ikiwiki
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ikiwiki is an open source software project for hosting a wiki on your own site that uses Git for storage and Xapian for search. Ikiwiki is written in Perl.
Ikiwiki is a wiki compiler; it generates static web pages from a directory tree of plain text files, by default written in Markdown. In this respect it is similar to Jekyll, however Ikiwiki provides a CGI-script, which allows authentication with OpenID (and others), online editing of pages, viewing the (Markdown) source of pages, etc. thus enabling online collaboration.
Ikiwiki can generate a website from plain files, however it integrates tightly with version control systems. Git is widely used, however Subversion, Bazaar and others are supported.
Ikiwiki has good support for blogs and other aggregations, like todo lists, bug tracking, forums. On the other side it is sometimes criticized for its default web design
IndieWeb Examples
IndieWeb community members using ikiwiki to run their primary site (and potentially more).
Georg Lehner
Georg Lehner uses ikiwiki on several sites.
He has modified ikiwiki to be able to blog with microformats2 h-feed and h-entry markup.
The technical details are explained in Microformats for IkiWiki on the MagmaSoft Tech Blog, which is selfdogfeeding on this.
Secondary Sites
People running ikiwiki as a secondary site or on a subdomain:
Philip Durbin
Philip Durbin uses ikiwiki on http://wiki.greptilian.com/