Hi FarCoder, I am using Eclipse PDT and I have the code completion using the following workspace setup:
a) when I setup a CI project I put the Application and System folder at the same directory level.
instead of the default
APP_DIR --+-- system ------+--- application
! +--- cache
! +--- codeigniter
! +--- ...and so on
!
+-- user_guide
+-- .htaccess
+-- index.php
I use this structure
APP_DIR --+-- application -+--- config
! +--- controller
! +--- ...and so on
!
+-- system ------+--- cache
! +--- codeigniter
! +--- ...and so on
!
+-- user_guide
+-- .htaccess
+-- index.php
You can read this in the user guide’s setup page 
b) once in Eclipse I create TWO projects: the first one pointing to the system folder I called it CI_CORE.
The second one is the project of my application and it points to the application folder.
In the PROPERTIES of the second project (application) I add a reference (in the INCLUDE PATH tab) to the first project (CI_CORE).
c) after that I have autocompletion!!!
In my workspace I use just one CI_CORE project as a reference and then I can have as many projects (installations) I want pointing to that core project.
Please have a look at the screenshots.
I hope I was clear enough cheers!
Stefano
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