Fix Repository::Add to write index changes to disk
Fix Repository::Add to write index changes to disk

Without this, changes are not visible outside of the node process,
and seem to be lost. This makes the changes persistent.

gisenberg/git-utils,cblp/git-utils,cblp/git-utils,greensnark/git-utils,atom/git-utils,atom/git-utils,tjkr/git-utils,gisenberg/git-utils,tjkr/git-utils,atom/git-utils,greensnark/git-utils