diff --git a/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/META-INF/MANIFEST.MF b/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/META-INF/MANIFEST.MF
index ce222d61207..cee554fa5aa 100644
--- a/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/META-INF/MANIFEST.MF
+++ b/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: GDB Hardware Debugging Tests
 Bundle-SymbolicName: org.eclipse.cdt.debug.gdbjtag.core.tests;singleton:=true
-Bundle-Version: 1.0.0.qualifier
+Bundle-Version: 1.0.100.qualifier
 Bundle-Activator: org.eclipse.cdt.debug.gdbjtag.core.tests.Activator
 Require-Bundle: org.eclipse.core.runtime,
  org.eclipse.cdt.tests.dsf.gdb;bundle-version="2.3.0",
diff --git a/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/pom.xml b/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/pom.xml
index 3433133ec3c..673110bb578 100644
--- a/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/pom.xml
+++ b/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/pom.xml
@@ -11,7 +11,7 @@
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 
-	<version>1.0.0-SNAPSHOT</version>
+	<version>1.0.100-SNAPSHOT</version>
 	<artifactId>org.eclipse.cdt.debug.gdbjtag.core.tests</artifactId>
 	<packaging>eclipse-test-plugin</packaging>
 
diff --git a/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/src/org/eclipse/cdt/debug/gdbjtag/core/tests/launch/GDBJtagLaunchTest.java b/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/src/org/eclipse/cdt/debug/gdbjtag/core/tests/launch/GDBJtagLaunchTest.java
index 05167246fdf..9281bb5fc20 100644
--- a/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/src/org/eclipse/cdt/debug/gdbjtag/core/tests/launch/GDBJtagLaunchTest.java
+++ b/jtag/org.eclipse.cdt.debug.gdbjtag.core.tests/src/org/eclipse/cdt/debug/gdbjtag/core/tests/launch/GDBJtagLaunchTest.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2018 Kichwa Coders and others.
+ * Copyright (c) 2016, 2019 Kichwa Coders and others.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -67,8 +67,9 @@ public class GDBJtagLaunchTest extends BaseParametrizedTestCase {
 				setLaunchAttribute(IGDBLaunchConfigurationConstants.ATTR_GDB_INIT, X86_64_INIT);
 			}
 		} else {
-			setLaunchAttribute(IGDBJtagConstants.ATTR_INIT_COMMANDS, "file " + TEST_PROGRAM_NAME); //$NON-NLS-1$
-			setLaunchAttribute(IGDBJtagConstants.ATTR_RUN_COMMANDS, "run"); //$NON-NLS-1$
+			String comments = "# Commented line\n\n  \n  # Commented indented line\n";
+			setLaunchAttribute(IGDBJtagConstants.ATTR_INIT_COMMANDS, comments + "file " + TEST_PROGRAM_NAME); //$NON-NLS-1$
+			setLaunchAttribute(IGDBJtagConstants.ATTR_RUN_COMMANDS, comments + "run"); //$NON-NLS-1$
 		}
 	}
 
diff --git a/jtag/org.eclipse.cdt.debug.gdbjtag.core/src/org/eclipse/cdt/debug/gdbjtag/core/GDBJtagDSFFinalLaunchSequence.java b/jtag/org.eclipse.cdt.debug.gdbjtag.core/src/org/eclipse/cdt/debug/gdbjtag/core/GDBJtagDSFFinalLaunchSequence.java
index 59f169e6ed8..89c623f0640 100644
--- a/jtag/org.eclipse.cdt.debug.gdbjtag.core/src/org/eclipse/cdt/debug/gdbjtag/core/GDBJtagDSFFinalLaunchSequence.java
+++ b/jtag/org.eclipse.cdt.debug.gdbjtag.core/src/org/eclipse/cdt/debug/gdbjtag/core/GDBJtagDSFFinalLaunchSequence.java
@@ -489,6 +489,11 @@ public class GDBJtagDSFFinalLaunchSequence extends FinalLaunchSequence {
 			if (userCmd.length() > 0) {
 				String[] commands = userCmd.split("\\r?\\n"); //$NON-NLS-1$
 
+				// Remove empty or commented lines
+				commands = Arrays.stream(commands)
+						.filter(line -> !line.trim().isEmpty() && !line.trim().startsWith("#")) //$NON-NLS-1$
+						.toArray(String[]::new);
+
 				CountingRequestMonitor crm = new CountingRequestMonitor(getExecutor(), rm);
 				crm.setDoneCount(commands.length);
 				for (int i = 0; i < commands.length; ++i) {
@@ -715,6 +720,11 @@ public class GDBJtagDSFFinalLaunchSequence extends FinalLaunchSequence {
 				userCmd = VariablesPlugin.getDefault().getStringVariableManager().performStringSubstitution(userCmd);
 				String[] commands = userCmd.split("\\r?\\n"); //$NON-NLS-1$
 
+				// Remove empty or commented lines
+				commands = Arrays.stream(commands)
+						.filter(line -> !line.trim().isEmpty() && !line.trim().startsWith("#")) //$NON-NLS-1$
+						.toArray(String[]::new);
+
 				CountingRequestMonitor crm = new CountingRequestMonitor(getExecutor(), rm);
 				crm.setDoneCount(commands.length);
 				for (int i = 0; i < commands.length; ++i) {