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If I create a new Java project through Netbeans, it has this structure:
My question is, do I need to put build and dist under version control? Or will just putting src, build.xml, and manifest.mf be sufficient?
just src, build.xml and manifest.mf should be enough. The dist and build should be built by whatever you are using to build. (maven, NetBean etc)
If you commit the dist and build then you are duplicating your code. The src, build.xml and manifest.mf detail the human readable parts of the project. The build and dis are the machine converted parts of it.