I'd like to have Web Workbench automatically tick this checkboxes off when it sees that I have included the file in my styles.scss.
It is something CodeKit for Mac does atm, which I'm really happy with - I'd really be thrilled to have this functionality in my Visual Studio environment aswell.
I think a good way of doing this would be to check if a file is included in another file.
Another option could be to add the _ (underscore) prefix as Compass is using in their framework. All files that do not compile by themselves have the underscore prefix. An example file structure would look like this:
framework/ _mixins.scss _vars.scss _normalize.scss modules/ _mycomponent.scss _myothercomponent.scss _somerootlevelcomponent.scss print.scss styles.scss
in this example only print and styles.scss is compiled directly as default. The rest indicates by the prefixet _ that they are imports and might not work by itself.
The other way would be to check all scss files for @import rules and if a file is found in an @import rule it is not compiled directly unless specified manually in the Web Workbench config.