user-manual: update references discussion
user-manual: update references discussion

Since references may be packed, it's no longer as helpful to
introduce references as paths relative to .git.

Signed-off-by: "J. Bruce Fields" <51738506c1b2ccb0761f23bdc612c93babf738ea@citi.umich.edu>

destenson/git,destenson/git,destenson/git,destenson/git,destenson/git,destenson/git,destenson/git,destenson/git