Add $Id Management in the generator. With it, it is possible to

jsonschema2pojo-ant/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>jsonschema2pojo</artifactId>
         <groupId>org.jsonschema2pojo</groupId>
-        <version>1.2.2-SNAPSHOT</version>
+	    <version>1.2.2-Id-Management</version>
     </parent>
 
     <artifactId>jsonschema2pojo-ant</artifactId>

jsonschema2pojo-cli/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>jsonschema2pojo</artifactId>
         <groupId>org.jsonschema2pojo</groupId>
-        <version>1.2.2-SNAPSHOT</version>
+	    <version>1.2.2-Id-Management</version>
     </parent>
 
     <artifactId>jsonschema2pojo-cli</artifactId>

jsonschema2pojo-core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>jsonschema2pojo</artifactId>
         <groupId>org.jsonschema2pojo</groupId>
-        <version>1.2.2-SNAPSHOT</version>
+        <version>1.2.2-Id-Management</version>
     </parent>
 
     <artifactId>jsonschema2pojo-core</artifactId>

jsonschema2pojo-core/src/main/java/org/jsonschema2pojo/Jsonschema2Pojo.java

@@ -76,6 +76,7 @@ public static void generate(GenerationConfig config, RuleLogger logger) throws I
             URL source = sources.next();
 
             if (URLUtil.parseProtocol(source.toString()) == URLProtocol.FILE && URLUtil.getFileFromURL(source).isDirectory()) {
+            	parseRecursive(config, mapper, codeModel, defaultString(config.getTargetPackage()), Arrays.asList(URLUtil.getFileFromURL(source).listFiles(config.getFileFilter())));
                 generateRecursive(config, mapper, codeModel, defaultString(config.getTargetPackage()), Arrays.asList(URLUtil.getFileFromURL(source).listFiles(config.getFileFilter())));
             } else {
                 mapper.generate(codeModel, getNodeName(source, config), defaultString(config.getTargetPackage()), source);
@@ -139,6 +140,22 @@ private static void generateRecursive(GenerationConfig config, SchemaMapper mapp
             }
         }
     }
+    private static void parseRecursive(GenerationConfig config, SchemaMapper mapper, JCodeModel codeModel, String packageName, List<File> schemaFiles) throws IOException {
+
+        Collections.sort(schemaFiles, config.getSourceSortOrder().getComparator());
+
+        for (File child : schemaFiles) {
+            if (child.isFile()) {
+                if (config.getSourceType() == SourceType.JSON || config.getSourceType() == SourceType.YAML) {
+                    // any cached schemas will have ids that are fragments, relative to the previous document (and shouldn't be reused)
+                    mapper.getRuleFactory().getSchemaStore().clearCache();
+                }
+                mapper.parse(codeModel, getNodeName(child.toURI().toURL(), config), defaultString(packageName), child.toURI().toURL());
+            } else {
+            	parseRecursive(config, mapper, codeModel, childQualifiedName(packageName, child.getName()), Arrays.asList(child.listFiles(config.getFileFilter())));
+            }
+        }
+    }
 
     private static String childQualifiedName(String parentQualifiedName, String childSimpleName) {
         String safeChildName = childSimpleName.replaceAll(NameHelper.ILLEGAL_CHARACTER_REGEX, "_");

jsonschema2pojo-core/src/main/java/org/jsonschema2pojo/SchemaMapper.java

@@ -18,6 +18,7 @@
 
 import java.io.IOException;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 
 import org.jsonschema2pojo.rules.RuleFactory;
@@ -37,6 +38,7 @@
  * used to create type generation rules for this mapper.
  */
 public class SchemaMapper {
+
     private static final JsonNodeFactory NODE_FACTORY = JsonNodeFactory.instance;
 
     private final RuleFactory ruleFactory;
@@ -89,6 +91,35 @@ public JType generate(JCodeModel codeModel, String className, String packageName
 
         return ruleFactory.getSchemaRule().apply(className, schemaNode, null, jpackage, new Schema(null, schemaNode, null));
 
+    }
+    /**
+     * Reads a schema and register schema which may be used after during the generation.
+     *
+     * @param codeModel
+     *            the java code-generation context that should be used to
+     *            generated new types
+     * @param className
+     *            the name of the parent class the represented by this schema
+     * @param packageName
+     *            the target package that should be used for generated types
+     * @param schemaUrl
+     *            location of the schema to be used as input
+     */
+    public void parse(JCodeModel codeModel, String className, String packageName, URL schemaUrl) {
+
+			try {
+		        ObjectNode schemaNode = readSchema(schemaUrl);
+		        SchemaStore schemaStore = getRuleFactory().getSchemaStore();
+		        Schema schema = new Schema(schemaUrl.toURI(), schemaNode, null);
+		        schemaStore.registerId(schema, schemaUrl.toURI(), ruleFactory.getGenerationConfig().getRefFragmentPathDelimiters());
+
+			} catch (URISyntaxException e) {
+				e.printStackTrace();
+			}
+
+
+//        return ruleFactory.getSchemaRule().apply(className, schemaNode, null, jpackage, new Schema(null, schemaNode, null));
+
     }
 
     private ObjectNode readSchema(URL schemaUrl) {