This issue is a limitation of the default CertificateFactory in Java 6
(sun.security.provider.X509Factory). Starting with Java 7 comments are
properly skipped when parsing PEM files (see the readOneBlock() method
in X509Factory.java [1]).

Considering that OpenJDK6 is going to be removed for Jessie I suggest
marking this bug as wontfix.

Emmanuel Bourg

[1]
http://grepcode.com/file_/repository.grepcode.com/java/root/jdk/openjdk/7-b147/sun/security/provider/X509Factory.java/?v=source

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