Org-mode support todo lists, agendas, scheduling, recording time per task, latex export, references (with org-tef) and executing code in the document (with babel) and more.
To give you an idea of what the workflow is while I am working on my PhD thesis. I write text with references in sections with todo tags, add my python code, execute it and export to latex. Now I can track how much work I did today in what section and I can also see other files in a common agenda. All of this is in plain text files so git work as well and if you decide to migrate a python script can parse it.
All of this in a free and open source solution if you are happy to work with Emacs. In my opinion it is worth it even if you keep a running Emacs version only for this.