Unlike ST2, most of the built in stuff is now contained within .sublime-package files. That includes language definition files (.tmLanguage), snippets, macros and colour scheme (.tmTheme) files.
sublime-package files are in the Packages folder and are actually .zip files. So you can open them inside your favourite zip tool. Cobalt, like all included colour schemes, is in the file "Color Scheme - Default.sublime-package". Extract it to your user folder and modify to taste.