Stanford NLP Output Formatting
If you are using the command line you can use -outputFormat text to get a human readable version or -outputFormat json to get a json version.  In Java code you can use edu.stanford.nlp.pipeline.StanfordCoreNLP.prettyPrint() or edu.stanford.nlp.pipeline.StanfordCoreNLP.jsonPrint() to print out an Annotation.
Using the Stanford NLP, I want my text to go through lemmatization and coreference resolution.
So for an input.txt:     "Stanford is located in California.  It is a great University, founded in 1891."
I would want the output.txt:      "Stanford be located in California. Stanford be a great University, found in 1891."
I am also looking to get a table where the first column consists of the name-entities that were recognized in the text, and the second column is the name class they were identified as. Thus, for the example sentence above, it would be something like:
1st Column                    2nd Column
Stanford                      Location, Organization
California                    Location
Thus, in the table, the name-entities would occur only once. 
There's nothing I was able to find online about manipulating the default xml output or making direct changes to the input text file using the NLP.  Could you give me any tips on how to go about this?