diff --git a/java/com/google/gerrit/acceptance/AbstractDaemonTest.java b/java/com/google/gerrit/acceptance/AbstractDaemonTest.java
index fd61aa5054..a933dac851 100644
--- a/java/com/google/gerrit/acceptance/AbstractDaemonTest.java
+++ b/java/com/google/gerrit/acceptance/AbstractDaemonTest.java
@@ -124,6 +124,7 @@ import com.google.gerrit.server.query.change.ChangeData;
 import com.google.gerrit.server.query.change.InternalChangeQuery;
 import com.google.gerrit.server.restapi.change.Revisions;
 import com.google.gerrit.server.update.BatchUpdate;
+import com.google.gerrit.server.util.git.DelegateSystemReader;
 import com.google.gerrit.testing.ConfigSuite;
 import com.google.gerrit.testing.FakeEmailSender;
 import com.google.gerrit.testing.FakeEmailSender.Message;
@@ -135,6 +136,7 @@ import com.google.inject.Module;
 import com.google.inject.Provider;
 import com.jcraft.jsch.KeyPair;
 import java.io.ByteArrayOutputStream;
+import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -170,11 +172,14 @@ import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevSort;
 import org.eclipse.jgit.revwalk.RevTree;
 import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.transport.FetchResult;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.Transport;
 import org.eclipse.jgit.transport.TransportBundleStream;
 import org.eclipse.jgit.transport.URIish;
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -289,6 +294,7 @@ public abstract class AbstractDaemonTest {
   private ProjectResetter resetter;
   private List<Repository> toClose;
   private String systemTimeZone;
+  private SystemReader oldSystemReader;
 
   @Before
   public void clearSender() {
@@ -385,6 +391,10 @@ public abstract class AbstractDaemonTest {
   }
 
   protected void beforeTest(Description description) throws Exception {
+    // SystemReader must be overridden before creating any repos, since they read the user/system
+    // configs at initialization time, and are then stored in the RepositoryCache forever.
+    oldSystemReader = setFakeSystemReader(temporaryFolder.getRoot());
+
     this.description = description;
     GerritServer.Description classDesc =
         GerritServer.Description.forTestClass(description, configName);
@@ -447,6 +457,28 @@ public abstract class AbstractDaemonTest {
         methodDesc.useSystemTime(), methodDesc.useClockStep(), methodDesc.useTimezone());
   }
 
+  private static SystemReader setFakeSystemReader(File tempDir) {
+    SystemReader oldSystemReader = SystemReader.getInstance();
+    SystemReader.setInstance(
+        new DelegateSystemReader(oldSystemReader) {
+          @Override
+          public FileBasedConfig openJGitConfig(Config parent, FS fs) {
+            return new FileBasedConfig(parent, new File(tempDir, "jgit.config"), FS.detect());
+          }
+
+          @Override
+          public FileBasedConfig openUserConfig(Config parent, FS fs) {
+            return new FileBasedConfig(parent, new File(tempDir, "user.config"), FS.detect());
+          }
+
+          @Override
+          public FileBasedConfig openSystemConfig(Config parent, FS fs) {
+            return new FileBasedConfig(parent, new File(tempDir, "system.config"), FS.detect());
+          }
+        });
+    return oldSystemReader;
+  }
+
   private void setTimeSettings(
       boolean useSystemTime,
       @Nullable UseClockStep useClockStep,
@@ -602,6 +634,8 @@ public abstract class AbstractDaemonTest {
       server.close();
       server = null;
     }
+    SystemReader.setInstance(oldSystemReader);
+    oldSystemReader = null;
   }
 
   protected void closeSsh() {
diff --git a/java/com/google/gerrit/acceptance/StandaloneSiteTest.java b/java/com/google/gerrit/acceptance/StandaloneSiteTest.java
index a095daaf20..1d6f51f8f6 100644
--- a/java/com/google/gerrit/acceptance/StandaloneSiteTest.java
+++ b/java/com/google/gerrit/acceptance/StandaloneSiteTest.java
@@ -143,6 +143,11 @@ public abstract class StandaloneSiteTest {
     SystemReader oldSystemReader = SystemReader.getInstance();
     SystemReader.setInstance(
         new DelegateSystemReader(oldSystemReader) {
+          @Override
+          public FileBasedConfig openJGitConfig(Config parent, FS fs) {
+            return new FileBasedConfig(parent, new File(tempDir, "jgit.config"), FS.detect());
+          }
+
           @Override
           public FileBasedConfig openUserConfig(Config parent, FS fs) {
             return new FileBasedConfig(parent, new File(tempDir, "user.config"), FS.detect());
diff --git a/polygerrit-ui/app/rules.bzl b/polygerrit-ui/app/rules.bzl
index cd4819a914..93c662aa55 100644
--- a/polygerrit-ui/app/rules.bzl
+++ b/polygerrit-ui/app/rules.bzl
@@ -22,8 +22,6 @@ def polygerrit_bundle(name, srcs, outs, app):
         dependency_mode = "PRUNE_LEGACY",
     )
 
-    # TODO(davido): Remove JSC_REFERENCE_BEFORE_DECLARE when this is fixed upstream:
-    # https://github.com/Polymer/polymer-resin/issues/7
     closure_js_library(
         name = name + "_closure_lib",
         srcs = [appName + ".js"],
@@ -32,9 +30,7 @@ def polygerrit_bundle(name, srcs, outs, app):
         # and remove this supression
         suppress = [
             "JSC_JSDOC_MISSING_TYPE_WARNING",
-            "JSC_REFERENCE_BEFORE_DECLARE",
             "JSC_UNNECESSARY_ESCAPE",
-            "JSC_UNUSED_LOCAL_ASSIGNMENT",
         ],
         deps = [
             "//lib/polymer_externs:polymer_closure",