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Is sqldiff meant to detect "NOT NULL" differences?
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Your initial belief on this was entirely reasonable given what the doc page and sqldiff's --help output said.

The doc page has been clarified to emphasize that the (usual) comparison is on content and to note the limited effect of the --schema option.

The sqldiff utility has been modified to make it possible to compare schema among databases more completely, via the option:<code>
   --table sqlite_schema
</code>.

These changes are available now in the SQLite code and doc repositories. They should be conveniently available at the next release.