:	KineticHub.h
-
-ifeq ($(USE_GSL),1)
-#Optional: Comment out the following two items if not using GSL.
-$(GSL_OBJ) : $(HEADERS)
-#StateScanner.o:	StateScanner.h
-endif # !USE_GSL
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(GSL_FLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg -I../kinetics -I../mesh -I../external/muparser/include -I../builtins $< -c
-
-$(TARGET):		$(OBJ) $(GSL_OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(GSL_OBJ) $(GSL_LIBS) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/mesh/Makefile b/mesh/Makefile
deleted file mode 100644
index 9e211655654da3faa2c5d294e44000b7ddcde74a..0000000000000000000000000000000000000000
--- a/mesh/Makefile
+++ /dev/null
@@ -1,55 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _mesh.o
-
-OBJ = \
-	ChemCompt.o	\
-	MeshCompt.o	\
-	MeshEntry.o	\
-	CubeMesh.o	\
-	CylBase.o	\
-	CylMesh.o	\
-	NeuroNode.o	\
-	NeuroMesh.o	\
-	SpineEntry.o	\
-	SpineMesh.o	\
-	PsdMesh.o	\
-	testMesh.o	\
-
-HEADERS = \
-	../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-MeshEntry.o:	MeshEntry.h
-Boundary.o:	Boundary.h
-ChemCompt.o:	VoxelJunction.h ChemCompt.h MeshEntry.h Boundary.h
-MeshCompt.o:	VoxelJunction.h ChemCompt.h MeshCompt.h MeshEntry.h Boundary.h
-CylBase.o:	../utility/Vec.h CylBase.h
-CylMesh.o:	../utility/Vec.h VoxelJunction.h ChemCompt.h CylBase.h CylMesh.h MeshEntry.h Boundary.h
-CubeMesh.o:	VoxelJunction.h ChemCompt.h CubeMesh.h MeshEntry.h Boundary.h
-NeuroNode.o: CylBase.h NeuroNode.h
-NeuroMesh.o: ../basecode/SparseMatrix.h ChemCompt.h CylBase.h NeuroNode.h NeuroMesh.h
-SpineMesh.o: ../basecode/SparseMatrix.h VoxelJunction.h ChemCompt.h CylBase.h NeuroNode.h NeuroMesh.h ../utility/Vec.h SpineEntry.h SpineMesh.h
-SpineEntry.o: VoxelJunction.h ChemCompt.h CylBase.h ../utility/Vec.h SpineEntry.h
-PsdMesh.o: ../basecode/SparseMatrix.h VoxelJunction.h ChemCompt.h CylBase.h ../utility/Vec.h SpineEntry.h SpineMesh.h
-testMesh.o:	../basecode/SparseMatrix.h CylBase.h NeuroNode.h MeshEntry.h ChemCompt.h CylMesh.h Boundary.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
-
diff --git a/mpi/Makefile b/mpi/Makefile
deleted file mode 100644
index a127fb78de6ffe176ee224b266771deb17c782a3..0000000000000000000000000000000000000000
--- a/mpi/Makefile
+++ /dev/null
@@ -1,34 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2013 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _mpi.o
-
-OBJ = \
-	PostMaster.o	\
-	testMpi.o \
-
-HEADERS = \
-	../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-Postmaster.o:	PostMaster.h
-testMpi.o:	PostMaster.h 
-
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/msg/Makefile b/msg/Makefile
deleted file mode 100644
index 1a373925f150d72886420d1b1fbd243d038334b0..0000000000000000000000000000000000000000
--- a/msg/Makefile
+++ /dev/null
@@ -1,44 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _msg.o
-
-OBJ = \
-	Msg.o	\
-	DiagonalMsg.o	\
-	OneToAllMsg.o	\
-	OneToOneMsg.o	\
-	SingleMsg.o	\
-	SparseMsg.o	\
-	OneToOneDataIndexMsg.o	\
-	testMsg.o	\
-
-HEADERS = \
-	../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-DiagonalMsg.o:	DiagonalMsg.h
-OneToAll.o:	OneToAll.h
-OneToOne.o:	OneToOne.h
-OneToOneDataIndex.o:	OneToOneDataIndex.h
-SingleMsg.o:	SingleMsg.h
-SparseMsg.o:	SparseMsg.h
-testMsg.o: DiagonalMsg.h OneToAllMsg.h OneToOneMsg.h SingleMsg.h SparseMsg.h OneToOneDataIndexMsg.h ../basecode/SetGet.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/pymoose/Makefile b/pymoose/Makefile
deleted file mode 100644
index 1c8abeca9e00a0b2bd0c0b36cf9fb222ebfbdd5d..0000000000000000000000000000000000000000
--- a/pymoose/Makefile
+++ /dev/null
@@ -1,22 +0,0 @@
-# Makefile
-# 
-# Author: Subhasis Ray
-# Created: 2011-03-10 12:10:32 (+0530)
-TARGET = _pymoose.o
-# CXXFLAGS += -I../basecode -I../msg -I../shell
-CXXFLAGS += -DQUIET_MODE
-NUMPY_WARNING_FLAG = -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
-.PHONY: clean
-
-HEADERS = moosemodule.h ../basecode/global.h PyRun.h
-
-OBJ = moosemodule.o mfield.o vec.o melement.o test_moosemodule.o PyRun.o
-
-$(TARGET): $(OBJ) $(HEADERS) ../basecode/main.cpp ../utility/_utility.o ../basecode/_basecode.o
-	$(LD) -r -o $(TARGET) $(OBJ) $(LDFLAGS)
-
-.cpp.o: $(HEADERS)
-	$(CXX) $(CXXFLAGS) $(NUMPY_WARNING_FLAG) -I.. -I../basecode $< -c
-clean: 
-	-rm -f *.o
-
diff --git a/randnum/Makefile b/randnum/Makefile
deleted file mode 100644
index 259bbb4c7882c99a7c45a5970251d0a9f49ac921..0000000000000000000000000000000000000000
--- a/randnum/Makefile
+++ /dev/null
@@ -1,51 +0,0 @@
-CXXFLAGS += -I..
-# the line below are for easy inclusion of libxml++
-#CXXFLAGS += $(shell pkg-config libxml++-2.6 --CXXFLAGS) 
-
-TARGET = _randnum.o
-
-OBJ = \
-	mt19937ar.o	\
-	RandGenerator.o	\
-	UniformRng.o	\
-	Uniform.o	\
-	Exponential.o	\
-	ExponentialRng.o	\
-	Binomial.o	\
-	Normal.o	\
-	Poisson.o	\
-	Gamma.o		\
-	PoissonRng.o	\
-	NormalRng.o	\
-	BinomialRng.o	\
-	GammaRng.o	\
-
-HEADERS = \
-	../basecode/header.h	\
-	randnum.h	\
-	Probability.h	\
-	RandGenerator.h	\
-	UniformRng.h	\
-	Uniform.h	\
-	Exponential.h	\
-	ExponentialRng.h	\
-	Binomial.h	\
-	Gamma.h		\
-	Poisson.h	\
-	PoissonRng.h	\
-	Normal.h	\
-	NormalRng.h	\
-	BinomialRng.h	\
-	GammaRng.h	\
-
-default: $(TARGET)
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $< -c
-#	$(CXX) $(CXXFLAGS) $(shell pkg-config libxml++-2.6 --CXXFLAGS) $< -c
-
-$(TARGET): $(OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ)
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/scheduling/Makefile b/scheduling/Makefile
deleted file mode 100644
index 2061a090a4a12a018e047a11c1db4c2416c0b4e9..0000000000000000000000000000000000000000
--- a/scheduling/Makefile
+++ /dev/null
@@ -1,34 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2009 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _scheduling.o
-
-OBJ = \
-	Clock.o	\
-	testScheduling.o \
-
-HEADERS = \
-	../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-Clock.o:	Clock.h
-testScheduling.o:	Clock.h 
-
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/.pre-commit-config.yaml b/scripts/pre-commit-config.yaml
similarity index 100%
rename from .pre-commit-config.yaml
rename to scripts/pre-commit-config.yaml
diff --git a/shell/Makefile b/shell/Makefile
deleted file mode 100644
index 543301438d3e165da180a7ee2109b498a1bd4023..0000000000000000000000000000000000000000
--- a/shell/Makefile
+++ /dev/null
@@ -1,49 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _shell.o
-
-OBJ = \
-	Shell.o	\
-	ShellCopy.o	\
-	ShellThreads.o	\
-	LoadModels.o \
-	SaveModels.o \
-	Neutral.o	\
-	Wildcard.o	\
-	testShell.o	\
-
-HEADERS = \
-	../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-#Shell.o:	Shell.h Neutral.h ../scheduling/Clock.h ../sbml/MooseSbmlWriter.h ../sbml/MooseSbmlReader.h
-Shell.o:	Shell.h Neutral.h ../scheduling/Clock.h
-ShellCopy.o:	Shell.h Neutral.h ../scheduling/Clock.h
-ShellSetGet.o:	Shell.h
-ShellThreads.o:	Shell.h Neutral.h ../scheduling/Clock.h
-LoadModels.o:	Shell.h Neutral.h ../biophysics/SwcSegment.h ../biophysics/ReadSwc.h
-SaveModels.o:	Shell.h Neutral.h
-Neutral.o:	Neutral.h ../basecode/ElementValueFinfo.h
-Wildcard.o:	Wildcard.h Shell.h Neutral.h ../basecode/ElementValueFinfo.h
-testShell.o:	Wildcard.h Shell.h Neutral.h ../builtins/Arith.h ../basecode/SparseMatrix.h ../msg/SparseMsg.h ../msg/SingleMsg.h ../basecode/SetGet.h ../basecode/HopFunc.h ../basecode/OpFuncBase.h ../basecode/OpFunc.h
-
-#../kinetics/ReadKkit.h ../biophysics/ReadCell.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I.. -I../basecode -I../msg $< -c
-
-$(TARGET):		$(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) 
-
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/signeur/Makefile b/signeur/Makefile
deleted file mode 100644
index ad8c507467241ca0853937796d8b21b8e10b9b8f..0000000000000000000000000000000000000000
--- a/signeur/Makefile
+++ /dev/null
@@ -1,36 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           Copyright (C) 2003-2012 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-CXXFLAGS += -I..
-# the line below are for easy inclusion of libxml++
-#CXXFLAGS += $(shell pkg-config libxml++-2.6 --cflags) 
-
-TARGET = _signeur.o
-
-OBJ = \
-	Adaptor.o	\
-	testSigNeur.o
-
-
-HEADERS = \
-	../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-Adaptor.o:	Adaptor.h
-testSigNeur.o:	Adaptor.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) -I.. -I../basecode $< -c
-
-$(TARGET): $(OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) 
-clean:
-	-rm -f *.o $(TARGET) core core.*
diff --git a/synapse/Makefile b/synapse/Makefile
deleted file mode 100644
index bbf82b990c89bb574aab8b2fd4ff27857a97a6d1..0000000000000000000000000000000000000000
--- a/synapse/Makefile
+++ /dev/null
@@ -1,50 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _synapse.o
-
-OBJ = \
-	SynHandlerBase.o	\
-	SimpleSynHandler.o	\
-	STDPSynHandler.o	\
-	GraupnerBrunel2012CaPlasticitySynHandler.o	\
-	Synapse.o	\
-	STDPSynapse.o	\
-	RollingMatrix.o	\
-	SeqSynHandler.o \
-	testSynapse.o	\
-
-# GSL_LIBS = -L/usr/lib -lgsl
-
-HEADERS = \
-	../basecode/header.h \
-	../utility/numutil.h \
-
-
-default: $(TARGET)
-
-$(OBJ)	: $(HEADERS)
-SynHandlerBase.o:	SynHandlerBase.h Synapse.h 
-SimpleSynHandler.o:	SynHandlerBase.h Synapse.h SimpleSynHandler.h SynEvent.h
-STDPSynHandler.o:	SynHandlerBase.h STDPSynapse.h STDPSynHandler.h SynEvent.h
-GraupnerBrunel2012CaPlasticitySynHandler.o:	SynHandlerBase.h Synapse.h GraupnerBrunel2012CaPlasticitySynHandler.h SynEvent.h
-Synapse.o:	Synapse.h SynHandlerBase.h
-STDPSynapse.o:	STDPSynapse.h SynHandlerBase.h
-RollingMatrix.o:	RollingMatrix.h
-SeqSynHandler.o:	SynHandlerBase.h Synapse.h SimpleSynHandler.h SeqSynHandler.h RollingMatrix.h SynEvent.h
-testSynapse.o: SynHandlerBase.h Synapse.h SimpleSynHandler.h SeqSynHandler.h RollingMatrix.h SynEvent.h
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg -I .. -I../external/muparser/include $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
-	rm -f *.o $(TARGET) core core.*
diff --git a/tests/python/test_hsolve_externalCalcium.py b/tests/python/test_hsolve_externalCalcium.py
index 1a831b607abc3d146f1d0a081bc138410192f1b0..92f5e68ec50ef00465709423b7d1567b10913fa5 100644
--- a/tests/python/test_hsolve_externalCalcium.py
+++ b/tests/python/test_hsolve_externalCalcium.py
@@ -1,3 +1,6 @@
+# Test scripts are always called from BUILD directory by cmake. 
+
+import os
 import sys
 import numpy as np
 import time
@@ -11,11 +14,11 @@ print('Using moose from %s' % moose.__file__ )
 difshell_no = 3
 difbuf_no = 0
 
+script_dir_ = os.path.dirname( os.path.abspath( __file__ ) )
 
-p_file = "soma.p"
-cond = {'CaL12':30*0.35e-5,
-        'SK':0.5*0.35e-6}
+p_file = os.path.join( script_dir_, "soma.p" )
 
+cond = {'CaL12':30*0.35e-5, 'SK':0.5*0.35e-6}
 
 if __name__ =='__main__':
     for tick in range(0, 7):
@@ -63,7 +66,9 @@ if __name__ =='__main__':
     t_stop = 10.
     moose.reinit()
     moose.start(t_stop)
-    print len(np.where(sktab.vector<1e-19)[0]), len(np.where(shelltab.vector>50e-6)[0])
-    
-    
+    print( sktab.vector )
+    print( shelltab.vector )
+    print(len(np.where(sktab.vector<1e-19)[0]), 
+            len(np.where(shelltab.vector>50e-6)[0])
+            )
     
diff --git a/utility/Makefile b/utility/Makefile
deleted file mode 100644
index 87af0b7dc6bf3ae2edd3e7517cc15831d4e4679c..0000000000000000000000000000000000000000
--- a/utility/Makefile
+++ /dev/null
@@ -1,45 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#**           Copyright (C) 2003-2012 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-CXXFLAGS += -I..
-# the line below are for easy inclusion of libxml++
-#CXXFLAGS += $(shell pkg-config libxml++-2.6 --cflags) 
-
-TARGET = _utility.o
-
-OBJ = \
-	strutil.o	\
-	types.o 	\
-	setupenv.o	\
-	numutil.o	\
-	Annotator.o	\
-	cnpy.o 		\
-	Vec.o	\
-
-
-HEADERS = \
-	strutil.h 	\
-	numutil.h	\
-	../basecode/header.h \
-	cnpy.hpp 	\
-
-default: $(TARGET)
-
-strutil.o: strutil.h
-Annotator.o: Annotator.h
-Vec.o: Vec.h ../basecode/doubleEq.h
-cnpy.o : cnpy.hpp
-
-.cpp.o:
-	$(CXX) $(CXXFLAGS) -I.. -I../basecode $< -c
-
-$(TARGET): $(OBJ) $(HEADERS)
-	$(LD) -r -o $(TARGET) $(OBJ) 
-clean:
-	-rm -f *.o $(TARGET) core core.*