Hopefully you can see those files. I retract my advice to use darktable's retouch tool -- there is a lot of sensor dust.
I ended up scaling the image by 50% because it was taking so long, but skyfill did happily work on the original full sized image.
I used the full sky replacement option (-fsr), which basically examines every pixel in the detected sky and assigns a probability that the pixel should be considered true sky. If the probability is large enough it will be overwritten -- so magically all the sensor dust disappears. That one spot near the horizon on the right where there is a black mask leaves some artifacts, because of some feathering at the edge of the mask where pixels were not completely black.
I will better document the -fsr option in the next tutorial for skyfill.
There is a shell script which shows the flags I used (just -fsr and a number of -tm flags). I had to mask a few of the sensor dust spots because they were too severe and caused end of sky detection to stop at them. The -tm mask tells skyfill to ignore that area for testing to see if the end of sky is there, and to not use that area as sample data to build the HSV sky model.
There are two runs of skyfill in the script, one with the -d3 option (debug level 3), which creates an image that shows the start of sky detected, end of sky detected, and where the masks are at.
A couple of other things:
Notice how that brown smear in the sky near the black-mask at the right is gone -- full sky replacement fixed that too.
The original full sized image caused a real problem to show up -- the large vertical shift in the sky data about at about 60% of the image width. The problem is (and has been the biggest problem for skyfill), is pixels near the edges of the data can be just "wrong". I'm not sure where the problem comes from, but in this example it is because the pixels on the edge near x=16278,y=551 are too dark. Skyfill in the first few steps will fill in pixels just to the left of that vertical edge because it is not perfectly vertical, and is using a localized rgb model to extrapolate and create pixels to make the edge perfectly vertical. Those dark pixels pollute the localized estimate of sky color...