I've started using Joplin after OneNote managed to delete all my data.
It has a rich text editor built in but I'd recommend using the Markdown editor (write in Markdown with a WYSIWYG output to see your changes in real time). One of the really nice things is you can copy and paste images directly into the Markdown editor and Joplin will handle the action and ...
The first tool that comes to mind is Obsidian. Have you already check it out? It might fit all your needs. The way you can link notes is like no other app I've seen before and it's also available for macOS, Windows, and more.
Hope this helps.
Visual Studio Code
Visual Studio Code is a free, open source, fast, lightweight editor perfect for your basic needs, but also extensible enough that you could mostly replace Visual Studio with it if you wanted to.
A directory structure of your choosing should provide the tree organization you are looking for.
I use Ctrl+Shift+F to ...
The image part requires some heavy lifting so I don't think anybody wrote software to do that -- it is certainly not impossible.
For the rest of the requirements, I think this answer (by me) offers the exact (and free) solution:
QOwnNotes seems to meet all your requirements:
Screenshot of QOwnNotes (source: QOwnNotes; click to enlarge)
notes stored separately in form of md-files or some other mark-up text format: Yes, Markdown even is its primary format
to store tags within note's body: it somewhere stores tags, but I didn't check where exactly (it's quite a while ago I used it ...
The Desktop Wiki zim is written in python and fulfills all your requirements.
You can write text quickly with a minimal markup and use LaTeX for Formulas.
Have a look at the nice screenshots on https://zim-wiki.org/screenshots.html
I'm a big fan of DokuWiki, we're run it "internally" on a local network and "externally" on a web-accessible server (shared hosting etc.) which means we can log in from anywhere and read / edit.
It's not perfect, but it does all the basics very well and reliably (I've been using it for over a decade and it's never failed) and since it ...
You can start by looking at Wiki matrix - the Wiki Comparison Site.
Use their choice wizard which will ask you series of questions.
At each stage it tells you how many wikis match your criteria, and at the end you can choose some to compare.
image snipped, but there is a lot of detail.
Many years ago, I hit on DokuWiki and have using it ever since. I wish ...
VirtualChemist (https://www.rosoft.website) may fit your need. Using reactant Lewis structure as the only user input, it can (1) describe detailed reaction mechanisms at the level of electron flows in elementary reaction steps, ensuring that all reaction steps are not only atom and electron balanced but also atom-mapped; and (2) track molecular 3-D structure ...
sorry for the very late answer…
I use Xournal exactly for ①, ② and ③.
Xournal is available for Linux and Windows, I'm not aware of a Mac version. As far as I can tell, it's no more actively developed but it's available and reasonably maintained on major Linux distributions, while the Windows version probably is in a less sane state.
From Xournal's site:
As already mentioned, Pocket is indeed a good app. Although I have recently replaced Pocket for Raindrop and won't be looking back. It works like a charm and will probably meet all your needs. Raindrop checks the bolded, important items off your list, and even more. Below just an overview of how many options you have for sorting the bookmarks.