As soon as a scan is started it will not bother you for anything nor require further user interaction.
One of the biggest advantages of Arachni is its highly modular nature.
The framework can be extended indefinitely by the addition of components like path extractors, modules, plug-ins, or even user interfaces.
Arachni is not only meant to serve as a security scanner but also as a platform for any sort of black box testing or data scraping; full fledged applications can be converted into framework plug-ins so as to take advantage of the framework's power and resources.
Arachni's flexibility goes so far as to enable system components (like plug-ins) to create their own component types and reap the benefits of a modular design as well.
Changelog - Version 0.2.2.2 (March 22, 2011)
Arachni: WebUI v0.1-pre screencast