There are many times I need to rename a file (such as a JPG) and with it sitting there in the files list it is extremely frustrating to not be able to change it.
Yes I know that you have a "Rename..." in the Refactor menu but sometimes I just want to rename and not refactor. If you fear people will just rename and never learn about refactor you could put up a dialog telling them about the refactor option with a "Don't show this again" checkbox.
While you are at it, could you please move "New..." to the "File" menu where 99.9% of other apps have it? If you don't I'm sure many others will have to hunt for it and waste 1/2 or more because it never occurs to them that it might be located under the "Edit" menu.
Just use keyboard shortcuts. Also use "Search for action" (via its shortcut too) to not remember where in the menu stuff are.
If you are absolutely set on doing it your way could you at least add the options to the menu and when people select them give them a help dialog that explains to them your way of doing things?
FWIW I'm going to be doing a lot of WordPress developer training in 2010 and I want to recommend this product to people who take my courses. While I'm mostly loving WebIDE at the moment I'm concerned that many of my future students will find WebIDE too confusing to use because of your choice to make them learn a menu interface which is different for the most fundamental operations (File New, Save As, Rename) than practically ever other app they have used. Please understand that most of the people doing PHP development are not professional programmers but people who learned to program in order to modify an open source app to meet their needs. Those people will have a harder time if you force them to learn your way of doing things even before they can get comfortable.
JMTCW.
Just trying to be constructive and find the most appropriate solution.