Apparently you need to put this in config.php
$CFG->textfilter1 = 'mod/glossary/dynalink.php';
But alas, I do not see autolinks (if I am understanding what they are).
I put the above in my config.php, and saved it. (Here is the top of my config.php)
<?PHP // $Id: config.php,v 1.19 2003/09/26 08:04:48 moodler Exp $
// config.php - allows admin to edit all configuration variables
require_once("../config.php");
$CFG->textfilter1 = 'mod/glossary/dynalink.php';
Then I added a glossary to week 0 of my file. It is a secondary glossary so the students can add to it.
Then I added two entries. One is an entry (word) that appears in one of my resources. The other is an entry that appears on the comment of week 0. Both are entered exactly as they are in their respective places in the course.
I have waited now for about 5 minutes. No, 15 minutes. I think that I heard in reference to the library that there is a cron or something that parses the database every X minutes, updating links. Perhaps I need to wait for longer. Or I am waiting for the wrong thing. I was anticipating that the instances of the words that I had entered in the glossary would be magically linked to the respective entries. This would be really great for language teachers.
It is not quite as good as the idea of a library because I don't think that I will be getting too many of my students to come to the glossary and make entries. They are shy for one thing. But maybe they will. The chances that they would come to the glossary and make entries would be radically increased if there were marks for glossary entries. In the longer term the possibility of grading would be nice, but either way a default point or .01 point per glossary entry would be nice. But this is all an aside, since what I am really wondering about is the lack of automatic linking and for your kind suggestions about what I might have done wrong. Hold on a minute. Perhaps I need to upload a later version of the glossary?
I will try that. I have yet to to use the "cvs." It will be a big challenge. I am sorry if this is just because I have an old version. But perhaps this will serve as a warning?
Update
I tried uploading the latest CVS of the dynalink.php to my glossary module. This did not seem to do anything. I also updated style.php from one of the standard themes to my custom theme (vanity). That did not do anything either. Then I downloaded the latest "nightly" (hourly?) changed my glossary to "oldglossary" and uploaded the whole thing, plonk. Then the below appeared in my latest activities framething on the right. (I now have turned latest activities off!).
Fatal error: Cannot redeclare glossary_upgrade() (previously declared in /home/tim/mootim/moodle/mod/glossary/db/mysql.php:5) in /home/tim/mootim/moodle/mod/oldglossary/db/mysql.php on line 5
One of my two glossary entries has dissappeared. I don't mind the fact that it has dissappeared but I hope it does not cause a database corruption that has nasty side effects.
Then I tried reentering the missing entry. I was taken to a pink message saying that the entry alread exist. And then to a page which says "Glossary module needs upgrading" and a lot of success signs, with
Fatal error: Cannot redeclare glossary_add_instance() (previously declared in /home/tim/mootim/moodle/mod/glossary/lib.php:13) in /home/tim/mootim/moodle/mod/oldglossary/lib.php on line 15
Aha! I realise the problem. It is no good leaving the old glossary as "oldglossary" in the mod directory since it will be treated as a glossary and will clash with the new one, as above.
Back to work.
But I'm half blind anyway... 
(and I think Tom Floyd too.. 
)
