Subversion stores everything it needs to know about the files in your repositories and working copies at the ‘folder level’. You can configure special Subversion properties for both folders and files, but folders have a different set of configurable properties than regular files.
When you add or modify a file, you can commit just that one file. But, when you have scheduled a file for deletion, keep in mind that Subversion considers that a change to the folder that contains the file, instead of to the file itself. It's easy to get the hang of, as long as you remember that folders are special in Subversion—and we mean that in a good way.
See the section titled Working copies for a primer on adding, deleting and committing changes.