Martin's update to the Wikispaces formatter fixes the problem with the
link array for tiddlers not be calculated accurately when using
alternate formatters. The solution involves having the Wikispaces
formatter hijack Tiddler.prototype.changed. Eg: 
http://trac.tiddlywiki.org/changeset/9028

Closing the ticket.

Thanks Martin!
Saq

On Mar 9, 8:23 am, Saq Imtiaz <[email protected]> wrote:
> Martin,
>
> My apologies. I had not tested MediaWiki formatter but assumed the
> same problem as the Wikispaces formatter since they use the same
> syntax. I've just verified that this problem does not affect the
> MediaWiki formatter but does affect the Wikispaces formatter.
>
> Suspect this is related to the fact that the MediaWiki formatter
> hijacks Tiddler.prototype.changed to work around the issues explained
> in the ticket.  A fix for the Wikispaces formatter would be greatly
> appreciated.
> Cheers,
> Saq
>
> On Mar 8, 4:38 pm, Martin Budden <[email protected]> wrote:
>
> > Saq,
>
> > most of the formatters don't keep the tiddler references up to date.
> > However the MediaWiki formatter does. Can you confirm that this
> > problem actually occurs with the MediaWiki formatter, or were you just
> > citing this as an example?
>
> > The Wikispaces formatter definitely does not keep references up to
> > date. I'll look into this and try and post a fix within the next few
> > days.
>
> > Martin
>
> > On Mar 8, 11:29 am, Saq Imtiaz <[email protected]> wrote:
>
> > > I've just come across a bug which renders the references command
> > > erratic and useless when using different formatters from the TW
> > > default (Wikispaces, MediaWiki etc). This is a critical issue for
> > > users of the StudentNotebook (over 300 students). Navigation by
> > > references and tags is one of the key advantages to the students of
> > > using a TiddlyWiki.
>
> > > I've filed a ticket with details:http://trac.tiddlywiki.org/ticket/967
> > > However I'm unsure as to what the correct approach to solving this
> > > problem is which is why I'm unable to submit a patch.
>
> > > I would greatly appreciate some assistance from the core development
> > > team (Jeremy, Martin) or anyone else that might be able to help.
>
> > > Saq
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