The latest code in HEAD has extension registry caching enabled. This mechanism is similar to that found in regular Eclipse where the extension registry is cached between runs (this eliminates the costly reparsing of plugin.xml etc). The standard related command line options have also be reintroducted. To recap they are
-noregistrycache = turn off the use of registry caching
-noLazyRegistryCacheLoading = if using registry caching, lazily load parts of the registry from the cache.
If you are experiencing problems and suspect the registry caching you can either delete the .registry file in your workspace metadata area or use -noregistrycache.
Comments/issue/bugs to this list or bugzilla as appropriate.