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The .cer and .crt file should be interchangable as far as importing them into a keystore.
Take a look at the contents of the .cer file. Erase anything before the -----BEGIN CERTIFICATE----- line and after the -----END CERTIFICATE----- line. You'll be left with the BEGIN/END lines with a bunch of Base64-encoded stuff between them.
-----BEGIN CERTIFICATE-----
MIIDQTCCAqqgAwIBAgIJALQea21f1bVjMA0GCSqGSIb3DQEBBQUAMIG1MQswCQYD
...
pfDACIDHTrwCk5OefMwArfEkSBo/
-----END CERTIFICATE-----
Then just import it into your keyfile using keytool.
keytool -import -alias myalias -keystore my.keystore -trustcacerts -file mycert.cer