Make CLI module use MongoDB
Allow configuration during the initialization of a repository
Merge branch 'initial-configuration' into mongo-cli

Conflicts:
	src/cli/src/main/java/org/geogit/cli/CLIInjectorBuilder.java
Add MongoStorageModule to version control
Use preconfigured connection parameters if they are present
Resolve conflicts from upstream
Add MongoStorageModule
Add more flexibility in Mongo connection configuration
Changed iterator used during import, so it can replace fid and feature type

That functionality had been mistakenly left aside after changes made to improve performance
Fix for checkout —theirs or checkout —ours not working if theirs or ours was a deleted node.
Fixed some issues with handling deleted features while resolving merge conflicts.
Propagate conflicts on end transaction.
Fixed incorrect exceptions in unit tests.
added --tree-stats option to diff-tree
added export-diff op and shp wrapper
added py4j entry point
Merge remote-tracking branch 'origin/pr/555'
Merge remote-tracking branch 'origin/pr/542'
Merge remote-tracking branch 'origin/pr/540'
Revert "Fixed incorrect exceptions in unit tests."

This reverts commit 69352838800b6be8cceffb4b7139e79c53aa9856.