remove dead nodes when loading the cluster log

This is to avoid inserting a cluster uuid into the location log when
only dead nodes in the cluster contain the content of a key.

One reason why this is necessary is Remote.keyLocations, which excludes
dead repositories from the list. But there are probably many more.

Implementing this was challenging, because Logs.Location importing
Logs.Cluster which imports Logs.Trust which imports Remote.List resulted
in an import cycle through several other modules.

Resorted to making Logs.Location not import Logs.Cluster, and instead
it assumes that Annex.clusters gets populated when necessary before it's
called.

That's done in Annex.Startup, which is run by the git-annex command
(but not other commands) at early startup in initialized repos. Or,
is run after initialization.

Note that is Remote.Git, it is unable to import Annex.Startup, because
Remote.Git importing Logs.Cluster leads the the same import cycle.
So ensureInitialized is not passed annexStartup in there.

Other commands, like git-annex-shell currently don't run annexStartup
either.

So there are cases where Logs.Location will not see clusters. So it won't add
any cluster UUIDs when loading the log. That's ok, the only reason to do
that is to make display of where objects are located include clusters,
and to make commands like git-annex get --from treat keys as being located
in a cluster. git-annex-shell certainly does not do anything like that,
and I'm pretty sure Remote.Git (and callers to Remote.Git.onLocalRepo)
don't either.

Command/Assistant.hs

@@ -17,6 +17,7 @@ import qualified BuildInfo
 import Utility.HumanTime
 import Assistant.Install
 import Remote.List
+import Annex.Startup
 
 import Control.Concurrent.Async
 
@@ -63,7 +64,7 @@ start o
 		stop
 	| otherwise = do
 		liftIO ensureInstalled
-		ensureInitialized remoteList
+		ensureInitialized startupAnnex remoteList
 		Command.Watch.start True (daemonOptions o) (startDelayOption o)
 
 startNoRepo :: AssistantOptions -> IO ()

Command/ConfigList.hs

@@ -16,6 +16,7 @@ import Git.Types
 import Remote.GCrypt (coreGCryptId)
 import qualified CmdLine.GitAnnexShell.Fields as Fields
 import CmdLine.GitAnnexShell.Checks
+import Annex.Startup
 
 cmd :: Command
 cmd = noCommit $ dontCheck repoExists $
@@ -47,7 +48,7 @@ findOrGenUUID = do
 		else ifM (Annex.Branch.hasSibling <||> (isJust <$> Fields.getField Fields.autoInit))
 			( do
 				liftIO checkNotReadOnly
-				initialize Nothing Nothing
+				initialize startupAnnex Nothing Nothing
 				getUUID
 			, return NoUUID
 			)

Command/Init.hs

@@ -12,6 +12,7 @@ module Command.Init where
 import Command
 import Annex.Init
 import Annex.Version
+import Annex.Startup
 import Types.RepoVersion
 import qualified Annex.SpecialRemote
 
@@ -77,7 +78,7 @@ perform os = do
 			Just v | v /= wantversion ->
 				giveup $ "This repository is already a initialized with version " ++ show (fromRepoVersion v) ++ ", not changing to requested version."
 			_ -> noop
-	initialize
+	initialize startupAnnex
 		(if null (initDesc os) then Nothing else Just (initDesc os))
 		(initVersion os)
 	unless (noAutoEnable os)

Command/Reinit.hs

@@ -10,6 +10,7 @@ module Command.Reinit where
 import Command
 import Annex.Init
 import Annex.UUID
+import Annex.Startup
 import qualified Remote
 import qualified Annex.SpecialRemote
 	
@@ -36,6 +37,6 @@ perform s = do
 		then return $ toUUID s
 		else Remote.nameToUUID s
 	storeUUID u
-	checkInitializeAllowed $ initialize' Nothing
+	checkInitializeAllowed $ initialize' startupAnnex Nothing
 	Annex.SpecialRemote.autoEnable
 	next $ return True

Command/Upgrade.hs

@@ -11,6 +11,7 @@ import Command
 import Upgrade
 import Annex.Version
 import Annex.Init
+import Annex.Startup
 
 cmd :: Command
 cmd = dontCheck
@@ -46,6 +47,6 @@ start (UpgradeOptions { autoOnly = True }) =
 start _ =
 	starting "upgrade" (ActionItemOther Nothing) (SeekInput []) $ do
 		whenM (isNothing <$> getVersion) $ do
-			initialize Nothing Nothing
+			initialize startupAnnex Nothing Nothing
 		r <- upgrade False latestVersion
 		next $ return r