Collatex

- Bug fix for the "non progressive alignment" exception in the command-line tool

- Major rewrite of the matching phase of the Dekker algorithm. The MatchTable approach used in versions 1.2 - 1.6 of
CollateX would match the tokens of the witness to be aligned against the tokens present on the vertices of the variant
graph one witness at a time. This approach did not scale very well and it was unable to look ahead. The new
implementation of the matching phase builds a token index of all tokens of all witnesses before the alignment phase
based on sorting the tokens. This approach is faster and returns a complete overview of all the possible matches
including 1) the number of tokens present in a block, 2) in how many witnesses the block occurs and 3) how frequent
the block occurs in the complete witness set.
- Optimizations of the alignment phase of the Dekker algorithm. A priority queue is now used instead of a multiple
value map to select the best possible match. The detection of possible overlap between possible matches now has a fast
path in case of complete overlap or no overlap between two possible blocks.
- The alignment phase of algorithm (including the transposition detection) has stayed the same. There are same quality
improvements however based on the fact that the possible matches are now based on the tokens of the complete witness
set.

- Added servlet module for easy deployment on servlet containers such as the Apache Tomcat web-server.
Implementation is based on JAX-RS and Jersey 2.

- JSON processing: fix regression bug due to which "tokenComparator" and "algorithm" turned into mandatory fields

- new algorithm based on Greedy String Tiling
- Java 8 now required
- provide our own implementation of variant graphs
- remove optional and seldomly used integrations with Neo4j and Apache Cocoon
- turn collatex-core into a self-contained library, independent of other components
- package collatex-tools as a self-contained, shaded JAR

- Extended the normalization in the javascript alignment table rendering to not only trim
whitespace but also lowercase the tokens.
- Update of Google Guava to v15.0.