So, new playthrough. I decided to go through the game this time, read every unclassified document I had access to first, take notes on each one, and then go back to the confidential/secret ones. After I finished reading each document, I filed it.
If I saw interesting names or case numbers, I copied them, went to the ARC and BRD tabs and pasted them. I found tag clouds on the BRD page (or nothing) that aggregated documents I'd already read. I just found documents I'd already read on the ARC page (or nothing). Searching on either page didn't seem to unlock anything.
Just by reading and filing unclassified documents, I was promoted to SECRET and reached level 2.
When I went back through the confidential and secret documents the same way - read, take notes, file - I found that all redactions I was able to interact with in previous playthroughs had been automatically filled out just by having SECRET clearance. I managed to get through all documents and arrive at "No documents pending." without filing a single challenge. I searched things, clicked on tags, copied and pasted lots of names and case numbers and things into the archive search or the cross-reference board tag search, and there was never any indication that anything at all was happening.
I opened up the game in an incognito window and did a speedrun for comparison: file unclassified documents until I got promoted to secret, then file the rest of them. I still got Source Contact 1, 2 and 3, even without searching for the term they told me to search for. There are 64 documents in the archive and 41 connections on the cross-reference board both in my slow playthrough and my speedrun.
I have no redactions to challenge and searching names and numbers doesn't seem to do anything, no matter how many I try. Nothing seems to trigger anything, it just seems like I'm doing completely normal searches with no impact.