In general, a filesystem copy should be sufficient. If you run into problems with your projects, try removing the project from the workspace (without deleting the files) and then re-add the project, which will rebuild the metadata.
You need to copy the whole folder which you select as your workspace at startup (or you once selected). All settings are included in there (even the opened files).
I use rsync for this. Works great.
You shouldn't have any issues with a straight filesystem copy as long as your eclipse versions match up.
If they don't, the project metadata may not load correctly
Make sure you shut down eclipse before you copy the workspace, and that the target computer has the same (or higher) eclipse version, including the same plugins.
Check that your workspace actually contains all the projects - when creating a project, it's possible to have its files situated outside the workspace.
If your projects use any external libraries installed on the system, install these on the other system in the same place (or adjust the paths).
Then, there should be no problem.
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