Try merging de.prob.core/build.gradle into the top-level one

build.gradle

@@ -29,6 +29,8 @@ install.dependsOn bMotionStudioHelpCustumBuild
 completeInstall.dependsOn bMotionStudioHelpCustumBuild*/
 
 project(':de.prob.core') {
+	apply plugin: "java"
+
 	repositories {
 		mavenCentral()
 	}
@@ -36,6 +38,10 @@ project(':de.prob.core') {
 	def parser_version = '2.5.1'
 
 	dependencies {
+		// Note: After changing/updating dependencies or their versions here,
+		// you also need to update the corresponding entries in META-INF/MANIFEST.MF!
+		// To be safe, you should probably also update the Eclipse .classpath file
+		// (it might be used by the Tycho build - not sure).
 		implementation group: "de.hhu.stups", name: "answerparser", version: parser_version
 		implementation group: "de.hhu.stups", name: "bparser", version: parser_version
 		implementation group: "de.hhu.stups", name: "ltlparser", version: parser_version
@@ -44,6 +50,15 @@ project(':de.prob.core') {
 		implementation group: "de.hhu.stups", name: "unicode", version: parser_version
 		implementation group: "de.hhu.stups", name: "theorymapping", version: parser_version
 		implementation 'commons-lang:commons-lang:2.6'
+		implementation 'commons-codec:commons-codec:1.8'
+		implementation 'com.thoughtworks.xstream:xstream:1.4.19'
+		// Current versions of XStream depend on MXParser, but not any specific version of it.
+		// To avoid the version number changing unexpectedly and breaking the MANIFEST.MF classpath entries,
+		// hardcode a specific MXParser version here.
+		// It *should* be safe to update this when a new version is released.
+		implementation group: 'io.github.x-stream', name: 'mxparser', version: '1.2.2'
+		implementation group: 'net.java.dev.jna', name: 'jna', version: '3.4.0'
+		implementation group: 'de.hhu.stups', name: 'ptolemy-jfmi', version: '1.1.0'
 	}
 }
 

de.prob.core/build.gradle

-apply plugin: 'java'
-
-def parser_version = '2.5.1'
-
-dependencies {
-	// Note: After changing/updating dependencies or their versions here,
-	// you also need to update the corresponding entries in META-INF/MANIFEST.MF!
-	// To be safe, you should probably also update the Eclipse .classpath file
-	// (it might be used by the Tycho build - not sure).
-	implementation group: "de.hhu.stups", name: "answerparser", version: parser_version
-	implementation group: "de.hhu.stups", name: "bparser", version: parser_version
-	implementation group: "de.hhu.stups", name: "ltlparser", version: parser_version
-	implementation group: "de.hhu.stups", name: "parserbase", version: parser_version
-	implementation group: "de.hhu.stups", name: "prologlib", version: parser_version
-	implementation group: "de.hhu.stups", name: "unicode", version: parser_version
-	implementation group: "de.hhu.stups", name: "theorymapping", version: parser_version
-	implementation 'commons-lang:commons-lang:2.6'
-	implementation 'commons-codec:commons-codec:1.8'
-	implementation 'com.thoughtworks.xstream:xstream:1.4.19'
-	// Current versions of XStream depend on MXParser, but not any specific version of it.
-	// To avoid the version number changing unexpectedly and breaking the MANIFEST.MF classpath entries,
-	// hardcode a specific MXParser version here.
-	// It *should* be safe to update this when a new version is released.
-	implementation group: 'io.github.x-stream', name: 'mxparser', version: '1.2.2'
-	implementation group: 'net.java.dev.jna', name: 'jna', version: '3.4.0'
-	implementation group: 'de.hhu.stups', name: 'ptolemy-jfmi', version: '1.1.0'
-}