[[!comment format=mdwn
 username="david.j.buckmaster@984ff2704feacab53415ac5647206517d18f88f8"
 nickname="david.j.buckmaster"
 avatar="http://cdn.libravatar.org/avatar/1650cdf23a0999fd0e03650e20c90ee7"
 subject="comment 2"
 date="2019-02-24T07:01:35Z"
 content="""
In case this is NOT a bug but rather an incompatibility between borg/git-annex, the bash snippet below seems to sidestep the issue if run AFTER a borg operation but BEFORE any other annex commit/sync. Unsure if I'm the only person in the world that wants a not-permanently-append-only borg repository in an unlocked+thin git-annex...but...after a borg operation that truncates+deletes files, the function uses the status printout to identify all missing, borg-controlled files, and for each

1. Reverts the deletion (git checkout -- ..)
2. Checks if the restored file is a (dead) file pointer (file contents start with /annex/objects). If no, redo the delete and continue loop; if yes, truncate (but do not delete) the file and stage a commit.

Truncations are then committed to force annex to see that contents have changed, and all deletions are repeated. After that, git annex add-ing a new file with old content restores the annex content that borg truncated, rather than ending up with a pointer file and missing contents.

Test case:

	set -x && \
		mkdir tmp && cd tmp && \
		git init && \
		git-annex init  --version 7 base && \
		git-annex config --set annex.thin true && \
		\
		echo \"bar\">foo && cat foo && git-annex add foo && ls -l && git-annex sync && git-annex unlock foo && git-annex sync && \
		echo \"barbar\">foo && cat foo && rm foo && \
		\
		git checkout -- foo && truncate -s 0 foo && git add foo && git-annex sync && \
		rm foo && git-annex sync && \
		\
		echo \"bar\">ffoo && cat ffoo && git-annex add ffoo && git-annex sync && cat ffoo

Bash function:

	handleborgdeletes() {
		echo \"(handleborgdeletes\"
		
		local PTRFILES=()
		local HAVETRUNCS=
		local f
		
		for f in $(IFS=$'\n' $GITANNEX status | grep ^D | grep -E '(index|hints|integrity|data/)'); do
			f=${f:2}
			
			$GIT checkout -- \"$f\" #restore
			if [ -n \"$(grep -F --text '/annex/objects' $f)\" ]; then #is broken annex pointer file
				echo \"$f is a pointer file\"
				HAVETRUNCS=1
				truncate -s 0 \"$f\" #truncate
				PTRFILES+=(\"$f\") #track
				$GIT add \"$f\" #stage content change
			else
				echo \"$f is not a pointer file\"
				rm \"$f\"
			fi
		done
		
		if [ -n \"$HAVETRUNCS\" ]; then
			$GIT commit -m \"truncating borg deletions\" #commit content changes
			
			for f in ${PTRFILES[@]}; do
				rm \"$f\" #repeat delete to be committed later
			done
		fi
		echo \"handleborgdeletes)\"
	}
"""]]
