diff --git a/fix-imports.cabal b/fix-imports.cabal
--- a/fix-imports.cabal
+++ b/fix-imports.cabal
@@ -1,5 +1,5 @@
 name: fix-imports
-version: 1.0.1
+version: 1.0.2
 cabal-version: >= 1.6
 build-type: Simple
 synopsis: Program to manage the imports of a haskell module
@@ -13,7 +13,11 @@
     It's most convenient if bound to an editor key.
     .
     Recent major changes:
+    * version 1.0.2
     .
+    * Fix bug where a qualified import with >1 dot wasn't found.  And don't
+    mess with Prelude.
+    .
     * version 1.0.1
     .
     * Fix a bunch of bugs: properly recognize unqualified imports as imports,
@@ -53,5 +57,5 @@
     main-is: Main.hs
     hs-source-dirs: src
     build-depends: base >= 3 && < 5, containers, directory, filepath, process,
-        haskell-src-exts >= 1.11, uniplate, split, cpphs, text
+        haskell-src-exts >= 1.13.2, uniplate, split, cpphs, text
     ghc-options: -Wall -fno-warn-name-shadowing
diff --git a/src/Config.hs b/src/Config.hs
--- a/src/Config.hs
+++ b/src/Config.hs
@@ -15,7 +15,7 @@
 
 data Config = Config {
     -- | Additional directories to search for local modules.  Taken from the
-    -- -i flag.
+    -- -i flag and 'include' config line.
     configIncludes :: [FilePath]
     -- | Format the import block.
     , configShowImports :: [Types.ImportLine] -> String
@@ -25,9 +25,9 @@
         -> Maybe (Maybe Index.Package, Types.ModuleName)
     }
 
-config :: ImportOrder -> Priorities -> Config
-config order prios = Config
-    { configIncludes = []
+config :: [FilePath] -> ImportOrder -> Priorities -> Config
+config include order prios = Config
+    { configIncludes = include
     , configShowImports = formatGroups order
     , configPickModule = pickModule prios
     }
diff --git a/src/FixImports.hs b/src/FixImports.hs
--- a/src/FixImports.hs
+++ b/src/FixImports.hs
@@ -51,7 +51,9 @@
 import qualified Data.Set as Set
 
 import qualified Language.Haskell.Exts.Annotated as Haskell
+import qualified Language.Haskell.Exts.Extension as Extension
 import qualified Language.Preprocessor.Cpphs as Cpphs
+
 import qualified System.Console.GetOpt as GetOpt
 import qualified System.Directory as Directory
 import qualified System.Environment
@@ -75,8 +77,9 @@
     (modulePath, (verbose, includes)) <-
         parseArgs =<< System.Environment.getArgs
     text <- IO.getContents
-    fixed <- fixModule (config { Config.configIncludes = includes })
-            modulePath text
+    config <- return $ config
+        { Config.configIncludes = includes ++ Config.configIncludes config }
+    fixed <- fixModule config modulePath text
         `Exception.catch` (\(exc :: Exception.SomeException) ->
             return $ Left $ "exception: " ++ show exc)
     case fixed of
@@ -86,15 +89,14 @@
             System.Exit.exitFailure
         Right (Result text added removed) -> do
             IO.putStr text
-            when (verbose
-                    && (not (Set.null added) || not (Set.null removed))) $
-                IO.hPutStrLn IO.stderr $ "added: " ++ names added
-                    ++ "; removed: " ++ names removed
+            let names = Util.join ", " . map Types.moduleName . Set.toList
+                (addedMsg, removedMsg) = (names added, names removed)
+            when (verbose && (not (null addedMsg) || not (null removedMsg))) $
+                IO.hPutStrLn IO.stderr $ Util.join "; " $ filter (not . null)
+                    [ if null addedMsg then "" else "added: " ++ addedMsg
+                    , if null removedMsg then "" else "removed: " ++ removedMsg
+                    ]
             System.Exit.exitSuccess
-    where
-    names xs
-        | Set.null xs = "[]"
-        | otherwise = (Util.join ", " . map Types.moduleName . Set.toList) xs
 
 data Flag = Verbose | Include String
     deriving (Eq, Show)
@@ -141,6 +143,7 @@
     parse = Haskell.parseFileContentsWithComments $
         Haskell.defaultParseMode
             { Haskell.parseFilename = modulePath
+            , Haskell.extensions = Extension.haskell2010
             -- The meaning of Nothing is undocumented, but I think it means
             -- to not check for fixity ambiguity at all, which is what I want.
             , Haskell.fixities = Nothing
@@ -265,9 +268,10 @@
         then concat <$> mapM (findFiles (depth-1) file)
             (filter isModuleDir subdirs)
         else return []
-    return $ filter ((==file) . FilePath.takeFileName) fns ++ subfns
+    return $ filter sameSuffix fns ++ subfns
     where
     isModuleDir = all Char.isUpper . take 1 . FilePath.takeFileName
+    sameSuffix fn = fn == file || ('/' : file) `List.isSuffixOf` fn
 
 
 -- * figure out existing imports
@@ -305,18 +309,20 @@
 importInfo :: Types.Module -> [Haskell.Comment]
     -> (Set.Set Types.Qualification, Set.Set Types.ModuleName,
         [(Types.ImportDecl, [Types.Comment])], (Int, Int))
-    -- ^ (missingImports, removedModules, moduleToImport, rangeOfImportBlock).
-importInfo mod cmts = (missing, removed, declCmts, range)
+    -- ^ (missingImports, unusedImports, unchangedImports, rangeOfImportBlock).
+importInfo mod cmts = (missing, unused, declCmts, range)
     where
-    removed = Set.difference (Set.fromList modules)
+    unused = Set.difference (Set.fromList modules)
         (Set.fromList (map (Types.importDeclModule . fst) declCmts))
     missing = Set.difference used imported
-    imported = Set.fromList quals
+    -- If the Prelude isn't explicitly imported, it's implicitly imported, so
+    -- if I see Prelude.x it doesn't mean to add an import.
+    imported = Set.fromList $ prelude : qualifiedImports
 
     -- Get from the qualified import name back to the actual module name so
     -- I can return that.
     modules = map Types.importDeclModule imports
-    quals = map Types.importDeclQualification imports
+    qualifiedImports = map Types.importDeclQualification imports
     used = Set.fromList (moduleQNames mod)
     imports = moduleImportDecls mod
     declCmts =
@@ -325,8 +331,13 @@
         , keepImport decl
         ]
     -- Keep unqualified imports, but only keep qualified ones if they are used.
-    keepImport decl = Set.member (Types.importDeclQualification decl) used
+    -- Prelude is considered always used if it appears, because removing it
+    -- changes import behavour.
+    keepImport decl =
+        Set.member (Types.importDeclQualification decl)
+            (Set.insert prelude used)
         || not (Haskell.importQualified decl)
+    prelude = Types.Qualification "Prelude"
     range = importRange mod
 
 filterImportCmts :: (Int, Int) -> [Haskell.Comment] -> [Haskell.Comment]
diff --git a/src/Main.hs b/src/Main.hs
--- a/src/Main.hs
+++ b/src/Main.hs
@@ -20,21 +20,26 @@
 
 main :: IO ()
 main = do
-    let deflt = (Config.ImportOrder [], Config.defaultPriorities, [])
-    (order, prios, warns) <- fmap (maybe deflt parse) $
+    let deflt = ([], Config.ImportOrder [], Config.defaultPriorities, [])
+    (include, order, prios, warns) <- fmap (maybe deflt parse) $
         Util.catchENOENT $ Text.IO.readFile ".fix-imports"
     unless (null warns) $
         IO.hPutStrLn IO.stderr $
             "warnings unrecognized fields in .fix-imports: "
             ++ List.intercalate ", " warns
-    FixImports.runMain (Config.config order prios)
+    FixImports.runMain (Config.config include order prios)
 
-parse :: Text.Text -> (Config.ImportOrder, Config.Priorities, [String])
-parse text = (order, prios, extra)
+parse :: Text.Text
+    -> ([FilePath], Config.ImportOrder, Config.Priorities, [String])
+parse text = (include, order, prios, extra)
     where
     extra = Map.keys config List.\\ valid
-    valid = ["import-order", "prio-package-high", "prio-package-low",
-        "prio-module-high", "prio-module-low"]
+    valid =
+        [ "include", "import-order"
+        , "prio-package-high", "prio-package-low"
+        , "prio-module-high", "prio-module-low"
+        ]
+    include = get "include"
     order = Config.ImportOrder (getModules "import-order")
     prios = Config.Priorities (get "prio-package-high", get "prio-package-low")
         (getModules "prio-module-high", getModules "prio-module-low")