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Build Automatically doesn't work as expected. In my project, I run 'make clean' at the command line. In this case it is because the Makefile originally generated a javadocs/ directory and it's annoying me. When I go back to Eclipse and click Refresh, Eclipse doesn't build the project. If I go to the Project menu I can't Build All or Build Project because they are greyed out. I have to turn off Build Automatically to be able to build my project. This is very counter-intuitive. I have seen other bugs that are similar to this, but they are confused with issues of CDT. I find it difficult to tell what the overall conclusion is; I see Verified Fixed but I still see the bug. If you do assign this as a duplicate of another bug, please can you tell me why they are a duplicate, as the similar bugs that I've seen don't seem to be the same (and it obviously isn't fixed, otherwise I wouldn't be logging this bug).
Moving to JDT/Core to comment on the fact, what should happen if clients delete the output folder outside Eclipse and do a refresh.
Dirk, I noticed you moved this bug to Core. That suggests that you believe the problem of not building automatically after refresh is the real bug here, rather than the menu items being greyed out. Is this correct? I don't see why the Build All needs to be greyed out if building automatically is turned on. Some users might want to build anyway, just to make sure. That action might be wrong, but they might want to do it. If a user upgrades from a previous version, Build Automatically is turned on, and they're used to being able to use Build All. That change is not intuitive.
Build All stands for "manual build" (in opposite to automatic build). In previous releases Eclipse offered a Rebuild All, which got replaced by the Clean action. So may be you are locking for this ?
That is probably true, yes.
The output folder is owned by the Java builder. Tempering with this folder is not supported. There is no plan to support this. As Dirk suggested, you must manually do Project>Clean if you temper with the output folder.
Sorry I meant "tampering" not "tempering"