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Problem

If you use Tomcat to run Java apps such as Atlassian Confluence (the page you're looking at now), JIRA, etc, via HTTPS, you might have noticed that your app will not support any 256 bit ciphers, however it will support 128 and 168 bit ciphers, as well as the lame 40 and 56 bit ciphers. The sslscan tool confirms this, and reports:

Accepted  SSLv3  128 bits  DHE-RSA-AES128-SHA 
Accepted  SSLv3  128 bits  AES128-SHA
Accepted  SSLv3  168 bits  EDH-RSA-DES-CBC3-SHA
Accepted  SSLv3  56 bits   EDH-RSA-DES-CBC-SHA
Accepted  SSLv3  40 bits   EXP-EDH-RSA-DES-CBC-SHA
Accepted  SSLv3  168 bits  DES-CBC3-SHA
Accepted  SSLv3  56 bits   DES-CBC-SHA
Accepted  SSLv3  40 bits   EXP-DES-CBC-SHA
Accepted  SSLv3  128 bits  RC4-SHA
Accepted  SSLv3  128 bits  RC4-MD5
Accepted  SSLv3  40 bits   EXP-RC4-MD5
Accepted  TLSv1  128 bits  DHE-RSA-AES128-SHA
Accepted  TLSv1  128 bits  AES128-SHA
Accepted  TLSv1  168 bits  EDH-RSA-DES-CBC3-SHA
Accepted  TLSv1  56 bits   EDH-RSA-DES-CBC-SHA
Accepted  TLSv1  40 bits   EXP-EDH-RSA-DES-CBC-SHA
Accepted  TLSv1  168 bits  DES-CBC3-SHA
Accepted  TLSv1  56 bits   DES-CBC-SHA
Accepted  TLSv1  40 bits   EXP-DES-CBC-SHA
Accepted  TLSv1  128 bits  RC4-SHA
Accepted  TLSv1  128 bits  RC4-MD5
Accepted  TLSv1  40 bits   EXP-RC4-MD5

So what's the problem here?

The issue lies in the so-called policy files of JDK6. According to Sun:

Due to import control restrictions for some countries, the Java Cryptography Extension (JCE) policy files shipped with the Java SE Development Kit and the Java SE Runtime Environment allow strong but limited cryptography to be used.

Enable 256 bit ciphers

From the Sun website, download the JCE Unlimited Strength Jurisdiction Policy Files 6 Release Candidate.
Unpack the ZIP file - it will contain two jar files: local_policy.jar and US_export_policy.jar.
On our Ubuntu boxes we use the packages sun-java6-jdk, sun-java6-bin, and sun-java6-jre. The files in question are stored in /usr/lib/jvm/java-6-sun/jre/lib/security. Replace the default jar files with the ones you downloaded, then restart your app. It should now support 256 bit ciphers:

Accepted  SSLv3  256 bits  DHE-RSA-AES256-SHA
Accepted  SSLv3  256 bits  AES256-SHA
Accepted  TLSv1  256 bits  DHE-RSA-AES256-SHA
Accepted  TLSv1  256 bits  AES256-SHA

Disable 40 and 56 bit ciphers

By default, also 40 and 56 bit ciphers are supported - you probably want to disable these. To do so you have to explicitly configure the allowed ciphers: take the previous list, include the 256 bit ciphers, leave out the 40 and 56 bit ones, then put the official names (not the OpenSSL equivalent) of the remaining ciphers in your HTTPS config (in my case at the bottom of server.xml). This will look like this:

After restarting your app, you can verify with sslscan that now 256 bit ciphers are supported and preferred, and no 40 and 56 bits ones are available anymore:

./sslscan --no-failed my.site.org:443
[...]
  Supported Server Cipher(s):
    Accepted  SSLv3  256 bits  DHE-RSA-AES256-SHA
    Accepted  SSLv3  256 bits  AES256-SHA
    Accepted  SSLv3  128 bits  DHE-RSA-AES128-SHA
    Accepted  SSLv3  128 bits  AES128-SHA
    Accepted  SSLv3  168 bits  EDH-RSA-DES-CBC3-SHA
    Accepted  SSLv3  168 bits  DES-CBC3-SHA
    Accepted  SSLv3  128 bits  RC4-SHA
    Accepted  SSLv3  128 bits  RC4-MD5
    Accepted  TLSv1  256 bits  DHE-RSA-AES256-SHA
    Accepted  TLSv1  256 bits  AES256-SHA
    Accepted  TLSv1  128 bits  DHE-RSA-AES128-SHA
    Accepted  TLSv1  128 bits  AES128-SHA
    Accepted  TLSv1  168 bits  EDH-RSA-DES-CBC3-SHA
    Accepted  TLSv1  168 bits  DES-CBC3-SHA
    Accepted  TLSv1  128 bits  RC4-SHA
    Accepted  TLSv1  128 bits  RC4-MD5

  Prefered Server Cipher(s):
    SSLv3  256 bits  DHE-RSA-AES256-SHA
    TLSv1  256 bits  DHE-RSA-AES256-SHA

For apache the following will have the same result:

SSLCipherSuite ALL:!ADH:!EXP:!DES:RC4+RSA:+HIGH:+MEDIUM!SSLv2
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