[cfssljson] parsing bundle and root certificate

Maybe I'm misunderstanding something but I think #842 should be reverted? When using `cfssljson` against the result of sign request submitted via API, I can either generate `ca-bundle.pem` + `ca-root.pem` by using the argument `-bare` or generate `ca.pem` by not using the `-bare` argument but there's no way to generate the 3 files out of only 1 command.

When submitting a sign request via the API (`/api/v1/cfssl/sign`), we get the following type of response:
```
{
"result": {
"bundle": {
"bundle": "-----BEGIN CERTIFICATE----- < redacted > -----END CERTIFICATE-----\n-----BEGIN CERTIFICATE----- < redacted > -----END CERTIFICATE-----\n-----BEGIN CERTIFICATE----- < redacted > -----END CERTIFICATE-----",
"root": "-----BEGIN CERTIFICATE----- < redacted > -----END CERTIFICATE-----",
},
},
}
```

Now if you pipe that to `cfssljson` with the argument `-bare`, the whole json blob is going to be put in `input` (`err = json.Unmarshal(fileData, &input)`) and the data structure in `input` will remain the same than the one returned by the API.

Which means that `cert` will never be populated (as `input["certificate"]` and `input["cert"]` don't exist, only `input["result"]["certificate"]` and `input["result"]["bundle"]["cert"]` exist):
```
if contents, ok := input["cert"]; ok {
cert = contents.(string)
} else if contents, ok = input["certificate"]; ok {
cert = contents.(string)
}
```
And therefore `ca.pem` will never be generated:
```
if cert != "" {
outs = append(outs, outputFile{
Filename: baseName + ".pem",
Contents: cert,
Perms: 0664,
})
}
```

Now if you don't use the `-bare` argument, you're going to get `input = response.Result` (L.97) which means that the data structure of `input` won't be similar to what was return by the API. Instead it will be something like:
```
"bundle": {
"bundle": "-----BEGIN CERTIFICATE----- < redacted > -----END CERTIFICATE-----\n-----BEGIN CERTIFICATE----- < redacted > -----END CERTIFICATE-----\n-----BEGIN CERTIFICATE----- < redacted > -----END CERTIFICATE-----",
"root": "-----BEGIN CERTIFICATE----- < redacted > -----END CERTIFICATE-----",
},
}
```

With that data structure, the test L.157 fails (`if result, ok := input["result"].(map[string]interface{}); ok {`) and, as a result, the `ca-bundle.pem` + `ca-root.pem` doesn't get generated.