Retrieved files may not be placed properly when the project has multiple configured source roots

This was originally reported in the discussion groups:

https://groups.google.com/a/illuminatedcloud.com/g/qanda/c/FYQbs9WlPeA/m/7BrPQ8_EBgAJ

What I found upon examining the logs is that if a metadata file/meta.xml file pair are retrieved and the metadata file is processed first, the meta.xml file is not properly recognized as a supporting meta.xml file because its companion file has already been moved out of the same parent directory.

The solution is to process all retrieved meta.xml files before processing other files.

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