Did that stop the riots and assaults or did they continue?

It stopped the riots and the assaults, yes. At least, AFAIK - maybe you have some different information?

There was a riot and a massive disruption that happened in June, and Portland PB cleared it out. There then was a small group of people who maintained a continuous protest ever since.

The people who have been protesting the last 100 days haven't been doing the things that happened at the riot, so the police can't "throw the book at them" or treat them as if they were doing the same things as happened at the riot. The windows are boarded up because of what happened at the riot, not because of what the 100-day protestors have been doing.

The article was from June 15, 2029 or so. Doesn't it strike you as odd that these disturbances have been ongoing for several months now and neither the city nor the state is doing the slightest thing to deal with it?

No, because it's not the same disturbance. What happened in June was a massive protest that devolved into violence. Since then, there have been a small group of people continuing to protest. It's not a massive protest and riot that's been ongoing for three months. It was a big problem that was addressed by Portland PB, followed by a minor protest that's been ongoing.

Please don't go back to the "protests [I] don't like" thing; that's a red herring: the peace is being disturbed, federal agents are being threatened and violently attacked night after night and the residents have to put up with this on a daily basis.

Are federal agents being violently attacked night after night? Do you have a link that shows that? Seems unlikely - this is an ICE office, these are federal law enforcement officials who have arrest authority, and if someone violently attacked them they would almost certainly respond with force and arrest them. Yes, the protest is almost certainly noisy - though I doubt that the ICE office is in a residential neighborhood, which is going to limit the applicability of many noise ordinances.

Again, if you've got links that show that people were rioting or breaking into ICE or the like for 100 days straight, rather than downshifting into just ordinary protesting, I would certainly stand corrected. But that doesn't seem to be the case, which is almost certainly why Portland hasn't bothered driving them off.