improve logging in various places

[jeanetteclark]

it's hard to track down exceptions when they are just printed to stdout or stderror without being logged properly.

Here is an example:

https://github.com/NCEAS/metadig-engine/blob/896ec0c5e09cbb576abeee51192eda57e0ae0ef4/src/main/java/edu/ucsb/nceas/mdqengine/store/StoreFactory.java#L18

Look for all of these and replace with an actual log.error() statement

[jeanetteclark]

Some of these were resolved but not all, so leaving open for now