diff --git a/framework/core/Constants.pm b/framework/core/Constants.pm
index b5fd92992..92a3988fb 100644
--- a/framework/core/Constants.pm
+++ b/framework/core/Constants.pm
@@ -48,7 +48,7 @@ our @ISA = qw(Exporter);
 my $dir = dirname(abs_path(__FILE__));
 
 # Enable debugging and verbose output
-our $DEBUG = 0;
+our $DEBUG = $ENV{'D4J_DEBUG'} // 0;
 
 =pod
 
@@ -232,8 +232,6 @@ unshift(@INC, $SCRIPT_DIR);
 unshift(@INC, $LIB_DIR);
 # Append Major's executables to the PATH -> ant may not be installed by default
 $ENV{PATH}="$ENV{PATH}:$MAJOR_ROOT/bin";
-# set name of mml file that provides definitions of used mutation operators
-$ENV{MML}="$MAJOR_ROOT/mml/all_mutants.mml.bin" unless defined $ENV{'MML'};
 
 # Constant strings used for errors
 our $ARG_ERROR       = "Invalid number of arguments!";
diff --git a/framework/core/Project.pm b/framework/core/Project.pm
index ad51d739a..b156cddba 100644
--- a/framework/core/Project.pm
+++ b/framework/core/Project.pm
@@ -767,7 +767,11 @@ sub mutate {
     $ENV{MML} = $mml_bin;
 
     # Mutate and compile sources
-    if (! $self->_call_major("mutate")) {
+    my $ret = $self->_call_major("mutate");
+
+    delete($ENV{MML});
+
+    if (! $ret) {
         return -1;
     }
 
@@ -1031,9 +1035,14 @@ sub _call_major {
     @_ >= 2 or die $ARG_ERROR;
     my ($self, $target, $option_str, $log_file, $ant_cmd) =  @_;
     $option_str = "-Dbuild.compiler=major.ant.MajorCompiler " . ($option_str // "");
+    # Prepend path with Major's executables
+    my $path = $ENV{PATH};
     $ENV{PATH}="$MAJOR_ROOT/bin:$ENV{PATH}";
     $ant_cmd = "$MAJOR_ROOT/bin/ant" unless defined $ant_cmd;
-    return $self->_ant_call($target, $option_str, $log_file, $ant_cmd);
+    my $ret = $self->_ant_call($target, $option_str, $log_file, $ant_cmd);
+    # Reset path for downstream calls to ant
+    $ENV{PATH} = $path;
+    return($ret);
 }
 
 #
diff --git a/framework/projects/defects4j.build.xml b/framework/projects/defects4j.build.xml
index 03aee7ce5..0ed95311e 100644
--- a/framework/projects/defects4j.build.xml
+++ b/framework/projects/defects4j.build.xml
@@ -60,6 +60,8 @@ project-specific build file ("project_id"/"project_id".build.xml) for the
 
     <!-- Location of customized JUnit formatter-->
     <property name="formatter.jar" value="${d4j.home}/framework/lib/formatter.jar"/>
+    <!-- Directory of compiled test-gen classes -->
+    <property name="d4j.dir.classes.testgen" value="${d4j.workdir}/.classes_testgen"/>
     <!-- Directory of instrumented classes (e.g., for coverage analysis)-->
     <property name="d4j.dir.classes.instrumented" value="${d4j.workdir}/.classes_instrumented"/>
     <!-- Directory of mutated classes-->
@@ -143,7 +145,7 @@ project-specific build file ("project_id"/"project_id".build.xml) for the
             <classpath>
                 <pathelement path="${formatter.jar}" />
                 <pathelement path="${junit.jar}" />
-                <pathelement path="${build.home}/gen-tests" />
+                <pathelement path="${d4j.dir.classes.testgen}" />
                 <path refid="d4j.test.classpath"/>
                 <!-- Add dependencies to runtime libraries of test generation tools -->
                 <path refid="d4j.lib.testgen.rt"/>
@@ -184,7 +186,7 @@ project-specific build file ("project_id"/"project_id".build.xml) for the
 <!--
     Run mutation analysis
 -->
-    <target name="mutation.test" depends="compile.tests,update.all.tests" description="Perform mutation analysis">
+    <target name="mutation.test" depends="update.all.tests" description="Perform mutation analysis">
         <!-- Test a generated test suite -->
         <if><isset property="d4j.test.include"/>
             <then>
@@ -229,7 +231,7 @@ project-specific build file ("project_id"/"project_id".build.xml) for the
 
             <classpath>
                 <pathelement location="${d4j.dir.classes.mutated}" />
-                <pathelement path="${build.home}/gen-tests" />
+                <pathelement path="${d4j.dir.classes.testgen}" />
                 <path refid="d4j.test.classpath"/>
                 <!-- Add dependencies to runtime libraries of test generation tools -->
                 <path refid="d4j.lib.testgen.rt"/>
@@ -254,10 +256,10 @@ project-specific build file ("project_id"/"project_id".build.xml) for the
         <echo message="classes.dir: ${classes.dir}" />
         <echo message="build.home: ${build.home}" />
 
-        <delete dir="${build.home}/gen-tests" quiet="true" />
-        <mkdir dir="${build.home}/gen-tests" />
+        <delete dir="${d4j.dir.classes.testgen}" quiet="true" />
+        <mkdir dir="${d4j.dir.classes.testgen}" />
         <javac srcdir="${d4j.test.dir}"
-               destdir="${build.home}/gen-tests"
+               destdir="${d4j.dir.classes.testgen}"
                debug="true"
                deprecation="false"
                optimize="false">
@@ -288,7 +290,7 @@ project-specific build file ("project_id"/"project_id".build.xml) for the
                 <!-- Make sure that instrumented classes appear at the beginning of the
                      classpath -->
                 <pathelement location="${d4j.dir.classes.instrumented}" />
-                <pathelement path="${build.home}/gen-tests" />
+                <pathelement path="${d4j.dir.classes.testgen}" />
                 <pathelement path="${formatter.jar}" />
                 <pathelement path="${junit.jar}" />
                 <pathelement path="${classes.dir}" />