I have to do (as root)
update-tracker-ontology -c Music -a audio/x-flac
in order for tracker to pick up FLAC, even with extra decoder support added. This was happenning before the patch, and may have come up from PR1.3

This patch works. I used to have problem with cover.jpg cover arts not becoming visible but this fixes it.

However, I still have a problem with id tags in M4A files (I assume that these are aac files becouse they were created by iTunes or purchased from there). Every time Tracker indexes my media files it somehow skips over some of these files which results them beeing seen as "unknown artist". This is annoying.

I can't fix the database by reindexing because every time different songs are skipped. Mussorgsky can't help either because it does not work with aac files (it just shows that id tags seem to lag information but does not allow to fix them). Is there any way to force Tracker to index/scan just a one file/folder so that I could manually add the missed songs to song library?

It would be great if these could be included in the CSSU. Do you have plans for that?

Yes. I am actually considering upgrading to the Harmattan version of tracker (but that would be for the -testing branch).

If anything breaks I'll probably settle with my current patched tracker, though, as I do not think I will have time to fix lots of breakage

By the way, the patched tracker on my site just got a new patch that helps if you have mountpoints under non-indexed roots (maemo tracker currently always indexes sdcard/mmc mountpoints even if they're on a .config/tracker exclusion list).