When using the Autotools plugin to build a relatively large C project (e.g. newlib) for the first time, there is a stage between configuration and build that is called refresh. This stage takes a very long time to complete and there is no real feedback on %complete (0 or done). The cause of the delay should be investigated to see if it can be addressed and if not, some better form of progress should be displayed.
Problem is actually caused when populating the Make Target dialog for Build Special Targets. The interface provided only allows one Make Target at a time to be added and it ends up rewriting .cdtproject. This causes events to be triggered. Fix was to added to Autotools 0.0.8.1 to provide new interface. Time between configure and build for newlib project goes down from >10 minutes to about 4 seconds.