What do you mean by the manual field? There's a manual tab in citoid...

yes, the manual tab.

In particular:

Click "cite", click "manual" tab, click "basic form", paste a URL in the box, click "insert".

(The "web" option in "manual" inserts a {{Cite web}} template, that seems to work fine.)

At least, that's what appears to have been done for:
https://fr.wikipedia.org/w/index.php?title=Association_pour_le_droit_de_mourir_dans_la_dignit%C3%A9&type=revision&diff=117276171&oldid=117275911
https://fr.wikipedia.org/w/index.php?title=France_aux_Jeux_olympiques_d%27%C3%A9t%C3%A9_de_2016&type=revision&diff=117288174&oldid=117251042
https://fr.wikipedia.org/w/index.php?title=Soci%C3%A9t%C3%A9_fran%C3%A7aise_d%27%C3%A9nergie_nucl%C3%A9aire&type=revision&diff=117277333&oldid=114440706 (scroll down)

This is a big problem for wikis which do not have any citation templates set up: there is only the "basic" option for citations, which shows you a text box, and if you paste an URL there, it won't work. It's very counterintuitive.

So there are two problems:

1. People pasting into basic instead of Citoid - this seems like a user education problem. I'm surprised it's happening at all given the first box we show you is Citoid.
2. Wikis which don't have Citoid.

For 2 I think the ideal solution is to find a way to give them Citoid. If it's impossible for them to create citation templates, then we can have a fallback which generates some sensible output based on parameters which are universal to all references (title/url?).

It seems to be mostly "power users" who "know how to add refs".

I think (1) adding proper autolink support to VE (is there a phab ticket for that?) will help a lot. I'm working on patches for that.

@Esanders also mentioned (2) a DataTransferHandler for paste that would detect wikitext (and bare links) and wiki-fy them before pasting (just feed them through wt2html in parsoid). That would also help a lot in general with our <nowiki>s, a bunch of which seem to be caused by pasting wikitext into VE.

The last bit is people manually typing a URL into the manual cite field. VE autolinks (as in google docs, etc) will happen on the first whitespace after a link, so it's possible if you just type the URL and close the dialog you'll still get an unlinked (nowiki'ed) URL. There might be (3) some sort of hack we can play where we invoke autolinking on dialog close or something like that. Let's do (1) and (2) first and see whether we really need (3).

https://gerrit.wikimedia.org/r/230145 addresses (1) -- autolink support in VE.
https://gerrit.wikimedia.org/r/230146 addresses (2) -- paste of wikitext.

Change 231145 had a related patch set uploaded (by Cscott):
Autolink pasted links

https://gerrit.wikimedia.org/r/231145

VE patches to autolink URLs when typing have landed (e17415501bf18ca55b8b4fdffb1f1e055f7aaa3a).

Still in the review queue are the patches to autolink pasted URLs (https://gerrit.wikimedia.org/r/231145 and related pull-through patch https://gerrit.wikimedia.org/r/231156). These are the patches which I expect will actually address the issue discussed here, pasted URLs in citations.

Change 231145 merged by jenkins-bot:
Autolink pasted links

https://gerrit.wikimedia.org/r/231145