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My first thought was did the User Lowercase File Names box get checked?
Not sure it affects that folder but check it anyway.
We've been running with that box checked for a long time now. I always thought it odd that the output folder would still generate as mergedProjects, even with lowercase specified, but that has just been a fact of life. Until now.
Curiouser and curiouser...
I'm not sure it does make a difference to that folder, in fact thinking some more about it, I don't think it does. Nonetheless, please just check it. What version are you on? Maybe something has changed.
I'm off to bed now but post back and I'll take another look in the morning.
Download my merged webhelp demo if you want something ready made to test with.
Quick thought. Maybe it didn't make a difference with the GUI but does with the command line?
I'm on RH6. All our projects have the lowercase output option selected. This past week is the first time I've done serious generation with the command line. (Overall, I'm quite pleased with it, BTW. ) Of the three parent projects I generated from the command line, two generated mergedProjects and one generated mergedprojects. The project that grabbed the bit between its teeth now continues to produce mergedprojects regardless of whether I generate via GUI or command line.
I manually cleaned out the output folder before generation, just to be certain that I didn't have any old folders that would confuse the issue. That wasn't it. From the command line, one project still generates mergedProjects, and the other generates mergedprojects.