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software-and-syntax.mdwn
Wiki: More Fun Links and Ideas
https://en.wikipedia.org/wiki/Wiki_markup
https://en.wikipedia.org/wiki/Lightweight_markup_language
http://www.wikicreole.org/wiki/Home
https://en.wikipedia.org/wiki/Haskell_(programming_language)
http://johnmacfarlane.net/pandoc/
Here’s the thing. You need to choose your tools for creating content. Even though right now you have very little experience with professional tools which allow maximal reuse and easy collaboration (editing LaTeX by hand, Emacs, etc.), you must choose the tool box for writing your base format, a lightweight markup language like Markdown or Wiki Syntax.
The tool I suggest is Pandoc, which is design-wise perfect for conversions: It has a native document tree representation, and file formats can be converted to it and from it. It probably already has everything you need, but you can always add formats using Haskell/Lua.
However, Pandoc is good mainly if you use Markdown, because my other suggestion - Wiki Syntax - has an issue: Pandoc does support Wikimedia syntax, but it doesn’t support a not-very-popular wiki language called Creole, which tries to create a unified syntax for many/all wikis to suppport. You can visit their site linked above and see if they have software support or even a Pandoc reader/writer, which would be perfect.
After that you’ll need to choose wiki software, i.e. how the wiki content is converted into web pages. For editing, it is not necessary because people can edit the Markdown using their favorite desktop software. But it would allow all the people with internet access in the world to see a beautifully formatted version of the content and could potentially provide an interface for editing, would would be awesone for non-technical people who just want to make small/special changes like fixing a typo or translating pages.
You already have a simple initial list of wiki software that may be interesting, but IIRC it contains just ikiwiki and gitit at the moment. That’s fine. Also, you can always for and hack them to suit your needs. Also, using any other wiki software (e.g. dokuwiki) and putting its plain-text content in git can work. Of course it may be a problem for wikis that use an SQL database.
Another thing, you can use your own language dialect and implement it either by creating a Pandoc module or by applying a preprocessor (preprocess, gpp, M4, etc.) to your text. The problem with that would be gedit’s highlighting, but you can also create a syntax description for it. That’s still a problem because it’s specific to gedit, but I guess it’s possible to port it to other tools gradually.