Added GIT_ANNEX_VECTOR_CLOCK environment variable

Can be used to override the default timestamps used in log files in the
git-annex branch. This is a dangerous environment variable; use with
caution.

Note that this only affects writing to the logs on the git-annex branch.
It is not used for metadata in git commits (other env vars can be set for
that).

There are many other places where timestamps are still used, that don't
get committed to git, but do touch disk. Including regular timestamps
of files, and timestamps embedded in some files in .git/annex/, including
the last fsck timestamp and timestamps in transfer log files.

A good way to find such things in git-annex is to get for getPOSIXTime and
getCurrentTime, although some of the results are of course false positives
that never hit disk (unless git-annex gets swapped out..)

So this commit does NOT necessarily make git-annex comply with some HIPPA
privacy regulations; it's up to the user to determine if they can use it in
a way compliant with such regulations.

Benchmarking: It takes 0.00114 milliseconds to call getEnv
"GIT_ANNEX_VECTOR_CLOCK" when that env var is not set. So, 100 thousand log
files can be written with an added overhead of only 0.114 seconds. That
should be by far swamped by the actual overhead of writing the log files
and making the commit containing them.

This commit was supported by the NSF-funded DataLad project.

Logs/Transitions.hs

@@ -14,13 +14,13 @@
 
 module Logs.Transitions where
 
-import Data.Time.Clock.POSIX
-import qualified Data.Set as S
-
 import Annex.Common
+import Annex.VectorClock
 import Logs.TimeStamp
 import Logs.Line
 
+import qualified Data.Set as S
+
 transitionsLog :: FilePath
 transitionsLog = "transitions.log"
 
@@ -30,7 +30,7 @@ data Transition
 	deriving (Show, Ord, Eq, Read)
 
 data TransitionLine = TransitionLine
-	{ transitionStarted :: POSIXTime
+	{ transitionStarted :: VectorClock
 	, transition :: Transition
 	} deriving (Show, Ord, Eq)
 
@@ -43,8 +43,8 @@ describeTransition ForgetDeadRemotes = "forget dead remotes"
 noTransitions :: Transitions
 noTransitions = S.empty
 
-addTransition :: POSIXTime -> Transition -> Transitions -> Transitions
-addTransition ts t = S.insert $ TransitionLine ts t
+addTransition :: VectorClock -> Transition -> Transitions -> Transitions
+addTransition c t = S.insert $ TransitionLine c t
 
 showTransitions :: Transitions -> String
 showTransitions = unlines . map showTransitionLine . S.elems
@@ -67,7 +67,7 @@ showTransitionLine (TransitionLine ts t) = unwords [show t, show ts]
 
 parseTransitionLine :: String -> Maybe TransitionLine
 parseTransitionLine s = TransitionLine
-	<$> parsePOSIXTime ds
+	<$> (VectorClock <$> parsePOSIXTime ds)
 	<*> readish ts
   where
 	ws = words s