diff --git a/cabal-install/src/Distribution/Client/CmdClean.hs b/cabal-install/src/Distribution/Client/CmdClean.hs
index 956552b3f06..aea3661e6e2 100644
--- a/cabal-install/src/Distribution/Client/CmdClean.hs
+++ b/cabal-install/src/Distribution/Client/CmdClean.hs
@@ -8,6 +8,8 @@ import Distribution.Client.DistDirLayout
     ( DistDirLayout(..), defaultDistDirLayout )
 import Distribution.Client.ProjectConfig
     ( findProjectRoot )
+import Distribution.Client.ScriptUtils
+    ( getScriptCacheDirectoryRoot )
 import Distribution.Client.Setup
     ( GlobalFlags )
 import Distribution.ReadE ( succeedReadE )
@@ -22,9 +24,14 @@ import Distribution.Simple.Utils
 import Distribution.Verbosity
     ( normal )
 
+import Control.Monad
+    ( forM, forM_, mapM )
+import qualified Data.Set as Set
 import System.Directory
     ( removeDirectoryRecursive, removeFile
-    , doesDirectoryExist, getDirectoryContents )
+    , doesDirectoryExist, doesFileExist
+    , getDirectoryContents, listDirectory
+    , canonicalizePath )
 import System.FilePath
     ( (</>) )
 
@@ -80,16 +87,18 @@ cleanAction CleanFlags{..} extraArgs _ = do
         mdistDirectory = flagToMaybe cleanDistDir
         mprojectFile   = flagToMaybe cleanProjectFile
 
-    unless (null extraArgs) $
-        die' verbosity $ "'clean' doesn't take any extra arguments: "
-                         ++ unwords extraArgs
+    -- assume all files passed are the names of scripts
+    notScripts <- filterM (fmap not . doesFileExist) extraArgs
+    unless (null notScripts) $
+        die' verbosity $ "'clean' extra arguments should be script files: "
+                         ++ unwords notScripts
 
-    projectRoot <- either throwIO return =<< findProjectRoot Nothing mprojectFile
+    if null extraArgs then do
+        projectRoot <- either throwIO return =<< findProjectRoot Nothing mprojectFile
 
-    let distLayout = defaultDistDirLayout projectRoot mdistDirectory
+        let distLayout = defaultDistDirLayout projectRoot mdistDirectory
 
-    if saveConfig
-        then do
+        if saveConfig then do
             let buildRoot = distBuildRootDirectory distLayout
 
             buildRootExists <- doesDirectoryExist buildRoot
@@ -103,7 +112,20 @@ cleanAction CleanFlags{..} extraArgs _ = do
             info verbosity ("Deleting dist-newstyle (" ++ distRoot ++ ")")
             handleDoesNotExist () $ removeDirectoryRecursive distRoot
 
-    removeEnvFiles (distProjectRootDirectory distLayout)
+        removeEnvFiles (distProjectRootDirectory distLayout)
+    else do
+        -- when cleaning script builds, also clean orphaned caches
+        toClean  <- Set.fromList <$> mapM canonicalizePath extraArgs
+        cacheDir <- getScriptCacheDirectoryRoot
+        caches   <- listDirectory cacheDir
+        paths    <- fmap concat . forM caches $ \cache -> do
+            let locFile = cacheDir </> cache </> "scriptlocation"
+            exists <- doesFileExist locFile
+            if exists then pure . (,) (cacheDir </> cache) <$> readFile locFile else return []
+        forM_ paths $ \(cache, script) -> do
+            exists <- doesFileExist script
+            unless (exists && script `Set.notMember` toClean) $ do
+                removeDirectoryRecursive cache
 
 removeEnvFiles :: FilePath -> IO ()
 removeEnvFiles dir =
diff --git a/cabal-install/src/Distribution/Client/ScriptUtils.hs b/cabal-install/src/Distribution/Client/ScriptUtils.hs
index 153c8f922f5..42e00a605d2 100644
--- a/cabal-install/src/Distribution/Client/ScriptUtils.hs
+++ b/cabal-install/src/Distribution/Client/ScriptUtils.hs
@@ -6,7 +6,7 @@
 -- | Utilities to help commands with scripts
 --
 module Distribution.Client.ScriptUtils (
-    getScriptCacheDirectory,
+    getScriptCacheDirectoryRoot, getScriptCacheDirectory,
     withTempTempDirectory,
     getContextAndSelectorsWithScripts
   ) where
@@ -65,25 +65,37 @@ import Distribution.Types.PackageName.Magic
          ( fakePackageId )
 import Language.Haskell.Extension
          ( Language(..) )
+import Distribution.Client.HashValue
+         ( hashValue, showHashValue )
 
 import Control.Exception
-        ( bracket )
+         ( bracket )
 import qualified Data.ByteString.Char8 as BS
+import Data.ByteString.Lazy ()
 import qualified Text.Parsec as P
 import System.Directory
-         ( getTemporaryDirectory, removeDirectoryRecursive, doesFileExist, makeAbsolute )
+         ( getTemporaryDirectory, removeDirectoryRecursive, doesFileExist, canonicalizePath )
 import System.FilePath
          ( (</>), takeExtension )
 
+
+-- | Get the directory where script builds are cached.
+--
+-- <cabal_dir>/script-builds
+getScriptCacheDirectoryRoot :: IO FilePath
+getScriptCacheDirectoryRoot = do
+    cabalDir <- getCabalDir
+    return $ cabalDir </> "script-builds"
+
 -- | Get the directory for caching a script build.
 --
 -- The only identity of a script is it's absolute path, so append that path
 -- to <cabal_dir>/script-builds/ to get the cache directory.
 getScriptCacheDirectory :: FilePath -> IO FilePath
 getScriptCacheDirectory script = do
-    scriptAbs <- dropWhile (\c -> c == '/' || c == '\\') <$> makeAbsolute script
-    cabalDir <- getCabalDir
-    return $ cabalDir </> "script-builds" </> scriptAbs
+    cacheDir <- getScriptCacheDirectoryRoot
+    scriptHash <- showHashValue . hashValue . fromString <$> canonicalizePath script
+    return $ cacheDir </> scriptHash
 
 -- | Create a new temporary directory inside the directory for temporary files
 -- and delete it after use.
@@ -117,7 +129,7 @@ getContextAndSelectorsWithScripts flags@NixStyleFlags {..} targetStrings globalF
           then do
             cacheDir <- getScriptCacheDirectory script
             ctx <- withProjectOrGlobalConfig verbosity ignoreProject globalConfigFlag with (without cacheDir)
-            BS.readFile script >>= handleScriptCase verbosity pol ctx cacheDir
+            BS.readFile script >>= handleScriptCase verbosity pol ctx cacheDir script
           else reportTargetSelectorProblems verbosity err
 
     -- We pass the baseCtx made with tmpDir to readTargetSelectors and only create a ctx with cacheDir
@@ -206,9 +218,10 @@ handleScriptCase
   -> PlainOrLiterate
   -> ProjectBaseContext
   -> FilePath
+  -> FilePath
   -> BS.ByteString
   -> IO (ProjectBaseContext, [TargetSelector])
-handleScriptCase verbosity pol baseCtx dir scriptContents = do
+handleScriptCase verbosity pol baseCtx dir scriptPath scriptContents = do
   (executable, contents') <- readScriptBlockFromScript verbosity pol scriptContents
 
   -- We need to create a dummy package that lives in our dummy project.
@@ -245,6 +258,7 @@ handleScriptCase verbosity pol baseCtx dir scriptContents = do
     pkgId = fakePackageId
 
   writeGenericPackageDescription (dir </> "fake-package.cabal") genericPackageDescription
+  writeFile (dir </> "scriptlocation") =<< canonicalizePath scriptPath
   BS.writeFile (dir </> mainName) contents'
 
   let