diff --git a/CHANGELOG b/CHANGELOG
index e58c6eedaf..0c5b6db83b 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,5 +1,8 @@
 git-annex (6.20160512) UNRELEASED; urgency=medium
 
+  * Split lines in the git-annex branch on \r as well as \n, to deal
+    with \r\n terminated lines written by some versions of git-annex on
+    Windows. This fixes strange displays in some cases.
   * Change git annex info remote encryption description to use wording
     closer to what's used in initremote.
   * webapp: Avoid confusing display of dead remotes.
diff --git a/COPYRIGHT b/COPYRIGHT
index 6620962b6b..119bbf6c61 100644
--- a/COPYRIGHT
+++ b/COPYRIGHT
@@ -95,6 +95,38 @@ License: MIT-twitter
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
 
+Files: Logs/Line.hs
+Copyright: 2001, The University Court of the University of Glasgow.
+License: other
+  All rights reserved.
+  .
+  Redistribution and use in source and binary forms, with or without
+  modification, are permitted provided that the following conditions are met:
+  .
+  - Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+  .
+  - Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+  .
+  - Neither name of the University nor the names of its contributors may be
+  used to endorse or promote products derived from this software without
+  specific prior written permission.
+  .
+  THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY COURT OF THE UNIVERSITY OF
+  GLASGOW AND THE CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+  INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+  UNIVERSITY COURT OF THE UNIVERSITY OF GLASGOW OR THE CONTRIBUTORS BE LIABLE
+  FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+  DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+  CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+  LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+  OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+  DAMAGE.
+
 License: GPL-3+
  The full text of version 3 of the GPL is distributed as doc/license/GPL in
  this package's source, or in /usr/share/common-licenses/GPL-3 on
diff --git a/Logs/Line.hs b/Logs/Line.hs
new file mode 100644
index 0000000000..a7e17190e2
--- /dev/null
+++ b/Logs/Line.hs
@@ -0,0 +1,51 @@
+{- 
+
+The Glasgow Haskell Compiler License
+
+Copyright 2001, The University Court of the University of Glasgow.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+- Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+- Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+- Neither name of the University nor the names of its contributors may be
+used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY COURT OF THE UNIVERSITY OF
+GLASGOW AND THE CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+UNIVERSITY COURT OF THE UNIVERSITY OF GLASGOW OR THE CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+-}
+
+module Logs.Line where
+
+-- This is the same as Data.List.lines, with \r added.
+-- This works around some versions of git-annex which wrote \r
+-- into git-annex branch files on Windows. Those \r's sometimes
+-- accumulated over time, so a single line could end with multiple \r's
+-- before the \n.
+splitLines :: String -> [String]
+splitLines "" =  []
+splitLines s =  cons (case break (\c -> c == '\n' || c == '\r') s of
+	(l, s') -> (l, case s' of
+		[]      -> []
+		_:s''   -> splitLines s''))
+  where
+	cons ~(h, t) = h : t
diff --git a/Logs/MapLog.hs b/Logs/MapLog.hs
index d5bb67f686..097439ac58 100644
--- a/Logs/MapLog.hs
+++ b/Logs/MapLog.hs
@@ -18,6 +18,7 @@ import Data.Time.Clock.POSIX
 
 import Common
 import Logs.TimeStamp
+import Logs.Line
 
 data TimeStamp = Unknown | Date POSIXTime
 	deriving (Eq, Ord, Show)
@@ -38,7 +39,7 @@ showMapLog fieldshower valueshower = unlines . map showpair . M.toList
 		unwords ["0", fieldshower f, valueshower v]
 
 parseMapLog :: Ord f => (String -> Maybe f) -> (String -> Maybe v) -> String -> MapLog f v
-parseMapLog fieldparser valueparser = M.fromListWith best . mapMaybe parse . lines
+parseMapLog fieldparser valueparser = M.fromListWith best . mapMaybe parse . splitLines
   where
 	parse line = do
 		let (ts, rest) = splitword line
diff --git a/Logs/Presence/Pure.hs b/Logs/Presence/Pure.hs
index e2ec3f13d3..7955c8da31 100644
--- a/Logs/Presence/Pure.hs
+++ b/Logs/Presence/Pure.hs
@@ -12,6 +12,7 @@ import qualified Data.Map as M
 
 import Annex.Common
 import Logs.TimeStamp
+import Logs.Line
 import Utility.QuickCheck
 
 data LogLine = LogLine {
@@ -25,7 +26,7 @@ data LogStatus = InfoPresent | InfoMissing | InfoDead
 
 {- Parses a log file. Unparseable lines are ignored. -}
 parseLog :: String -> [LogLine]
-parseLog = mapMaybe parseline . lines
+parseLog = mapMaybe parseline . splitLines
   where
 	parseline l = LogLine
 		<$> parsePOSIXTime d
diff --git a/Logs/SingleValue.hs b/Logs/SingleValue.hs
index 9b1306c985..201e205eb2 100644
--- a/Logs/SingleValue.hs
+++ b/Logs/SingleValue.hs
@@ -16,6 +16,7 @@ module Logs.SingleValue where
 import Annex.Common
 import qualified Annex.Branch
 import Logs.TimeStamp
+import Logs.Line
 
 import qualified Data.Set as S
 import Data.Time.Clock.POSIX
@@ -37,7 +38,7 @@ showLog = unlines . map showline . S.toList
 	showline (LogEntry t v) = unwords [show t, serialize v]
 
 parseLog :: (Ord v, SingleValueSerializable v) => String -> Log v
-parseLog = S.fromList . mapMaybe parse . lines
+parseLog = S.fromList . mapMaybe parse . splitLines
   where
 	parse line = do
 		let (ts, s) = splitword line
diff --git a/Logs/Transitions.hs b/Logs/Transitions.hs
index 5440047688..07667c4074 100644
--- a/Logs/Transitions.hs
+++ b/Logs/Transitions.hs
@@ -19,6 +19,7 @@ import qualified Data.Set as S
 
 import Annex.Common
 import Logs.TimeStamp
+import Logs.Line
 
 transitionsLog :: FilePath
 transitionsLog = "transitions.log"
@@ -50,7 +51,7 @@ showTransitions = unlines . map showTransitionLine . S.elems
 
 {- If the log contains new transitions we don't support, returns Nothing. -}
 parseTransitions :: String -> Maybe Transitions
-parseTransitions = check . map parseTransitionLine . lines
+parseTransitions = check . map parseTransitionLine . splitLines
   where
 	check l
 		| all isJust l = Just $ S.fromList $ catMaybes l
diff --git a/Logs/UUIDBased.hs b/Logs/UUIDBased.hs
index 5613c6fb41..97ecd10113 100644
--- a/Logs/UUIDBased.hs
+++ b/Logs/UUIDBased.hs
@@ -35,6 +35,7 @@ import Common
 import Types.UUID
 import Logs.MapLog
 import Logs.TimeStamp
+import Logs.Line
 
 type Log v = MapLog UUID v
 
@@ -50,7 +51,7 @@ parseLog :: (String -> Maybe a) -> String -> Log a
 parseLog = parseLogWithUUID . const
 
 parseLogWithUUID :: (UUID -> String -> Maybe a) -> String -> Log a
-parseLogWithUUID parser = M.fromListWith best . mapMaybe parse . lines
+parseLogWithUUID parser = M.fromListWith best . mapMaybe parse . splitLines
   where
 	parse line
 		-- This is a workaround for a bug that caused
diff --git a/doc/bugs/Whereis_reports_same_UUID_multiple_times/comment_5_2355fd90d4ff8dd440bf11348a8daa73._comment b/doc/bugs/Whereis_reports_same_UUID_multiple_times/comment_5_2355fd90d4ff8dd440bf11348a8daa73._comment
new file mode 100644
index 0000000000..5ae6c2b1f4
--- /dev/null
+++ b/doc/bugs/Whereis_reports_same_UUID_multiple_times/comment_5_2355fd90d4ff8dd440bf11348a8daa73._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 5"""
+ date="2016-05-27T15:40:16Z"
+ content="""
+I've developed a patch which yields a good whereis display in this repo.
+
+Still remains to be seen if there's some code path that currently causes
+'\r' to get added in the current version of git-annex on Windows.
+"""]]