In my data model, I have something to this effect:
@Entity
public class Target {
    @Id 
    @GeneratedValue
    private Long id;
    /* ...etc... */
}
@Entity
public class Dependency {
    @Id
    @GeneratedValue
    private Long id;
    @ManyToOne(optional=false)
    @Column(name="target_id")
    private Target target;
    /* ...etc... */
}
I'm already serializing Target just fine, but I need to serialize Dependency. Essentially, what I need is something like this:
<dependency>
    <id>100</id>
    <targetId>200</targetId>
</dependency>
Is there a way to do this in JAXB annotations without modifying my model?
You could use an XmlAdapter for this use case:
package forum7278406;
import javax.xml.bind.annotation.adapters.XmlAdapter;
public class TargetAdapter extends XmlAdapter<Long, Target> {
    @Override
    public Long marshal(Target target) throws Exception {
        return target.getId();
    }
    @Override
    public Target unmarshal(Long id) throws Exception {
        Target target = new Target();
        target.setId(id);
        return target;
    }
}
The XmlAdapter is registered on the Dependency class using the @XmlJavaTypeAdapter annotation:
package forum7278406;
import javax.persistence.*;
import javax.xml.bind.annotation.*;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
@Entity
@XmlRootElement
@XmlAccessorType(XmlAccessType.FIELD)
public class Dependency {
    @Id
    @GeneratedValue
    private Long id;
    @ManyToOne(optional=false)
    @Column(name="target_id")
    @XmlJavaTypeAdapter(TargetAdapter.class)
    private Target target;
    public Long getId() {
        return id;
    }
    public void setId(Long id) {
        this.id = id;
    }
    public Target getTarget() {
        return target;
    }
    public void setTarget(Target target) {
        this.target = target;
    }
}
Going Further
Instead of just creating a new instance of Target we could use an EntityManager to query the corresponding instance from the database.  Our XmlAdapter would be changed to look something like:
package forum7278406;
import javax.persistence.EntityManager;
import javax.xml.bind.annotation.adapters.XmlAdapter;
public class TargetAdapter extends XmlAdapter<Long, Target> {
    EntityManager entityManager;
    public TargetAdapter() {
    }
    public TargetAdapter(EntityManager entityManager) {
        this.entityManager = entityManager;
    }
    @Override
    public Long marshal(Target target) throws Exception {
        return target.getId();
    }
    @Override
    public Target unmarshal(Long id) throws Exception {
        Target target = null;
        if(null != entityManager) {
            target = entityManager.find(Target.class, id);
        }
        if(null == target) {
            target = new Target();
            target.setId(id);
        }
        return target;
    }
}
Now to set the instance of EntityManager on our XmlAdapter, we can do the following:
Unmarshaller umarshaller = jaxbContext.createUnmarshaller();
TargetAdapter targetAdatper = new TargetAdapter(entityManager);
unmarshaller.setAdapter(targetAdapter);
                        It works for EclipseLink MOXy with XmlID and XmlIDRef (but fails for sun JAXB, where XmlID must be string)
@Entity
@XmlRootElement
public class Target {
    @Id
    @GeneratedValue
    @XmlID
    @XmlElement
    private Long id;
}
@Entity
@XmlRootElement
public class Dependency {
    @Id
    @GeneratedValue
    @XmlElement
    private  Long id;
    @ManyToOne(optional = false)
    @Column(name = "target_id")
    @XmlIDREF
    @XmlElement(name = "targetId")
    private Target target;
}
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