Generally when someone links to something no github they are linking to 
something that isn't tiddlywiki as an example of what they would like to 
see in tiddlywiki. In those cases we can't just give you something to put 
into your wiki and try it out because it doesn't exist. You can completely 
ignore git and github and you won't miss anything.

>From your list it sounds like you need some dedicated custom software on 
your own server. What you want isn't simple and pieces of it are going to 
be pretty complex.

Now, for your list:

You have complete control over any wikis you have. I don't know what else 
you want here.

Making it accessible to the web requires you to have somewhere to host it. 
You can try tiddlyspot if you don't like any other web hosting solutions. 
TiddlyWiki needs to be hosted somewhere to be accessible online, just like 
any other webpage. That isn't a tiddlywiki problem.

The encryption tiddlywiki has is pretty secure, but I think you are asking 
for the wrong thing here.

You want to know who is logging into what? TiddlyWiki is a single file 
application, there is no server to take care of this. Also if you are going 
to do medical records please ask someone who knows something about security 
and privacy about facebooks business model before handing them your users 
medical data.

Letting a user edit one part of a wiki and not another in a secure fashion 
may be impossible. TiddlyWiki is a single file application and if you give 
a user write permissions and they know what they are doing than they can 
change any part of it.

You can have read only wikis, but the note above applies to any edits you 
want to let users make.

Leaving comments either uses a third party service like the google form 
commenting system (once again, ask someone who does security and privacy 
things about googles business model before sharing all the data with them 

Creating a separate wiki for each user is something that requires you to 
have a server and your own hosting. It isn't particularly difficult to do 
but it isn't part of tiddlywiki.

The system that you want is going to have pieces that are far outside of 
what tiddlywiki is because it is going no require its own server. It sounds 
like this is something that needs an actual database backend and probably 
some dedicated developers to make. You may want to look into a CMS like 
Drupal, but once again, please talk to someone who has a background in 
security and privacy.

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