I am writing a master's thesis in engineering. It is quite literature-heavy, and I'm using Zotero with BibTeX to manage my references. For the most part, I use [Zotero's browser extension](https://chrome.google.com/webstore/detail/zotero-connector/ekhagklcjbdpajgpjgmbionohlpdbjgc) to create Zotero entries, but when necessary (e.g. for PDFs that were only published on a university server), I also create some from scratch. Sometimes, I want to cite websites of software tools without a publication. I could gather as much information as possible from those websites, but since these references are really only made in passing, I find that giving the reader a URL suffices. Also, my sources list is quite long already, so I try to avoid going out of my way to add extra references just for the sake of mentioning a single name. So, a URL it is.

What **is** and what **ought be** the best practice to include such a naked URL into a master's thesis, or even a research paper? There are essentially three possible ways to do this:

1. Footnote with the link (e.g. using `\url{ }` from `hyperref`): ugly, but visible to people who print the work on physical paper -- and lose the digital version, so that the only way to visit the URL is copying it letter by letter manually.
2. Embedded hyperlink in the text (with an unobtrusive colour to indicate the text is clickable). Looks neat, but not accessible in print. This is what I'm currently doing.
3. Have a list of raw URLs as a subsection of my sources list, and use some LaTeX magic to annotate and jump to the correct link from the text.

Worth mentioning: our department has 1. no standard citation style and 2. stopped requiring physical thesis prints since 2020, hence why 1. I have the freedom to choose the citation style and 2. I am embracing hyperlinks currently. My thesis is in NLP, so my own style most closely resembles that of the ACL (see [this paper](https://aclanthology.org/2021.iwslt-1.31.pdf) as an example), but this is not a hard constraint.

I am asking for an **ought** as well because of this freedom. If the standard is (1), but there are better arguments for (2), then I prefer (2).

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Note: I am *not* asking [how to cite a website](https://academia.stackexchange.com/questions/8098/how-should-i-cite-a-website-url). As explained above, I've made up my mind on this: I want to only cite a URL, not have a whole BibTeX entry for it. The question is how/where to do the citation.