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Now you have a file with a PEM encoded certificate, say e.g. C:\Temp\MyCA.cer.
To add this to your JDK's cacerts, go to the directory where the cacerts resides, like e.g.:
C:\Program Files\Java\jdk1.6.0_43\jre\lib\security\cacerts
Here, enter the command:
keytool -import -keystore cacerts -alias "My AD CA" -file C:\Temp\MyCA.cer -storepass changeit
You may want to repeat this for the JRE in e.g. C:\Program Files\Java\jre6\lib\security\cacerts.
Now restart the Tomcat instance that PWM uses.
Again, note that the latest build have a wizard in the configuration editor to import the certificates of all connected LDAP servers automatically.
Regards,
Menno