String xml = "...";
Document doc = parseXML(xml);
Element data = doc.getDocumentElement();
Element sign = ru.smevx.crypto.smev3.xmldsig.XmlDSignUtils.sign(privateKey, cert, data);

var CAPICOM_ENCODE_BASE64 = 0;
...
if (args.toSign) {
    try {
        var oHashedData = yield cadesplugin.CreateObjectAsync("CAdESCOM.HashedData");
        oHashedData.Algorithm = cadesplugin.CADESCOM_HASH_ALGORITHM_CP_GOST_3411; // ГОСТ Р 34.11-94
        oHashedData.DataEncoding = cadesplugin.CADESCOM_BASE64_TO_BINARY;
        yield oHashedData.Hash(args.toSign);

        var oRawSignature = yield cadesplugin.CreateObjectAsync("CAdESCOM.RawSignature");
        var signHash;
        var certData;
        // Вычисляем значение подписи
        try {
            signHash = yield oRawSignature.SignHash(oHashedData, oCertificate);
        } catch (err) {
            alert("Failed to create signature. Error: " + cadesplugin.getLastError(err));
            return;
        }

        var signature = Base64.encode(utils.reverse(utils.hexToString(signHash)));
        args.sig = signature;

        certData = yield oCertificate.Export(CAPICOM_ENCODE_BASE64);
        args.cert = certData;
    } catch (err) {
        alert(err);
    }
}

<dependency>
    <groupId>JCPxml</groupId>
    <artifactId>JCPxml</artifactId>
    <version>2.0.0</version>
</dependency>
<dependency>
    <groupId>org.apache.santuario</groupId>
    <artifactId>xmlsec</artifactId>
    <version>1.5.8</version>
</dependency>

private static void initXmlSec() throws Exception {
    // При формировании элемента Signature будут убраны все разрывы между элементами.
    System.setProperty("org.apache.xml.security.ignoreLineBreaks", "true");

    //Добавил инициализацию из документации jsp : jcp-build-2.0.37027

    //Перед началом использования классов из библиотеки XML Security необходимо зарегистрировать ГОСТ алгоритмы.
    // Регистрируем реализации алгоритмов в xmlsec.
    if (!JCPXMLDSigInit.isInitialized()) {
        JCPXMLDSigInit.init();
    }

    // Реализация дополнительной трансформации.
    Transform.register(SmevTransformSpi.ALGORITHM_URN, SmevTransformSpi.class.getName());
    hackXmlsecIgnoreLineBreaks();
}

private static void hackXmlsecIgnoreLineBreaks() throws PrivilegedActionException {
    AccessController.doPrivileged(new PrivilegedExceptionAction < Boolean > () {
        @Override
        public Boolean run() throws Exception {
            Field f = XMLUtils.class.getDeclaredField("ignoreLineBreaks");
            f.setAccessible(true);
            f.set(null, true);
            return false;
        }
    });
}

final String xml = "<ns1:BreachRequest xmlns:ns1=\"urn://x-artefacts-gibdd-gov-ru/breach/root/1.0\" xmlns:ns2=\"urn://x-artefacts-gibdd-gov-ru/breach/commons/1.0\" xmlns:ns3=\"urn://x-artefacts-smev-gov-ru/supplementary/commons/1.0.1\" xmlns:ns4=\"xml:id\" Id=\"PERSONAL_SIGNATURE\"><ns1:RequestedInformation><ns2:RegPointNum>Т785ЕС57</ns2:RegPointNum></ns1:RequestedInformation><ns1:Governance><ns2:Name>ГИБДД РФ</ns2:Name><ns2:Code>GIBDD</ns2:Code><ns2:OfficialPerson><ns3:FamilyName>Загурский</ns3:FamilyName><ns3:FirstName>Андрей</ns3:FirstName><ns3:Patronymic>Петрович</ns3:Patronymic></ns2:OfficialPerson></ns1:Governance></ns1:BreachRequest>";
final Element doc = ru.it.poltava.xml.XMLTransformHelper.buildDocumentFromString(xml).getDocumentElement();

public String buildHashForSignByBusinessContent() throws XMLSecurityException {
    // Формируем с заполненными трасформ алгоритмами объект SignedInfo со сгенерированным DigestValue,
    XMLSignature xmlSignature = buildXMLSignatureTemplate(doc);
    // получаем массив byte[] с канокализированным значением SignedInfo
    byte[] canonicalizeOctetStream = xmlSignature.getSignedInfo().getCanonicalizedOctetStream();

    // необходимо посчитать хэш по алгоритму гост и закодировать его в шеснадцатерично-десятичном формате.
    String hash3411Base64 = CryptoUtil.buildHash3411Base64(canonicalizeOctetStream);
    return CryptoUtil.getHexadecimalHash(hash3411Base64);
}

private XMLSignature buildXMLSignatureTemplate() throws XMLSecurityException {
    Document document = doc.getOwnerDocument();
    XMLSignature xmlSignature = new XMLSignature(document, "", XMLDSIG_SIGN_METHOD, Transforms.TRANSFORM_C14N_EXCL_OMIT_COMMENTS);

    Transforms transforms = new Transforms(document);
    transforms.addTransform(Transforms.TRANSFORM_C14N_EXCL_OMIT_COMMENTS);
    transforms.addTransform(SmevTransformSpi.ALGORITHM_URN);

    String refURI = document.getDocumentElement().getAttribute("Id");
    if (!refURI.isEmpty() && !refURI.startsWith("#")) {
        refURI = "#" + refURI;
    }

    xmlSignature.addDocument(refURI, transforms, DIGEST_METHOD);

    xmlSignature.getSignedInfo().generateDigestValues();
    return xmlSignature;
}

static String buildHash3411Base64(byte[] data) {
    byte[] hash = buildHash3411(data);
    return hash != null ? Base64.encodeBase64String(data) : "";
}

static String getHexadecimalHash(String hashInBase64) {
    String hexadecimalHash = "";

    try {
        byte[] encodedBytes = Base64.decodeBase64(hashInBase64);

        hexadecimalHash = toHex(encodedBytes);
    } catch (Exception e) {
        LOGGER.log(Level.SEVERE, null, e);
    }

    return hexadecimalHash;
}

function signHashRawAndGetCertificate_Async(certListBoxId, handleFunction, args) {
    cadesplugin.async_spawn(function*(arg) {
        var CAPICOM_ENCODE_BASE64 = 0;
        var oCertificate;
        var certData;
        var oHashedData;
        var oRawSignature;
        var sRawSignature;

        var e = document.getElementById(arg[0]);
        var selectedCertID = e.selectedIndex;
        if (selectedCertID == -1) {
            alert("Select certificate");
            return;
        }

        var thumbprint = e.options[selectedCertID].value.split(" ").reverse().join("").replace(/\s/g, "").toUpperCase();
        try {
            var oStore = yield cadesplugin.CreateObjectAsync("CAdESCOM.Store");
            yield oStore.Open();
        } catch (err) {
            alert('Failed to create CAdESCOM.Store: ' + err.number);
            return;
        }

        var all_certs = yield oStore.Certificates;
        var oCerts = yield all_certs.Find(cadesplugin.CAPICOM_CERTIFICATE_FIND_SHA1_HASH, thumbprint);

        if ((yield oCerts.Count) == 0) {
            alert("Certificate not found");
            return;
        }
        oCertificate = yield oCerts.Item(1);

        try{

            // Создаем объект CAdESCOM.HashedData
            oHashedData = yield cadesplugin.CreateObjectAsync("CAdESCOM.HashedData");

            // Инициализируем объект заранее вычисленным хэш-значением
            // Алгоритм хэширования нужно указать до того, как будет передано хэш-значение
            oHashedData.Algorithm = cadesplugin.CADESCOM_HASH_ALGORITHM_CP_GOST_3411; // ГОСТ Р 34.11-94
            oHashedData.SetHashValue(args.toSign);

            if (args.toSign) {
                // Создаем объект CAdESCOM.RawSignature
                oRawSignature = yield cadesplugin.CreateObjectAsync("CAdESCOM.RawSignature");

                // Вычисляем значение подписи
                try {
                    sRawSignature = yield oRawSignature.SignHash(oHashedData, oCertificate);
                } catch (err) {
                    alert("Failed to create signature. Error: " + cadesplugin.getLastError(err));
                    return;
                }

                try {
                    oRawSignature.VerifyHash(oHashedData, oCertificate, sRawSignature);
                } catch (err) {
                    alert("Failed to verify signature. Error: " + cadesplugin.getLastError(err));
                }

                certData = yield oCertificate.Export(CAPICOM_ENCODE_BASE64);
            }

            args.sig = sRawSignature;
            args.cert = certData;

            handleFunction(args);
        }catch(err){
            alert(err);
        }
    }, certListBoxId); //cadesplugin.async_spawn
}

public String buildXmlSigDetached(String cspSignHexadecimal, String x509certificateBase64) throws Exception {
    String signatureValue = buildSignatureValueByCspSignHexadecimal(cspSignHexadecimal);

    Element personalSignature = buildSignatureTemplateByBusinessContent(doc, x509certificateBase64);
    personalSignature.getElementsByTagNameNS("http://www.w3.org/2000/09/xmldsig#", "SignatureValue")
            .item(0).setTextContent(signatureValue);

    return XMLTransformHelper.elementToString(personalSignature);
}

private String buildSignatureValueByCspSignHexadecimal(String cspSignHexadecimal) throws DecoderException {
    byte[] signBytes = Hex.decodeHex(cspSignHexadecimal.toCharArray());

    ArrayUtils.reverse(signBytes);

    return new Base64().encodeAsString(signBytes);
}

private Element buildSignatureTemplateByBusinessContent(String x509certificateBase64) throws XMLSecurityException, CertificateException, IOException {
	XMLSignature xmlSignature = buildXMLSignatureTemplate(doc);

    X509Certificate certificate = (X509Certificate) CertificateFactory.getInstance("X.509").generateCertificate(new ByteArrayInputStream(Base64.decodeBase64(x509certificateBase64)));

    xmlSignature.addKeyInfo(certificate);

    return xmlSignature.getElement();
}

var objHashedData = yield cadesplugin.CreateObjectAsync("CAdESCOM.HashedData");
objHashedData.Algorithm = cadesplugin.CADESCOM_HASH_ALGORITHM_CP_GOST_3411; // ГОСТ Р 34.11-94
objHashedData.Hash("");
var hashValue = yield objHashedData.Value;
console.log("Hash from empty string: " + hashValue);

981E5F3CA30C841487830F84FB433E13AC1101569B9C13584AC483234CD656C0

var objHashedData = yield cadesplugin.CreateObjectAsync("CAdESCOM.HashedData");
objHashedData.Algorithm = cadesplugin.CADESCOM_HASH_ALGORITHM_CP_GOST_3411; // ГОСТ Р 34.11-94
objHashedData.DataEncoding = cadesplugin.CADESCOM_BASE64_TO_BINARY;
objHashedData.Hash(args.toSign);
var hashValue = yield objHashedData.Value;
console.log("Hash from args.toSign: " + hashValue);

017ECC86FA1E9D463578987C3878C4E08A82C36E20F2481468EB8F698D310F70

var objHashedData = yield cadesplugin.CreateObjectAsync("CAdESCOM.HashedData");
objHashedData.Algorithm = cadesplugin.CADESCOM_HASH_ALGORITHM_CP_GOST_3411; // ГОСТ Р 34.11-94
tempHashedData2.Hash(Base64.decode(args.toSign));
var hashValue = yield objHashedData.Value;
console.log("Hash from decode string: " + hashValue);

CCE9DCB34BB3EA4B943C23B532821ADE52E4E5762B966F581B1FCD29C51253AA