Preserve initialization options stored inside Preferences.

- Also implement better workaround for JAXP limits on JDK24

Signed-off-by: Roland Grunberg <rgrunber@redhat.com>

Author: rgrunber

.github/workflows/codeql-analysis.yml

@@ -72,7 +72,7 @@ jobs:
     #   echo "Run, Build Application using script"
     #   ./location_of_script_within_repo/buildscript.sh
     - name: Manual build
-      run: ./mvnw clean package -f "pom.xml" -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip -DskipTests -Dmaven.test.skip.exec -Dlicense.skip=true -Drat.skip=true -Dspotless.check.skip=true -Djdk.xml.maxGeneralEntitySizeLimit=1000000 -Djdk.xml.totalEntitySizeLimit=1000000
+      run: ./mvnw clean package -f "pom.xml" -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip -DskipTests -Dmaven.test.skip.exec -Dlicense.skip=true -Drat.skip=true -Dspotless.check.skip=true
 
 
     - name: Perform CodeQL Analysis

.mvn/jvm.config

@@ -0,0 +1 @@
+-Djdk.xml.maxGeneralEntitySizeLimit=1000000 -Djdk.xml.totalEntitySizeLimit=1000000

org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/preferences/PreferenceManager.java

@@ -226,7 +226,12 @@ private static boolean updateTemplate(String templateId, String content) {
 	public void update(Map<String, Object> preferences) {
 		Map<String, Object> currMap = this.preferences.asMap();
 		currMap.putAll(preferences);
-		update(Preferences.createFrom(currMap));
+		Preferences newPreferences = Preferences.createFrom(currMap);
+		// Preserve preferences stored here that are never sent after initialization
+		newPreferences.setRootPaths(this.preferences.getRootPaths());
+		newPreferences.setTriggerFiles(this.preferences.getTriggerFiles());
+		newPreferences.setProjectConfigurations(this.preferences.getProjectConfigurations());
+		update(newPreferences);
 	}
 
 	public void update(Preferences preferences) {