Applying transformations to the features (after extracting them)
Applying transformations to the features (after extracting them), and fixing montage optimization parameters
Small script fixes
Added sift parameters to command line and set default values.
Merge branch 'master' of https://github.com/cmor/FijiBento

Conflicts:
	src/main/java/org/janelia/alignment/ComputeSiftFeatures.java
Adding a script to execute MatchBeMaxPMCC
Fetching meshes for the entire image
Adding support for multiple sections in a json file, and the tile layer to the tilespec
Minor changes to the java files
Pulling from FijiBento master branch