Perhaps I have misunderstood the nature of the problem reported above.  Are
you trying to run "fossil rebuild" or "fossil reconstruct"?  I've been
assuming "fossil rebuild", but now I'm thinking I misunderstood.

There is an inefficiency in "fossil reconstruct", I think.  And I think I
have a simple fix.  But I need to fix some inefficiencies in
"fossil deconstruct" first, so that I can construct a large set of files
from which to test "fossil reconstruct".  I'll try to post a patch soon....