Crypto providers need to be installed into the JRE extension directory
(e.g. $JRE_HOME/lib/ext) and an entry must be added to
$JRE_HOME/lib/security/java.security to install the provider.  For
example:

security.provider.5=org.bouncycastle.jce.provider.BouncyCastleProvider

Note the 5 above; each provider needs a unique number and the ordering
determines which provider is used for a given crypto primitive
obtained by code like the following:

Cipher c1 = Cipher.getInstance("DES");

If BC is before the Sun provider, you'll use the BC DES
implementation.  Put it last if in doubt.  (Although it's arguably
better than Sun in many cases.)

M

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