File / Data / Script management as a PhD
In general I would distinguish between two approaches or a combination of both before ending in a very time consuming categorization of all your files

top-down
This means you use intelligent software to find again files you are looking for and don't worry too much about where it is stored. For example reference manager (Mendeley, Zotero,...), a Desktop search engine (Copernic). In the desktop search engine or with windows search (indexing turned on) you should see which file was changed at the latest. Most of your ideas and sketches you save in Onenote or something else that can link to files and www links.

bottom-up
This means you come up your self with a distinct structure like you did with a rough categorization (raw data, devices, projects). But don't complexify this, when most of the files can be identified by the file type/ending, then it may be more convenient to order it by projects and keep all file types within such subfolders.


Additionally, one trick I use is tagging files in their filename like &quot;#phdthesis&quot; or &quot;#interesting&quot; or &quot;#cite&quot; or &quot;#collaboration&quot;.
Sample files (data, images of samples) always get a date ProjectnameDayMonthYear independent of their file type.
Don't make your system too complex or too time consuming. For instance most of PDFs I read and download end in one folder. No point in categorizing them, this will not work/help over years and decades. Defining content-relative filenames takes too much time, most of them I find again over my desktop search engine months or years later if they were memorizable with keywords and search operators or self-created #tags.
For files which the PI or teammembers have to have the possibility to retrace them you anyway have to arrange a common plan how to structure and save the files everyone understands and can contribute. I would either suggest cloud storage or a local wiki here (moinmoinwiki for instance).
The most productive system is probably the one &quot;invented&quot; by Stephen Wolfram, but it took probably even more time to set it up than writing his article. But you get a lot of ideas, so I'm not sure it is future-proof to organize yourself with a propertiary software.
A personal opensource free wiki like moinmoinwiki or tiddlywiki is also an alternative and combination of bottom-up top-down and file system. So my experience is a wiki is only worth the additional time and effort at least with 2 or more team members, otherwise your personal choice and mixture of bottom-up and top-down is more time-efficient and humanities/experimental research/programming single reaserchers will end up with very different management system due to available time, number of files, work-flow and necessity to document and retrace everything.
File systems and desktop search engines will never die out, so my general tip is not to rely too much on fancy software like onenote, mathematica or alternatives to have a future-proof system.