diff --git a/README.md b/README.md
index ece13e1d33d1c989123ee8f931ce46990f8d667e..8dc9cb91cd54717aa0f4a807ea006e09ef5a6384 100644
--- a/README.md
+++ b/README.md
@@ -10,10 +10,13 @@ Requirements
 
 Giraffe requires the MOOSE environment (including PETSc, libmesh, and MOOSE).  This can be installed according to the [MOOSE installation instructions](http://mooseframework.com/getting-started/).  After installation you must define the following environment variables:
 * `LIBMESH_DIR`: The top-level directory of your libmesh installation.  If you follow the MOOSE installation instructions, this should already be set in your environment.  A typical command is:
+
   ``` Shell
   export $LIBMESH_DIR="$HOME/projects/moose/libmesh/installed"
   ```
+
 * `MOOSE_DIR`:  The top-level directory of your MOOSE installation.  For Giraffe, this must be additionally set in your environment. A typical command is:
+
   ``` Shell
   export $MOOSE_DIR="$HOME/projects/moose/"
   ```
@@ -29,6 +32,7 @@ Giraffe must be separately compiled for each specific problem, since Nek5000 use
 3. In the subdirctory for the example problem, run `make`. 
 
 The complete steps for the `integration_example` problem are:
+
 ``` Shell
 $ cd giraffe
 $ ./bootstrap
@@ -55,6 +59,7 @@ $ ../../giraffe-opt -i coefficient_integration.i
 ```
 
 The Giraffe executable is output to the top-level Giraffe directory (in this case, `giraffe/giraffe-opt`) but must be run in the example subdirectory.  To run the simulation, use:
+
 ``` Shell
 $ cd examples/integration example/
 $ ../../giraffe-opt -i coefficient_integration.i
diff --git a/config/giraffe.mk.in b/config/giraffe.mk.in
index cba48d378e725a5c79488d0a14faab21389ad11d..b69ae5626f4055b28c0012cd997ebcaf5d715777 100644
--- a/config/giraffe.mk.in
+++ b/config/giraffe.mk.in
@@ -1,5 +1,5 @@
 # == Source and destination directories ============================================================
-VPATH    := @srcdir@/Nek5000/core:@srcdir@/Nek5000/core/cmt:@srcdir@/Nek5000/core/3rd_party:@srcdir@/Nek5000/jl
+VPATH    := @srcdir@/Nek5000/core:@srcdir@/Nek5000/core/cmt:@srcdir@/Nek5000/core/3rd_party:@srcdir@/Nek5000/jl:@srcdir@/src_nek
 srcdir   := @srcdir@
 builddir := @builddir@
 nek_objdir   := @builddir@/nek_obj
@@ -8,7 +8,7 @@ nek_includedir := @builddir@/include
 # == Discovered by autoconf script
 CASENAME     := @CASENAME@
 nek_CFLAGS   := @CFLAGS@
-nek_INCLUDES := -I$(builddir) -I$(nek_includedir) -I$(srcdir)/Nek5000/core -I$(srcdir)/Nek5000/core/cmt -I$(srcdir)/Nek5000/core/3rd_party -I$(srcdir)/Nek5000/jl
+nek_INCLUDES := -I$(builddir) -I$(nek_includedir) -I$(srcdir)/Nek5000/core -I$(srcdir)/Nek5000/core/cmt -I$(srcdir)/Nek5000/core/3rd_party -I$(srcdir)/Nek5000/jl -I$(srcdir)/src_nek
 nek_CPPFLAGS := @CPPFLAGS@ @DEFS@ @nek_DEFS@ $(nek_INCLUDES)
 nek_LDFLAGS  := @LDFLAGS@
 nek_LIBS     := @LIBS@
@@ -32,7 +32,7 @@ nek_core_f_obj := $(addprefix $(nek_objdir)/, $(addsuffix .$(obj-suffix), \
                   subs1 subs2 genbox gmres hsmg convect induct perturb navier5 \
                   navier6 navier7 navier8 fast3d fasts calcz postpro \
                   cvode_driver vprops qthermal cvode_aux makeq_aux papi nek_in_situ \
-                  readat_new @CASENAME@))
+                  readat_new nek_moose @CASENAME@))
 
 nek_math_obj   := $(addprefix $(nek_objdir)/, $(addsuffix .$(obj-suffix), math))
 nek_blas_obj   := $(addprefix $(nek_objdir)/, $(addsuffix .$(obj-suffix), @nek_blas_obj@))   # blas.o | null
diff --git a/src/nek/NEKMOOSE b/src_nek/NEKMOOSE
similarity index 100%
rename from src/nek/NEKMOOSE
rename to src_nek/NEKMOOSE
diff --git a/src/nek/nek_moose.f b/src_nek/nek_moose.f
similarity index 100%
rename from src/nek/nek_moose.f
rename to src_nek/nek_moose.f