Bugfix: pipeline now reads number of features from packed grammars
bugfix: maxlen = 0 now means don't trim sentences, and ambiguous lattices are never pruned
fixes #130
Removed support for deprecated decoder invocation (passing config file without
-c or -config). Addresses issue #130.
Added test case to ensure sentences are trimmed for length but not lattices.
Added support for scientific notation on arc labels. Fixes #137.
Rewrote float[][] using a class that maps spans (i,j) to a one-dimensional array,
saving quadratic space. This should be done more generically so the DotChart and Chart
classes can use it, too
Got rid of two-dimensional arrays in Chart, DotChart, Lattice, and Sentence in favor
of a new generic ChartSpan class.

This saves quadratic memory per sentence decoded (in the length), and preliminary
tests show significant decreases in decoding time.
Removed ChartArray class
Added MGIZA to ignore list
Removed old file
Small update to developer docs
Merge branch 'master' into gwenniger
Gideon : Added some info output and Assertions to DotChart (1)
as a first step to extending the code to implement soft constraints.
These assertions will later be again removed, but now served to
check wether the assumptions about were terminals and were nonterminals
are added are in fact true. For testing with Assert statements to work
in a java pipeline call, we needed also to have junit to be available
in th dependencies, build file and decoder, which is were the changes to
(2,3,4) come in .

  (1)    modified:   bin/joshua-decoder
  (2)    modified:   build.xml
  (3)    modified:   lib/ivy.xml
  (4)    modified:   src/joshua/decoder/chart_parser/DotChart.java
Gideon : Added a new test SoftSyntacticConstraintDecodingTest.java
that tests if soft syntactic constraint decoding matches, by checking if
the alternate derivations that are expected from soft matching of labels
are indeed generated. Currently this test still fails, as the new functionality is not
yet implemented. We are now thus well prepared to implement the new functionality.

As part of the effort to implement this new test, we also refactored the old
test code of ArtificialGrammarAndCorpusCreater and added new supporting classes
TestConfigFileCreater.java and ArtificialGrammarAndCorpusCreater.java that take care
of producing the required test files automatically.
Gideon : Refactored ../src/joshua/decoder/chart_parser/DotChart.java
by making the logic concerning the matching with respect to the boolean
"regExpMatching" produce a list of child_tnodes - or just one node if the boolean is set to false -
and have a generic block work with that list, rather than having an if/else block with a lot
of duplication were the only thing different is wether just one or a whole list of tnodes is produced
and processed.

This prepares for the next step: Creating a RuleMatcher class, that determines the matching behavior,
i.e. refactoring to strategy and getting rid of the boolean flag.
Gideon : Implemented a first working version of soft constraint Rule matching.
The new Interface RuleMatcher and implementation class RuleMatcherFactory
introduces methods that match rules, depending on whether what is matched is a non-terminal
or a terminal.
There are several implementations added, depending on whether regular expression matching is allowed and
whether soft syntactic constraint matching is allowed.
The test SoftSyntacticConstraintDecodingTest.java tests for a simple test grammar if the
right number of derivations is created, corresponding to alternate substitutions for the labels
of terminal rules.

       modified:   src/joshua/decoder/chart_parser/Chart.java
       modified:   src/joshua/decoder/chart_parser/DotChart.java
       new file:   src/joshua/decoder/chart_parser/RuleMatcher.java
       new file:   src/joshua/decoder/chart_parser/RuleMatcherFactory.java
       modified:   test/joshua/decoder/ArtificialGrammarAndCorpusCreater.java
       modified:   test/joshua/decoder/SoftSyntacticConstraintDecodingTest.java
       modified:   test/joshua/decoder/TestConfigFileCreater.java
Gideon : Extended the SoftSyntacticConstraintDecodingTest so it tests both normal decoding and decoding with soft syntactic constraints.
Adapted the JoshuaConfiguration so that it now contains a property that can be used to switch soft syntactic constraints decoding
on. Made some other minor improvements / clean ups of the code.

       modified:   src/joshua/decoder/JoshuaConfiguration.java
       modified:   src/joshua/decoder/chart_parser/Chart.java
       modified:   src/joshua/decoder/chart_parser/DotChart.java
       modified:   src/joshua/decoder/chart_parser/RuleMatcherFactory.java
       modified:   test/joshua/decoder/FeatureFunctionsTest.java
       modified:   test/joshua/decoder/SoftSyntacticConstraintDecodingTest.java
       modified:   test/joshua/decoder/TestConfigFileCreater.java