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Looking at journalctl -b -F BOOTCHART --full, it allows you to extract only exactly one bootchart correctly. If bootchart was manually run several times, the charts aren't even correctly concatenated, and the output is mixed/truncated and malformed XML.
Aside from manually iterating the journal in C, I don't see a consistent way to extract bootcharts with journalctl properly one-by-one.
See systemd/systemd#657.
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