Not all the theme() calls are being saved in references

Migrated issue

Reported by: jhodgdon

On both the newly-updated api.drupal.org and on my test site, I'm seeing cases where theme('xyz') calls are being made, but the references are not showing up on the theme_xyz() page as theme invokes. Some are being registered, but some aren't.

For instance, the function system_themes_page() makes one call to theme():

 return theme('system_themes_page', array('theme_groups' => $theme_groups, 'theme_group_titles' => $theme_group_titles)) . drupal_render($admin_form);

When I look at this function in the database, the parsing is marking this line up as:

<span class="php-keyword">return</span> <span class="php-function-or-constant">theme</span>(<span class="php-string potential-theme">'system_themes_page'</span>, <span class="php-keyword">array</span>(<span class="php-string potential-theme">'theme_groups'</span> =&gt; <span class="php-variable">$theme_groups</span>, <span class="php-string potential-theme">'theme_group_titles'</span> =&gt; <span class="php-variable">$theme_group_titles</span>)) . <span class="php-function-or-constant">drupal_render</span>(<span class="php-variable">$admin_form</span>);

So the parser is correctly recognizing that 'system_themes_page' is a theme call, and it's incorrectly thinking maybe 'theme_group_titles' and 'theme_groups' are also theme calls. Which they aren't, but that is probably OK.

But the real problem is that it is not storing system_themes_page in {api_reference_storage} as a theme call, so when you visit the theme_system_themes_page() page, you don't see the "1 function invokes this theme" link. On the other hand, those other two strings are stored. Need to investigate and figure out why this is happening.