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Header IDs are automatically added when you Generate a TOC, or when you Save. I'm not sure why its generating IDs when saving, but we'll look into that. Its possible someone once found that some readers had a problem if there were no IDs? But as mentioned they shouldn't cause any issue.
The meta tags are not deleted automatically. Can you give a step by step example of how to demonstrate this?
You have to wait for the next version in order to be able to stop Sigil's from using HTML Tidy to Pretty Print your code.
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