$ php refreshLinks.php --help
--redirects-only : Only fix redirects, not all links
which implies that "all links" includes "redirects".
But it really should be worded
--redirects-only : Only fix redirects, not all links EXCEPT REDIRECTS
Because without it, refreshLinks.php forgets to also refresh redirects.
This has in turn fooled the author of rebuildall.php into thinking
that he is "rebuilding all".
But to actually rebuild all, one needs
$ php rebuildall.php && php refreshLinks.php --redirects-only
So please fix the behavior of refreshLinks.php to reflect its
documentation (and not the documentation to reflect the behavior!)
By the way, the message "Rebuilding links tables" should add "and
category table". Also metion that table in the documentation too.
And perhaps the same for redirects, as that table does not have the word "links" in its name... which in fact you could use as an excuse to close this bug, but don't do that, as you still wouldn't have fixed the "implies" problem above.