While I have been tuning the system towards a direction where all user changes can be made into files that aren't affected by future upgrades, I'm not exactly aware what all users are doing to customize their WWB/iWiccle sites.

This question doesn't concern changes you have done using any of the interfaces provided; they are stored in the database, and carried over by definition. (Though you are of course welcome to tell about all the changes you've done using the ready tools! Perhaps in a separate thread, so we can keep focus here.)

Specifically, I'd like to know what files you've modified to tame the CMS to your needs.

How is this for specifics - so far - since I have been tracking all of my changes specifically with upgrades in mind (most if not all are simply from asking for support and then making the changes):

Oh and please forgive me that it took me a while to realize you spelled your name with a k.  I am slightly dyslectic.

• Core/class_elements.php and core/variables.php
  • both per thread here: http://www.wiccle.com/forums/public_forums/bugs__troubleshooting/thread/forum_zone_thread_error
  • Should be fixed in next release.
• core/class_templates.php
  •  
    • per forum thread: http://www.wiccle.com/forums/public_forums/install__modification/thread/module_menu_li_tags
    • should be fixed in next release.
• core/ajax/message.php
  • line 287 added a line per thread: http://www.wiccle.com/forums/public_forums/bugs__troubleshooting/thread/members_mailquote_bug
• core/config_mapper.php
  • added lines 44 - 47 per post: http://www.wiccle.com/forums/public_forums/bugs__troubleshooting/thread/cant_log_out
  • only needed it for when the site was accessed via IP address.  Don't need it anymore after site goes live.
• core/config_misc.php (Pro skin admin commented out)
  • commented out use of Pro Skin for admin on line 75 per post: http://www.wiccle.com/forums/public_forums/install__modification/thread/thread_buttons_site_pages_module_descrip
• Skin_wrappers.php
  • around line 310 changed margin and removed section with original logo included.
  • also much other stuff, such as the bg_top_... section
  • modified line 301 to make the module description go away on mouse out rather than onclick per post here: http://www.wiccle.com/forums/public_forums/install__modification/thread/thread_buttons_site_pages_module_descrip
• Skin_menus.php
  • modified line 115 per email from Marcus to me on August 4, 2010.
  • added to line 84 to make module description go away when cursor leaves menu item per post here:  http://www.wiccle.com/forums/public_forums/install__modification/thread/thread_buttons_site_pages_module_descrip
• Pro/modules/skin_members.php
  • Added Username display line 252 - 255, comments to other fields and 
  • deleted out some Member settings fields ( sex, birthday, phrase, current status) line 278 per post: http://www.wiccle.com/forums/public_forums/install__modification/thread/customize_member_basic_settings__member_
  • deleted Premium Members link line 287 per post: http://www.wiccle.com/forums/public_forums/install__modification/post/post_2359
• languages/en/lang_members.php
  • edited line 184 to change Name to Display Name for Member/Basic Settings per same post above under skin_members
• languages/en/lang_mail.php
  • Added new mail message language for admin: search for mail_reg_confirmation_approval_admin around line 138 - added from $lang... to WIC; having copied a section from directly above.
  • Also created a new subject for mail titled: mail_reg_confirmation_approval_admin_subject on line 125.  
  • Per post: http://www.wiccle.com/forums/public_forums/bugs__troubleshooting/thread/registration_email
• core/ajax/members.php (my customization)
  • changed mail_reg_confirmation_approval to mail_reg_confirmation_approval_admin on line 661 to insert the custom mail language for admin that I created in languages/en/lang_mail.php.
  • Also changed subject line to new subject I created, and added new msg rule: mail_reg_confirmation_approval_admin_subject on line 664 and 683
  • per post: http://www.wiccle.com/forums/public_forums/bugs__troubleshooting/thread/registration_email
  • also fixed line 963 per bug address on same post above.
• core/class_mailer.php - (bug fixed for future builds)
  • modified line 178 to remove double email subject header 
  • per post: http://www.wiccle.com/forums/public_forums/bugs__troubleshooting/thread/registration_email
• admin/admin_area_users.php -  (bug fixed for future builds)
  • fixed bug per post: http://www.wiccle.com/forums/public_forums/bugs__troubleshooting/thread/registration_email
• modules/members/members_class.php
  • modified from line 627 to fix Profile Builder multi-slect bug per post: http://www.wiccle.com/forums/public_forums/install__modification/thread/profile_builder_multiselect
• core/admin/admin_skin_users.php
  • removed section that allowed creating a new Admin password, with Marcus said is no longer in use.  per post: http://www.wiccle.com/forums/public_forums/bugs__troubleshooting/thread/users__administrators__password
• modules/forums/forums_config.php (line 136 - 137)
  • Part of Private Forums fix
  • add code to end per post: http://www.wiccle.com/forums/wiccle_forums/templates_and_modifications/thread/help_-_creating_a_private_forum_2383
• core/class_modules.php
  • part of private forums fix, per post: http://www.wiccle.com/forums/wiccle_forums/templates_and_modifications/thread/help_-_creating_a_private_forum_2383
  • modify multiple lines of code starting on line 181 and ending at line 205
• Images
• CSS files: 

•  
  • html.css 
  • menus.css
  • wrappers.css
  • units.css
  • globals.css (copyright stuff only so far)

Most people spell it wrong the first few dozen times around — no worries there, and thank you for sharing your changelog. Here are some notes on upgrades in general.

As a general principle, files under /core/* and /modules/*, except extension files (*_extensions.php, *_ext.php), are subject to being written over in future upgrades. Possible changes to configuration files are noted in detail.

From what I see from your list above, all changes in your list affecting files in these two folders are upcoming changes that match (or are the functional equivalent of) the files in the next public release.

Any possible changes under /templates/* and /languages/* will be noted in detail in upgrade notes to a new release — to give you the option of either 1) porting your customizations into the new file, or 2) porting the changes from the new file into your customized file.

Changes to template files in upgrades are generally in the range of a few changed lines of HTML fixing a display problem, or a HTML snippet that enables the display of a new feature. Again, most changes to template files are for dynamic content templates (skin_post.php etc.), and don't affect your main design PHP and CSS files (menus, units, wrappers).

Changes to language files are generally only due to the addition of new language strings.

Whenever I prepare an upgrade for release, I run a general file difference check to identify all files that have been changed, and then run a difference check to highlight all changed code between the two versions. During this, I do a final code "proofreading" to see that everything looks orderly, write the general version changelog, and make detailed notes for changes in files that our users may have customized.

There's more work to be done yet in terms of making the upgrades automagical and super slick, but if someone has understood the system enough to have made a customization or two, then there really should be nothing in our upgrades themselves that would pose a problem or challenge of any sort. (And if there is, we can do the upgrade on your behalf.)

So far our updates have been straight-forward enough: 1) upload changed files (primarily core and module improvements), and (sometimes) 2) click once or twice to go through the steps of an automatic database upgrade script.