diff --git a/Makefile b/Makefile
index 7b83dae..6c5b4a1 100644
--- a/Makefile
+++ b/Makefile
@@ -28,7 +28,7 @@ include make.config
 .PHONY: default clean veryclean archive configure 
 
 default: make.config
-	$(MAKE) -C $$PWD/src 
+	cd src && $(MAKE)
 
 clean:
 	- bash -c "[[ -f lib/libezfio.a ]] && rm $$PWD/lib/*"
diff --git a/build.ninja b/build.ninja
index 4d8bcc1..719f5ba 100644
--- a/build.ninja
+++ b/build.ninja
@@ -6,7 +6,7 @@ rule build_generated_ninja
    generator = 1
 
 rule run_ninja
-   command = bash -c 'source make.config ; bash -c "$$NINJA -f $in"'
+   command = bash -c 'source .make.config.sh ; exec bash -c "$$NINJA -f $in"'
    description = Building Fortran library
 
 rule build_archive
@@ -14,11 +14,11 @@ rule build_archive
    description = Building archive
 
 rule clean_all
-   command = bash -c 'source make.config ; bash -c "$$NINJA -f $in -t clean ; $$NINJA -t clean" ; rm -rf src/IRPF90_{temp,man} src/*.pyc'
+   command = bash -c 'source .make.config.sh ; bash -c "$$NINJA -f $in -t clean ; $$NINJA -t clean" ; rm -rf src/IRPF90_{temp,man} src/*.pyc'
    description = Cleaning directory
 
 
-build make.config generated.ninja: build_generated_ninja configure.py
+build make.config .make.config.sh generated.ninja: build_generated_ninja configure.py
 
 build all: run_ninja generated.ninja
 default all
diff --git a/configure.py b/configure.py
index 50eae69..8069e58 100755
--- a/configure.py
+++ b/configure.py
@@ -19,18 +19,16 @@ d_default = {
 
 def create_make_config():
 
-    if sys.argv[-1] == 'ninja':
-        fmt = '{0}="{1}"\n'
-    else:
-        fmt = '{0}={1}\n'
-
-    with open("make.config",'w') as out:
-        for var,default in d_default.iteritems():
-            try:
-                cur = os.environ[var] 
-            except KeyError:
-                cur = default
-            out.write(fmt.format(var,cur))
+    fmt = { "make.config" :'{0}={1}\n' , 
+            ".make.config.sh": '{0}="{1}"\n' }
+    for filename in fmt:
+        with open(filename,'w') as out:
+            for var,default in d_default.iteritems():
+                try:
+                    cur = os.environ[var] 
+                except KeyError:
+                    cur = default
+                out.write(fmt[filename].format(var,cur))
 
 
 def read_make_config():
@@ -39,8 +37,6 @@ def read_make_config():
         for line in f.readlines():
           try:
             key, value = line.strip().split('=',1)
-            if value.startswith('"') and value.endswith('"'):
-                value = value[1:-1]
           except:
             print "Error in make.config:"
             print line
@@ -51,8 +47,7 @@ def read_make_config():
 
 def create_build_ninja():
     
-    if "make.config" not in os.listdir(os.getcwd()):
-        create_make_config()
+    create_make_config()
 
     d = read_make_config()