When other modules change pwd, includes don't work.

yeah and this was the error message we were getting before we patched it:

# Warning: include_once() [function.include]: Failed opening 'sites/all/modules/advanced_forum/includes/core-overrides.inc' for inclusion (include_path='.:') in include_once() (line 516 of/var/www/vhosts/***.com/httpdocs/portal/sites/all/modules/advanced_forum/advanced_forum.module).
# Warning: include_once(sites/all/modules/advanced_forum/includes/mark-read.inc) [function.include-once]: failed to open stream: No such file or directory in include_once() (line 519 of/var/www/vhosts/***.com/httpdocs/portal/sites/all/modules/advanced_forum/advanced_forum.module).
# Warning: include_once() [function.include]: Failed opening 'sites/all/modules/advanced_forum/includes/mark-read.inc' for inclusion (include_path='.:') in include_once() (line 519 of/var/www/vhosts/***.com/httpdocs/portal/sites/all/modules/advanced_forum/advanced_forum.module).
# Warning: include_once(sites/all/modules/advanced_forum/includes/theme.inc) [function.include-once]: failed to open stream: No such file or directory in include_once() (line 510 of/var/www/vhosts/***.com/httpdocs/portal/sites/all/modules/advanced_forum/advanced_forum.module)

The issue started appearing when we changed the directory name of our drupal directory. We uninstalled, re-installed, cleared caches, uninstalled other modules, re-installed, but the error kept coming back.

the patch above fixes the issue.

I believe using module_load_include() is proper way to fix this.
Please, try attached patch and report back.

cool, thanks troky for the input, i will test it later on and report back.

Thanks for testing. Committed.