diff --git a/.gitignore b/.gitignore
index 40c74be..d092dc6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,4 +26,3 @@ out
 user.bazelrc
 !bazel-diff-example.sh
 .DS_Store
-integration/BUILD.bazel
diff --git a/integration/BUILD b/integration/BUILD
new file mode 100644
index 0000000..e69de29
diff --git a/integration/src/main/java/com/integration/BUILD b/integration/src/main/java/com/integration/BUILD
index 419206e..ae975c2 100644
--- a/integration/src/main/java/com/integration/BUILD
+++ b/integration/src/main/java/com/integration/BUILD
@@ -4,7 +4,7 @@ java_library(
     name = "bazel-diff-integration-lib",
     srcs = glob(["*.java"]),
     deps = [
-        "//src/main/java/com/integration/submodule:Submodule"
+        "//integration/src/main/java/com/integration/submodule:Submodule"
     ],
     visibility = ["//visibility:public"]
 )
diff --git a/integration/test/java/com/integration/BUILD b/integration/test/java/com/integration/BUILD
index 0d1bcfa..9e66c64 100644
--- a/integration/test/java/com/integration/BUILD
+++ b/integration/test/java/com/integration/BUILD
@@ -9,8 +9,9 @@ java_test(
 java_library(
     name = "bazel-diff-integration-test-lib",
     srcs = glob(["*.java"]),
+    testonly = True,
     deps = [
-        "//src/main/java/com/integration:bazel-diff-integration-lib",
+        "//integration/src/main/java/com/integration:bazel-diff-integration-lib",
         "@bazel_diff_maven//:junit_junit"
     ]
 )
diff --git a/src/main/java/com/bazel_diff/BazelClient.java b/src/main/java/com/bazel_diff/BazelClient.java
index 398500a..2ae2824 100644
--- a/src/main/java/com/bazel_diff/BazelClient.java
+++ b/src/main/java/com/bazel_diff/BazelClient.java
@@ -20,7 +20,6 @@
 
 interface BazelClient {
     List<BazelTarget> queryAllTargets() throws IOException;
-    Set<BazelSourceFileTarget> convertFilepathsToSourceTargets(Set<Path> filepaths) throws IOException, NoSuchAlgorithmException;
     Set<BazelSourceFileTarget> queryAllSourcefileTargets() throws IOException, NoSuchAlgorithmException;
 }
 
@@ -28,15 +27,24 @@ class BazelClientImpl implements BazelClient {
     private Path workingDirectory;
     private Path bazelPath;
     private Boolean verbose;
+    private Boolean keepGoing;
     private List<String> startupOptions;
     private List<String> commandOptions;
 
-    BazelClientImpl(Path workingDirectory, Path bazelPath, String startupOptions, String commandOptions, Boolean verbose) {
+    BazelClientImpl(
+            Path workingDirectory,
+            Path bazelPath,
+            String startupOptions,
+            String commandOptions,
+            Boolean verbose,
+            Boolean keepGoing
+    ) {
         this.workingDirectory = workingDirectory.normalize();
         this.bazelPath = bazelPath;
         this.startupOptions = startupOptions != null ? Arrays.asList(startupOptions.split(" ")): new ArrayList<String>();
         this.commandOptions = commandOptions != null ? Arrays.asList(commandOptions.split(" ")): new ArrayList<String>();
         this.verbose = verbose;
+        this.keepGoing = keepGoing;
     }
 
     @Override
@@ -45,19 +53,6 @@ public List<BazelTarget> queryAllTargets() throws IOException {
         return targets.stream().map( target -> new BazelTargetImpl(target)).collect(Collectors.toList());
     }
 
-    @Override
-    public Set<BazelSourceFileTarget> convertFilepathsToSourceTargets(Set<Path> filepaths) throws IOException, NoSuchAlgorithmException {
-        Set<BazelSourceFileTarget> sourceTargets = new HashSet<>();
-        for (List<Path> partition : Iterables.partition(filepaths, 100)) {
-            String targetQuery = partition
-                    .stream()
-                    .map(path -> String.format("'%s'", path.toString()))
-                    .collect(Collectors.joining(" + "));
-            sourceTargets.addAll(processBazelSourcefileTargets(performBazelQuery(targetQuery), false));
-        }
-        return sourceTargets;
-    }
-
     @Override
     public Set<BazelSourceFileTarget> queryAllSourcefileTargets() throws IOException, NoSuchAlgorithmException {
         return processBazelSourcefileTargets(performBazelQuery("kind('source file', deps(//...))"), true);
@@ -99,7 +94,9 @@ private List<Build.Target> performBazelQuery(String query) throws IOException {
         cmd.add("--output");
         cmd.add("streamed_proto");
         cmd.add("--order_output=no");
-        cmd.add("--keep_going");
+        if (keepGoing != null && keepGoing) {
+            cmd.add("--keep_going");
+        }
         cmd.addAll(this.commandOptions);
         cmd.add("--query_file");
         cmd.add(tempFile.toString());
diff --git a/src/main/java/com/bazel_diff/main.java b/src/main/java/com/bazel_diff/main.java
index c75015f..267e3f3 100644
--- a/src/main/java/com/bazel_diff/main.java
+++ b/src/main/java/com/bazel_diff/main.java
@@ -38,7 +38,13 @@ class GenerateHashes implements Callable<Integer> {
 
     @Override
     public Integer call() {
-        BazelClient bazelClient = new BazelClientImpl(parent.workspacePath, parent.bazelPath, parent.bazelStartupOptions, parent.bazelCommandOptions, BazelDiff.isVerbose());
+        BazelClient bazelClient = new BazelClientImpl(
+                parent.workspacePath,
+                parent.bazelPath,
+                parent.bazelStartupOptions,
+                parent.bazelCommandOptions,
+                BazelDiff.isVerbose(),
+                parent.keepGoing);
         TargetHashingClient hashingClient = new TargetHashingClientImpl(bazelClient, new FilesClientImp());
         try {
             Set<Path> seedFilepathsSet = new HashSet<>();
@@ -92,6 +98,9 @@ class BazelDiff implements Callable<Integer> {
     @Option(names = {"-co", "--bazelCommandOptions"}, description = "Additional space separated Bazel command options used when invoking Bazel", scope = ScopeType.INHERIT)
     String bazelCommandOptions;
 
+    @Option(names = {"-k", "--keep_going"}, negatable = true, description = "This flag controls if `bazel query` will be executed with the `--keep_going` flag or not. Disabling this flag allows you to catch configuration issues in your Bazel graph, but may not work for some Bazel setups. Defaults to `true`")
+    Boolean keepGoing = true;
+
     @Override
     public Integer call() throws IOException {
         if (startingHashesJSONPath == null || !startingHashesJSONPath.canRead()) {
@@ -103,7 +112,14 @@ public Integer call() throws IOException {
             return ExitCode.USAGE;
         }
         GitClient gitClient = new GitClientImpl(workspacePath);
-        BazelClient bazelClient = new BazelClientImpl(workspacePath, bazelPath, bazelStartupOptions, bazelCommandOptions, BazelDiff.isVerbose());
+        BazelClient bazelClient = new BazelClientImpl(
+                workspacePath,
+                bazelPath,
+                bazelStartupOptions,
+                bazelCommandOptions,
+                BazelDiff.isVerbose(),
+                keepGoing
+        );
         TargetHashingClient hashingClient = new TargetHashingClientImpl(bazelClient, new FilesClientImp());
         try {
             gitClient.ensureAllChangesAreCommitted();