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Restrict system library check to require Java nature
The validation of the project classpath introduced with 74d062b always fails, if the project doesn't have a Java nature (and thus usually no .classpath file). This causes issues when e.g. trying to open a source file with the Java editor or simply when trying to use the AST parser outside of a Java project. With this change, the check becomes more conservative and only fails, if both the Java nature exists and no system library is configured. Note that one can avoid this exception by disabling the binding resolution. But given that this requires changes in user code, it is more prudent to only fail in cases where this is the desired behavior. Resolves #3298
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