CDT/Archive/Flexible Project Structure
- Version control simply didn't work at all
- You can't make file system changes with links. For example, if you want to rename a file or folder, or move a file around, you can't do this with linked resources. It only changes the link itself, not the underlying resource.
- Creating new resources in a project with links is confusing at best. Let's say you have a project with a linked folder and file at the root. If you create a new file or folder at the root, it is created in the workspace, not where the other folder/file are in the file system. But if you create a new file under the linked folder, it gets created where you'd expect.
- The location of the .project/.cproject files are problematic. Some users will want to keep these in version control, while others won't. Those that do want them created in the source tree, but those that don't want them elsewhere, like the workspace. I forget now why this was a problem with linked resources, but there was something weird going on there.