Making sure that image_ids between a model and the database are consistent is a pain. The clear_points flag takes care of this by assigning the correct image_ids to images (consistent with the database) based on filenames. This makes things much easier for casual users, who don't need to read out the image_ids from the database. I would argue that enabling this by default is the better choice (especially since in many cases, one would re-triangulate from scratch anyways).

The PR sets the default value to true. It also adds a bit of documentation about the behavior described above to the --help argument.

If you prefer to keep clear_points set to false by default, I would suggest to add another flag that makes recomputing image_ids default behavior.