I would like suggest changing the default value the 
"Synchronize output directory" option under "Project
Properties - Compiler" in IntelliJ 3. I do not believe
it should be enabled by default. Here is my rational,
based on real world experience:

I am working on a project were we create extensions to
a commercial Java application. We have source code to
portions of the product, but not others. This allows
us to only extend only selected parts of the product.

The system is designed such that class files for custom
extensions live in a branch of the same codebase directory
as the rest of the product. So when creating my IntelliJ
project I set my output directory to the shared codebase
directory and accepted the defaults for new switches,
since I didn't really understand their effects.

With the "Synchronize output directory" option enabled,
as it is by default, IntelliJ will apparently delete all
of the class files in the output directory that I do not
corresponding source files in the source directory.
This can (and did for me) have very bad unintended effects.
A large number of class files (several hundred) that are
required for my application to run were deleted. Obviously
this behavior was not what I expected.

Synchronization is probably good in most cases, but can
be potentially damaging in some cases, as it was for me.

Ron
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