The built-in source code repository integration feature from the days of MantisBT 1.1.x has been removed in MantisBT 1.3.x. This feature is superseded by the SourceIntegration plugin available for use with MantisBT 1.2.0 and later versions. The old in-built system had very limited capabilities and hadn’t been properly maintained for some time.
SourceIntegration is a set of plugins developed by John Reese (MantisBT developer) which allows you to integrate your MantisBT instance with multiple source code repositories at the same time. Currently supported version control systems include Subversion, WebSVN, SourceForge SVN hosting, Gitweb and Github.
The main benefit of SourceIntegration is the modular design which allows you to quickly and effortlessly integrate MantisBT with different version control systems. A new plugin for HgWeb (Mercurial) support took around 2 hours to create inclusive of the learning curve of becoming familiar with how SourceIntegration works. You can expect this plugin and more to become available with future versions of SourceIntegration.
The official MantisBT bug tracker has been using the SourceIntegration plugin for months without issue. The reason you’ve been seeing prefixes such as “Fix #123456:” and “Issue #234567:” in commit messages is that SourceIntegration automatically links commits with bugs on the official tracker where one (or more) of those prefixes exists.
If you have any problems with SourceIntegration or would like to submit patches, please report your issues at John’s plugin bug tracker instead of at the official MantisBT bug tracker.
You are strongly urged to migrate from the old in-built system to SourceIntegration if you haven’t done so already. As of MantisBT 1.3.0 the in-built system will no longer exist (you won’t lose historical data however).