Fix FileSystem not updated on file deletion

[Hilderin]

• Fixes Found a bug when deleting file in the filesystem #95423

The issue was a regression from #93919. I removed the emission of the filesystem_changed signal in EditorFileSystem::update_files when is_scanning is true. When removing files in a large project, the scanning process can take a bit longer, enough to have the scanning_changes variable set to true when entering EditorFileSystem::update_files. I kept the if (!is_scanning()) condition for _process_update_pending to prevent the original issue; anyway, it's called at the end of the scanning process.

It's really difficult to reproduce. I had to be in debug mode with a couple of breakpoints in DependencyRemoveDialog::ok_pressed and EditorFileSystem::update_files to reproduce the problem.

[akien-mga]

Ok I misspoke in #95526 (comment), this is the last PR we'll merge for 4.3.stable :D

[akien-mga]

Thanks! ✨