freeswan 1.98b with x509patch-0.9.13 is missing the files /etc/x509cert.der and /usr/lib/ipsec/mkx509cert pluto is complaining about not finding the .der file. Aren't these files supposed to go away only in x509patch-1.0.0 and higher?
x509cert.der is obsolete and should not be supported.
The X.509 default certifcate /etc/x509cert.der and the PGP default certificate /etc/pgpcert.pgp have been obsoleted and are not available any more. Local X.509 certificates in base64 PEM and binary DER format are now exclusively loaded using the leftcert/rightcert parameters in /etc/ipsec.conf. See CHANGES from X.509 Patch documentation.
This bug applies only to old versions of freeswan.