You can write custom deserialiser or use @JsonAnySetter annotation. You can do it in that way:
- Deserialise 
JSON to middle POJO structure which uses @JsonAnySetter annotation 
- Convert middle 
POJO structure to Map 
- Convert 
Map to destination POJO structure. 
Deserialisation part and converting to Map could look like below:
class Fields {
    private Field[] fields;
    public Field[] getFields() {
        return fields;
    }
    public void setFields(Field[] fields) {
        this.fields = fields;
    }
    public Map<String, Object> toMap() {
        Map<String, Object> map = new HashMap<>();
        for (Field field : fields) {
            map.put(field.getTypeName(), field.getFieldValue().resolve());
        }
        return map;
    }
    @Override
    public String toString() {
        return "Fields{" +
                "fields=" + Arrays.toString(fields) +
                '}';
    }
}
class Field {
    private String typeName;
    private FieldValue fieldValue;
    @JsonAnySetter
    private void setValue(String propertyName, Object value) {
        FieldValueBuilder builder = new FieldValueBuilder();
        if (builder.accept(propertyName)) {
            this.fieldValue = builder.build(propertyName, value);
        }
    }
    public String getTypeName() {
        return typeName;
    }
    public void setTypeName(String typeName) {
        this.typeName = typeName;
    }
    public FieldValue getFieldValue() {
        return fieldValue;
    }
    public void setFieldValue(FieldValue fieldValue) {
        this.fieldValue = fieldValue;
    }
    @Override
    public String toString() {
        return "Field{" +
                "typeName='" + typeName + '\'' +
                ", fieldValue=" + fieldValue +
                '}';
    }
}
class FieldValueBuilder {
    private List<String> ignoreFields = Arrays.asList("multiple", "typeClass");
    public boolean accept(String propertyName) {
        return !ignoreFields.contains(propertyName);
    }
    public FieldValue build(String propertyName, Object value) {
        if (value instanceof String) {
            return new StringFieldValue(value.toString());
        }
        if (value instanceof List) {
            return deserialiseList((List) value);
        }
        System.out.println("Need to parse: key = " + propertyName + ", value = " + value);
        return null;
    }
    private FieldValue deserialiseList(List list) {
        if (list.isEmpty()) {
            return null;
        }
        // It is a tricky part. From example it looks like that value is always a single-element-array.
        // If not, handle it.
        Object item = list.get(0);
        if (item instanceof String) {
            return new StringFieldValue(item.toString());
        } else if (item instanceof Map) {
            List<Field> fields = new ArrayList<>();
            Map<String, Object> map = (Map<String, Object>) item;
            for (Object valueItem : map.values()) {
                if (valueItem instanceof Map) {
                    Map<String, Object> mapItem = (Map<String, Object>) valueItem;
                    Field field = new Field();
                    field.setTypeName(mapItem.get("typeName").toString());
                    field.setFieldValue(build("value", mapItem.get("value")));
                    fields.add(field);
                }
            }
            return new ListFieldValues(fields);
        } else {
            System.out.println(item);
        }
        return new NullFieldValue();
    }
}
interface FieldValue {
    Object resolve();
}
class StringFieldValue implements FieldValue {
    private final String value;
    public StringFieldValue(String value) {
        this.value = value;
    }
    public String getValue() {
        return value;
    }
    @Override
    public Object resolve() {
        return value;
    }
    @Override
    public String toString() {
        return "StringFieldValue{" +
                "value='" + value + '\'' +
                '}';
    }
}
class ListFieldValues implements FieldValue {
    private final List<Field> fields;
    public ListFieldValues(List<Field> fields) {
        this.fields = fields;
    }
    public List<Field> getFields() {
        return fields;
    }
    @Override
    public Object resolve() {
        Map<String, Object> map = new HashMap<>();
        for (Field field : fields) {
            map.put(field.getTypeName(), field.getFieldValue().resolve());
        }
        return map;
    }
    @Override
    public String toString() {
        return "ListFieldValues{" +
                "fields=" + fields +
                '}';
    }
}
class NullFieldValue implements FieldValue {
    @Override
    public Object resolve() {
        return null;
    }
}
Final POJO structure could look like below:
class Book {
    private String subject;
    private Author author;
    private Description dsDescription;
    private String dateOfDeposit;
    private String depositor;
    private String title;
    private Contact datasetContact;
    public String getSubject() {
        return subject;
    }
    public void setSubject(String subject) {
        this.subject = subject;
    }
    public Author getAuthor() {
        return author;
    }
    public void setAuthor(Author author) {
        this.author = author;
    }
    public Description getDsDescription() {
        return dsDescription;
    }
    public void setDsDescription(Description dsDescription) {
        this.dsDescription = dsDescription;
    }
    public String getDateOfDeposit() {
        return dateOfDeposit;
    }
    public void setDateOfDeposit(String dateOfDeposit) {
        this.dateOfDeposit = dateOfDeposit;
    }
    public String getDepositor() {
        return depositor;
    }
    public void setDepositor(String depositor) {
        this.depositor = depositor;
    }
    public String getTitle() {
        return title;
    }
    public void setTitle(String title) {
        this.title = title;
    }
    public Contact getDatasetContact() {
        return datasetContact;
    }
    public void setDatasetContact(Contact datasetContact) {
        this.datasetContact = datasetContact;
    }
    @Override
    public String toString() {
        return "Book{" +
                "subject='" + subject + '\'' +
                ", author=" + author +
                ", dsDescription=" + dsDescription +
                ", dateOfDeposit='" + dateOfDeposit + '\'' +
                ", depositor='" + depositor + '\'' +
                ", title='" + title + '\'' +
                ", datasetContact=" + datasetContact +
                '}';
    }
}
class Author {
    private String authorName;
    private String authorAffiliation;
    public String getAuthorName() {
        return authorName;
    }
    public void setAuthorName(String authorName) {
        this.authorName = authorName;
    }
    public String getAuthorAffiliation() {
        return authorAffiliation;
    }
    public void setAuthorAffiliation(String authorAffiliation) {
        this.authorAffiliation = authorAffiliation;
    }
    @Override
    public String toString() {
        return "Author{" +
                "authorName='" + authorName + '\'' +
                ", authorAffiliation='" + authorAffiliation + '\'' +
                '}';
    }
}
class Description {
    private String dsDescriptionValue;
    public String getDsDescriptionValue() {
        return dsDescriptionValue;
    }
    public void setDsDescriptionValue(String dsDescriptionValue) {
        this.dsDescriptionValue = dsDescriptionValue;
    }
    @Override
    public String toString() {
        return "Description{" +
                "dsDescriptionValue='" + dsDescriptionValue + '\'' +
                '}';
    }
}
class Contact {
    private String datasetContactEmail;
    private String datasetContactAffiliation;
    private String datasetContactName;
    public String getDatasetContactEmail() {
        return datasetContactEmail;
    }
    public void setDatasetContactEmail(String datasetContactEmail) {
        this.datasetContactEmail = datasetContactEmail;
    }
    public String getDatasetContactAffiliation() {
        return datasetContactAffiliation;
    }
    public void setDatasetContactAffiliation(String datasetContactAffiliation) {
        this.datasetContactAffiliation = datasetContactAffiliation;
    }
    public String getDatasetContactName() {
        return datasetContactName;
    }
    public void setDatasetContactName(String datasetContactName) {
        this.datasetContactName = datasetContactName;
    }
    @Override
    public String toString() {
        return "Contact{" +
                "datasetContactEmail='" + datasetContactEmail + '\'' +
                ", datasetContactAffiliation='" + datasetContactAffiliation + '\'' +
                ", datasetContactName='" + datasetContactName + '\'' +
                '}';
    }
}
Example usage of above code:
import com.fasterxml.jackson.annotation.JsonAnySetter;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class JsonTest {
    public static void main(String[] args) throws Exception {
        File jsonFile = new File("./resource/test.json").getAbsoluteFile();
        ObjectMapper mapper = new ObjectMapper();
        mapper.enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY);
        Fields fields = mapper.readValue(jsonFile, Fields.class);
        System.out.println(fields);
        Map<String, Object> map = fields.toMap();
        System.out.println(map);
        System.out.println(mapper.convertValue(map, Book.class));
    }
}
Above code prints:
Fields{fields=[Field{typeName='title', fieldValue=StringFieldValue{value='Shapefile Dataset'}}, Field{typeName='author', fieldValue=ListFieldValues{fields=[Field{typeName='authorName', fieldValue=StringFieldValue{value='Quigley, Elizabeth'}}, Field{typeName='authorAffiliation', fieldValue=StringFieldValue{value='Harvard University'}}]}}, Field{typeName='datasetContact', fieldValue=ListFieldValues{fields=[Field{typeName='datasetContactName', fieldValue=StringFieldValue{value='Quigley, Elizabeth'}}, Field{typeName='datasetContactAffiliation', fieldValue=StringFieldValue{value='Harvard University'}}, Field{typeName='datasetContactEmail', fieldValue=StringFieldValue{value='equigley@iq.harvard.edu'}}]}}, Field{typeName='dsDescription', fieldValue=ListFieldValues{fields=[Field{typeName='dsDescriptionValue', fieldValue=StringFieldValue{value='Dataset for shapefile'}}]}}, Field{typeName='subject', fieldValue=StringFieldValue{value='Earth and Environmental Sciences'}}, Field{typeName='depositor', fieldValue=StringFieldValue{value='Quigley, Elizabeth'}}, Field{typeName='dateOfDeposit', fieldValue=StringFieldValue{value='2015-07-13'}}]}
{author={authorName=Quigley, Elizabeth, authorAffiliation=Harvard University}, subject=Earth and Environmental Sciences, dsDescription={dsDescriptionValue=Dataset for shapefile}, dateOfDeposit=2015-07-13, depositor=Quigley, Elizabeth, title=Shapefile Dataset, datasetContact={datasetContactEmail=equigley@iq.harvard.edu, datasetContactAffiliation=Harvard University, datasetContactName=Quigley, Elizabeth}}
Book{subject='Earth and Environmental Sciences', author=Author{authorName='Quigley, Elizabeth', authorAffiliation='Harvard University'}, dsDescription=Description{dsDescriptionValue='Dataset for shapefile'}, dateOfDeposit='2015-07-13', depositor='Quigley, Elizabeth', title='Shapefile Dataset', datasetContact=Contact{datasetContactEmail='equigley@iq.harvard.edu', datasetContactAffiliation='Harvard University', datasetContactName='Quigley, Elizabeth'}}