Here is my foolproof aspiration for organizing my academic data. Take what you will and find what works for you!
Step -1: No Software
A few years ago my university shifted from physical lab books to a fancy digital note-taking software. I thought it was going to save my life! I have always been, and still am, incredibly disorganized. I thought having all my note-taking happen in a simple browser window would turn my research life around.
It did not.
Now, if you find a piece of software that works for you, by all means, use it and never let go! But if you have trouble adopting one, you may be suffering from digital cognitive friction. After all, in theory, you just need a stack of notebooks to stay organized. In theory that's all it should take me. And yet I am not even physically notebook-organized, which means that any successful organizational system must be even simpler than opening up a notebook and writing.
No logins. No menus. No side-by-side panes. We need to go all the way back to basics.
Step 0: Open a new folder
And pat yourself on the back. Organizing a project from the beginning is much better than trying to organize a sprawling disorganized year-old festering mess.
Step 1: Simple folders, simple files, simple filenames
Simple folders mean things are stored by kind. Here's a sample directory structure:
flux-capacitor_1985
|
|--papers
| |--Einstein_relativity_1915.pdf
| |--Brown_gigawatt-energy-requirements_1955.pdf
|
|--notes
| |--DeLoreans-are-cool_1980.md
| |--possible-teenage-collaborators.md
|
|--invoices
| |--Libyan-Glowies_1984-06-21.docx
[...]
If you can organize things more deeply into subfolders, good for you -- if you find yourself agonizing between "physics" and "mathematics" for Poincare's papers then don't bother. It is better to have a folder full of thousands of well-named simple files than to have an folder empty of files you couldn't organize because you couldn't pin down a sub-organization system to your liking. Remember that if they are well-named simple files then your computer can search through their contents for you. (This is an adaptation of the YODA principles for data organization.)
Simple files are, as far as possible, plain text. Store written documents as Markdown plain text files, which are both very readable in Notepad and very pretty when formatted. Store tables as column-separated plain text files for easy AWK-ing. Store plots as plain images (and generate them from scripts which have the filenames coded in, so you can search your scripts
directory for a plot's filename and have the relevant plot's name come up). Of course, you will have PDFs of journal articles, PPTXs of presentation slides, and binary output from instruments or programs you can't control -- but that should be just about it.
Simple filenames make it easy for either you or your computer to decide what's in a file based on its name. Here is an excellent presentation on how to name files -- read and apply it.
Step 2: Frequently backup
There are all the usual cloud solutions like Google Drive, Dropbox, OneDrive ... But if you have an external storage server, you can use SyncThing, and if you want to backup to a thumbdrive you can use FreeFileSync.
Notice that since you have organized your files using folder structures and filenames, the organization automatically travels with any backup.
Step 3: Version control
Are you not organized? Then here's the next level: turn your project folder into a version-controlled repository. Version control means you'll be able to track and revert changes across everything you do. No accidental deletions, no uncertainty about when a script suddenly stopped giving the "correct" results, and no more worrying that you won't be able to backtrack your steps.
If you can learn Git, you can even host your repository on GitHub! And guess what -- it automatically formats your Markdown files for you!
One Step At A Time
Notice how each step is worthwhile in itself. This way, no matter where you stop, even if you don't get all the way to creating a fancy-as research compendium, you can pat yourself on the back for being more organized than me than you would otherwise have been!
Also notice how the steps synergize with each other. Simple folders and files mean you can automatically apply version control, and mean that a GitHub repo will be as perfectly navigable as your desktop folder. They also make it easy to back up your work.
Also notice that this is a bare framework on which you can add things. You can absolutely run Mendeley or Zotero off your papers
subfolder (and thus make sure, by the way, that it can't corrupt anything else). You can experiment with Jupyter Notebooks or the DataLad system or anything else you please -- again, having a simple folder of simple, well-named subfolders and files can only help. You can almost certainly do better! But these suggestions, I think, are a good starting point.
All the best!