A small update:
The bug report about the missing tracker3 subcommands was closed due to it being an upstream issue. I disagree on this, but I can live with the workaround. The workaround is linking the subcommands from the
/usr/lib64/tracker-miners/tracker3 folder to
/usr/lib64/tracker/tracker3, which as far as I can tell solves the issue. Now I can run
tracker3 reset -s and this solves the SQLite errors from
tracker-extract-3 was apparently the main culprit for the CPU usage, and the two issues seem to be unrelated. From the syslog,
tracker-extract-3 seems to choke mostly on EPUBs and flac files.
Also after a shutdown
tracker-miner-fs-3 shows the same errors as before (less of them, thankfully), so there is something weirder than just a corrupted database.
I hope at least that the subcommands workaround is useful to others.