Are those files still in the svn repository? If you ran 'svn update' would they be resurrected?

Yes, the files remain in the subversion repository and if you perform an update, they are indeed restored to the project.

i'm not very familiar with rails & co.

could you please describe how to reproduce?

thanks

Certainly,

1) Create a new Ruby on Rails application

2) Import the application into a subversion repository.

3) Using the Rails Plugin Manager, add a plugin or two to the application.

4) Add all the new files to the repository and commit all changes.

5) Using the Rails Plugin Manager, remove one of the plugins you added in step 3.

6) Check the Subversion Window and you will see that the files are locally removed, but that you cannot identify that
you want to delete them from repository.

this is caused by the plugin manager which removes the whole plugin folder including svn metadata. The plugin files
don't exist on the disk anymore, svn lost track about them, but they are still present in the repository - thus remotely
new. 

reassigning for further evaluation

Is there any chance:
a) that the uninstall script called by the plugin manager would remove the files in a svn manner (svn remove instead of rm) 
b) or that the plugin folder would be removed via the netbeans filesystem before/instead of calling an external script?
That way the vcs modules would take over the delete and carry out the appropriate commands 

any other ideas?

thanks

I think we can do b), a) is more tricky since we'd need to modify the external script (although dynamically redefining 
certain methods could be an option). 

Integrated into 'main-golden', available in build *200808201401* on http://bits.netbeans.org/dev/nightly/
Changeset: http://hg.netbeans.org/main/rev/f66afd6bc28b
User: Tomas Stupka <tstupka@netbeans.org>
Log: #142698 - [65cat] [tools] Files deleted using component tools like Rails Plugin Manager cannot be deleted from SVN repository
partial fix - try to invoke a svn remove for externaly deleted files

Looking at this more closely, just removing a plugin via using the netbeans file system doesn't work, the plugin script 
also invokes an uninstall hook. I need to redefine the Plugin#uninstall method and load that before running the plugin 
script. 

Fixed, e3393d630853.

Integrated into 'main-golden', will be available in build *200809101401* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
Changeset: http://hg.netbeans.org/main/rev/e3393d630853
User: Erno Mononen <emononen@netbeans.org>
Log: #142698: [65cat] [tools] Files deleted using component tools like Rails Plugin Manager cannot be deleted from SVN repository