java.io.FileNotFoundException: /usr/lib/jvm/jdk1.6.0_31-jcp/jre/lib/security/cacerts (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:120)
at java.io.FileInputStream.<init>(FileInputStream.java:79)
at ru.CryptoPro.CAdES.b.d.a.a(Unknown Source)
at ru.CryptoPro.CAdES.b.d.a.<clinit>(Unknown Source)
at ru.CryptoPro.CAdES.CAdESSignature.addSigner(Unknown Source)
at ru.CryptoPro.CAdES.CAdESSignature.addSigner(Unknown Source)

Exception in thread "main" ru.CryptoPro.CAdES.exception.CAdESException: Error verifying the certificate CN=Leader, O=Earth, C=UN: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty
at ru.CryptoPro.CAdES.b.d.b.a(Unknown Source)
at ru.CryptoPro.CAdES.b.d.b.a(Unknown Source)
at ru.CryptoPro.CAdES.b.d.a.<init>(Unknown Source)
at ru.CryptoPro.CAdES.b.d.a.<init>(Unknown Source)
at ru.CryptoPro.CAdES.CAdESSignature.addSigner(Unknown Source)
at ru.CryptoPro.CAdES.CAdESSignature.addSigner(Unknown Source)

public class SimpleTest {

public static void main(String[] args) throws Exception {
KeyStore keyStore = KeyStore.getInstance("HDImageStore", "JCP");
keyStore.load(new FileInputStream(System.getProperty("cryptopro.trustStore")), "changeit".toCharArray());

PrivateKey key = (PrivateKey) keyStore.getKey("leadZeroTest", "qwerty".toCharArray());
List<X509Certificate> chain = new ArrayList<X509Certificate>();
chain.add((X509Certificate) keyStore.getCertificate("leadZeroTest"));

CAdESSignature signature = new CAdESSignature(true);
signature.addSigner(key, chain, CAdESType.CAdES_X_Long_Type_1, "http://www.cryptopro.ru/tsp/tsp.srf");
signature.sign("test".getBytes());
}
}

Здравствуйте.
Путь к доверенному хранилищу cacerts и пароль к нему зашиты в коде, и список доверенных сертификатов берется именно по этому пути (см. при включенном уровне логирования FINE). Попробуйте сделать символьную ссылку на перемещенный cacerts.