Delta encoding is still taking a significant amount of time, in particular the call to content_deltify() by add_one_mlink() in manifest.c.
Commenting out this call to content_deltify() allows cloning my smaller repository with "--nocompress" to go from 1 minute down to 4 seconds. I am not familiar enough with fossil to know all the implications of commenting this call out, but the resulting cloned repository seems to be fine. If the noCompress flag could be propagated down so that this particular call to content_deltify() is skipped when cloning with the flag enabled, the clone operation time could be reduced to a small fraction of what it is now.
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