After applying metadata with git-store-meta.pl --apply, the GUI tool gitk detects "local uncommitted changes" for all files with changed metadata.
After reading this comment on StackOverflow, I added

git update-index --refresh

to my post-checkout and post-merge hooks, and it seems to work now. Unfortunately I don't know Git well enough to determine whether this is the right command here.

Are the hooks even the right place to do this, or should this be done inside --apply?