diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
index af23ad1e3..cce83c00b 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
@@ -128,11 +128,8 @@ public void setUp() throws Exception {
 		if (!tmp.delete() || !tmp.mkdir())
 			throw new IOException("Cannot create " + tmp);
 
-		// measure timer resolution before the test to avoid time critical tests
-		// are affected by time needed for measurement
-		FS.getFileStoreAttributes(tmp.toPath().getParent());
-
 		mockSystemReader = new MockSystemReader();
+		SystemReader.setInstance(mockSystemReader);
 		mockSystemReader.userGitConfig = new FileBasedConfig(new File(tmp,
 				"usergitconfig"), FS.DETECTED);
 		// We have to set autoDetach to false for tests, because tests expect to be able
@@ -142,7 +139,12 @@ public void setUp() throws Exception {
 				null, ConfigConstants.CONFIG_KEY_AUTODETACH, false);
 		mockSystemReader.userGitConfig.save();
 		ceilTestDirectories(getCeilings());
-		SystemReader.setInstance(mockSystemReader);
+
+		// Measure timer resolution before the test to avoid time critical tests
+		// are affected by time needed for measurement.
+		// The MockSystemReader must be configured first since we need to use
+		// the same one here
+		FS.getFileStoreAttributes(tmp.toPath().getParent());
 
 		author = new PersonIdent("J. Author", "jauthor@example.com");
 		committer = new PersonIdent("J. Committer", "jcommitter@example.com");
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ConfigTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ConfigTest.java
index 0ce645139..1ce86d15e 100644
--- a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ConfigTest.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ConfigTest.java
@@ -43,14 +43,14 @@
 package org.eclipse.jgit.pgm;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
-import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.List;
+import java.util.HashMap;
+import java.util.Map;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
-import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.Before;
 import org.junit.Test;
@@ -65,6 +65,7 @@ public void setUp() throws Exception {
 		}
 	}
 
+	@SuppressWarnings("boxing")
 	@Test
 	public void testListConfig() throws Exception {
 		boolean isWindows = SystemReader.getInstance().getProperty("os.name")
@@ -73,19 +74,31 @@ public void testListConfig() throws Exception {
 				.equals("Mac OS X");
 
 		String[] output = execute("git config --list");
-		List<String> expect = new ArrayList<>();
-		expect.add("gc.autoDetach=false");
-		expect.add("core.filemode=" + !isWindows);
-		expect.add("core.logallrefupdates=true");
-		if (isMac)
-			expect.add("core.precomposeunicode=true");
-		expect.add("core.repositoryformatversion=0");
-		if (!FS.DETECTED.supportsSymlinks())
-			expect.add("core.symlinks=false");
-		expect.add(""); // ends with LF (last line empty)
-		assertEquals("expected default configuration",
-				Arrays.asList(expect.toArray()).toString(),
-				Arrays.asList(output).toString());
+
+		Map<String, String> options = parseOptions(output);
+
+		assertEquals(!isWindows, Boolean.valueOf(options.get("core.filemode")));
+		assertTrue((Boolean.valueOf(options.get("core.logallrefupdates"))));
+		if (isMac) {
+			assertTrue(
+					(Boolean.valueOf(options.get("core.precomposeunicode"))));
+		}
+		assertEquals(Integer.valueOf(0),
+				Integer.valueOf(options.get("core.repositoryformatversion")));
+	}
+
+	private Map<String, String> parseOptions(String[] output) {
+		Map<String, String> options = new HashMap<>();
+		Arrays.stream(output).forEachOrdered(s -> {
+			int p = s.indexOf('=');
+			if (p == -1) {
+				return;
+			}
+			String key = s.substring(0, p);
+			String value = s.substring(p + 1);
+			options.put(key, value);
+		});
+		return options;
 	}
 
 }