fix problem populating pointer files

This is a result of an audit of every use of getInodeCaches,
to find places that misbehave when the annex object is not in the inode
cache, despite pointer files for the same key being in the inode cache.

Unfortunately, that is the case for objects that were in v7 repos that
upgraded to v8. Added a note about this gotcha to getInodeCaches.

Database.Keys.reconcileStaged, then annex.thin is set, would fail to
populate pointer files in this situation. Changed it to check if the
annex object is unmodified the same way inAnnex does, falling back to a
checksum if the inode cache is not recorded.

Sponsored-by: Dartmouth College's Datalad project

Database/Keys.hs

@@ -36,6 +36,7 @@ import Annex.Common hiding (delete)
 import qualified Annex
 import Annex.LockFile
 import Annex.Content.PointerFile
+import Annex.Content.Presence.LowLevel
 import Annex.Link
 import Utility.InodeCache
 import Annex.InodeSentinal
@@ -182,7 +183,14 @@ addInodeCaches :: Key -> [InodeCache] -> Annex ()
 addInodeCaches k is = runWriterIO $ SQL.addInodeCaches k is
 
 {- A key may have multiple InodeCaches; one for the annex object, and one
- - for each pointer file that is a copy of it. -}
+ - for each pointer file that is a copy of it.
+ -
+ - When there are no pointer files, the annex object typically does not
+ - have its InodeCache recorded either, so the list will be empty.
+ -
+ - Note that, in repos upgraded from v7, there may be InodeCaches recorded
+ - for pointer files, but none recorded for the annex object.
+ -}
 getInodeCaches :: Key -> Annex [InodeCache]
 getInodeCaches = runReaderIO . SQL.getInodeCaches
 
@@ -375,12 +383,12 @@ reconcileStaged qh = do
 	reconcilepointerfile file key = do
 		ics <- liftIO $ SQL.getInodeCaches key (SQL.ReadHandle qh)
 		obj <- calcRepo (gitAnnexLocation key)
-		objic <- withTSDelta (liftIO . genInodeCache obj)
-		-- Like inAnnex, check the annex object's inode cache
+		mobjic <- withTSDelta (liftIO . genInodeCache obj)
+		-- Like inAnnex, check the annex object is unmodified
 		-- when annex.thin is set.
 		keypopulated <- ifM (annexThin <$> Annex.getGitConfig)
-			( maybe (pure False) (`elemInodeCaches` ics) objic
-			, pure (isJust objic)
+			( maybe (pure False) (\objic -> isUnmodifiedLowLevel addInodeCaches key obj objic ics) mobjic
+			, pure (isJust mobjic)
 			)
 		p <- fromRepo $ fromTopFilePath file
 		filepopulated <- sameInodeCache p ics
@@ -390,7 +398,7 @@ reconcileStaged qh = do
 					Nothing -> return ()
 					Just ic -> liftIO $
 						SQL.addInodeCaches key
-							(catMaybes [Just ic, objic])
+							(catMaybes [Just ic, mobjic])
 							(SQL.WriteHandle qh)
 			(False, True) -> depopulatePointerFile key p
 			_ -> return ()