Added additional plumbing commands (ls-tree, cat, rev-list, merge-base, diff-tree and show-ref).

Changed help command to show just porcelain commands.

Porcelain command for listing a path is now called "ls".

Added documentation for plumbing commands and removed it from manual
Merge pull request #246 from volaya/plumbing

Plumbing commands
Added blame command
Merge pull request #248 from volaya/blame

Blame command
Initial implementation of shallow clone.

Added depth commands to clone, fetch, and pull.
Initial implementation of sparse clone using a mapped repository.
Updated missing and incorrect licenses. Improved comments.
Use a test neo4j database on bdb je tests to speed them up
Add JavaDoc comments for PostOrderIterator
Added partial clone docs
Merge pull request #266 from dwins/postorderiterator-javadoc

Add JavaDoc comments for PostOrderIterator
remove non documentation related files added at 52fc5006bc
Documentation update and cleaning