If I change the current project's 'base path' setting, refreshing the project organizer should first re-read that setting before crawling the directory structure.
Good catch. I've introduced this regression when I added support for external directories. It should actually not be needed to refresh the project manually after confirming the project settings dialog - it should be reloaded automatically for you. #921 should fix this bug.
Closed #901 via #921.
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