Then you may need to improve your git-fu (or $vcs-fu). I use magit, so it's always easier to select only the lines/hunks/files that is for one specific change, stage and commit that. Before magit, I use sublime merge, Intellij vcs feature, and fugitive.

My flow state is for editing files. Once that's done and I've got something that work. It's always easy to convert those into sensible commits. Do not that the logs is not the like of "write database schema * add the index page * add the details page * add the new object form". They're more like "show the list of objects * allow object creation * show the details of a specific object". Those breaks to create the commits are more natural to the general flow state.