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If a target such as a Container target is selected and either the Run or Debug buttons of the launchbar are pressed, the build and run/debug work as expected, however, after the run/debug, the active target is set to default even though the pull-down menu shows different. This affects the indexer and clicking on the outline view will result in bringing up the local headers. The only way to change back is to change the target to something else and then back again as selecting the same target won't cause the target change to occur.
By default, sounds like you mean the config used by the indexer (not sure that qualifies it as a "default" but I get what you mean). In the managed build, we had a project setting to pick the build configuration to use for indexing. It would make sense to have something similar for Core build.
BTW, a similar issue I run into is what build config the Build Project menu item runs. In theory it's the last one set by the Launch Bar. Would be good to make that explicit as well.