This was caused by commit fb8ab2469d putting
an isPointerFile check in the wrong place. So if the file was not a pointer
file at that point, but got replaced by one before the file got locked
down, the pointer file would be ingested into the annex.
The fix is simply to move the isPointerFile check to after safeToAdd locks
down the file. Now if the file changes to a pointer file after the
isPointerFile check, ingestion will see that it changed after lockdown,
and will refuse to add it to the annex.
Sponsored-by: the NIH-funded NICEMAN (ReproNim TR&D3) project
They could be missing due to an interrupted git-annex at just the wrong
time during a prior graft, after which the tree objects got garbage
collected.
Or they could be missing because of manual messing with the git-annex
branch, eg resetting it to back before the graft commit.
Sponsored-by: Dartmouth College's OpenNeuro project
Fix a bug where interrupting git-annex while it is updating the git-annex
branch could lead to git fsck complaining about missing tree objects.
Interrupting git-annex while regraftexports is running in a transition
that is forgetting git-annex branch history would leave the
repository with a git-annex branch that did not contain the tree shas
listed in export.log. That lets those trees be garbage collected.
A subsequent run of the same transition then regrafts the trees listed
in export.log into the git-annex branch. But those trees have been lost.
Note that both sides of `if neednewlocalbranch` are atomic now. I had
thought only the True side needed to be, but I do think there may be
cases where the False side needs to be as well.
Sponsored-by: Dartmouth College's OpenNeuro project
