tools: Fix ndnsec-cert-gen to correctly infer prefix before KEY

This commit also includes a few help message corrections in cert-dump,
cert-gen, and key-gen.

Change-Id: I67977e62c144c35e0e17fa1228c53b9d3cff201e
Refs: #2052
tools: Accept `--sign-id` and `--cert-prefix` in ndnsec-cert-revoke

Also, this commit changes output format to base64 encoding.

Change-Id: I17037dafb0c5994c2e1598323a5eaeb532ce806f
Refs: #2058, #2059