Various fixes from sonarcloud

build.gradle

@@ -1,6 +1,7 @@
 plugins {
     id 'java'
     id 'application'
+    id 'jacoco'
     id 'org.sonarqube' version '6.0.1.5171'
 }
 
@@ -76,6 +77,17 @@ tasks.register('fatJar', Jar) {
     with jar
 }
 
+tasks.test {
+    finalizedBy(tasks.jacocoTestReport) // report is always generated after tests run
+}
+
+tasks.jacocoTestReport {
+    dependsOn(tasks.test) // tests are required to run before generating the report
+    reports {
+        xml.required.set(true)
+    }
+}
+
 // SonarQube configuration
 sonar {
     properties {

src/main/java/org/openmbee/flexo/cli/commands/InitCommand.java

@@ -213,18 +213,16 @@ private void waitForServices() throws Exception {
         // Wait for Fuseki (port 3030) and MMS (port 8080) to be available
         int maxAttempts = 30;
         int attempt = 0;
-        
+
         while (attempt < maxAttempts) {
             try {
-                // Check Fuseki
-                java.net.Socket fusekiSocket = new java.net.Socket();
-                fusekiSocket.connect(new java.net.InetSocketAddress("localhost", 3030), 1000);
-                fusekiSocket.close();
-
-                // Check MMS
-                java.net.Socket mmsSocket = new java.net.Socket();
-                mmsSocket.connect(new java.net.InetSocketAddress("localhost", 8080), 1000);
-                mmsSocket.close();
+                try (java.net.Socket fusekiSocket = new java.net.Socket()) {
+                    fusekiSocket.connect(new java.net.InetSocketAddress("localhost", 3030), 1000);
+                }
+
+                try (java.net.Socket mmsSocket = new java.net.Socket()) {
+                    mmsSocket.connect(new java.net.InetSocketAddress("localhost", 8080), 1000);
+                }
 
                 // Both services are up
                 ConsoleUtil.success("  Services are ready");

src/test/java/org/openmbee/flexo/cli/client/FlexoMmsClientTest.java

@@ -125,7 +125,7 @@ void testGetBranchSuccess() throws Exception {
 
         FlexoMmsClient client = createClientWithMockedHttp();
 
-        Branch branch = client.getBranch("org1", "repo1", "develop");
+        client.getBranch("org1", "repo1", "develop");
 
         // Branch might be null if parsing returns empty list
         // The test verifies the method completes without exception
@@ -155,7 +155,7 @@ void testCreateBranchSuccess() throws Exception {
 
         FlexoMmsClient client = createClientWithMockedHttp();
 
-        Branch branch = client.createBranch("org1", "repo1", "feature", null);
+        client.createBranch("org1", "repo1", "feature", null);
 
         // Verify PUT was executed twice (create + get)
         verify(mockHttpClient, atLeastOnce()).execute(any(HttpUriRequestBase.class));

src/test/java/org/openmbee/flexo/cli/config/FlexoConfigTest.java

@@ -15,17 +15,29 @@
 
 class FlexoConfigTest {
 
-    private Map<String, String> originalEnv;
+    /*
+     * These lifecycle methods are intentionally empty because:
+     * - System.getenv() cannot be modified or reset in Java, so storing the original
+     *   environment doesn't help with isolation between tests
+     * - FlexoConfig instances are independent and don't share mutable state
+     * - Each test creates fresh FlexoConfig instances that load from defaults/files
+     * - Test isolation is achieved through fresh config objects per test, not through
+     *   environment restoration which is not possible in Java
+     */
 
     @BeforeEach
     void setUp() {
-        // Store original environment variables
-        originalEnv = new HashMap<>(System.getenv());
+        // Lifecycle methods are intentionally empty.
+        // System.getenv() cannot be modified or reset in Java, so storing the original
+        // environment doesn't help with isolation between tests. Each test creates fresh
+        // FlexoConfig instances that load from defaults/files independently.
     }
 
     @AfterEach
     void tearDown() {
-        // Note: Cannot fully restore environment in Java, but tests are isolated
+        // Lifecycle methods are intentionally empty.
+        // Test isolation is achieved through fresh FlexoConfig objects per test,
+        // not through environment restoration which is not possible in Java.
     }
 
     @Test