diff --git a/gradle.properties b/gradle.properties
index 619a0679..ed246e6c 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,2 +1,2 @@
-version=1.1.0
+version=1.1.1
 
diff --git a/src/main/java/com/ibm/cldk/CodeAnalyzer.java b/src/main/java/com/ibm/cldk/CodeAnalyzer.java
index d1ea7c3f..40d2ff57 100644
--- a/src/main/java/com/ibm/cldk/CodeAnalyzer.java
+++ b/src/main/java/com/ibm/cldk/CodeAnalyzer.java
@@ -76,6 +76,9 @@ public class CodeAnalyzer implements Runnable {
     @Option(names = {"-v", "--verbose"}, description = "Print logs to console.")
     private static boolean verbose = false;
 
+    @Option(names = {"--no-clean-dependencies"}, description = "Do not attempt to auto-clean dependencies")
+    public static boolean noCleanDependencies = false;
+
     private static final String outputFileName = "analysis.json";
 
     public static Gson gson = new GsonBuilder()
diff --git a/src/main/java/com/ibm/cldk/utils/BuildProject.java b/src/main/java/com/ibm/cldk/utils/BuildProject.java
index 9a426b4f..33c2a057 100644
--- a/src/main/java/com/ibm/cldk/utils/BuildProject.java
+++ b/src/main/java/com/ibm/cldk/utils/BuildProject.java
@@ -18,6 +18,7 @@
 
 import static com.ibm.cldk.utils.ProjectDirectoryScanner.classFilesStream;
 import static com.ibm.cldk.CodeAnalyzer.projectRootPom;
+import static com.ibm.cldk.CodeAnalyzer.noCleanDependencies;
 
 public class BuildProject {
     public static Path libDownloadPath;
@@ -188,6 +189,17 @@ public static List<Path> buildProjectAndStreamClassFiles(String projectPath, Str
         return buildProject(projectPath, build) ? classFilesStream(projectPath) : new ArrayList<>();
     }
 
+    private static boolean mkLibDepDirs(String projectPath) {
+        if (!Files.exists(libDownloadPath)) {
+            try {
+                Files.createDirectories(libDownloadPath);
+            } catch (IOException e) {
+                Log.error("Error creating library dependency directory for " + projectPath + ": " + e.getMessage());
+                return false;
+            }
+        }
+        return true;
+    }
     /**
      * Downloads library dependency jars of the given project so that the jars can be used
      * for type resolution during symbol table creation.
@@ -198,17 +210,15 @@ public static List<Path> buildProjectAndStreamClassFiles(String projectPath, Str
     public static boolean downloadLibraryDependencies(String projectPath, String projectRootPom) throws IOException {
         // created download dir if it does not exist
         String projectRoot = projectRootPom != null ? projectRootPom : projectPath;
-        libDownloadPath = Paths.get(projectPath, LIB_DEPS_DOWNLOAD_DIR).toAbsolutePath();
-        if (!Files.exists(libDownloadPath)) {
-            try {
-                Files.createDirectory(libDownloadPath);
-            } catch (IOException e) {
-                Log.error("Error creating library dependency directory for " + projectPath + ": " + e.getMessage());
-                return false;
-            }
-        }
+
         File pomFile = new File(projectRoot, "pom.xml");
         if (pomFile.exists()) {
+            libDownloadPath = Paths.get(projectPath, "target", LIB_DEPS_DOWNLOAD_DIR).toAbsolutePath();
+            if (mkLibDepDirs(projectPath))
+                Log.debug("Dependencies found/created in " + libDownloadPath);
+            else
+                throw new IllegalStateException("Error creating library dependency directory in " + libDownloadPath);
+
             if (MAVEN_CMD == null || !commandExists(new File(MAVEN_CMD)).getKey()) {
                 String msg = MAVEN_CMD == null ?
                         "Could not find Maven or a valid Maven Wrapper" :
@@ -225,6 +235,12 @@ public static boolean downloadLibraryDependencies(String projectPath, String pro
             return buildWithTool(mavenCommand);
         } else if (new File(projectRoot, "build.gradle").exists() || new File(projectRoot, "build.gradle.kts").exists()) {
             if (GRADLE_CMD == null || !commandExists(new File(GRADLE_CMD)).getKey()) {
+                libDownloadPath = Paths.get(projectPath, "build", LIB_DEPS_DOWNLOAD_DIR).toAbsolutePath();
+                if (mkLibDepDirs(projectPath))
+                    Log.debug("Dependencies found/created in " + libDownloadPath);
+                else
+                    throw new IllegalStateException("Error creating library dependency directory in " + libDownloadPath);
+
                 String msg = GRADLE_CMD == null ?
                         "Could not find Gradle or valid Gradle Wrapper" :
                         MessageFormat.format("Could not verify that {0} exists", GRADLE_CMD);
@@ -249,20 +265,23 @@ public static boolean downloadLibraryDependencies(String projectPath, String pro
     }
 
     public static void cleanLibraryDependencies() {
+        if (noCleanDependencies) {
+            return;
+        }
         if (libDownloadPath != null) {
             Log.info("Cleaning up library dependency directory: " + libDownloadPath);
             try {
                 Files.walk(libDownloadPath).filter(Files::isRegularFile).map(Path::toFile).forEach(File::delete);
                 Files.delete(libDownloadPath);
             } catch (IOException e) {
-                Log.error("Error deleting library dependency directory: " + e.getMessage());
+                Log.warn("Unable to fully delete library dependency directory: " + e.getMessage());
             }
         }
         if (tempInitScript != null) {
             try {
                 Files.delete(tempInitScript);
             } catch (IOException e) {
-                Log.error("Error deleting temporary Gradle init script: " + e.getMessage());
+                Log.warn("Error deleting temporary Gradle init script: " + e.getMessage());
             }
         }
     }
diff --git a/src/main/java/com/ibm/cldk/utils/ProjectDirectoryScanner.java b/src/main/java/com/ibm/cldk/utils/ProjectDirectoryScanner.java
index d6178a15..fb138dca 100644
--- a/src/main/java/com/ibm/cldk/utils/ProjectDirectoryScanner.java
+++ b/src/main/java/com/ibm/cldk/utils/ProjectDirectoryScanner.java
@@ -7,6 +7,8 @@
 import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
 
 public class ProjectDirectoryScanner {
     public static List<Path> classFilesStream(String projectPath) throws IOException {
@@ -37,6 +39,30 @@ public static List<Path> jarFilesStream(String projectPath) throws IOException {
         return null;
     }
 
+    /**
+     * Returns a stream of class files inside the jars and class files in the project.
+     * @param projectPath
+     * @return
+     * @throws IOException
+     */
+    public static Stream<String> classesFromJarFileStream(String projectPath) throws IOException {
+        List<Path> jarPaths = jarFilesStream(projectPath);
+
+        if (jarPaths == null) {
+            return Stream.empty();
+        }
+
+        return jarPaths.stream().flatMap(jarPath -> {
+            try (ZipFile zip = new ZipFile(jarPath.toFile())) {
+                return zip.stream()
+                        .filter(entry -> !entry.isDirectory() && entry.getName().endsWith(".class"))
+                        .map(ZipEntry::getName);
+            } catch (IOException e) {
+                return Stream.empty();
+            }
+        });
+    }
+
     public static List<Path> sourceFilesStream(String projectPath) throws IOException {
         Path projectDir = Paths.get(projectPath);
         Log.info("Finding *.java files in " + projectDir);