diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
index cca24ac..652fce6 100644
--- a/.buildkite/pipeline.yml
+++ b/.buildkite/pipeline.yml
@@ -28,7 +28,7 @@ steps:
     artifact_paths:
       - "result/bin/*"
 
-  - command: nix run -f ci.nix xrefcheck-static -c xrefcheck --ignored 'tests/**/*'
+  - command: nix run -f ci.nix xrefcheck-static -c xrefcheck --ignored 'tests/markdowns/**/*' --ignored 'tests/golden/**/*'
     label: Xrefcheck itself
 
   - label: lint
diff --git a/CHANGES.md b/CHANGES.md
index 3c802db..b4cac2b 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -25,6 +25,10 @@ Unreleased
     as broken (with message `Link targets a local file outside repository`).
     Same for links that are using directories outside repository (e.g. `/../repo/a.md`),
     since such things are not supported by GitHub markdown renderer.
+* [#174](https://github.com/serokell/xrefcheck/pull/174)
+  + Make xrefcheck only scan files that are tracked by git.
+  + Fixed bug where links to ignored files were valid.
+  + Fixed bug where links with trailing slashes were invalid.
 
 0.2.1
 ==========
diff --git a/README.md b/README.md
index 7cfb98e..12b6da3 100644
--- a/README.md
+++ b/README.md
@@ -47,6 +47,10 @@ Both relative and absolute local links are supported out of the box.
 
 At the moment of writing, the listed solutions don't support ftp/ftps links.
 
+## Dependencies [↑](#xrefcheck)
+
+Xrefcheck requires you to have `git` version 2.18.0 or later in your PATH.
+
 ## Usage [↑](#xrefcheck)
 
 We provide the following ways for you to use xrefcheck:
diff --git a/package.yaml b/package.yaml
index cd2dfde..08d588e 100644
--- a/package.yaml
+++ b/package.yaml
@@ -82,7 +82,6 @@ library:
     - containers
     - cmark-gfm >= 0.2.5
     - data-default
-    - directory-tree
     - directory
     - dlist
     - exceptions
@@ -99,6 +98,7 @@ library:
     - mtl
     - o-clock
     - optparse-applicative
+    - process
     - regex-tdfa
     - req
     - tagsoup
diff --git a/src/Xrefcheck/Config/Default.hs b/src/Xrefcheck/Config/Default.hs
index 8f40464..4d14cf6 100644
--- a/src/Xrefcheck/Config/Default.hs
+++ b/src/Xrefcheck/Config/Default.hs
@@ -17,12 +17,7 @@ defConfigUnfilled =
 traversal:
   # Glob patterns describing files which we pretend do not exist
   # (so they are neither analyzed nor can be referenced).
-  ignored:
-    # Git files
-    - .git/**/*
-
-    # Stack files
-    - .stack-work/**/*
+  ignored: []
 
 # Verification parameters.
 verification:
diff --git a/src/Xrefcheck/Core.hs b/src/Xrefcheck/Core.hs
index c385b03..3c61828 100644
--- a/src/Xrefcheck/Core.hs
+++ b/src/Xrefcheck/Core.hs
@@ -122,8 +122,13 @@ makeLenses ''FileInfo
 instance Default FileInfo where
   def = diffToFileInfo mempty
 
-newtype RepoInfo = RepoInfo (Map FilePath FileInfo)
-  deriving stock (Show)
+-- | All tracked files and directories.
+data RepoInfo = RepoInfo
+ { riFiles       :: Map FilePath (Maybe FileInfo)
+   -- ^ Files from the repo with `FileInfo` attached to files that we can scan.
+ , riDirectories :: Set FilePath
+   -- ^ Tracked directories.
+ } deriving stock (Show)
 
 -----------------------------------------------------------
 -- Instances
@@ -171,7 +176,8 @@ instance Given ColorMode => Buildable FileInfo where
     ]
 
 instance Given ColorMode => Buildable RepoInfo where
-  build (RepoInfo m) = blockListF' "⮚" buildFileReport (M.toList m)
+  build (RepoInfo m _) =
+    blockListF' "⮚" buildFileReport (mapMaybe sequence $ M.toList m)
     where
       buildFileReport (name, info) = mconcat
         [ colorIfNeeded Cyan $ fromString name <> ":\n"
diff --git a/src/Xrefcheck/Scan.hs b/src/Xrefcheck/Scan.hs
index 4e23dec..9a6e372 100644
--- a/src/Xrefcheck/Scan.hs
+++ b/src/Xrefcheck/Scan.hs
@@ -24,13 +24,14 @@ module Xrefcheck.Scan
 import Universum
 
 import Data.Aeson (FromJSON (..), genericParseJSON)
-import Data.Foldable qualified as F
+import Data.List qualified as L
 import Data.Map qualified as M
 import Data.Reflection (Given)
 import Fmt (Buildable (..), nameF, (+|), (|+))
 import System.Directory (doesDirectoryExist)
-import System.Directory.Tree qualified as Tree
-import System.FilePath (dropTrailingPathSeparator, equalFilePath, takeDirectory, takeExtension)
+import System.FilePath
+  (dropTrailingPathSeparator, equalFilePath, splitDirectories, takeDirectory, takeExtension, (</>))
+import System.Process (cwd, readCreateProcess, shell)
 
 import Xrefcheck.Core
 import Xrefcheck.Progress
@@ -107,6 +108,31 @@ specificFormatsSupport formats = \ext -> M.lookup ext formatsMap
         , extension <- extensions
         ]
 
+-- | Process files that are tracked by git and not ignored by the config.
+readDirectoryWith
+  :: forall a. TraversalConfig
+  -> (FilePath -> IO a)
+  -> FilePath
+  -> IO [(FilePath, a)]
+readDirectoryWith config scanner root =
+  traverse scanFile
+  . filter (not . isIgnored)
+  . fmap (location </>)
+  . L.lines =<< readCreateProcess (shell "git ls-files"){cwd = Just root} ""
+  where
+    scanFile :: FilePath -> IO (FilePath, a)
+    scanFile = sequence . (normaliseWithNoTrailing &&& scanner)
+
+    isIgnored :: FilePath -> Bool
+    isIgnored = matchesGlobPatterns root $ tcIgnored config
+
+    -- Strip leading "." and trailing "/"
+    location :: FilePath
+    location =
+      if root `equalFilePath` "."
+        then ""
+        else dropTrailingPathSeparator root
+
 scanRepo
   :: MonadIO m
   => Rewrite -> FormatsSupport -> TraversalConfig -> FilePath -> m ScanResult
@@ -116,36 +142,33 @@ scanRepo rw formatsSupport config root = do
   when (not $ isDirectory root) $
     die $ "Repository's root does not seem to be a directory: " <> root
 
-  _ Tree.:/ repoTree <- liftIO $ Tree.readDirectoryWithL processFile root
-  let (errs, fileInfos) = gatherScanErrs &&& gatherFileInfos
-        $ dropSndMaybes . F.toList
-        $ Tree.zipPaths $ location Tree.:/ repoTree
-  return . ScanResult errs $ RepoInfo (M.fromList fileInfos)
-  where
-    isDirectory = readingSystem . doesDirectoryExist
-    gatherScanErrs = foldMap (snd . snd)
-    gatherFileInfos = map (bimap normaliseWithNoTrailing fst)
+  (errs, fileInfos) <- liftIO
+    $ (gatherScanErrs &&& gatherFileInfos)
+    <$> readDirectoryWith config processFile root
 
+  let dirs = fromList $ foldMap (getDirs . fst) fileInfos
+
+  return . ScanResult errs $ RepoInfo (M.fromList fileInfos) dirs
+  where
+    isDirectory :: FilePath -> Bool
+    isDirectory = readingSystem . doesDirectoryExist
+
+    -- Get all directories from filepath.
+    getDirs :: FilePath -> [FilePath]
+    getDirs = scanl (</>) "" . splitDirectories . takeDirectory
+
+    gatherScanErrs
+      :: [(FilePath, Maybe (FileInfo, [ScanError]))]
+      -> [ScanError]
+    gatherScanErrs = fold . mapMaybe (fmap snd . snd)
+
+    gatherFileInfos
+      :: [(FilePath, Maybe (FileInfo, [ScanError]))]
+      -> [(FilePath, Maybe FileInfo)]
+    gatherFileInfos = map (second (fmap fst))
+
+    processFile :: FilePath -> IO $ Maybe (FileInfo, [ScanError])
     processFile file = do
       let ext = takeExtension file
       let mscanner = formatsSupport ext
-      if isIgnored file
-        then pure Nothing
-        else forM mscanner ($ file)
-    dropSndMaybes l = [(a, b) | (a, Just b) <- l]
-
-    isIgnored = matchesGlobPatterns root $ tcIgnored config
-
-    -- The context location of the root.
-    -- This is done by removing the last component from the path.
-    -- > root = "./folder/file.md"       ==> location = "./folder"
-    -- > root = "./folder/subfolder"     ==> location = "./folder"
-    -- > root = "./folder/subfolder/"    ==> location = "./folder"
-    -- > root = "./folder/subfolder/./"  ==> location = "./folder/subfolder"
-    -- > root = "."                      ==> location = ""
-    -- > root = "/absolute/path"         ==> location = "/absolute"
-    -- > root = "/"                      ==> location = "/"
-    location =
-      if root `equalFilePath` "."
-        then ""
-        else takeDirectory $ dropTrailingPathSeparator root
+      forM mscanner ($ file)
diff --git a/src/Xrefcheck/Verify.hs b/src/Xrefcheck/Verify.hs
index e8f8aaa..67271de 100644
--- a/src/Xrefcheck/Verify.hs
+++ b/src/Xrefcheck/Verify.hs
@@ -57,8 +57,8 @@ import Network.HTTP.Req
   HttpMethod, NoReqBody (..), defaultHttpConfig, ignoreResponse, req, runReq, useURI)
 import Network.HTTP.Types.Header (hRetryAfter)
 import Network.HTTP.Types.Status (Status, statusCode, statusMessage)
-import System.Directory (doesDirectoryExist, doesFileExist)
-import System.FilePath (makeRelative, normalise, splitDirectories, takeDirectory, (</>))
+import System.FilePath
+  (equalFilePath, joinPath, makeRelative, normalise, splitDirectories, takeDirectory, (</>))
 import Text.ParserCombinators.ReadPrec qualified as ReadPrec (lift)
 import Text.Regex.TDFA.Text (Regex, regexec)
 import Text.URI (Authority (..), ParseExceptionBs, URI (..), mkURIBs)
@@ -260,13 +260,16 @@ verifyRepo
   config@VerifyConfig{..}
   mode
   root
-  repoInfo'@(RepoInfo repoInfo)
+  repoInfo'@(RepoInfo files _)
     = do
   let toScan = do
-        (file, fileInfo) <- M.toList repoInfo
+        (file, fileInfo) <- M.toList files
         guard . not $ matchesGlobPatterns root vcNotScanned file
-        ref <- _fiReferences fileInfo
-        return (file, ref)
+        case fileInfo of
+          Just fi -> do
+            ref <- _fiReferences fi
+            return (file, ref)
+          Nothing -> empty -- no support for such file, can do nothing
 
   progressRef <- newIORef $ initVerifyProgress (map snd toScan)
 
@@ -312,7 +315,7 @@ verifyReference
   config@VerifyConfig{..}
   mode
   progressRef
-  (RepoInfo repoInfo)
+  (RepoInfo files dirs)
   root
   fileWithReference
   ref@Reference{..}
@@ -417,11 +420,30 @@ verifyReference
       unless (isVirtual referredFile) do
         checkReferredFileIsInsideRepo referredFile
         checkReferredFileExists referredFile
-        case M.lookup referredFile repoInfo of
+        case lookupFilePath referredFile $ M.toList files of
           Nothing -> pass  -- no support for such file, can do nothing
           Just referredFileInfo -> whenJust mAnchor $
             checkAnchor referredFile (_fiAnchors referredFileInfo)
 
+    lookupFilePath :: FilePath -> [(FilePath, Maybe FileInfo)] -> Maybe FileInfo
+    lookupFilePath fp = snd <=< find (equalFilePath (expandIndirections fp) . fst)
+
+    -- expands ".." and "."
+    -- expandIndirections "a/b/../c"      = "a/c"
+    -- expandIndirections "a/b/c/../../d" = "a/d"
+    -- expandIndirections "../../a"       = "../../a"
+    -- expandIndirections "a/./b"         = "a/b"
+    -- expandIndirections "a/b/./../c"    = "a/c"
+    expandIndirections :: FilePath -> FilePath
+    expandIndirections = joinPath . reverse . expand 0 . reverse . splitDirectories
+      where
+        expand :: Int -> [FilePath] -> [FilePath]
+        expand acc ("..":xs) = expand (acc+1) xs
+        expand acc (".":xs)  = expand acc xs
+        expand 0 (x:xs)      = x : expand 0 xs
+        expand acc (_:xs)    = expand (acc-1) xs
+        expand acc []        = replicate acc ".."
+
     checkReferredFileIsInsideRepo file = unless
       (noNegativeNesting $ makeRelative root file) $
         throwError (LocalFileOutsideRepo file)
@@ -439,11 +461,17 @@ verifyReference
         nestingChange _ = 1
 
     checkReferredFileExists file = do
-      let fileExists = readingSystem $ doesFileExist file
-      let dirExists = readingSystem $ doesDirectoryExist file
-
       unless (fileExists || dirExists) $
         throwError (LocalFileDoesNotExist file)
+      where
+        matchesFilePath :: FilePath -> Bool
+        matchesFilePath = equalFilePath $ expandIndirections file
+
+        fileExists :: Bool
+        fileExists = any matchesFilePath $ M.keys files
+
+        dirExists :: Bool
+        dirExists = any matchesFilePath dirs
 
     checkAnchor file fileAnchors anchor = do
       checkAnchorReferenceAmbiguity file fileAnchors anchor
diff --git a/tests/Test/Xrefcheck/TooManyRequestsSpec.hs b/tests/Test/Xrefcheck/TooManyRequestsSpec.hs
index ea68dac..c57e827 100644
--- a/tests/Test/Xrefcheck/TooManyRequestsSpec.hs
+++ b/tests/Test/Xrefcheck/TooManyRequestsSpec.hs
@@ -198,7 +198,7 @@ test_tooManyRequests = testGroup "429 response tests"
     verifyReferenceWithProgress reference progRef = do
       fmap wrlItem <$> verifyReference
         ((cVerification $ defConfig GitHub) { vcIgnoreRefs = [] }) FullMode
-        progRef (RepoInfo M.empty) "." "" reference
+        progRef (RepoInfo M.empty mempty) "." "" reference
 
     -- | When called for the first time, returns with a 429 and `Retry-After: @retryAfter@`.
     -- Subsequent calls will respond with @status@.
diff --git a/tests/Test/Xrefcheck/TrailingSlashSpec.hs b/tests/Test/Xrefcheck/TrailingSlashSpec.hs
index 267c9f8..c56ae39 100644
--- a/tests/Test/Xrefcheck/TrailingSlashSpec.hs
+++ b/tests/Test/Xrefcheck/TrailingSlashSpec.hs
@@ -26,7 +26,7 @@ test_slash = testGroup "Trailing forward slash detection" $
     testCase ("All the files within the root \"" <>
       root <>
       "\" should exist") $ do
-        (ScanResult _ (RepoInfo repoInfo)) <- allowRewrite False $ \rw ->
+        (ScanResult _ (RepoInfo repoInfo _)) <- allowRewrite False $ \rw ->
           scanRepo rw format TraversalConfig{ tcIgnored = [] } root
         nonExistentFiles <- lefts <$> forM (keys repoInfo) (\filePath -> do
           predicate <- doesFileExist filePath
diff --git a/tests/configs/github-config.yaml b/tests/configs/github-config.yaml
index 6276020..9714dd4 100644
--- a/tests/configs/github-config.yaml
+++ b/tests/configs/github-config.yaml
@@ -2,12 +2,7 @@
 traversal:
   # Glob patterns describing files which we pretend do not exist
   # (so they are neither analyzed nor can be referenced).
-  ignored:
-    # Git files
-    - .git/**/*
-
-    # Stack files
-    - .stack-work/**/*
+  ignored: []
 
 # Verification parameters.
 verification:
diff --git a/tests/golden/check-git/check-git.bats b/tests/golden/check-git/check-git.bats
new file mode 100644
index 0000000..34a6633
--- /dev/null
+++ b/tests/golden/check-git/check-git.bats
@@ -0,0 +1,58 @@
+#!/usr/bin/env bats
+
+# SPDX-FileCopyrightText: 2022 Serokell <https://serokell.io>
+#
+# SPDX-License-Identifier: MPL-2.0
+
+load '../helpers/bats-support/load'
+load '../helpers/bats-assert/load'
+load '../helpers/bats-file/load'
+load '../helpers'
+
+@test "Git: not a repo" {
+  cd $TEST_TEMP_DIR
+
+  run xrefcheck
+
+  assert_output --partial "fatal: not a git repository"
+}
+
+@test "Git: file not tracked" {
+  cd $TEST_TEMP_DIR
+
+  git init
+
+  echo "[a](/a.md)" >> "git.md"
+
+  run xrefcheck
+
+  assert_output --partial "All repository links are valid."
+}
+
+@test "Git: file tracked, check failure" {
+  cd $TEST_TEMP_DIR
+
+  git init
+
+  echo "[a](./a.md)" >> "git.md"
+
+  git add git.md
+
+  to_temp xrefcheck
+
+  assert_diff - <<EOF
+=== Invalid references found ===
+
+  ➥  In file git.md
+      bad reference (relative) at src:1:1-11:
+        - text: "a"
+        - link: ./a.md
+        - anchor: -
+
+      ⛀  File does not exist:
+          a.md
+
+
+Invalid references dumped, 1 in total.
+EOF
+}
diff --git a/tests/golden/check-ignored/check-ignored.bats b/tests/golden/check-ignored/check-ignored.bats
index 17426c0..722e543 100644
--- a/tests/golden/check-ignored/check-ignored.bats
+++ b/tests/golden/check-ignored/check-ignored.bats
@@ -37,5 +37,47 @@ load '../helpers'
 @test "Ignore file with broken xrefcheck annotation: directory, check failure" {
   to_temp xrefcheck --ignored ./to-ignore/inner-directory/
 
-  assert_diff expected.gold
+  assert_diff - <<EOF
+=== Scan errors found ===
+
+  ➥  In file to-ignore/inner-directory/broken_annotation.md
+  scan error at src:9:1-30:
+
+  ⛀  Annotation "ignore file" must be at the top of markdown or right after comments at the top
+
+
+
+Scan errors dumped, 1 in total.
+EOF
+}
+
+@test "Ignore referenced file, check error" {
+  to_temp xrefcheck --ignored referenced-file.md
+
+  assert_diff - <<EOF
+=== Scan errors found ===
+
+  ➥  In file to-ignore/inner-directory/broken_annotation.md
+     scan error at src:9:1-30:
+
+     ⛀  Annotation "ignore file" must be at the top of markdown or right after comments at the top
+
+
+Scan errors dumped, 1 in total.
+
+
+=== Invalid references found ===
+
+  ➥  In file check-ignored.md
+     bad reference (absolute) at src:7:1-37:
+       - text: "Good reference"
+       - link: /referenced-file.md
+       - anchor: -
+
+     ⛀  File does not exist:
+        ./referenced-file.md
+
+
+Invalid references dumped, 1 in total.
+EOF
 }
diff --git a/tests/golden/check-ignored/check-ignored.md b/tests/golden/check-ignored/check-ignored.md
new file mode 100644
index 0000000..6a6583f
--- /dev/null
+++ b/tests/golden/check-ignored/check-ignored.md
@@ -0,0 +1,7 @@
+<!--
+ - SPDX-FileCopyrightText: 2022 Serokell <https://serokell.io>
+ -
+ - SPDX-License-Identifier: MPL-2.0
+ -->
+
+[Good reference](/referenced-file.md)
diff --git a/tests/golden/check-ignored/expected.gold b/tests/golden/check-ignored/expected.gold
deleted file mode 100644
index e38e002..0000000
--- a/tests/golden/check-ignored/expected.gold
+++ /dev/null
@@ -1,10 +0,0 @@
-=== Scan errors found ===
-
-  ➥  In file ./to-ignore/inner-directory/broken_annotation.md
-  scan error at src:9:1-30:
-
-  ⛀  Annotation "ignore file" must be at the top of markdown or right after comments at the top
-
-
-
-Scan errors dumped, 1 in total.
diff --git a/tests/golden/check-ignored/referenced-file.md b/tests/golden/check-ignored/referenced-file.md
new file mode 100644
index 0000000..25690a3
--- /dev/null
+++ b/tests/golden/check-ignored/referenced-file.md
@@ -0,0 +1,7 @@
+<!--
+ - SPDX-FileCopyrightText: 2022 Serokell <https://serokell.io>
+ -
+ - SPDX-License-Identifier: MPL-2.0
+ -->
+
+referenced file
diff --git a/tests/golden/check-local-refs/dir1/dir2/d2f1.md b/tests/golden/check-local-refs/dir1/dir2/d2f1.md
index 59db474..f9ee512 100644
--- a/tests/golden/check-local-refs/dir1/dir2/d2f1.md
+++ b/tests/golden/check-local-refs/dir1/dir2/d2f1.md
@@ -14,11 +14,8 @@
 [existing-file-rel-3](../dir2/.././d1f1.md)
 [existing-file-rel-4](d2f3.yaml)
 
-Currently our behavior is wrong, see https://github.com/serokell/xrefcheck/issues/195
 [slash-file-rel](d2f2.md/)
 
-
-
 [existing-dir-rel-1](..)
 [existing-dir-rel-2](../dir2)
 [existing-dir-rel-3](../dir2/)
diff --git a/tests/golden/check-local-refs/expected1.gold b/tests/golden/check-local-refs/expected1.gold
index 219ed54..4cb9900 100644
--- a/tests/golden/check-local-refs/expected1.gold
+++ b/tests/golden/check-local-refs/expected1.gold
@@ -10,17 +10,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:18:1-26:
-       - text: "slash-file-rel"
-       - link: d2f2.md/
-       - anchor: -
-
-     ⛀  File does not exist:
-        dir1/dir2/d2f2.md/
-
-
-  ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:30:1-43:
+     bad reference (relative) at src:27:1-43:
        - text: "bad-file-rel"
        - link: ../a/b/c/unexisting-file.md
        - anchor: -
@@ -30,7 +20,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:31:1-31:
+     bad reference (relative) at src:28:1-31:
        - text: "bad-casing-file-rel"
        - link: D2F2.md/
        - anchor: -
@@ -40,7 +30,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:32:1-32:
+     bad reference (relative) at src:29:1-32:
        - text: "bad-casing-folder-rel"
        - link: ../DIR2
        - anchor: -
@@ -50,7 +40,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:34:1-38:
+     bad reference (relative) at src:31:1-38:
        - text: "bad-anchor-rel-1"
        - link: d2f2.md
        - anchor: bad-anchor
@@ -59,7 +49,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:35:1-49:
+     bad reference (relative) at src:32:1-49:
        - text: "bad-anchor-rel-2"
        - link: unexisting-file.md
        - anchor: bad-anchor
@@ -69,7 +59,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:45:1-22:
+     bad reference (absolute) at src:42:1-22:
        - text: "file-abs-2"
        - link: /d1f1.md
        - anchor: -
@@ -79,7 +69,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:46:1-27:
+     bad reference (absolute) at src:43:1-27:
        - text: "file-abs-3"
        - link: /dir2/d2f2.md
        - anchor: -
@@ -89,7 +79,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:47:1-32:
+     bad reference (absolute) at src:44:1-32:
        - text: "file-abs-4"
        - link: /./dir2/../d1f1.md
        - anchor: -
@@ -99,7 +89,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:48:1-37:
+     bad reference (absolute) at src:45:1-37:
        - text: "file-abs-slash"
        - link: /./dir2/../d1f1.md/
        - anchor: -
@@ -109,7 +99,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:49:1-55:
+     bad reference (absolute) at src:46:1-55:
        - text: "anchor-abs-3"
        - link: /./dir2/../d1f1.md
        - anchor: existing-anchor-d1f1
@@ -119,7 +109,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:60:1-16:
+     bad reference (absolute) at src:57:1-16:
        - text: "A"
        - link: /../../a.md
        - anchor: -
@@ -129,7 +119,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:61:1-18:
+     bad reference (absolute) at src:58:1-18:
        - text: "B"
        - link: /b/../../b.md
        - anchor: -
@@ -138,4 +128,4 @@
         ./b/../../b.md
 
 
-Invalid references dumped, 14 in total.
+Invalid references dumped, 13 in total.
diff --git a/tests/golden/check-local-refs/expected2.gold b/tests/golden/check-local-refs/expected2.gold
index 9bb2c96..a518c86 100644
--- a/tests/golden/check-local-refs/expected2.gold
+++ b/tests/golden/check-local-refs/expected2.gold
@@ -10,17 +10,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:18:1-26:
-       - text: "slash-file-rel"
-       - link: d2f2.md/
-       - anchor: -
-
-     ⛀  File does not exist:
-        dir1/dir2/d2f2.md/
-
-
-  ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:30:1-43:
+     bad reference (relative) at src:27:1-43:
        - text: "bad-file-rel"
        - link: ../a/b/c/unexisting-file.md
        - anchor: -
@@ -30,7 +20,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:31:1-31:
+     bad reference (relative) at src:28:1-31:
        - text: "bad-casing-file-rel"
        - link: D2F2.md/
        - anchor: -
@@ -40,7 +30,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:32:1-32:
+     bad reference (relative) at src:29:1-32:
        - text: "bad-casing-folder-rel"
        - link: ../DIR2
        - anchor: -
@@ -50,7 +40,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:34:1-38:
+     bad reference (relative) at src:31:1-38:
        - text: "bad-anchor-rel-1"
        - link: d2f2.md
        - anchor: bad-anchor
@@ -59,7 +49,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:35:1-49:
+     bad reference (relative) at src:32:1-49:
        - text: "bad-anchor-rel-2"
        - link: unexisting-file.md
        - anchor: bad-anchor
@@ -69,7 +59,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:39:1-29:
+     bad reference (absolute) at src:36:1-29:
        - text: "file-abs-1"
        - link: /dir1/./d1f1.md
        - anchor: -
@@ -79,7 +69,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:40:1-21:
+     bad reference (absolute) at src:37:1-21:
        - text: "folder-abs-1"
        - link: /dir1
        - anchor: -
@@ -89,7 +79,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:41:1-30:
+     bad reference (absolute) at src:38:1-30:
        - text: "folder-abs-2"
        - link: /dir1/dir2/../
        - anchor: -
@@ -99,7 +89,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:42:1-58:
+     bad reference (absolute) at src:39:1-58:
        - text: "anchor-abs-1"
        - link: /dir1/../dir1/d1f1.md
        - anchor: existing-anchor-d1f1
@@ -109,7 +99,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:43:1-73:
+     bad reference (absolute) at src:40:1-73:
        - text: "anchor-abs-2"
        - link: /dir1/dir2/../../dir1/./dir2/d2f2.md
        - anchor: existing-anchor-d2f2
@@ -119,17 +109,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:48:1-37:
-       - text: "file-abs-slash"
-       - link: /./dir2/../d1f1.md/
-       - anchor: -
-
-     ⛀  File does not exist:
-        dir1/./dir2/../d1f1.md/
-
-
-  ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:54:1-42:
+     bad reference (relative) at src:51:1-42:
        - text: "path-through-top-dir"
        - link: ../../dir1/d1f1.md
        - anchor: -
@@ -139,7 +119,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:55:1-75:
+     bad reference (relative) at src:52:1-75:
        - text: "path-through-top-dir-with-anchor"
        - link: ../../dir1/d1f1.md
        - anchor: existing-anchor-d1f1
@@ -149,7 +129,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:56:1-26:
+     bad reference (relative) at src:53:1-26:
        - text: "ref-to-d0"
        - link: ../../d0f1.md
        - anchor: -
@@ -159,7 +139,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:60:1-16:
+     bad reference (absolute) at src:57:1-16:
        - text: "A"
        - link: /../../a.md
        - anchor: -
@@ -169,7 +149,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:61:1-18:
+     bad reference (absolute) at src:58:1-18:
        - text: "B"
        - link: /b/../../b.md
        - anchor: -
@@ -178,4 +158,4 @@
         dir1/b/../../b.md
 
 
-Invalid references dumped, 18 in total.
+Invalid references dumped, 16 in total.
diff --git a/tests/golden/check-local-refs/expected3.gold b/tests/golden/check-local-refs/expected3.gold
index 94b997c..08bda13 100644
--- a/tests/golden/check-local-refs/expected3.gold
+++ b/tests/golden/check-local-refs/expected3.gold
@@ -10,17 +10,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:18:1-26:
-       - text: "slash-file-rel"
-       - link: d2f2.md/
-       - anchor: -
-
-     ⛀  File does not exist:
-        dir1/dir2/d2f2.md/
-
-
-  ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:30:1-43:
+     bad reference (relative) at src:27:1-43:
        - text: "bad-file-rel"
        - link: ../a/b/c/unexisting-file.md
        - anchor: -
@@ -30,7 +20,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:31:1-31:
+     bad reference (relative) at src:28:1-31:
        - text: "bad-casing-file-rel"
        - link: D2F2.md/
        - anchor: -
@@ -40,7 +30,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:34:1-38:
+     bad reference (relative) at src:31:1-38:
        - text: "bad-anchor-rel-1"
        - link: d2f2.md
        - anchor: bad-anchor
@@ -49,7 +39,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:35:1-49:
+     bad reference (relative) at src:32:1-49:
        - text: "bad-anchor-rel-2"
        - link: unexisting-file.md
        - anchor: bad-anchor
@@ -59,7 +49,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:39:1-29:
+     bad reference (absolute) at src:36:1-29:
        - text: "file-abs-1"
        - link: /dir1/./d1f1.md
        - anchor: -
@@ -69,7 +59,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:40:1-21:
+     bad reference (absolute) at src:37:1-21:
        - text: "folder-abs-1"
        - link: /dir1
        - anchor: -
@@ -79,7 +69,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:41:1-30:
+     bad reference (absolute) at src:38:1-30:
        - text: "folder-abs-2"
        - link: /dir1/dir2/../
        - anchor: -
@@ -89,7 +79,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:42:1-58:
+     bad reference (absolute) at src:39:1-58:
        - text: "anchor-abs-1"
        - link: /dir1/../dir1/d1f1.md
        - anchor: existing-anchor-d1f1
@@ -99,7 +89,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:43:1-73:
+     bad reference (absolute) at src:40:1-73:
        - text: "anchor-abs-2"
        - link: /dir1/dir2/../../dir1/./dir2/d2f2.md
        - anchor: existing-anchor-d2f2
@@ -109,17 +99,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (absolute) at src:48:1-37:
-       - text: "file-abs-slash"
-       - link: /./dir2/../d1f1.md/
-       - anchor: -
-
-     ⛀  File does not exist:
-        dir1/./dir2/../d1f1.md/
-
-
-  ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:54:1-42:
+     bad reference (relative) at src:51:1-42:
        - text: "path-through-top-dir"
        - link: ../../dir1/d1f1.md
        - anchor: -
@@ -129,7 +109,7 @@
 
 
   ➥  In file dir1/dir2/d2f1.md
-     bad reference (relative) at src:55:1-75:
+     bad reference (relative) at src:52:1-75:
        - text: "path-through-top-dir-with-anchor"
        - link: ../../dir1/d1f1.md
        - anchor: existing-anchor-d1f1
@@ -138,4 +118,4 @@
         dir1/dir2/../../dir1/d1f1.md
 
 
-Invalid references dumped, 14 in total.
+Invalid references dumped, 12 in total.
diff --git a/tests/golden/check-scan-errors/expected.gold b/tests/golden/check-scan-errors/expected.gold
index 7505380..cec78c6 100644
--- a/tests/golden/check-scan-errors/expected.gold
+++ b/tests/golden/check-scan-errors/expected.gold
@@ -1,42 +1,43 @@
 === Scan errors found ===
 
-  ➥  In file ./check-scan-errors.md
+
+  ➥  In file check-scan-errors.md
      scan error at src:9:1-30:
 
      ⛀  Annotation "ignore file" must be at the top of markdown or right after comments at the top
 
 
-  ➥  In file ./check-scan-errors.md
+  ➥  In file check-scan-errors.md
      scan error at src:13:1-36:
 
      ⛀  Expected a PARAGRAPH after "ignore paragraph" annotation, but found HEADING
 
 
-  ➥  In file ./check-scan-errors.md
+  ➥  In file check-scan-errors.md
      scan error at src:17:1-31:
 
      ⛀  Expected a LINK after "ignore link" annotation
 
 
-  ➥  In file ./check-scan-errors.md
+  ➥  In file check-scan-errors.md
      scan error at src:21:1-50:
 
      ⛀  Unrecognised option "unrecognised-annotation" perhaps you meant <"ignore link"|"ignore paragraph"|"ignore file">
 
 
-  ➥  In file ./check-second-file.md
+  ➥  In file check-second-file.md
      scan error at src:9:1-30:
 
      ⛀  Annotation "ignore file" must be at the top of markdown or right after comments at the top
 
 
-  ➥  In file ./no_link_eof.md
+  ➥  In file no_link_eof.md
      scan error at src:9:1-31:
 
      ⛀  Expected a LINK after "ignore link" annotation
 
 
-  ➥  In file ./no_paragraph_eof.md
+  ➥  In file no_paragraph_eof.md
      scan error at src:9:1-36:
 
      ⛀  Expected a PARAGRAPH after "ignore paragraph" annotation, but found EOF
diff --git a/xrefcheck.nix b/xrefcheck.nix
index 846cf05..057f5ce 100644
--- a/xrefcheck.nix
+++ b/xrefcheck.nix
@@ -8,7 +8,7 @@ let
   src = (import ./ci.nix).project-src;
   pkgs = if linux-static then nixpkgs.pkgsCross.musl64 else if windows then nixpkgs.pkgsCross.mingwW64 else nixpkgs;
   project = pkgs.haskell-nix.stackProject {
-    src = pkgs.haskell-nix.haskellLib.cleanGit { src = ./.; };
+    src = pkgs.haskell-nix.haskellLib.cleanGit { src = ./.; keepGitDir = true; };
     modules = [{
       packages.xrefcheck = {
         ghcOptions =
@@ -38,6 +38,7 @@ let
             '';
             testFlags = [ "--ftp-host" "ftp://localhost:2221" ];
           };
+          xrefcheck-tests.build-tools = [ pkgs.git ];
         };
       };
     }];