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Pragma compile_options does not show some options
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Just an observation.  There are many defaults that are set at various places various header and source files but are not reflected in the output from compile_options.

For example, the default for the define SQLITE_DEFAULT_MEMSTATUS is 1 and that default is set long after ctime.c has been processed in the amalgamation.

This means that the output of pragma compile_options reflects compile settings and not the as-built settings (that is, if DEFAULT_MEMSTATUS does not appear in the pragma compile_list then the code was compiled either with that option actively disabled *or* perhaps it is enabled by default -- it appears in the pragma output only if it was specifically enabled.)