Personally I just use my own pmwiki instance to store my personal notes. It doesn't really have a "native" solution, but as you know you can access a website from almost any platform. If you need offline access, there are CLI editors.
I've found PmWiki to be easier to set up and use than Dokuwiki. More or less just download and extract the .zip archive. I've always had permissions issues with Dokuwiki, and while that might be worth the trouble for an online wiki, there's no reason to mess around with a big installation for a personal wiki.
Also, recent versions of PHP come with a built-in webserver that will work for an offline wiki (whether Dokuwiki or PmWiki). Go to the root directory of your wiki, run
php -S localhost:8001
and access it at
localhost:8001/pmwiki.php
or
localhost:8001/doku.php
You don't need to run a web server like Apache, and you don't need to mess around with an existing web server if you've already got one running.
By "small private usage" do you mean you want a standalone wiki (i.e., running on your local computer) or one that you have on your web server but only you access?
I use PmWiki. It's dead simple to set it up either way, uses plain text files rather than a database, updating is trivial, and is easy to customize.
Another alternative is Tiddlywiki.
I will recommend Media Wiki because is is the current standard of Wiki software. You can try Iki Wiki if you want to avoid database or if you want a static site instead of a dynamic site.
There is something called PmWiki which is what tvtropes runs on that uses a different wiki markup than Media Wiki, I don't know if you would like that better.
I've been using PmWiki (http://www.pmwiki.org/) as my personal lab notebook for 4-5 months, now. It's not perfect, but it's fast and has a decent user community who have created lots of extensions. I run it on a public Web server (it's PHP-based), so that I can reach it from anywhere. The access control was pretty easy to configure and most of it was configured for privacy, out of the box.
>and all of the wiki builders I have seen are tied into a subdomain when I am looking to use a standalone domain.
It seems you are using hosted wiki, you can use "standalone domain" if you setup it yourself. Get a web hosting and a domain name. Some of wiki that may or may not be fulfill your requirements:
I tried several and found I like PmWiki the best. It's file-based by default but I use the sqlite database option. Also added markdown and LaTeX/MathJax extensions (called recipes in their idiom).
I think you just need to flip your perspective.
When you're reading something like this do you identify then locate each and every note?
Is your thought process "That's an A... so that's... here... Then C#... so... here..."?
Because that's a HUGE waste of time.
You look at it, see that it's in D major (key signatures exist for a reason) and ranges from G to E, find a good spot on the guitar that puts those notes under your fingers, then focus on how the notes move. The only note you need to identify and locate by name is the first one.
Yes, that's a simple example, but that same sort of mental process happens with more complicated pieces as well.
The only thing I can say for sure uses flat files is PmWiki... "PmWiki stores all data in flat files, so there is no need for MySQL or other utilities". I used to use it ages ago, but found that ideas tended to get lost in the maze of pages and I spent too much time just organising things. Then I had a folder of LyX files, but that didn't really work out as I never remembered what was in which file and it was too much effort to open it up and go poking about for the right thing. So now... yeah, I use Trello.
( And you got me thinking howhardcoulditbe to make a little local web front end to a folder of files, I got enough unfinished webrick weekend projects... )
If you prefer doing things your own way, I suggest pmwiki. Uses PHP and flat files, no database. Easy to set up, back up, or move to other hosts. On OS X can be dropped in the web folder and run locally. And it has a deeper feature set when you find that there is something you can't live without, or didn't know you needed when you started.