Refactoring is scaring.
Without support from an IDE, it becomes even difficult. However, git can help. I have done refactoring for an express.js web application several times recently. I summaries the following rules to make the process less scaring.
Rule 1. branch before refactoring
If the refactoring is not going well, you can always go back. In most cases, I have to touch the model, the view, and the controller. If you named your files according to RESTful resource name, it is very likely you need to update the file names.
Rule 2. rename files and then commit before touch the codes inside files
After add new files and rm old ones, git will recognized the changes are renaming files. If you make changes inside a renamed file, then the renaming will be lost in git history.
In this sequence, you will be able to have a testable application after each code modification. When M-V-C are updated, and all tests passed, you can merge the refactoring branch back to the original one.