自動生成したJavaコードに手を加えても綺麗にマージしてくれるJmerge ref: http://qiita.com/ko2ic/items/eb8107bd74ab510e0a6d

EclipseJavaMerger.java

public class EclipseJavaMerger {

    private final JMerger merger = new JMerger(buildMergeRule());

    public String merge(String source, String target) {
        try {
            if (target == null) {
                return source;
            }
            merger.setSourceCompilationUnit(merger.createCompilationUnitForContents(source));
            merger.setTargetCompilationUnit(merger.createCompilationUnitForContents(target));
            merger.merge();
            return merger.getTargetCompilationUnitContents();
        } finally {
            merger.reset();
        }
    }

    private JControlModel buildMergeRule() {
        JControlModel controlModel = new JControlModel();
        String configFileUri = getClass().getResource("/emf-merge.xml").toString();
        controlModel.initialize(new ASTFacadeHelper(), configFileUri);
        return controlModel;
    }
}

emf-merge.xml

<?xml version="1.0" encoding="UTF-8"?>
<merge:options 
  indent="  "  
  braceStyle="matching"  
  redirect="Gen"
  block="\s*@\s*generated\s*NOT\s*(?:\n\r?|\r\n?)"
  noImport="\s*//\s*import\s+([\w.*]*)\s*;\s*(?:\n\r?|\r\n?)"
  xmlns:merge="http://www.eclipse.org/org/eclipse/emf/codegen/jmerge/Options">

<!-- Tabbed Standard

  indent="&#x9;"  
  braceStyle="standard"  

-->

  <!-- this accepts both new and old style markup. -->

  <merge:dictionaryPattern
    name="modelMembers" 
    select="Member/getComment" 
    match="@\s*(model)"/>

  <merge:dictionaryPattern
    name="generatedUnmodifiableMembers" 
    select="Member/getComment" 
    match="@\s*(gen)erated\s*(This field/method[^(?:\n\r?|\r\n?)]*)*(?:\n\r?|\r\n?)"/>

  <merge:dictionaryPattern
    name="generatedModifiableMembers" 
    select="Member/getComment" 
    match="@\s*generated\s*(modifiable)\s*(?:\n\r?|\r\n?)"/>

  <!-- This is like the above, but for backward compatibility -->
  <merge:dictionaryPattern
    name="generatedLastGenMembers" 
    select="Member/getComment" 
    match="@\s*(lastgen).*(?:\n\r?|\r\n?)"/>

  <merge:dictionaryPattern
    name="orderedMembers" 
    select="Member/getComment" 
    match="@\s*(ordered)\s*(?:\n\r?|\r\n?)"/>

  <!-- Only push Annotations for the Members marked by gen-->
  <merge:push targetParentMarkup="^gen$" select="Annotation"/>

  <merge:pull 
    sourceMarkup="^modifiable$"
    sourceGet="Member/getComment"
    sourceTransfer="(\s*&lt;!--\s*begin-user-doc.*?end-user-doc\s*-->\s*)(?:\n\r?|\r\n?)"
    targetMarkup="^modifiable$"
    targetPut="Member/setComment"/>
  <merge:pull 
    sourceMarkup="^gen$"
    sourceGet="Member/getComment"
    sourceTransfer="(\s*&lt;!--\s*begin-user-doc.*?end-user-doc\s*-->\s*)(?:\n\r?|\r\n?)"
    targetMarkup="^gen$"
    targetPut="Member/setComment"/>
  <merge:pull 
    sourceGet="Member/getFlags"
    targetMarkup="^gen$"
    equals="Member/getName"
    targetPut="Member/setFlags"/>

  <merge:pull 
    sourceMarkup="^gen$"
    sourceGet="AbstractType/getComment"
    sourceTransfer="(\s*&lt;!--\s*begin-user-doc.*?end-user-doc\s*-->\s*)(?:\n\r?|\r\n?)"
    targetMarkup="^modifiable$"
    targetPut="AbstractType/setComment"/>

  <merge:pull 
    sourceGet="Type/getTypeParameters"
    targetMarkup="^lastgen$|^gen$|^modifiable$|^model$"
    targetPut="Type/setTypeParameters"/>
  <merge:pull 
    sourceGet="Type/getSuperclass"
    targetMarkup="^lastgen$|^gen$|^modifiable$|^model$"
    targetPut="Type/setSuperclass"/>
  <merge:pull 
    sourceGet="Type/getSuperInterfaces"
    sourceTransfer="(\s*@\s*extends|\s*@\s*implements)(.*?)(?:&lt;!--|(?:\n\r?|\r\n?))"
    targetMarkup="^lastgen$|^gen$|^modifiable$|^model$"
    targetPut="Type/addSuperInterface"/>

  <merge:pull 
    sourceGet="Enum/getSuperInterfaces"
    sourceTransfer="(\s*@\s*extends|\s*@\s*implements)(.*?)(?:&lt;!--|(?:\n\r?|\r\n?))"
    targetMarkup="^lastgen$|^gen$|^modifiable$|^model$"
    targetPut="Enum/addSuperInterface"/>

  <merge:pull 
    sourceGet="EnumConstant/getArguments"
    targetMarkup="^lastgen$|^gen$|^modifiable$|^model$"
    targetPut="EnumConstant/setArguments"/>
  <merge:pull 
    sourceGet="EnumConstant/getBody"
    targetMarkup="^lastgen$|^gen$|^modifiable$|^model$$"
    targetPut="EnumConstant/setBody"/>

  <merge:pull 
    sourceGet="AnnotationTypeMember/getType"
    targetMarkup="^gen$"
    targetPut="AnnotationTypeMember/setType"/>
  <merge:pull 
    sourceGet="AnnotationTypeMember/getDefaultValue"
    targetMarkup="^gen$"
    targetPut="AnnotationTypeMember/setDefaultValue"/>

  <merge:pull 
    sourceGet="Initializer/getBody"
    targetMarkup="^gen$"
    targetPut="Initializer/setBody"/>

  <merge:pull 
    sourceGet="Field/getType"
    targetMarkup="^gen$"
    targetPut="Field/setType"/>
  <merge:pull 
    sourceGet="Field/getInitializer"
    targetMarkup="^gen$"
    targetPut="Field/setInitializer"/>

  <merge:pull 
    sourceGet="Method/getTypeParameters"
    targetMarkup="^gen$"
    targetPut="Method/setTypeParameters"/>
  <merge:pull 
    sourceGet="Method/getReturnType"
    targetMarkup="^gen$|^model$"
    targetPut="Method/setReturnType"/>
  <merge:pull 
    sourceGet="Method/getParameters"
    targetMarkup="^gen$"
    targetPut="Method/setParameters"/>
  <merge:pull 
    sourceGet="Method/getBody"
    targetMarkup="^gen$"
    targetPut="Method/setBody"/>
  <merge:pull 
    sourceGet="Method/getExceptions"
    targetMarkup="^gen$"
    targetPut="Method/addException"/>

  <merge:sweep markup="^gen$" select="Member"/>
  <merge:sweep markup="^org.eclipse.emf.ecore.EMetaObject$" select="Import"/>
  <merge:sweep markup="^org.eclipse.emf.ecore.impl.EMetaObjectImpl$" select="Import"/>
  <merge:sweep markup="^org.eclipse.emf.ecore.util.EObjectCompositeEList$" select="Import"/>
  <merge:sweep markup="^org.eclipse.emf.ecore.util.EObjectCompositeWithInverseEList$" select="Import"/>
  <merge:sweep markup="^org.eclipse.emf.common.util.AbstractEnumerator$" select="Import"/>

  <merge:sort markup="^ordered$" select="Field"/>
  <merge:sort markup="^ordered$" select="EnumConstant"/>

<!-- Basic Rules

    <merge:pull 
      sourceGet="CompilationUnit/getHeader"
      targetPut="CompilationUnit/setHeader"/>

    <merge:pull 
      sourceGet="Package/getName"
      targetPut="Package/setName"/>

    <merge:pull 
      sourceGet="Member/getFlags"
      targetPut="Member/setFlags"/>
    <merge:pull 
      sourceGet="Member/getComment"
      targetPut="Member/setComment"/>

    <merge:pull 
      sourceGet="Type/getSuperclass"
      targetPut="Type/setSuperclass"/>
    <merge:pull 
      sourceGet="Type/getSuperInterfaces"
      targetPut="Type/addSuperInterface"/>

    <merge:pull 
      sourceGet="Initializer/getBody"
      targetPut="Initializer/setBody"/>

    <merge:pull 
      sourceGet="Field/getType"
      targetPut="Field/setType"/>
    <merge:pull 
      sourceGet="Field/getInitializer"
      targetPut="Field/setInitializer"/>

    <merge:pull 
      sourceGet="Method/getBody"
      targetPut="Method/setBody"/>
    <merge:pull 
      sourceGet="Method/getReturnType"
      targetPut="Method/setReturnType"/>
    <merge:pull 
      sourceGet="Method/getExceptions"
      targetPut="Method/addException"/>
-->

<!-- Push Enum Constants only for generated Enums -->
<!-- 
  <merge:push targetParentMarkup="^gen$" select="EnumConstant"/>
-->

<!-- Push Annotation Type Members only for generated Annotation Types -->
<!--
  <merge:push targetParentMarkup="^gen$" select="AnnotationTypeMember"/>
-->

<!-- Sets the content of annotations if the parent is marked with gen --> 
<!--
    <merge:pull 
      sourceGet="Annotation/getContents"
      targetParentMarkup="^gen$"
      targetPut="Annotation/setContents"/>
-->      

<!-- Remove annotations of generated target nodes if the annotation is not in the source -->
<!--
  <merge:sweep parentMarkup="^gen$" select="Annotation"/>
-->    

<!-- 
    <merge:pull 
      sourceMarkup="^modifiable$"
      sourceGet="Member/getComment"
      targetMarkup="^gen$"
      targetPut="Member/setComment"/>
-->

</merge:options>

file0.txt

    /**
     * method1.<br/>
     * @generated
     */
    public void method1() {        
        System.out.println("a");
    }

    /**
     * method2.<br/>
     * @generated
     */
    public void method2() {        
        System.out.println("a");
    }

file1.txt

    /**
     * method1.<br/>
     * @generated
     */
    public void method1() {        
        System.out.println("あ");
    }

    /**
     * method2.<br/>
     */
    public void method2() {        
        System.out.println("あ");
    }

file2.txt

    /**
     * method1.<br/>
     * @generated
     */
    public void method1() {        
        System.out.println("a");
    }

    /**
     * method2.<br/>
     */
    public void method2() {        
        System.out.println("あ");
    }

その後に手修正したコード.java

    /**
     * method1.<br/>
     * @generated
     */
    public void method1() {        
        System.out.println("あ");
    }

    /**
     * method2.<br/>
     */
    public void method2() {        
        System.out.println("あ");
    }

もう一度自動生成させたコード.java

    /**
     * method1.<br/>
     * @generated
     */
    public void method1() {        
        System.out.println("a");
    }

    /**
     * method2.<br/>
     */
    public void method2() {        
        System.out.println("あ");
    }

元々の自動生成コード.java

    /**
     * method1.<br/>
     * @generated
     */
    public void method1() {        
        System.out.println("a");
    }

    /**
     * method2.<br/>
     * @generated
     */
    public void method2() {        
        System.out.println("a");
    }