Make JGitAPIImpl default behavior match CliGitAPIImpl default

Previously, if JGitAPIImpl was constructed with a null workspace, it
would later throw exceptions. If CliGitAPIImpl was constructed with a null
workspace, it would use the current working directory as the workspace.

Since CliGitAPIImpl is the reference implementation, make JGitAPIImpl
match it.
Update bugs link in README

Projects were renamed in Jira
Note that javadoc improvements are in progress
Merge remote-tracking branch 'upstream/master' into master-add-file-perm-test