diff --git a/generators.py b/generators.py
index e177424ef..f23ec20c8 100755
--- a/generators.py
+++ b/generators.py
@@ -141,6 +141,17 @@ class Generator():
             args.append(fname)
         return args
 
+    def generate_configure_files(self):
+        for cf in self.build.get_configure_files():
+            infile = os.path.join(self.environment.get_source_dir(),
+                                  cf.get_subdir(),
+                                  cf.get_source_name())
+            outdir = os.path.join(self.environment.get_build_dir(),
+                                   cf.get_subdir())
+            os.makedirs(outdir, exist_ok=True)
+            outfile = os.path.join(outdir, cf.get_target_name())
+            do_conf_file(infile, outfile, self.interpreter.get_variables())
+
 class NinjaGenerator(Generator):
 
     def __init__(self, build, interp):
@@ -150,6 +161,7 @@ class NinjaGenerator(Generator):
     def generate(self):
         outfilename = os.path.join(self.environment.get_build_dir(), self.ninja_filename)
         outfile = open(outfilename, 'w')
+        self.generate_configure_files()
         outfile.write('# This is the build file for project "%s"\n' % self.build.get_project())
         outfile.write('# It is autogenerated. Do not edit by hand.\n\n')
         self.generate_rules(outfile)
@@ -324,7 +336,7 @@ class NinjaGenerator(Generator):
         build = 'build %s: %s %s %s\n' % \
         (ninja_quote(abs_obj), compiler_name, ninja_quote(abs_src),
          pch_dep)
-        flags = ' FLAGS = %s\n\n' % ' '.join([ninja_quote(t) for t in commands])
+        flags = ' FLAGS = %s\n\n' % ' '.join(["'" + ninja_quote(t) + "'" for t in commands])
         outfile.write(build)
         outfile.write(flags)
         return abs_obj
@@ -460,17 +472,6 @@ echo Run compile.sh before this or bad things will happen.
         cpcommand = ' '.join(shell_quote(cpcommand)) + ' || exit\n'
         outfile.write(cpcommand)
 
-    def generate_configure_files(self):
-        for cf in self.build.get_configure_files():
-            infile = os.path.join(self.environment.get_source_dir(),
-                                  cf.get_subdir(),
-                                  cf.get_source_name())
-            outdir = os.path.join(self.environment.get_build_dir(),
-                                   cf.get_subdir())
-            os.makedirs(outdir, exist_ok=True)
-            outfile = os.path.join(outdir, cf.get_target_name())
-            do_conf_file(infile, outfile, self.interpreter.get_variables())
-
     def generate_data_install(self, outfile):
         prefix = self.environment.get_prefix()
         dataroot = os.path.join(prefix, self.environment.get_datadir())
diff --git a/run_tests.py b/run_tests.py
index 0f39a6de3..fcf56a6d6 100755
--- a/run_tests.py
+++ b/run_tests.py
@@ -20,9 +20,9 @@ import os, subprocess, shutil
 test_build_dir = 'work area'
 install_dir = os.path.join(os.path.split(os.path.abspath(__file__))[0], 'install dir')
 builder_command = './builder.py'
-compile_commands = [os.path.join(test_build_dir, 'compile.sh')]
-test_commands = [os.path.join(test_build_dir, 'run_tests.sh')]
-install_commands = [os.path.join(test_build_dir, 'install.sh')]
+compile_commands = ['compile.sh']
+test_commands = ['run_tests.sh']
+install_commands = ['install.sh']
 
 def run_test(testdir):
     shutil.rmtree(test_build_dir)
@@ -34,15 +34,15 @@ def run_test(testdir):
     p.wait()
     if p.returncode != 0:
         raise RuntimeError('Generating the build system failed.')
-    pc = subprocess.Popen(compile_commands)
+    pc = subprocess.Popen(compile_commands, cwd=test_build_dir)
     pc.wait()
     if pc.returncode != 0:
         raise RuntimeError('Compiling source code failed.')
-    pt = subprocess.Popen(test_commands)
+    pt = subprocess.Popen(test_commands, cwd=test_build_dir)
     pt.wait()
     if pt.returncode != 0:
         raise RuntimeError('Running unit tests failed.')
-    pi = subprocess.Popen(install_commands)
+    pi = subprocess.Popen(install_commands, cwd=test_build_dir)
     pi.wait()
     if pi.returncode != 0:
         raise RuntimeError('Running install failed.')