- Committed stage 2 of the theme system improvements!  Patch by CodeMonkeyX.

- Fixed bug in update of taxonomy links.

  keep their settings.
- Change author fields in marvin and example theme. Dries is picky about his
  name ;)

Committing Changes by Moshe Weitzman:
- admin_user_account(), user_edit(), and user_view() no longer have any
  hard code for authentication modules. instead authentication modules
  implement the _user hook.
- fixed a couple 'help' typos.
- linked the 'REGISTER' text in the login block to the register page.
  this page now advertises DA better if site employs DA.
- admins may now edit everything about a user account (was a feature
  request).
- user #1 may now login immediately, in addition to receiving his
  password via email.

Other changes:
- modules and themes are now enabled/disabled in the administrative /
  settings / modules | themes pages. Requires SQL update and things must
  be enabled before your site returns to normal. TODO: enable all
  functionality. (For now just do UPDATE system SET status = 1;)
- removed $themes from conf.php.
- added a $theme->system() function where theme can specify settings.
  All themes in the Drupal CVS have been updated to use this.
- added _system hook to modules. TODO: update modules to use this.
- changed strange use of sprintf to the usual strtr. The disadvantage of
  sprintf is that it requires translations to keep the string order,
  which may not be possible in all languages.
- an invalid/nonexisting theme in a user profile will now fallback to the
  BaseTheme instead of crashing.

  http://list.drupal.org/drupal-devel/2002-February/thread.html#6678
  http://list.drupal.org/drupal-devel/2002-February/thread.html#6629
- removed references to $this->user() from themes.
- removed $BaseTheme->user(). It was deprecated a while back.

NOTE: this update will break custom themes, so make sure you update your
themes before updating!

- A large batch of updates, amongst them a rewritten node system.  More
  information available on the mailing list.

  easier. Also changed the <? tag to <?php in some cases.

- Updated example.theme: it's being reduced to a minimum as it can inherit
  most/all of its functions from the BaseTheme.

- added a comment() function to the base theme: you don't have to overload
  it in your custom themes

- moved 'theme_account()' to the base theme as '$theme->user()' so that it
  can be themed.

- Added the new user module!

- Changed the authentication and login scheme as discussed on the mailing
  list.
- Fixed the export function in book.module (patch my Julian).
- Fixed the comment alignment (comments got truncated).

- format_username() now takes a second optional parameter which gives the
  real name of the user.

Rest
- updated the calls to format_username() where appropriate to show the name
  of the user instead of the account id. Clicking on a name will still give you
  the account info etc. If you find a place where the real name is not shown
  let me know.

Update of the box function in themes to allow a difference in style/output/look of a box() depending on the position on the page.
Basically this is a 'nice version' of a hack that you could do as a theme author.
I've updated all the standard themes, but 3rd party themes will of course have to be updated by their authors, in the following manner:

- Replace the box() declaration:
< function box($subject, $content) {
> function box($subject, $content, $region = "main") {

- Replace the theme_account call:
< theme_account($this);
> theme_account("region", $this);

Note that you'll have to replace "region" with the correct region that the box is placed in. However if you have a one-column theme, you should use "all", and not for example "left" (if all boxes are on the left).
Usually the "region" here should be the same as the nearest theme_blocks() call.

Those theme authors who want to can make boxes that appear in the center look different from those that appear in the sides for example.

- Tidied up some stuff in account.php and theme.inc.
- Tidied up the box() API.

Extremely large commit:

- Fixed tiny quote problem in account.php.

- Fixed tiny bug in comment.inc.

- Fixed tiny bug in comment.module.

- Fixed tiny bug in meta.module.

- Simplified user_access() API.

- Rewrote link system: still needs fine-tuning and testing so don't
  upgrade if you are running a production site. ;)

  Updated all modules and themes to reflect this change.  All other
  themes and modules need updating too!

  '=' instead of ';' and ':'.  It is considered to be more readable.
  --> A _first_ step towards and improved index.module.  Stay tuned
      for more.

  + Important:
     If you update from CVS - apply the queries in 2.00-to-x.xx.sql!

- Changed all 'attribute' to 'attributes'.

  + Important:
     If you update from CVS - apply the queries in 2.00-to-x.xx.sql!

  + Important:
     This might require to ieni-wieni small update to your custom
     themes and/or node-related modules:
      - themes: node_index($node->attribute) -> node_index($node)
      - node modules: attribute -> attributes

- fixed the trailing | in some cases.
- removed theme_morelinks().
- added node_links().
- simplified BaseTheme->links().
- updated themes.

Notes
- the new links system is taking form, but concider it beta. There might still
  be some major changes ahead so I suggest waiting a little longer before
  modifying your theme to take advantage of it.

This a rather large commit that needs a lot of fine-tuning.  If you
update, you'll break your site as you need switching from structure
to index.module: so this can be considered an intermediate commit.

If you upgrade, and you are welcome to, just create a collection
called "section" (for now) and assign your nodes some attributes
in the described format.

Feedback and bugreports are welcomed.  Questions will be answered.

CHANGES:

- comment system:
   + when replying to a node (rather then to a comment), that
     node is displayed above the reply form.
   + when replying to a comment (rather then to a node), that
     comment is displayd above the reply form.

- removed structure.inc, removed structure.module.

- node.inc:
   + added 2 new node functions called 'node_attribute_edit()' and
     'node_attribute_save()' used to 'hook in' any indexing system
    including your home-brewed stuff if you'd want to.  Currently,
    index.module is the facto default index system.

    See story.module for usage.

- book.module, story.module, poll.module, page.module, forum.module:
   + added preview functionality to administration section (via node
     module).
   + removed all references to structure.inc (category, topic).

- moderate.module:
   + removed all references to structure.inc (category, topic).

- book.module, story.module, page.module, forum.module:
   + increased the sizes of some textareas.

- submit.php:
   + removed all references to structure.inc (category, topic).

- marvin.theme:
   + removed dead code: function story() was depricated.

- unconed.theme:
   + removed hardcoded references to drop.org.

- marvin.theme, unconed.theme, jeroen.theme, yaroon.theme, example.theme:
   + removed all references to structure.inc (category, topic).

TODO:

- file.module, trip_link.module:
   + update preview functionality:
       see story.module for example.
   + remove references to 'cid' and 'tid', use 'attribute' instead:
       see story.module for example.

- extend and build upon index.module as well as making it configurable

- created a BaseTheme class in theme.inc.
- added links($links = array(), $status = 0, $node = 0) to BaseTheme.
- modified all themes to extend from BaseTheme.
- modiefied theme_link() to take advantage of $theme->links().
- theme_morelink() does not require a $theme argument.

Todo
- add the other standard variables and functions to BaseTheme.
- some themes could use some more modifications.

Weird
- marvin.theme still has a story() function.

- Added $theme->foreground and $theme->background vars to provide some general usable colors outside of a theme.
- Updated poll.module to use the new $theme color variables

- Replaced $theme->story() by a more generic $theme->node().  All themes
  required an update (and so will your custom themes).

  They both return a linked string with the respective category,
  or topic name.  Updated all themes to use these new functions.

- (stripped tabs from emsa files, nevermind)

Another big update so please read this carefully because there is important information hidden in it.

Made it so that we can disable/enable comments on a category by category basis. In order to accomplish this I had to make a few (*temporary*) changes.

I moved all comment code from the "module level" (eg. story.module) to the "node level".  It was nothing but the logical next step in nodifying drupal.  This enables us to add comments to all existing content types including book entries.  But also for book entries, this to can be toggled on and off. :-)

Moreover module writers don't have to worry about the complex comment logic: it is "abstracted" away.  This implies that story.module got smaller, faster and easier to comprehend. :-)

In order to accomplish this, I had to update ALL THEMES, which I did - and on my way I updated Goofy, Oranzh and UnConeD - with the previous changes.  All themes are up-to-date now!  I also had to remove the [ reply to this story ] links, and temporally re-introcuded the "Add comment" button in the "Comment control".  Tempora lly that is, UnConeD. ;)

I plan to upgrade drop.org either tommorow or wednesday so test away if you have some time to kill. ;)

Oh, I also fixed a few bugs and made various small improvements.

Large commit, read it carefully, and make the required changes to
your theme:

- corrected some missing translations in story.module.  Oops!
- grealty simplified the "moderation threshold mechanism"(tm) so
  that module writers don't have to worry about this.  As a result
  story.module and book.module became a bit smaller and easier to
  grasp.
- greatly simplified new "category" and "topic" code which is soon
  going to replace the "section" code.  Needs more work though so
  hang on thight.
- includes/section.inc and modules/section.module are replaced by
  includes/structure.module and modules/structure.module.
- beautified example.theme a bit without adding HTML complexity:
  it is a good example but still useful as a theme
- made theme example use "categories" and "topics"
    --> TAKE A LOOK AT IT AND UPDATE YOUR THEME
- made theme marvin use "categories" and "topics"
    --> TAKE A LOOK AT IT AND UPDATE YOUR THEME
- added 2 new "story listings" to administrator interface of
  story.module to verify story integrity.
- optimized comment table a bit (work in progress)

- improved submit.php:
  it now uses the new category code, incl content bindings.
  You can setup different "categories" which map on a content
  type.  Example:
    review   -> review.module
    article  -> story.module
    column   -> story.module
    announc. -> story.module
    addons   -> file.module
    themes   -> file.module
- "generalised" story.module and book.module's output.
- fixed bug in includes/timer.inc
- fixed glitch in theme example.theme: it said "$how by" but
  the variable $how has never been declared.
- added "drupal development settings" to display some timings
- more work on the categories/topics -> does NOT work yet

- added new variable: theme_footer which can be used to provide a
  footer message like a copyright notice. Themes should use this!
- small improvement to example theme
- added theme_footer to theme marvin
- small improvement to database.inc

A lot of small changes (search-n-replace) make a big commit:

  - fixed update bug in book.module
  - provide a log message when both adding and updating book pages
  - all configurable variables are now accessed through "variable_get()":
  - rewrote watchdog and submission throttle and removed watchdog.inc
  - improved robustness of sections.inc
  - imporved story.module
  - updated ./database/database.sql

Commiting my work of last Sunday:

 - removed ban.inc and ban.module and integrated it in account.module
   under the name "access control" --> the ban code was not really up
   to standard so this has now been dealt with.  This refactoring and
   reintegration cuts down the code size with 100 lines too.  :-)
   (The ban.module code was really old and it showed.)

 - added node.module and made the other modules reuse some of this
   code --> cut down the code size of modules by at least 100 lines
   and adds stability.

 - added a status() function to admin.php to display a conform status
   message where appropriate.  See admin.php for usage.

 - removed $theme->control() and made comments.inc handle this itself
   wrapped in a $theme->box().  No need to clutter the themes with
   such complexity --> updated all themes already. :-)

 - some small visual changes to some administration pages to be more
   consistent across different modules.

- fixed "you-have-to-logout-and-login-before-permissions-change" bug
  (reported by UnConeD)
- added "add node" link to book selection box and made it display the
  current location
- removed tabs and whitespaces from themes - done automatically

- visual improvements to example.theme, simplified HMTL code (- 20
  lines)
- made node.inc more robust: it should roll-back when something goes
  fubar and it should work in subdirectories

- fixed small problem in example.theme

- large commit of everything else that has been queued in my backlog:
  it's not 100% stable yet

- themes now get there header/footer links through theme_link();
- tidied up example.theme

- fixed potential quote problem: wrapped $story->section in a check_output
- removed all $story->update related logic - the update field is redundant

During my nigthly session I fixed a few glitches in the example theme.
Read them carefully because the other theme might need updating too (I
don't think so though).  I could only commit it now because I didn't
had the time to write up these comments/remarks yet.  So here goes:

1. the comment() function only takes 2 arguments - $thread is no longer
   needed and shouldn't be used in the code either.

2. I added 2 COLSPAN's to fix a <TD> problem in the story() function.

3. <A HREF="">home</A> is will not work properly when using drupal in
   a subdirectory!  Simply use <A HREF="index.php">home</A> instead -
   it does matters. ;-)

4. Removed the $timestamp = format_timestamp(...)'s and used them
   "directly" just like this is done for format_username and others.
   It's generally more consistent now. :-)

OK, lets hope this works... I should've added a directory example/ in themes/ and in example/ there should be example.theme

Jeroen.