diff --git a/tycho-cleancode-plugin/pom.xml b/tycho-cleancode-plugin/pom.xml
index 74848cd3c8..0ae5e2c50b 100644
--- a/tycho-cleancode-plugin/pom.xml
+++ b/tycho-cleancode-plugin/pom.xml
@@ -36,12 +36,57 @@
 			<groupId>org.eclipse.jdt</groupId>
 			<artifactId>org.eclipse.jdt.ui</artifactId>
 			<version>3.33.200</version>
+			<exclusions>
+				<exclusion>
+					<groupId>*</groupId>
+					<artifactId>*</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.eclipse.jdt</groupId>
 			<artifactId>org.eclipse.jdt.core.manipulation</artifactId>
 			<version>1.21.300</version>
+			<exclusions>
+				<exclusion>
+					<groupId>*</groupId>
+					<artifactId>*</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
+		<dependency>
+			<groupId>org.eclipse.platform</groupId>
+			<artifactId>org.eclipse.ltk.core.refactoring</artifactId>
+			<version>3.14.600</version>
+			<exclusions>
+				<exclusion>
+					<groupId>*</groupId>
+					<artifactId>*</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.platform</groupId>
+			<artifactId>org.eclipse.ui.workbench</artifactId>
+			<exclusions>
+				<exclusion>
+					<groupId>*</groupId>
+					<artifactId>*</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.platform</groupId>
+			<artifactId>org.eclipse.ui.ide</artifactId>
+			<version>3.22.400</version>
+			<exclusions>
+				<exclusion>
+					<groupId>*</groupId>
+					<artifactId>*</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+
 	</dependencies>
 
 	<build>
diff --git a/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/CleanUp.java b/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/CleanUp.java
index 6c85f26204..5d87ac6e91 100644
--- a/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/CleanUp.java
+++ b/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/CleanUp.java
@@ -20,6 +20,7 @@
 
 import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.ProjectScope;
+import org.eclipse.core.runtime.CoreException;
 import org.eclipse.jdt.core.ICompilationUnit;
 import org.eclipse.jdt.core.IJavaElement;
 import org.eclipse.jdt.core.IJavaProject;
@@ -41,10 +42,12 @@
 public class CleanUp extends AbstractEclipseBuild<CleanupResult> {
 
 	private Map<String, String> customProfile;
+	private boolean applyCleanupsIndividually;
 
-	CleanUp(Path projectDir, boolean debug, Map<String, String> customProfile) {
+	CleanUp(Path projectDir, boolean debug, Map<String, String> customProfile, boolean applyCleanupsIndividually) {
 		super(projectDir, debug);
 		this.customProfile = customProfile;
+		this.applyCleanupsIndividually = applyCleanupsIndividually;
 	}
 
 	@Override
@@ -54,27 +57,38 @@ protected CleanupResult createResult(IProject project) throws Exception {
 		ICleanUp[] cleanups = getCleanups(result, options);
 		if (cleanups.length > 0) {
 			List<ICompilationUnit> units = getCompilationUnits(project);
-			final CleanUpRefactoring refactoring = new CleanUpRefactoring(project.getName());
-			for (ICompilationUnit cu : units) {
-				refactoring.addCompilationUnit(cu);
-			}
-			refactoring.setUseOptionsFromProfile(false);
-			for (ICleanUp cleanUp : cleanups) {
-				refactoring.addCleanUp(cleanUp);
-			}
-			final RefactoringStatus status = refactoring.checkAllConditions(this);
-			if (status.isOK()) {
-				Change change = refactoring.createChange(this);
-				change.initializeValidationData(this);
-				PerformChangeOperation performChangeOperation = new PerformChangeOperation(change);
-				performChangeOperation.run(this);
-			} else if (status.hasError()) {
-				throw new RuntimeException("Refactoring failed: " + status);
+			if (applyCleanupsIndividually) {
+				for (ICleanUp cleanUp : cleanups) {
+					applyCleanups(project, new ICleanUp[] { cleanUp }, units);
+				}
+			} else {
+				applyCleanups(project, cleanups, units);
 			}
 		}
 		return result;
 	}
 
+	private void applyCleanups(IProject project, ICleanUp[] cleanups, List<ICompilationUnit> units)
+			throws CoreException {
+		final CleanUpRefactoring refactoring = new CleanUpRefactoring(project.getName());
+		for (ICompilationUnit cu : units) {
+			refactoring.addCompilationUnit(cu);
+		}
+		refactoring.setUseOptionsFromProfile(false);
+		for (ICleanUp cleanUp : cleanups) {
+			refactoring.addCleanUp(cleanUp);
+		}
+		final RefactoringStatus status = refactoring.checkAllConditions(this);
+		if (status.isOK()) {
+			Change change = refactoring.createChange(this);
+			change.initializeValidationData(this);
+			PerformChangeOperation performChangeOperation = new PerformChangeOperation(change);
+			performChangeOperation.run(this);
+		} else if (status.hasError()) {
+			throw new RuntimeException("Refactoring failed: " + status);
+		}
+	}
+
 	private List<ICompilationUnit> getCompilationUnits(IProject project) throws JavaModelException {
 		IJavaProject javaProject = JavaCore.create(project);
 		List<ICompilationUnit> units = new ArrayList<ICompilationUnit>();
diff --git a/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/CleanUpMojo.java b/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/CleanUpMojo.java
index 21e390e323..94123c62ea 100644
--- a/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/CleanUpMojo.java
+++ b/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/CleanUpMojo.java
@@ -40,6 +40,9 @@ public class CleanUpMojo extends AbstractEclipseBuildMojo<CleanupResult> {
 	@Parameter
 	private Map<String, String> cleanUpProfile;
 
+	@Parameter
+	private boolean applyCleanupsIndividually;
+
 	@Override
 	protected String[] getRequireBundles() {
 		return new String[] { "org.eclipse.jdt.ui" };
@@ -52,7 +55,7 @@ protected String getName() {
 
 	@Override
 	protected CleanUp createExecutable() {
-		return new CleanUp(project.getBasedir().toPath(), debug, cleanUpProfile);
+		return new CleanUp(project.getBasedir().toPath(), debug, cleanUpProfile, applyCleanupsIndividually);
 	}
 
 	@Override
@@ -65,6 +68,7 @@ protected void handleResult(CleanupResult result)
 		builder.h3("The following cleanups where applied:");
 		result.cleanups().forEach(cleanup -> {
 			builder.addListItem(cleanup);
+			getLog().info("CleanUp: " + cleanup);
 		});
 		builder.newLine();
 		builder.newLine();
diff --git a/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/QuickFixMojo.java b/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/QuickFixMojo.java
index bdb96a57b9..911b59f317 100644
--- a/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/QuickFixMojo.java
+++ b/tycho-cleancode-plugin/src/main/java/org/eclipse/tycho/cleancode/QuickFixMojo.java
@@ -53,14 +53,13 @@ protected void handleResult(QuickFixResult result) throws MojoFailureException {
 		MarkdownBuilder builder = new MarkdownBuilder(reportFileName);
 		List<String> fixes = result.fixes().toList();
 		builder.h3("The following " + (fixes.size() > 0 ? "warnings" : "warning") + " has been resolved:");
-		builder.newLine();
-		fixes.forEach(fix -> builder.addListItem(fix));
+		fixes.forEach(fix -> {
+			builder.addListItem(fix);
+			getLog().info("QuickFix: " + fix);
+		});
 		builder.newLine();
 		builder.newLine();
 		builder.write();
-		for (String fix : fixes) {
-			getLog().info("Fixed: " + fix);
-		}
 	}
 
 	@Override