Public bug reported:

Sun Java 6 does not use the Debian/Ubuntu ca-certificates system for SSL
root certificates. This means that, for example, installing a corporate
CA certificate using the system-wide ca-certificates mechanism will NOT
result in it being trusted by Sun Java 6.

This can be fixed by symlinking /etc/java-6-sun/security/cacerts to 
/etc/ssl/certs/java/cacerts. However, that will result in the following CAs 
(which are currently trusted in Java 6) no longer being trusted. If that 
presents a problem, they should be added to ca-certificates. The certificates 
are:
    CN=Baltimore CyberTrust Code Signing Root, OU=CyberTrust, O=Baltimore, C=IE
    CN=GTE CyberTrust Root 5, OU="GTE CyberTrust Solutions, Inc.", O=GTE 
Corporation, C=US
    CN=TC TrustCenter Class 2 CA II, OU=TC TrustCenter Class 2 CA, O=TC 
TrustCenter GmbH, C=DE
    CN=TC TrustCenter Class 4 CA II, OU=TC TrustCenter Class 4 CA, O=TC 
TrustCenter GmbH, C=DE
    CN=TC TrustCenter Universal CA I, OU=TC TrustCenter Universal CA, O=TC 
TrustCenter GmbH, C=DE
    OU=Security Communication EV RootCA1, O="SECOM Trust Systems CO.,LTD.", C=JP

** Affects: ca-certificates (Ubuntu)
     Importance: Undecided
         Status: New

** Affects: sun-java6 (Ubuntu)
     Importance: Undecided
         Status: New

** Also affects: ca-certificates (Ubuntu)
   Importance: Undecided
       Status: New

-- 
Sun Java 6 JRE does not use ca-certificates for SSL
https://bugs.launchpad.net/bugs/346609
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