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:

metadig-engine/src/main/java/edu/ucsb/nceas/mdqengine/store/StoreFactory.java

Line 18 in 896ec0c

e.printStackTrace();

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