diff --git a/org.eclipse.jdt.core/.settings/.api_filters b/org.eclipse.jdt.core/.settings/.api_filters
index c2585475019..f9c56a5b6fc 100644
--- a/org.eclipse.jdt.core/.settings/.api_filters
+++ b/org.eclipse.jdt.core/.settings/.api_filters
@@ -1,13 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.jdt.core" version="2">
-    <resource path="META-INF/MANIFEST.MF">
-        <filter comment="https://github.com/eclipse-jdt/eclipse.jdt.core/pull/4385" id="929038356">
-            <message_arguments>
-                <message_argument value="3.43.100"/>
-                <message_argument value="org.eclipse.jdt.core.compiler.batch"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="dom/org/eclipse/jdt/core/dom/AbstractTagElement.java" type="org.eclipse.jdt.core.dom.AbstractTagElement">
         <filter id="576725006">
             <message_arguments>
diff --git a/org.eclipse.jdt.core/META-INF/MANIFEST.MF b/org.eclipse.jdt.core/META-INF/MANIFEST.MF
index 3653c75a3b3..ddd26cefc7f 100644
--- a/org.eclipse.jdt.core/META-INF/MANIFEST.MF
+++ b/org.eclipse.jdt.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %pluginName
 Bundle-SymbolicName: org.eclipse.jdt.core; singleton:=true
-Bundle-Version: 3.43.100.qualifier
+Bundle-Version: 3.44.0.qualifier
 Bundle-Activator: org.eclipse.jdt.core.JavaCore
 Bundle-Vendor: %providerName
 Bundle-Localization: plugin
diff --git a/org.eclipse.jdt.core/formatter/org/eclipse/jdt/core/formatter/DefaultCodeFormatterConstants.java b/org.eclipse.jdt.core/formatter/org/eclipse/jdt/core/formatter/DefaultCodeFormatterConstants.java
index a61d640159a..023bea9493d 100644
--- a/org.eclipse.jdt.core/formatter/org/eclipse/jdt/core/formatter/DefaultCodeFormatterConstants.java
+++ b/org.eclipse.jdt.core/formatter/org/eclipse/jdt/core/formatter/DefaultCodeFormatterConstants.java
@@ -1510,6 +1510,19 @@ public class DefaultCodeFormatterConstants {
 	 */
 	public final static String FORMATTER_COMMENT_FORMAT_JAVADOC_COMMENT = "org.eclipse.jdt.core.formatter.comment.format_javadoc_comments"; //$NON-NLS-1$
 
+	/**
+	 * <pre>
+	 * FORMATTER / Option to control whether markdown comments are formatted
+	 *     - option id:         "org.eclipse.jdt.core.formatter.comment.format_markdown_comments"
+	 *     - possible values:   { TRUE, FALSE }
+	 *     - default:           TRUE
+	 * </pre>
+	 * @see #TRUE
+	 * @see #FALSE
+	 * @since 3.44
+	 */
+	public final static String FORMATTER_COMMENT_FORMAT_MARKDOWN_COMMENT = "org.eclipse.jdt.core.formatter.comment.format_markdown_comments"; //$NON-NLS-1$
+
 	/**
 	 * <pre>
 	 * FORMATTER / Option to control whether the header comment of a Java source file is formatted
diff --git a/org.eclipse.jdt.core/formatter/org/eclipse/jdt/internal/formatter/DefaultCodeFormatterOptions.java b/org.eclipse.jdt.core/formatter/org/eclipse/jdt/internal/formatter/DefaultCodeFormatterOptions.java
index ba287c35099..04ca7bf0201 100644
--- a/org.eclipse.jdt.core/formatter/org/eclipse/jdt/internal/formatter/DefaultCodeFormatterOptions.java
+++ b/org.eclipse.jdt.core/formatter/org/eclipse/jdt/internal/formatter/DefaultCodeFormatterOptions.java
@@ -238,6 +238,7 @@ public static DefaultCodeFormatterOptions getJavaConventionsSettings() {
 	public boolean comment_new_lines_at_javadoc_boundaries;
 	public boolean comment_javadoc_do_not_separate_block_tags;
 	public boolean comment_format_javadoc_comment;
+	public boolean comment_format_markdown_comment;
 	public boolean comment_format_line_comment;
 	public boolean comment_format_line_comment_starting_on_first_column;
 	public boolean comment_format_block_comment;
@@ -667,6 +668,7 @@ public Map<String, String> getMap() {
 		options.put(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_HEADER, this.comment_format_header ? DefaultCodeFormatterConstants.TRUE : DefaultCodeFormatterConstants.FALSE);
 		options.put(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_HTML, this.comment_format_html ? DefaultCodeFormatterConstants.TRUE : DefaultCodeFormatterConstants.FALSE);
 		options.put(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_JAVADOC_COMMENT, this.comment_format_javadoc_comment ? DefaultCodeFormatterConstants.TRUE : DefaultCodeFormatterConstants.FALSE);
+		options.put(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_MARKDOWN_COMMENT, this.comment_format_markdown_comment ? DefaultCodeFormatterConstants.TRUE : DefaultCodeFormatterConstants.FALSE);
 		options.put(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_LINE_COMMENT, this.comment_format_line_comment ? DefaultCodeFormatterConstants.TRUE : DefaultCodeFormatterConstants.FALSE);
 		options.put(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_LINE_COMMENT_STARTING_ON_FIRST_COLUMN, this.comment_format_line_comment_starting_on_first_column ? DefaultCodeFormatterConstants.TRUE : DefaultCodeFormatterConstants.FALSE);
 		options.put(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_SOURCE, this.comment_format_source ? DefaultCodeFormatterConstants.TRUE : DefaultCodeFormatterConstants.FALSE);
@@ -1570,6 +1572,10 @@ public void set(Map<String, String> settings) {
 		if (commentFormatJavadocCommentOption != null) {
 			this.comment_format_javadoc_comment = DefaultCodeFormatterConstants.TRUE.equals(commentFormatJavadocCommentOption);
 		}
+		final Object commentFormatMarkdownCommentOption = settings.get(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_MARKDOWN_COMMENT);
+		if (commentFormatMarkdownCommentOption != null) {
+			this.comment_format_markdown_comment = DefaultCodeFormatterConstants.TRUE.equals(commentFormatMarkdownCommentOption);
+		}
 		final Object commentFormatBlockCommentOption = settings.get(DefaultCodeFormatterConstants.FORMATTER_COMMENT_FORMAT_BLOCK_COMMENT);
 		if (commentFormatBlockCommentOption != null) {
 			this.comment_format_block_comment = DefaultCodeFormatterConstants.TRUE.equals(commentFormatBlockCommentOption);
@@ -3063,6 +3069,7 @@ public void setDefaultSettings() {
 		this.comment_clear_blank_lines_in_javadoc_comment = false;
 		this.comment_format_block_comment = true;
 		this.comment_format_javadoc_comment = true;
+		this.comment_format_markdown_comment = true;
 		this.comment_format_line_comment = true;
 		this.comment_format_line_comment_starting_on_first_column = true;
 		this.comment_format_header = false;
@@ -3468,6 +3475,7 @@ public void setJavaConventionsSettings() {
 		this.comment_clear_blank_lines_in_javadoc_comment = false;
 		this.comment_format_block_comment = true;
 		this.comment_format_javadoc_comment = true;
+		this.comment_format_markdown_comment = true;
 		this.comment_format_line_comment = true;
 		this.comment_format_line_comment_starting_on_first_column = false;
 		this.comment_format_header = false;
diff --git a/org.eclipse.jdt.core/pom.xml b/org.eclipse.jdt.core/pom.xml
index 9f31673ac20..f0201b985ea 100644
--- a/org.eclipse.jdt.core/pom.xml
+++ b/org.eclipse.jdt.core/pom.xml
@@ -17,7 +17,7 @@
     <version>4.38.0-SNAPSHOT</version>
   </parent>
   <artifactId>org.eclipse.jdt.core</artifactId>
-  <version>3.43.100-SNAPSHOT</version>
+  <version>3.44.0-SNAPSHOT</version>
   <packaging>eclipse-plugin</packaging>
 
   <properties>