Merge pull request #1 from AlessioDeAngelis/index

Index
BookParser implemented (test included)
comment added
file service implementation + test
some warnings avoided
ignore index files
ignore index files
jUnit tests
book parser cleanup and jUnit test
removed unnecessary imports
fixed null pointer access in ICDIndexer
some plumbing
added missing tagsoup library
skipping empty MedDocuments

MedDocument containing a chapter from book will be added to collection
only if it contains sentences
plumbing
ignore output
got rid of jsonwriter
fix of matching service
ignore class files
query returns Set to contain unique hits, logging