> so, the main question is: why isn't "mtxrun --generate" run?

It is run. But this has been broken since the very beginning.

When you run "mtxrun --generate" from withit mtx-update in creates a
different database and updates that one (at least that used to be a
problem in past; I didn't check that recently, but it is one of few
longstanding nasty bugs (the other one is inability to properly set
the platform in a decent way)).

Most of the time it is not as nasty since formats for MKIV are rebuild
later anyway, so often one would not notice the problem. At the end
there are two databases then.

It would help to know how you calculate the md5 hash and why it
chooses two different hashes ... But I will try to check again.

Mojca
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