HeaderSection.java

package sandbox.maildata;

import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

public class HeaderSection {

    private final Map<String, List<String>> map = new HashMap<>();

    public void put(String key, String value) {
        map.put(key, new ArrayList<>(Arrays.asList(value)));
    }

    public void add(String key, String value) {
        List<String> list = map.get(key);
        if (list == null) {
            list = new ArrayList<>();
            map.put(key, list);
        }
        list.add(value);
    }

    public String get(String key) {
        if (!map.containsKey(key))
            return null;
        List<String> list = map.get(key);
        if (list.size() != 1)
            throw new InvalidHeaderException("HeaderSection has " + list.size() + " values for '"
                    + key + "', not 1");
        return list.get(1);
    }

    public List<String> getList(String key) {
        return map.get(key);
    }

    void parse(String headerField) {
        String key = headerField.substring(0, headerField.indexOf(": "));
        String value = headerField.substring(headerField.indexOf(": ") + 2);
        add(key, value);
    }

    @Override
    public String toString() {
        return map.toString();
    }

    public void writeTo(OutputStream out) throws IOException {
        OutputStreamWriter writer = new OutputStreamWriter(out);
        for (Map.Entry<String, List<String>> entry : map.entrySet()) {
            for (Object value : entry.getValue()) {
                writer.write(entry.getKey() + ": " + value + "\r\n");
            }
            writer.flush();
        }

    }
}

InvalidHeaderException.java

package sandbox.maildata;

public class InvalidHeaderException extends RuntimeException {

    public InvalidHeaderException(String msg) {
        super(msg);
    }
}

MailData.java

package sandbox.maildata;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FilterOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.Reader;
import java.util.Scanner;


public class MailData {

    private File file;

    public MailData(File file) {
        this.file = file;
    }

    public HeaderSection parseHeaders() throws FileNotFoundException {
        Scanner in = new Scanner(new FileReader(file));
        HeaderSection headers = new HeaderSection();
        StringBuilder buf = new StringBuilder();
        boolean prevCont = false;
        while (in.hasNextLine()) {
            String ln = in.nextLine();
            boolean cont = !ln.trim().equals(ln);
            if (!cont && buf.length() > 0) {
                headers.parse(buf.toString());
                buf.setLength(0);
            }
            if (ln.isEmpty())
                break;
            buf.append(ln.trim());
            prevCont = cont;
        }
        return headers;
    }

    public InputStream decodeBody(HeaderSection headers) throws IOException {
        InputStream in = new FileInputStream(file);
        boolean prev = false;
        for (int ch; (ch = in.read()) != -1;) {
            if (ch == '\r' && prev) {
                in.read();
                break;
            }
            prev = ch == '\n';
        }
        return in;
    }

    public OutputStream output() throws FileNotFoundException {
        File tmpfile = new File(file.getAbsolutePath() + "_TMP");
        final FileOutputStream out = new FileOutputStream(tmpfile);
        return new FilterOutputStream(out) {

            @Override
            public void write(byte[] b, int off, int len) throws IOException {
                out.write(b, off, len);
            }

            @Override
            public void close() throws IOException {
                out.close();
                file.delete();
                tmpfile.renameTo(file);
                file = tmpfile;
            }

        };
    }
}

MailDataTest.java

package sandbox.maildata;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;

public class MailDataTest {

    public static void main(String[] args) throws FileNotFoundException, IOException {
        MailData mail = new MailData(new File("/home/attila/mzn.eml"));
        HeaderSection headers = mail.parseHeaders();
        InputStream in = mail.decodeBody(headers);
        headers.add("X-MailData-Test", "a");
        headers.put("X-MailData-Test", "b");
        headers.add("X-MailData-Test", "c");
        try (OutputStream out = mail.output()) {
            headers.writeTo(out);
            for(int ch; (ch = in.read()) != -1;)
                out.write(ch);
        }
    }

}