AE/SentimentFinderAE.java: Remove unused import
AE/CoCitationExtractorAE.java: Remove unused imports
Renaming
AE/PatternAnnotatorAE.java: Ignore the CASE when matching patterns.
CitationSentimentAnalysisTS.xml: Add correct & valid features to
Sentiment annotation + regenerate JCAS.
WF/TestWF04.java: Checking whether the syntax+workflow was able to match
multi-words patterns
XML/PubMedXMLParser.java: Some articles, probably old ones, use
ref-type="bib" instead of "bibr".

This is incorrect according to
http://jats.nlm.nih.gov/archiving/tag-library/0.4/n-cyk2.html but fix it anyway.
src/main/java/jgreg/internship/nii/AE/CitationContextAnnotatorAE.java
src/main/java/jgreg/internship/nii/AE/PatternAnnotatorAE.java
src/main/java/jgreg/internship/nii/CR/DirectoryReaderCR.java
src/main/java/jgreg/internship/nii/Utils/Utils.java:

Fix missing "silent" checks.
AE/CitationContextAnnotatorAE.java: Use an ArrayList for citations in every cases.
XML/PubMedXMLParser.java: Improve a comment + Be sure to only store
bibliographic references (not figures or tables).