diff --git a/exist-core/pom.xml b/exist-core/pom.xml
index 1db30a1dd9..972742d1d0 100644
--- a/exist-core/pom.xml
+++ b/exist-core/pom.xml
@@ -180,7 +180,8 @@
             <artifactId>jing</artifactId>
             <version>20241231</version>
             <exclusions>
-                <exclusion> <!-- conflicts with Xerces dependency on xml-apis -->
+                <exclusion>
+                    <!-- NOTE(AR): conflicts with com.evolvedbinary.thirdparty.xml-apis:xml-apis -->
                     <groupId>xml-apis</groupId>
                     <artifactId>xml-apis</artifactId>
                 </exclusion>
@@ -332,12 +333,6 @@
             <artifactId>xercesImpl</artifactId>
             <version>${xerces.version}</version>
             <classifier>jdk14-xml-schema-1.1</classifier>
-            <exclusions>
-                <exclusion>  <!-- conflicts with Java 21's javax.xml module -->
-                    <groupId>com.evolvedbinary.thirdparty.xml-apis</groupId>
-                    <artifactId>xml-apis</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
 
         <dependency>
@@ -353,13 +348,10 @@
             </exclusions>
         </dependency>
 
-        <!-- conflicts with Java 21's javax.xml module -->
-        <!--
         <dependency>
             <groupId>com.evolvedbinary.thirdparty.xml-apis</groupId>
             <artifactId>xml-apis</artifactId>
         </dependency>
-        -->
 
         <dependency>
             <groupId>com.evolvedbinary.thirdparty.org.apache.ws.commons.util</groupId>
@@ -381,7 +373,8 @@
             <artifactId>xmlresolver</artifactId>
             <version>${xmlresolver.version}</version>
             <exclusions>
-                <exclusion> <!-- conflicts with Java 21's javax.xml module -->
+                <exclusion>
+                    <!-- NOTE(AR): conflicts with com.evolvedbinary.thirdparty.xml-apis:xml-apis -->
                     <groupId>xml-apis</groupId>
                     <artifactId>xml-apis</artifactId>
                 </exclusion>
@@ -400,7 +393,8 @@
             <classifier>data</classifier>
             <scope>runtime</scope>
             <exclusions>
-                <exclusion> <!-- conflicts with Java 21's javax.xml module -->
+                <exclusion>
+                    <!-- NOTE(AR): conflicts with com.evolvedbinary.thirdparty.xml-apis:xml-apis -->
                     <groupId>xml-apis</groupId>
                     <artifactId>xml-apis</artifactId>
                 </exclusion>
@@ -419,12 +413,6 @@
             <artifactId>xpath2</artifactId>
             <version>1.2.1.1</version>
             <scope>runtime</scope>
-            <exclusions>
-                <exclusion>  <!-- conflicts with Java 21's javax.xml module -->
-                    <groupId>com.evolvedbinary.thirdparty.xml-apis</groupId>
-                    <artifactId>xml-apis</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>edu.princeton.cup</groupId>
@@ -2364,7 +2352,7 @@ The BaseX Team. The original license statement is also included below.]]></pream
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
                 <configuration>
-                    <excludePackageNames>org.exist.xquery.parser:org.exist.xquery.xqdoc.parser</excludePackageNames>
+                    <sourcepath>${project.build.sourceDirectory}:${project.build.directory}/generated-sources/annotations:${project.build.directory}/generated-sources/antlr</sourcepath>
                 </configuration>
             </plugin>
 
diff --git a/extensions/indexes/ngram/pom.xml b/extensions/indexes/ngram/pom.xml
index 5b5f1f017f..0e3c84dfcb 100644
--- a/extensions/indexes/ngram/pom.xml
+++ b/extensions/indexes/ngram/pom.xml
@@ -86,6 +86,12 @@
             <artifactId>xml-apis</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>com.evolvedbinary.j8fu</groupId>
+            <artifactId>j8fu</artifactId>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
@@ -104,6 +110,12 @@
             <scope>test</scope>
         </dependency>
 
+        <dependency>
+            <groupId>org.xmlunit</groupId>
+            <artifactId>xmlunit-core</artifactId>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>org.xmlunit</groupId>
             <artifactId>xmlunit-matchers</artifactId>
diff --git a/extensions/modules/expathrepo/pom.xml b/extensions/modules/expathrepo/pom.xml
index 9b55ddb399..c550a66213 100644
--- a/extensions/modules/expathrepo/pom.xml
+++ b/extensions/modules/expathrepo/pom.xml
@@ -92,6 +92,11 @@
             <artifactId>xml-apis</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>com.google.code.findbugs</groupId>
+            <artifactId>jsr305</artifactId>
+        </dependency>
+
         <!-- test -->
         <dependency>
             <groupId>junit</groupId>