First, let's find every PHP file where the application calls a mysql function:
find . -name '*.php' -exec grep -Hil 'mysql_' {} \;
-H with filename
-i ignore case (because PHP is case-insensitive, MYSQL_ is possible but quite rare)
-l list only the filename, with no context for the match
Results in:
./FREDts/content/geshi/geshi/php-brief.php
./FREDts/content/geshi/geshi/php.php
./components/com_user/user.php
./installation/install2.php
./installation/install4.php
./installation/index.php
./modules/mod_stats.php
./administrator/components/com_checkin/admin.checkin.php
./administrator/components/com_admin/admin.admin.html.php
./includes/feedcreator.class.php
./includes/phpInputFilter/class.inputfilter.php
./includes/database.php
./includes/getids.php
Hmm. FRED doesn't offer a clean separation of database functionality,
either by database (everything is calling the mysql_ functions directly inline)
or by type of functionality (for example, there isn't a *_db.php file corresponding
to each subdirectory).
One way of proceeding would be to abstract the database functionality into a
separate layer so that the correct database implementation can be loaded based
on a configuration option.