I use PHP Development Tools in Eclipse IDE. I did refactoring and move some scripts to the new folders of PHP project. Now no refactored folders or files are displayed in PHP Explorer View although they are present in the file system.
The problem occurs regularly after moving or renaming files. I sent bug report to Eclipse technical support but so far they have not solved it.
There is radical solution - to re-create the workspace, but then it's too expensive restore all my settings, reimport all projects, restore all working sets, etc.
All described above causes a lot of discomfort in my development work. So I decided to try to resolve it myself, because there is the only Eclipse workspace and a bug can be hidden within it.
I make a simple search on the file system and found three files that mention the name of my PHP project:
For me this happened multiple times, on different project and different folders. Opening+closing or refreshing the project yield no success.
In my case, I have found out that this is related to the Working sets. It seems by default new subfolders and files of a project are not marked belonging to the set, so the project has a mix of old folders (included) and new folders (excluded).
To fix this, you can disable the working sets or edit the active working set and check the project's checkbox (which will check all subfolders).
Bonus tip: on large projects, having this mixed state working set made opening the folder structure (and other operations) very slow (3-5 seconds per level). Turning off the working set filter made it instantaneous.