Misc changes and fixes for new API internals.
Fixed package.d rule with new resolver.
Refactoring ModuleNamingRules
Updated API, removed usages of DeeProjetModuleResolver.
Fix bug in AbstractUIOperation.
getFilePath API fixes and changes, marked other stuff as deprecated.
Fixed concurrent modification bug.
Fixed failure in tests, perhaps due to Eclipse bug??
Fixed UI tests for the past changes is project API.