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Currently netbeans supports databases over the services tab / databases. Even though this is a very useful tool for server databases, where connections are generic pointed to a database url like localhost, for the embedded databases it is not working properly. Embedded databases in my point of view are regarded both as a central resource for all projects (like the server equivalent) but also should be project specific. Currently when you create an embedded database (for example a derbydb embedded database) the usual path to do this is .netbeans-derby on the user folder (in windows: c:\document and settings\<user>\.netbeans-derby\<database>). When you create this database, you can use the reference to jpa/persistence/ create entity beans from database features, yet this is not the project database, but rather resides as a generic database connection. Afterwards it creates the corresponding database on the target project location, but yet the data you control are being controlled from the user folder and not from the live data of the real project created database. Also when using the database desktop wizard with an embedded database, netbeans believes there is a duplicate reference (to the home dir) so it throws exceptions. Embedded databases should be project oriented. You create a project, and if you want to attach a database within there should be an option from the project name. Right clicking project name and attaching/detaching a database there. That database could create a true reference path to the database explorer (if you want to keep the databases organized there tidy and etc, netbeans way, if there is such), or a variable pointing to $nbprojectpath/db/$dbname. For example, let's just say that in windows I have a project called project1 to c:\java\projects\project1. If I want to attach a javadb called "embdb" there, netbeans should add that to c:\java\projects\project1\embdb\ or c:\java\projects\project1\db\embdb\. That would be added to databases ready to process / alter data. The thing about that is, that the path would be relative to the project, thus if for any reason I move to another os (example linux) and my project is now /home/user/project1/ the database should be on /home/user/project1/db/embdb/ and reflected there accordingly from netbeans of the current platform.
Reassigned to new owner.