save: always push parents when entering a subtree

Once we enter the subtree, all of the parents must be on the stack for
subsequent operations to work correctly (like the _pop() in the
following "if not file:" section).

Consider the case where /some/empty/dir was indexed, but removed before
save.  Without this fix, the metadata read for "dir" would fail and the
pending directory stack (parts) would include /some/empty instead of
/some/empty/dir.

Signed-off-by: Rob Browning <rlb@defaultvalue.org>
Tested-by: Rob Browning <rlb@defaultvalue.org>