fsck: When run with --all or --unused, while .gitattributes annex.numcopies cannot be honored since it's operating on keys instead of files, make it honor the global numcopies setting, and the annex.numcopies git config setting.

Command/Fsck.hs

@@ -68,7 +68,7 @@ seek ps = do
 	from <- getOptionField fsckFromOption Remote.byNameWithUUID
 	i <- getIncremental
 	withKeyOptions
-		(startKey i)
+		(\k -> startKey i k =<< getNumCopies)
 		(withFilesInGit $ whenAnnexed $ start from i)
 		ps
 
@@ -162,18 +162,19 @@ performRemote key file backend numcopies remote =
 			)
 	dummymeter _ = noop
 
-startKey :: Incremental -> Key -> CommandStart
-startKey inc key = case Backend.maybeLookupBackendName (Types.Key.keyBackendName key) of
+startKey :: Incremental -> Key -> NumCopies -> CommandStart
+startKey inc key numcopies =
+	case Backend.maybeLookupBackendName (Types.Key.keyBackendName key) of
 		Nothing -> stop
-	Just backend -> runFsck inc (key2file key) key $ performAll key backend
+		Just backend -> runFsck inc (key2file key) key $
+			performKey key backend numcopies
 
-{- Note that numcopies cannot be checked in --all mode, since we do not
- - have associated filenames to look up in the .gitattributes file. -}
-performAll :: Key -> Backend -> Annex Bool
-performAll key backend = check
+performKey :: Key -> Backend -> NumCopies -> Annex Bool
+performKey key backend numcopies = check
 	[ verifyLocationLog key (key2file key)
 	, checkKeySize key
 	, checkBackend backend key Nothing
+	, checkKeyNumCopies key (key2file key) numcopies
 	]
 
 check :: [Annex Bool] -> Annex Bool
@@ -357,7 +358,7 @@ checkBackendOr' bad backend key file postcheck =
 				, return True
 				)
 
-checkKeyNumCopies :: Key -> FilePath -> NumCopies -> Annex Bool
+checkKeyNumCopies :: Key -> String -> NumCopies -> Annex Bool
 checkKeyNumCopies key file numcopies = do
 	(untrustedlocations, safelocations) <- trustPartition UnTrusted =<< Remote.keyLocations key
 	let present = NumCopies (length safelocations)

debian/changelog

@@ -12,6 +12,10 @@ git-annex (5.20140211) UNRELEASED; urgency=medium
     of annexed files within a view.
   * Add progress display for transfers to/from external special remotes.
   * unused: Fix to actually detect unused keys when in direct mode.
+  * fsck: When run with --all or --unused, while .gitattributes
+    annex.numcopies cannot be honored since it's operating on keys
+    instead of files, make it honor the global numcopies setting,
+    and the annex.numcopies git config setting.
   * Windows webapp: Can set up box.com, Amazon S3, and rsync.net remotes
   * Windows webapp: Can create repos on removable drives.
   * Windows: Ensure HOME is set, as needed by bundled cygwin utilities.

doc/bugs/Numcopies_not_checked_when_running_with_--all.mdwn

@@ -22,3 +22,19 @@ Linux (Ubuntu 13.10)
 
 # End of transcript or log.
 """]]
+
+> It's expected that --all (and --unused) make .gitattributes
+> annex.numcopies settings be ignored, because with these options git-annex
+> is operating on keys, it does not know or care what filename they're
+> associated with, and so cannot look them up in .gitattributes. I have
+> improved the documentation of .gitattributes files to mention this
+> limitation.
+> 
+> I also notice that fsck --all is not checking .git/config's
+> annex.numcopies or the new global numcopies setting. It certianly makes
+> sense for those numcopies settings to be paid attention to.
+> [[fixed|done]] --[[Joey]]
+> 
+> (--all is faster because it can quickly scan through .git/annex/objects
+> to find everything, rather than looking at the symlink target of every
+> file in the work tree.)

doc/git-annex.mdwn

@@ -1625,6 +1625,15 @@ for flac files:
 
 Note that setting numcopies to 0 is very unsafe.
 
+These settings are honored by git-annex whenever it's operating on a
+matching file. However, when using --all, --unused, or --key to specify
+keys to operate on, git-annex is operating on keys and not files, so will
+not honor the settings from .gitattributes.
+
+Also note that when using views, only the toplevel .gitattributes file is
+preserved in the view, so other settings in other files won't have any
+efffect.
+
 # FILES
 
 These files are used by git-annex: