validate: Clarify output messages

[tsibley]

Distinguishes between schema validation and internal consistency (e.g.
data) checks and includes filenames in top-level messages so the subject
is clear.

Resolves #440.

[jameshadfield]

Much improved 👍

Note that during augur export v2, if the call to verifyMainJSONIsInternallyConsistent raises an error, which it can, then we print "Validation of ... failed ..." but the dataset file still remains and the augur command still exits with code 0. This is different from a call to augur validate export-v2 which will return a non-zero exit code. Not sure what's best practice here.

[tsibley]

Note that during augur export v2, if the call to verifyMainJSONIsInternallyConsistent raises an error, which it can, then we print "Validation of ... failed ..." but the dataset file still remains and the augur command still exits with code 0. This is different from a call to augur validate export-v2 which will return a non-zero exit code. Not sure what's best practice here.

Ah, yeah, thanks for noting that. I was focused on augur validate, not augur export. If a JSON produced by augur export fails internal validation, I think the command should exit with an error status to indicate failure but leave the JSON file as-is for troubleshooting/debugging. Pushed a commit to do so.

[emmahodcroft]

@tsibley , sorry for the delay! Thanks for tackling this - it has irked me occasionally that these messages weren't very clear at all, so I think this is a good improvement. It generally looks good to me!