Restructure the project folder

Moved java files into a src directory.

	renamed:    BPGDistance.java -> src/BPGDistance.java
	renamed:    BPGPath.java -> src/BPGPath.java
	renamed:    CommonGene.java -> src/CommonGene.java
	renamed:    Contig.java -> src/Contig.java
	renamed:    EdgeForMWM.java -> src/EdgeForMWM.java
	renamed:    GeneGroup.java -> src/GeneGroup.java
	renamed:    GeneInfo.java -> src/GeneInfo.java
	renamed:    GenePair.java -> src/GenePair.java
	renamed:    GenomeAdj.java -> src/GenomeAdj.java
	renamed:    GenomeInGeneInfo.java -> src/GenomeInGeneInfo.java
	renamed:    GenomeInString.java -> src/GenomeInString.java
	renamed:    GenomePair.java -> src/GenomePair.java
	renamed:    Homolog.java -> src/Homolog.java
	renamed:    OMGMEC.java -> src/OMGMEC.java
	renamed:    PositionInAGenome.java -> src/PositionInAGenome.java
	renamed:    SubgenomeRanges.java -> src/SubgenomeRanges.java
	renamed:    TestCountValues.java -> src/TestCountValues.java
	renamed:    TestGetContigInput.java -> src/TestGetContigInput.java
	renamed:    TestGetContigOutput.java -> src/TestGetContigOutput.java
	renamed:    TestGetContigOutputAndScaffoldInput.java -> src/TestGetContigOutputAndScaffoldInput.java
	renamed:    TestGetContigOutputAndScaffoldInputNoSubgenomeInfo.java -> src/TestGetContigOutputAndScaffoldInputNoSubgenomeInfo.java
	renamed:    TestGetGenomes.java -> src/TestGetGenomes.java
	renamed:    TestScaffoldInput.java -> src/TestScaffoldInput.java
	renamed:    TestScaffoldInputOLdData.java -> src/TestScaffoldInputOLdData.java
	renamed:    TestScaffoldOutput.java -> src/TestScaffoldOutput.java
	renamed:    TestScaffoldOutputNoSubgenomeInfo.java -> src/TestScaffoldOutputNoSubgenomeInfo.java
Move README to markdown format

	renamed:    README -> README.md
Fix compiler errors in command line parsing

	modified:   src/TestScaffoldOutput.java
add building for java files

The ant task will build all the java files in the src directory. Update
the .gitignore to include the build directory.

	modified:   .gitignore
	new file:   build.xml
Add documentation to the README

The README now includes a title and build documentation.

	modified:   README.md