I do not like CI directory structure!

[eluser]webthink[/eluser]
I don't like applications being inside system either that's why we separate them but if this is really your only issue...

Every time i look at the directoyry structure in Eclipse , i could n’t find which file i was working...mainly because duplicating directory structure in application level and system level confuses me.

Why don't you just set you project directory as the application folder in eclipse and forget system even exists?

There's lots of reasons why system and application should be separated but I wouldn't think that's tops on the list