Use Spoon to detect imports.

dependencies/dependencies.groovy

 ///////////////////////////// Dependencies
 @Grapes([
-		@Grab(group='com.github.javaparser', module='javaparser-core', version='3.6.7')]
-)
-import com.github.javaparser.JavaParser
-import groovy.io.FileType
+		@Grab(group = 'fr.inria.gforge.spoon', module = 'spoon-core', version = '7.0.0')
+])
 import groovy.transform.Field
+import spoon.*
+import spoon.reflect.declaration.*
+import spoon.reflect.visitor.*
 
 import java.nio.charset.StandardCharsets
 import java.nio.file.Files
-import java.nio.file.Path
 import java.nio.file.Paths
 import java.util.stream.Collectors
-import static java.lang.System.exit
-
 
+import static java.lang.System.exit
 
 ///////////////////////////// Configuration
 @Field final SCRIPT_LOCATION = new File(this.class.protectionDomain.codeSource.location.path).parent
@@ -75,31 +74,31 @@ padding = Math.max(padding as int, 150)
 
 
 ///////////////////////////// Generate JSON string
-Optional<String> parseJavaFile(Path p) {
-	String ex = exclude
-	def cu = JavaParser.parse(p)
-	def pkg = cu.packageDeclaration
-					.map{pd -> pd.nameAsString}
-					.orElse('')
-	def base = p.fileName.toString().replaceFirst('[.][^.]+$', '')
-	def name = "${pkg}.${base}"
-	if (name.matches(ex)) {
-		return Optional.empty()
+def entries = []
+def launcher = new Launcher();
+launcher.addInputResource(input)
+launcher.environment.noClasspath = true
+launcher.buildModel()
+launcher.factory.CompilationUnit().map.values().each {
+	def name = it.declaredPackage.qualifiedName + "." +
+			it.file.name.replaceFirst('[.][^.]+$', '')
+	if (name.matches((String) exclude)) {
+		return
+	}
+	def imports = new HashSet<CtImport>()
+	it.declaredTypes.each {
+		ImportScanner scanner = new ImportScannerImpl()
+		scanner.scan(it)
+		imports.addAll(scanner.getAllImports())
 	}
-	def imports = String.join(',',
-			cu.imports.stream()
-					.map{i -> i.nameAsString}
-					.filter{i -> !i.matches(ex)}
+	def importsStr = String.join(',',
+			imports.stream()
+					.map{i -> i.reference}
+					.map{i -> i.toString()}
+					.filter{i -> !i.isEmpty()}
 					.map{i -> "\"${i}\""}
 					.collect(Collectors.toList()))
-	return Optional.of('{"name":"'+name+'","size":1,"imports":['+imports+']}')
-}
-
-def entries = []
-new File(input).eachFileRecurse(FileType.FILES) {
-	if (it.name.endsWith(".java")) {
-		parseJavaFile(it.toPath()).ifPresent({ e -> entries << e })
-	}
+	entries << '{"name":"'+name+'","size":1,"imports":['+importsStr+']}'
 }
 def json = '[' + String.join(',', entries) + ']'