changed how volume and conference insert strings are formatted, so commented out the query format strings.  Converence had too few fields and we needed to address nulls.
in the utility method formatstring, backslashes are now removed.  Some of the journal of cell biology citation context (text to left and right) had the unfortunate situation of ending with a backslash, so MySQL interprests that string as not ending, but having an escaped quote
in the volume ID generator, the get from the hashmap was using the volId instead of volKey, so it was doing a get for null, so each article had a separate volume entry which caused a lot of duplicates
changed the creation of the volume string to no longer use the format string.
add comments on setting up logging
moved functionality to PubmedCentral class as part of the need to track articles already added
combined dataset operations class into this one.  Added code to track if an ID had already been added and log if it has.  Made traverse program a queue of directories to process instead of recursive (still recursive for finding the directories)
moved getting of article-meta element and ID to the constructor so the Pubmedcentral class can decide if the article is a duplicate that should not be parsed
changed getPubmedId to return a string that's of the format ID:IDtype instead of just ID since the type indicates whether it is pmid, PMC, DOI, or something else.  Although DOI would be different, the pmid and pmc number ranges are not mutually exclusive.
jar added for Trevor with the fixes for duplicates and some other bug fixes