Eclipse Helios - files and directories missing from Working Set

When I create a working set - with no filters - I see all my PHP files in the directory heirachy EXCEPT for in the last nested directory. In this directory the PHP files are not shown in PHP Explorer even though they certainly exist in the directory. This does not happen when viewing the project without a working set defined.

Any ideas?

Edit I have now found that it is happening with other projects and whole directories with javascript files are going missing. I just recreated the problem like this:

1. created a PHP project and imported source for a clean wordpress installation
2. created a working set based on the whole project

3. took a screen shot of it; notice the directory my_wordpress.co.uk/wp-includes/js/crop/; here is the screen shot:

   

   _{(source: internetsolutionsni.co.uk)}

4. edit the current active working set and unticked (removed) the directory wp-content now the working set is minus the wp-content folder, but also several other folders have 'disappeared' including my_wordpress.co.uk/wp-includes/js/crop/; see the resulting screen shot:

   

   _{(source: internetsolutionsni.c开发者_StackOverflow社区o.uk)}

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I have a (hacky) fix to this problem:

Create your working sets, it doesn't matter that they're missing files or directories, just get them all created using the wizard.

Close eclipse completely.

Open /workspace/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml

In each workingSet element, add the following as the first child element:

<item elementID="=WORKINGSET_NAME" factoryID="org.eclipse.dltk.ui.PersistableModelElementFactory"/>

When you restart eclipse you should find it works as expected, need to do some more testing on adding new directories etc. but so far all looks good!