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It would make sense to be able to set the JDK Compliance level against a project. This would allow for compiling different projects under different level of compiler. The main reason for being able to this is that you may want to compile say a applet project with 1.1 compliance, but be developing new projects with 1.4 compliance. Currently JRE is definable at the project level and to make this useful would also require the JDK compliance at the project level.
Currently all settings are global indeed. Per project settings are not currently on the 2.0 plan.
Will reconsider post 2.0
Reopening
Clearing resolution
Variable values per project are along the same line as option values per project. *** This bug has been marked as a duplicate of 7091 ***
Solved in latest, IJavaProject can be specified custom options, in particular compliance can be toggled on a project basis (once UI surfaces it).