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sqlite header and source version mismatch
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It has nothing whatsoever to do with the database being accessed.

The message means that the version of the sqlite3 shell program being executed was built so as to use the "system shared library", and that the "system shared library" being loaded is a "different version" of the code than the version of the code that was used to build that sqlite3 shell program.

In other words, there is more than one "package" of sqlite3 stuffs on your computer and they do not represent the same version of sqlite3.

The version of the "system shared library" is 2018-12-01 12:34:55 bf8c1b2b7a5960c282e543b9c293686dccff272512d08865f4600fb58238alt1  
but the version of the sqlite3 CLI application is 2013-10-17 12:57:35 c78be6d786c19073b3a6730dfe3fb1be54f5657a

You need to use the package manager for your OS to upgrade (or downgrade) one or the other components so the are the same or otherwise make them consistent (perhaps by downloading and compiling the current version).

Although the version mismatch is for the most part immaterial, the sqlite3 shell program complains about the difference because use of a diagnostic tool in an inconsistent state might result in inconsistent and irreproducible results.