I created the project and tried to pull choice 1 (apex/VF) from production org, got this error:

Factory exception occurred when marshalling package manifest into DOM document, please make sure package manifest is well-form and present in proper location.

Reason:

com.salesforce.ide.api.metadata.types.Metadata$JaxbAccessorF_fullName can not case to com.sum.xml.internal.bind.v2.runtime.reflect.Accessor

Please let me know what i need to do to proceed. Thank you!