Solution
Full import/export is more properly designated for the backup/restore type of operation. There is no way to exclude pieces, either on export or import, although this is possible with a script that iterates over all projects (or at least all that are not part of CloudBees CD (CloudBees Flow) and/or plugins) and export each one of them. Then you can import them into the other system.
The procedure for exporting individual projects is attached.
Notes regarding the procedure:
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This procedure should work for Commander 5.x and CloudBees CD (CloudBees Flow) 6.x and above.
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By default, this procedure imports itself into a project called "EA Testing".
You need to either create this project (if it does not exist) or provide an import path such as
ectool import export_procedure_Export\ All\ Projects.xml --path /projects/<projectName >/procedure/<procedureName >
(again, <projectName> is the name of an existing project).
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This procedure has three steps:
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create a list of all projects and store it in a property
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export the procedure itself (for convenience)
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export projects into the job’s workspace
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Review the code to see if you need to adjust anything (for example, project filters in the first step).