With all of Drupal's myriad functions, we thought it'd be nice to be able to differentiate between them and PHP's functions. jEdit allows users to write and modify the XML files that define its syntax highlighting, so we're providing instructions to achieve this.
First off, download the attached file and put it in jEdit's 'modes' directory. Now we need to tell jEdit about it. Open up the 'catalog' file in the 'modes' directory. Between any two <MODE> tags insert the following:
<MODE NAME="drupal" FILE="drupal.xml" />
I put it after "doxygen" to maintain alphabetical order.
Next open up php.xml from the same directory (preferably in jEdit, it'll catch mistakes with ErrorList). In it you'll find a section that is a list of all the keywords in the PHP language. Right before that section, before the <KEYWORDS> tag, insert the following code:
With all the files saved, jEdit should highlight Drupal functions like theme() and db_query() as KEYWORD4. The appearance of KEYWORD4 can be changed under Utilities >> Global Options >> Syntax Highlighting. By default PHP mode doesn't use KEYWORD4, so there should be no conflicts.