From 3f85f675ff9d4465bee1348d543ab25b27cc66c6 Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Mon, 2 May 2022 17:45:29 +0930
Subject: [PATCH 01/20] added ui component to ignore unlinked files

---
 .idea/runConfigurations/JabRef_Main.xml       |  5 +++--
 .../FileIgnoreUnlinkedFiles.java              | 20 +++++++++++++++++++
 .../externalfiles/UnlinkedFilesDialog.fxml    | 12 ++++++-----
 .../UnlinkedFilesDialogView.java              |  7 +++++++
 .../UnlinkedFilesDialogViewModel.java         | 14 +++++++++++++
 .../jabref/logic/util/StandardFileType.java   |  4 +++-
 src/main/resources/l10n/JabRef_en.properties  |  1 +
 7 files changed, 55 insertions(+), 8 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java

diff --git a/.idea/runConfigurations/JabRef_Main.xml b/.idea/runConfigurations/JabRef_Main.xml
index a588730b31a..7b96690299e 100644
--- a/.idea/runConfigurations/JabRef_Main.xml
+++ b/.idea/runConfigurations/JabRef_Main.xml
@@ -1,7 +1,8 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="JabRef Main" type="Application" factoryName="Application" singleton="true">
+    <option name="ALTERNATIVE_JRE_PATH" value="17" />
+    <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="true" />
     <option name="MAIN_CLASS_NAME" value="org.jabref.gui.JabRefMain" />
-    <module name="JabRef.main" />
     <option name="VM_PARAMETERS" value="--patch-module test=fastparse_2.12-1.0.0.jar --patch-module test2=fastparse-utils_2.12-1.0.0.jar --patch-module test3=sourcecode_2.12-0.1.4.jar --patch-module org.jabref=build/resources/main --add-exports javafx.controls/com.sun.javafx.scene.control=org.jabref --add-exports org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref --add-opens javafx.controls/javafx.scene.control=org.jabref --add-opens org.controlsfx.controls/org.controlsfx.control.textfield=org.jabref --add-exports javafx.graphics/com.sun.javafx.scene=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.scene.traversal=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control.inputmap=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.event=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.collections=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.runtime=org.controlsfx.controls --add-exports javafx.web/com.sun.webkit=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls --add-opens javafx.controls/javafx.scene.control.skin=org.controlsfx.controls --add-opens javafx.graphics/javafx.scene=org.controlsfx.controls --add-exports com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle --add-exports javafx.graphics/com.sun.javafx.stage=com.jfoenix --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix" />
     <option name="WORKING_DIRECTORY" value="$MODULE_WORKING_DIR$" />
     <RunnerSettings RunnerId="Profile ">
@@ -11,4 +12,4 @@
       <option name="Make" enabled="true" />
     </method>
   </configuration>
-</component>
+</component>
\ No newline at end of file
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java b/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
new file mode 100644
index 00000000000..584e64a4f7b
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
@@ -0,0 +1,20 @@
+package org.jabref.gui.externalfiles;
+
+import java.util.List;
+
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.FileType;
+
+public class FileIgnoreUnlinkedFiles {
+    private final String description;
+    private final List<String> filesToIgnore;
+
+    FileIgnoreUnlinkedFiles(FileType fileType) {
+        this.description = Localization.lang("%0", fileType.getName());
+        this.filesToIgnore = fileType.getExtensionsWithDot();
+    }
+
+    public String getDescription() {
+        return this.description;
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
index e3d2b8b9133..15155694716 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
@@ -52,12 +52,14 @@
 
                 <Label text="%File type" GridPane.columnIndex="0" GridPane.rowIndex="1"/>
                 <ComboBox fx:id="fileTypeCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="1"/>
-                <Label text="%Last edited:" GridPane.columnIndex="0" GridPane.rowIndex="2"/>
-                <ComboBox fx:id="fileDateCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="2"/>
-                <Label text="%Sort by:" GridPane.columnIndex="0" GridPane.rowIndex="3"/>
-                <ComboBox fx:id="fileSortCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="3"/>
+                <Label text="%Ignore Unlinked Files" GridPane.columnIndex="0" GridPane.rowIndex="2"/>
+                <ComboBox fx:id="unlinkedFileCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="2"/>
+                <Label text="%Last edited:" GridPane.columnIndex="0" GridPane.rowIndex="3"/>
+                <ComboBox fx:id="fileDateCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="3"/>
+                <Label text="%Sort by:" GridPane.columnIndex="0" GridPane.rowIndex="4"/>
+                <ComboBox fx:id="fileSortCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="4"/>
                 <Button fx:id="scanButton" onAction="#scanFiles" text="%Search"
-                        GridPane.columnIndex="2" GridPane.rowIndex="3">
+                        GridPane.columnIndex="2" GridPane.rowIndex="4">
                     <tooltip>
                         <Tooltip text="%Searches the selected directory for unlinked files."/>
                     </tooltip>
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
index 2d1af899d12..273ee1f6207 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
@@ -55,6 +55,7 @@ public class UnlinkedFilesDialogView extends BaseDialog<Void> {
 
     @FXML private TextField directoryPathField;
     @FXML private ComboBox<FileExtensionViewModel> fileTypeCombo;
+    @FXML private ComboBox<FileIgnoreUnlinkedFiles> unlinkedFileCombo;
     @FXML private ComboBox<DateRange> fileDateCombo;
     @FXML private ComboBox<ExternalFileSorter> fileSortCombo;
     @FXML private CheckTreeView<FileNodeViewModel> unlinkedFilesList;
@@ -159,6 +160,12 @@ private void initDirectorySelection() {
         fileSortCombo.setItems(viewModel.getSorters());
         fileSortCombo.valueProperty().bindBidirectional(viewModel.selectedSortProperty());
         fileSortCombo.getSelectionModel().selectFirst();
+        new ViewModelListCellFactory<FileIgnoreUnlinkedFiles>()
+                .withText(FileIgnoreUnlinkedFiles::getDescription)
+                .install(unlinkedFileCombo);
+        unlinkedFileCombo.setItems(viewModel.unlinkedFileFilter());
+        unlinkedFileCombo.valueProperty().bindBidirectional(viewModel.selectedFileIgnoreProperty());
+        unlinkedFileCombo.getSelectionModel().selectFirst();
     }
 
     private void initUnlinkedFilesList() {
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
index 7d19b2bdc98..af3c6282bc7 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
@@ -55,6 +55,7 @@ public class UnlinkedFilesDialogViewModel {
     private final ImportHandler importHandler;
     private final StringProperty directoryPath = new SimpleStringProperty("");
     private final ObjectProperty<FileExtensionViewModel> selectedExtension = new SimpleObjectProperty<>();
+    private final ObjectProperty<FileIgnoreUnlinkedFiles> selectedFileIgnore = new SimpleObjectProperty<>();
     private final ObjectProperty<DateRange> selectedDate = new SimpleObjectProperty<>();
     private final ObjectProperty<ExternalFileSorter> selectedSort = new SimpleObjectProperty<>();
 
@@ -69,6 +70,7 @@ public class UnlinkedFilesDialogViewModel {
     private final ObservableList<FileExtensionViewModel> fileFilterList;
     private final ObservableList<DateRange> dateFilterList;
     private final ObservableList<ExternalFileSorter> fileSortList;
+    private final ObservableList<FileIgnoreUnlinkedFiles> unlinkedFileFilter;
 
     private final DialogService dialogService;
     private final PreferencesService preferences;
@@ -105,6 +107,10 @@ public UnlinkedFilesDialogViewModel(DialogService dialogService,
                 new FileExtensionViewModel(StandardFileType.BIBTEX_DB, externalFileTypes),
                 new FileExtensionViewModel(StandardFileType.PDF, externalFileTypes));
 
+        this.unlinkedFileFilter = FXCollections.observableArrayList(
+                new FileIgnoreUnlinkedFiles(StandardFileType.DEF),
+                new FileIgnoreUnlinkedFiles(StandardFileType.IUF));
+
         this.dateFilterList = FXCollections.observableArrayList(DateRange.values());
 
         this.fileSortList = FXCollections.observableArrayList(ExternalFileSorter.values());
@@ -205,6 +211,10 @@ public ObservableList<FileExtensionViewModel> getFileFilters() {
         return this.fileFilterList;
     }
 
+    public ObservableList<FileIgnoreUnlinkedFiles> unlinkedFileFilter() {
+        return this.unlinkedFileFilter;
+    }
+
     public ObservableList<DateRange> getDateFilters() {
         return this.dateFilterList;
     }
@@ -266,6 +276,10 @@ public ObjectProperty<ExternalFileSorter> selectedSortProperty() {
         return this.selectedSort;
     }
 
+    public ObjectProperty<FileIgnoreUnlinkedFiles> selectedFileIgnoreProperty() {
+        return this.selectedFileIgnore;
+    }
+
     public StringProperty directoryPathProperty() {
         return this.directoryPath;
     }
diff --git a/src/main/java/org/jabref/logic/util/StandardFileType.java b/src/main/java/org/jabref/logic/util/StandardFileType.java
index ffdb7e63e93..60211487ff2 100644
--- a/src/main/java/org/jabref/logic/util/StandardFileType.java
+++ b/src/main/java/org/jabref/logic/util/StandardFileType.java
@@ -44,7 +44,9 @@ public enum StandardFileType implements FileType {
     YAML("YAML Markup", "yaml"),
     CFF("CFF", "cff"),
     ANY_FILE("Any", "*"),
-    CER("SSL Certificate", "cer");
+    CER("SSL Certificate", "cer"),
+    IUF("Include all Files", "*"),
+    DEF("Default", "");
 
     private final List<String> extensions;
     private final String name;
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index e1aa756a5ae..aa0726b6e43 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2483,3 +2483,4 @@ Success\!\ Finished\ writing\ metadata.=Success! Finished writing metadata.
 
 Custom\ API\ key=Custom API key
 Check\ %0\ API\ Key\ Setting=Check %0 API Key Setting
+Ignore\ Unlinked\ Files=Ignore Unlinked Files

From 05ae9effcee760c27b75f5f8fcbf41d8d8819365 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=9Czhaoqingying123=E2=80=9C?= <710870305@qq.com>
Date: Wed, 11 May 2022 11:14:36 +0930
Subject: [PATCH 02/20] ignore the files in ".gitignore" when searching for
 unlinked local files

---
 .gitignore                                    |  1 +
 .../gui/externalfiles/FileFilterUtils.java    | 36 +++++++++++----
 .../jabref/gui/externalfiles/FileIgnore.java  | 46 +++++++++++++++++++
 .../externalfiles/UnlinkedFilesCrawler.java   |  4 +-
 4 files changed, 76 insertions(+), 11 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/externalfiles/FileIgnore.java

diff --git a/.gitignore b/.gitignore
index fd187d3f735..ab2cd6b84b9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,6 +47,7 @@ gradle.properties
 *.ipr
 *.iml
 
+
 # UNKNWON
 jabref.xml
 *.sonargraph
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
index 28e1f20929a..53a622e4f00 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
@@ -6,8 +6,7 @@
 import java.nio.file.attribute.FileTime;
 import java.time.LocalDateTime;
 import java.time.ZoneId;
-import java.util.Comparator;
-import java.util.List;
+import java.util.*;
 import java.util.stream.Collectors;
 
 import org.slf4j.Logger;
@@ -16,7 +15,8 @@
 public class FileFilterUtils {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(FileFilterUtils.class);
-    
+    private static final Set<String> FILEIGNORESET = FileIgnore.getInstance().getIgnoreFileSet();
+
     /* Returns the last edited time of a file as LocalDateTime. */
     public static LocalDateTime getFileTime(Path path) {
         FileTime lastEditedTime = null;
@@ -33,28 +33,28 @@ public static LocalDateTime getFileTime(Path path) {
         return localDateTime;
     }
 
-    /* Returns true if a file with a specific path 
+    /* Returns true if a file with a specific path
      * was edited during the last 24 hours. */
     public boolean isDuringLastDay(LocalDateTime fileEditTime) {
         LocalDateTime NOW = LocalDateTime.now(ZoneId.systemDefault());
         return fileEditTime.isAfter(NOW.minusHours(24));
     }
 
-    /* Returns true if a file with a specific path 
+    /* Returns true if a file with a specific path
      * was edited during the last 7 days. */
     public boolean isDuringLastWeek(LocalDateTime fileEditTime) {
         LocalDateTime NOW = LocalDateTime.now(ZoneId.systemDefault());
         return fileEditTime.isAfter(NOW.minusDays(7));
     }
 
-    /* Returns true if a file with a specific path 
+    /* Returns true if a file with a specific path
      * was edited during the last 30 days. */
     public boolean isDuringLastMonth(LocalDateTime fileEditTime) {
         LocalDateTime NOW = LocalDateTime.now(ZoneId.systemDefault());
         return fileEditTime.isAfter(NOW.minusDays(30));
     }
 
-    /* Returns true if a file with a specific path 
+    /* Returns true if a file with a specific path
      * was edited during the last 365 days. */
     public boolean isDuringLastYear(LocalDateTime fileEditTime) {
         LocalDateTime NOW = LocalDateTime.now(ZoneId.systemDefault());
@@ -75,7 +75,25 @@ public static boolean filterByDate(Path path, DateRange filter) {
         return isInDateRange;
     }
 
-    /* Sorts a list of Path objects according to the last edited date 
+    /* Returns true if a file should be ignored by .gitignore */
+    public static boolean filterByFileExtension(Path path) {
+        try {
+            String fileExtension = "";
+            int i = path.toString().lastIndexOf('.');
+            if (i > 0) {
+                fileExtension = path.toString().substring(i + 1);
+            }
+            if (fileExtension != "" && FILEIGNORESET.contains(fileExtension)) {
+                return false;
+            }
+        } catch (Exception e) {
+            LOGGER.info("Not file");
+        }
+
+        return true;
+    }
+
+    /* Sorts a list of Path objects according to the last edited date
      * of their corresponding files, from newest to oldest. */
     public List<Path> sortByDateAscending(List<Path> files) {
         return files.stream()
@@ -86,7 +104,7 @@ public List<Path> sortByDateAscending(List<Path> files) {
                 .collect(Collectors.toList());
     }
 
-    /* Sorts a list of Path objects according to the last edited date 
+    /* Sorts a list of Path objects according to the last edited date
      * of their corresponding files, from oldest to newest. */
     public List<Path> sortByDateDescending(List<Path> files) {
         return files.stream()
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java b/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java
new file mode 100644
index 00000000000..b6183366fd3
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java
@@ -0,0 +1,46 @@
+package org.jabref.gui.externalfiles;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
+import java.util.HashSet;
+import java.util.Set;
+
+public class FileIgnore {
+
+    private static FileIgnore instance;
+    private static Set<String> IgnoreFileSet = new HashSet<>();
+    private static final Logger LOGGER = LoggerFactory.getLogger(FileIgnore.class);
+    private String gitIgnorePath = ".gitignore";
+
+    public FileIgnore() {
+        try (BufferedReader br = new BufferedReader(new InputStreamReader(
+                new FileInputStream(gitIgnorePath)
+        ))) {
+            String line = "";
+            line = br.readLine();
+            while (line != null) {
+                line = br.readLine();
+                if (line != null && line.length() > 2 && line.charAt(0) == '*') {
+                    IgnoreFileSet.add(line.substring(2));
+                }else if (line != null && line.length() > 1 && line.charAt(0) == '.'){
+                    IgnoreFileSet.add(line.substring(1));
+                }
+            }
+        } catch (IOException e) {
+            LOGGER.error("No such file.");
+        }
+    }
+
+    public Set<String> getIgnoreFileSet(){
+        return IgnoreFileSet;
+    }
+
+    public static FileIgnore getInstance(){
+        if (instance == null){
+            return new FileIgnore();
+        }
+        return instance;
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index 53ebad10fc5..674316a6927 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -66,7 +66,7 @@ protected FileNodeViewModel call() throws IOException {
      * 'state' must be set to 1, to keep the recursion running. When the states value changes, the method will resolve
      * its recursion and return what it has saved so far.
      * <br>
-     * The files are filtered according to the {@link DateRange} filter value 
+     * The files are filtered according to the {@link DateRange} filter value
      * and then sorted according to the {@link ExternalFileSorter} value.
      *
      * @throws IOException if directory is not a directory or empty
@@ -102,7 +102,7 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
         // filter files according to last edited date.
         List<Path> filteredFiles = new ArrayList<Path>();
         for (Path path : files) {
-            if (FileFilterUtils.filterByDate(path, dateFilter)) {
+            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterByFileExtension(path)) {
                 filteredFiles.add(path);
             }
         }

From 849bb4fc3f74dcd71eb95668a2c0719f5c3dc6fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=9Czhaoqingying123=E2=80=9C?= <710870305@qq.com>
Date: Wed, 11 May 2022 21:11:20 +0930
Subject: [PATCH 03/20] ignore the name of files and the extention in
 ".gitignore" when searching for unlinked local files

---
 .gitignore                                                   | 4 ++--
 .../java/org/jabref/gui/externalfiles/FileFilterUtils.java   | 5 +++++
 src/main/java/org/jabref/gui/externalfiles/FileIgnore.java   | 3 +++
 .../org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java   | 2 +-
 4 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index ab2cd6b84b9..44e91193de7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -240,7 +240,7 @@ fabric.properties
 *.zip
 *.tar.gz
 *.rar
-
+AAGenerator.cpp
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
 
@@ -419,7 +419,7 @@ Thumbs.db
 Thumbs.db:encryptable
 ehthumbs.db
 ehthumbs_vista.db
-
+data.tsv
 # Dump file
 *.stackdump
 
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
index 53a622e4f00..40b6b073f45 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
@@ -92,6 +92,11 @@ public static boolean filterByFileExtension(Path path) {
 
         return true;
     }
+    public static boolean filterByFileName(Path path) {
+        if (FILEIGNORESET.contains(path.getFileName().toString())){
+            return false;}
+        return true;
+        }
 
     /* Sorts a list of Path objects according to the last edited date
      * of their corresponding files, from newest to oldest. */
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java b/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java
index b6183366fd3..d72546e5099 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java
@@ -26,7 +26,10 @@ public FileIgnore() {
                     IgnoreFileSet.add(line.substring(2));
                 }else if (line != null && line.length() > 1 && line.charAt(0) == '.'){
                     IgnoreFileSet.add(line.substring(1));
+                }else if (line != null && line.length() > 1 &&(!line.contains("/"))){
+                    IgnoreFileSet.add(line);
                 }
+
             }
         } catch (IOException e) {
             LOGGER.error("No such file.");
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index 674316a6927..f50436f5659 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -102,7 +102,7 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
         // filter files according to last edited date.
         List<Path> filteredFiles = new ArrayList<Path>();
         for (Path path : files) {
-            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterByFileExtension(path)) {
+            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterByFileExtension(path)&&FileFilterUtils.filterByFileName(path)) {
                 filteredFiles.add(path);
             }
         }

From c0926a503401c729b56a7d40d004d5efde185240 Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Fri, 13 May 2022 04:01:06 +0930
Subject: [PATCH 04/20] linked ui to the logic & refactored the code

---
 .../gui/externalfiles/FileFilterUtils.java    | 39 +++++++-------
 .../jabref/gui/externalfiles/FileIgnore.java  | 49 -----------------
 .../FileIgnoreUnlinkedFiles.java              | 53 +++++++++++++++----
 .../externalfiles/UnlinkedFilesCrawler.java   |  8 +--
 .../UnlinkedFilesDialogView.java              |  2 +-
 .../UnlinkedFilesDialogViewModel.java         |  7 ++-
 .../jabref/logic/util/StandardFileType.java   |  4 +-
 7 files changed, 72 insertions(+), 90 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/externalfiles/FileIgnore.java

diff --git a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
index 40b6b073f45..fe1b4774eed 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
@@ -6,7 +6,9 @@
 import java.nio.file.attribute.FileTime;
 import java.time.LocalDateTime;
 import java.time.ZoneId;
-import java.util.*;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.slf4j.Logger;
@@ -15,8 +17,7 @@
 public class FileFilterUtils {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(FileFilterUtils.class);
-    private static final Set<String> FILEIGNORESET = FileIgnore.getInstance().getIgnoreFileSet();
-
+    private static Set<String> FILEIGNORESET = null;
     /* Returns the last edited time of a file as LocalDateTime. */
     public static LocalDateTime getFileTime(Path path) {
         FileTime lastEditedTime = null;
@@ -76,27 +77,25 @@ public static boolean filterByDate(Path path, DateRange filter) {
     }
 
     /* Returns true if a file should be ignored by .gitignore */
-    public static boolean filterByFileExtension(Path path) {
-        try {
-            String fileExtension = "";
-            int i = path.toString().lastIndexOf('.');
-            if (i > 0) {
-                fileExtension = path.toString().substring(i + 1);
-            }
-            if (fileExtension != "" && FILEIGNORESET.contains(fileExtension)) {
-                return false;
+    public static boolean filterForUnlinkedFiles(Path path, FileIgnoreUnlinkedFiles unlinkedFileFilter) {
+        if (unlinkedFileFilter.equals(FileIgnoreUnlinkedFiles.DEFAULT)) {
+            try {
+                FILEIGNORESET = FileIgnoreUnlinkedFiles.getIgnoreFileSet();
+                String fileExtension = "";
+                int i = path.toString().lastIndexOf('.');
+                if (i > 0) {
+                    fileExtension = path.toString().substring(i + 1);
+                }
+                if (!fileExtension.equals("") && FILEIGNORESET.contains(fileExtension)) {
+                    return false;
+                }
+            } catch (Exception e) {
+                LOGGER.info("Not file");
             }
-        } catch (Exception e) {
-            LOGGER.info("Not file");
+            return !FILEIGNORESET.contains(path.getFileName().toString());
         }
-
         return true;
     }
-    public static boolean filterByFileName(Path path) {
-        if (FILEIGNORESET.contains(path.getFileName().toString())){
-            return false;}
-        return true;
-        }
 
     /* Sorts a list of Path objects according to the last edited date
      * of their corresponding files, from newest to oldest. */
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java b/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java
deleted file mode 100644
index d72546e5099..00000000000
--- a/src/main/java/org/jabref/gui/externalfiles/FileIgnore.java
+++ /dev/null
@@ -1,49 +0,0 @@
-package org.jabref.gui.externalfiles;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.*;
-import java.util.HashSet;
-import java.util.Set;
-
-public class FileIgnore {
-
-    private static FileIgnore instance;
-    private static Set<String> IgnoreFileSet = new HashSet<>();
-    private static final Logger LOGGER = LoggerFactory.getLogger(FileIgnore.class);
-    private String gitIgnorePath = ".gitignore";
-
-    public FileIgnore() {
-        try (BufferedReader br = new BufferedReader(new InputStreamReader(
-                new FileInputStream(gitIgnorePath)
-        ))) {
-            String line = "";
-            line = br.readLine();
-            while (line != null) {
-                line = br.readLine();
-                if (line != null && line.length() > 2 && line.charAt(0) == '*') {
-                    IgnoreFileSet.add(line.substring(2));
-                }else if (line != null && line.length() > 1 && line.charAt(0) == '.'){
-                    IgnoreFileSet.add(line.substring(1));
-                }else if (line != null && line.length() > 1 &&(!line.contains("/"))){
-                    IgnoreFileSet.add(line);
-                }
-
-            }
-        } catch (IOException e) {
-            LOGGER.error("No such file.");
-        }
-    }
-
-    public Set<String> getIgnoreFileSet(){
-        return IgnoreFileSet;
-    }
-
-    public static FileIgnore getInstance(){
-        if (instance == null){
-            return new FileIgnore();
-        }
-        return instance;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java b/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
index 584e64a4f7b..7e3d26671fa 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
@@ -1,20 +1,53 @@
 package org.jabref.gui.externalfiles;
 
-import java.util.List;
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.HashSet;
+import java.util.Set;
 
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.FileType;
 
-public class FileIgnoreUnlinkedFiles {
-    private final String description;
-    private final List<String> filesToIgnore;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
-    FileIgnoreUnlinkedFiles(FileType fileType) {
-        this.description = Localization.lang("%0", fileType.getName());
-        this.filesToIgnore = fileType.getExtensionsWithDot();
+public enum FileIgnoreUnlinkedFiles {
+    DEFAULT(Localization.lang("Default")),
+    INCLUDE_ALL(Localization.lang("Include All Files"));
+
+    private static FileIgnoreUnlinkedFiles instance;
+    private static String gitIgnorePath = ".gitignore";
+    private static Set<String> IgnoreFileSet = new HashSet<>();
+    private static final Logger LOGGER = LoggerFactory.getLogger(FileIgnoreUnlinkedFiles.class);
+
+    private final String fileIgnoreOption;
+    FileIgnoreUnlinkedFiles(String fileIgnoreOption) {
+        this.fileIgnoreOption = fileIgnoreOption;
+    }
+
+    public String getFileIgnoreOption() {
+        return fileIgnoreOption;
     }
 
-    public String getDescription() {
-        return this.description;
+    public static Set<String> getIgnoreFileSet() {
+        try (BufferedReader br = new BufferedReader(new InputStreamReader(
+                new FileInputStream(gitIgnorePath)
+        ))) {
+            String line = br.readLine();
+            while (line != null) {
+                line = br.readLine();
+                if (line != null && line.length() > 2 && line.charAt(0) == '*') {
+                    IgnoreFileSet.add(line.substring(2));
+                } else if (line != null && line.length() > 1 && line.charAt(0) == '.') {
+                    IgnoreFileSet.add(line.substring(1));
+                } else if (line != null && line.length() > 1 && (!line.contains("/"))) {
+                    IgnoreFileSet.add(line);
+                }
+            }
+        } catch (IOException e) {
+            LOGGER.error("No such file.");
+        }
+        return IgnoreFileSet;
     }
 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index f50436f5659..ada85a29f8c 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -36,14 +36,16 @@ public class UnlinkedFilesCrawler extends BackgroundTask<FileNodeViewModel> {
     private final ExternalFileSorter sorter;
     private final BibDatabaseContext databaseContext;
     private final FilePreferences filePreferences;
+    private final FileIgnoreUnlinkedFiles unlinkedFileFilter;
 
-    public UnlinkedFilesCrawler(Path directory, Filter<Path> fileFilter, DateRange dateFilter, ExternalFileSorter sorter, BibDatabaseContext databaseContext, FilePreferences filePreferences) {
+    public UnlinkedFilesCrawler(Path directory, Filter<Path> fileFilter, DateRange dateFilter, ExternalFileSorter sorter, BibDatabaseContext databaseContext, FilePreferences filePreferences, FileIgnoreUnlinkedFiles unlinkedFileFilter) {
         this.directory = directory;
         this.fileFilter = fileFilter;
         this.dateFilter = dateFilter;
         this.sorter = sorter;
         this.databaseContext = databaseContext;
         this.filePreferences = filePreferences;
+        this.unlinkedFileFilter = unlinkedFileFilter;
     }
 
     @Override
@@ -66,7 +68,7 @@ protected FileNodeViewModel call() throws IOException {
      * 'state' must be set to 1, to keep the recursion running. When the states value changes, the method will resolve
      * its recursion and return what it has saved so far.
      * <br>
-     * The files are filtered according to the {@link DateRange} filter value
+     * The files are filtered according to the {@link DateRange} filter value & the {@link FileIgnoreUnlinkedFiles} filter value
      * and then sorted according to the {@link ExternalFileSorter} value.
      *
      * @throws IOException if directory is not a directory or empty
@@ -102,7 +104,7 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
         // filter files according to last edited date.
         List<Path> filteredFiles = new ArrayList<Path>();
         for (Path path : files) {
-            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterByFileExtension(path)&&FileFilterUtils.filterByFileName(path)) {
+            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterForUnlinkedFiles(path, unlinkedFileFilter)) {
                 filteredFiles.add(path);
             }
         }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
index 273ee1f6207..14f8728024b 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
@@ -161,7 +161,7 @@ private void initDirectorySelection() {
         fileSortCombo.valueProperty().bindBidirectional(viewModel.selectedSortProperty());
         fileSortCombo.getSelectionModel().selectFirst();
         new ViewModelListCellFactory<FileIgnoreUnlinkedFiles>()
-                .withText(FileIgnoreUnlinkedFiles::getDescription)
+                .withText(FileIgnoreUnlinkedFiles::getFileIgnoreOption)
                 .install(unlinkedFileCombo);
         unlinkedFileCombo.setItems(viewModel.unlinkedFileFilter());
         unlinkedFileCombo.valueProperty().bindBidirectional(viewModel.selectedFileIgnoreProperty());
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
index af3c6282bc7..e1e40d3909b 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
@@ -107,9 +107,7 @@ public UnlinkedFilesDialogViewModel(DialogService dialogService,
                 new FileExtensionViewModel(StandardFileType.BIBTEX_DB, externalFileTypes),
                 new FileExtensionViewModel(StandardFileType.PDF, externalFileTypes));
 
-        this.unlinkedFileFilter = FXCollections.observableArrayList(
-                new FileIgnoreUnlinkedFiles(StandardFileType.DEF),
-                new FileIgnoreUnlinkedFiles(StandardFileType.IUF));
+        this.unlinkedFileFilter = FXCollections.observableArrayList(FileIgnoreUnlinkedFiles.values());
 
         this.dateFilterList = FXCollections.observableArrayList(DateRange.values());
 
@@ -125,12 +123,13 @@ public UnlinkedFilesDialogViewModel(DialogService dialogService,
     public void startSearch() {
         Path directory = this.getSearchDirectory();
         Filter<Path> selectedFileFilter = selectedExtension.getValue().dirFilter();
+        FileIgnoreUnlinkedFiles selectedUnlinkedFileIgnoreFilter = selectedFileIgnore.getValue();
         DateRange selectedDateFilter = selectedDate.getValue();
         ExternalFileSorter selectedSortFilter = selectedSort.getValue();
         progressValueProperty.unbind();
         progressTextProperty.unbind();
 
-        findUnlinkedFilesTask = new UnlinkedFilesCrawler(directory, selectedFileFilter, selectedDateFilter, selectedSortFilter, bibDatabase, preferences.getFilePreferences())
+        findUnlinkedFilesTask = new UnlinkedFilesCrawler(directory, selectedFileFilter, selectedDateFilter, selectedSortFilter, bibDatabase, preferences.getFilePreferences(), selectedUnlinkedFileIgnoreFilter)
                 .onRunning(() -> {
                     progressValueProperty.set(ProgressIndicator.INDETERMINATE_PROGRESS);
                     progressTextProperty.setValue(Localization.lang("Searching file system..."));
diff --git a/src/main/java/org/jabref/logic/util/StandardFileType.java b/src/main/java/org/jabref/logic/util/StandardFileType.java
index 60211487ff2..ffdb7e63e93 100644
--- a/src/main/java/org/jabref/logic/util/StandardFileType.java
+++ b/src/main/java/org/jabref/logic/util/StandardFileType.java
@@ -44,9 +44,7 @@ public enum StandardFileType implements FileType {
     YAML("YAML Markup", "yaml"),
     CFF("CFF", "cff"),
     ANY_FILE("Any", "*"),
-    CER("SSL Certificate", "cer"),
-    IUF("Include all Files", "*"),
-    DEF("Default", "");
+    CER("SSL Certificate", "cer");
 
     private final List<String> extensions;
     private final String name;

From 4be3ce4634a45f7c090a14e635e7bf619611ccb9 Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Sun, 15 May 2022 01:38:51 +0930
Subject: [PATCH 05/20] adding localization key

---
 src/main/resources/l10n/JabRef_en.properties | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index aa0726b6e43..ae00eebb829 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2484,3 +2484,4 @@ Success\!\ Finished\ writing\ metadata.=Success! Finished writing metadata.
 Custom\ API\ key=Custom API key
 Check\ %0\ API\ Key\ Setting=Check %0 API Key Setting
 Ignore\ Unlinked\ Files=Ignore Unlinked Files
+Include\ All\ Files=Include All Files

From 713b954c6adfaa8cd79447dd8497b14552ff2cea Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Mon, 16 May 2022 05:21:30 +0930
Subject: [PATCH 06/20] changelog updated

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 81d801e29f3..40cb8fa1c7b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We added a fetcher for [Biodiversity Heritage Library)](https://www.biodiversitylibrary.org/) [8539](https://github.com/JabRef/jabref/issues/8539)
 - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
+- We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [#373](https://github.com/koppor/jabref/issues/373)
 
 ### Changed
 

From 77cf1857414e8d9a4afb572ce7a2e4dfb90a9d28 Mon Sep 17 00:00:00 2001
From: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
Date: Mon, 16 May 2022 21:38:12 +0200
Subject: [PATCH 07/20] Update .gitignore

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 44e91193de7..94554d89725 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,7 +47,6 @@ gradle.properties
 *.ipr
 *.iml
 
-
 # UNKNWON
 jabref.xml
 *.sonargraph

From 65c1de5af87b5adb7ca52b992e6e64ad66ca774c Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Tue, 17 May 2022 15:24:16 +0930
Subject: [PATCH 08/20] changes after review

---
 .gitignore                                    |  3 +-
 .../gui/externalfiles/FileFilterUtils.java    | 11 +++---
 .../FileIgnoreUnlinkedFiles.java              | 37 +------------------
 .../externalfiles/UnlinkedFilesDialog.fxml    |  2 +-
 .../UnlinkedFilesDialogViewModel.java         | 27 ++++++++++++++
 src/main/resources/l10n/JabRef_en.properties  |  2 +-
 6 files changed, 36 insertions(+), 46 deletions(-)

diff --git a/.gitignore b/.gitignore
index 44e91193de7..c0ab1a12442 100644
--- a/.gitignore
+++ b/.gitignore
@@ -240,7 +240,7 @@ fabric.properties
 *.zip
 *.tar.gz
 *.rar
-AAGenerator.cpp
+
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
 
@@ -419,7 +419,6 @@ Thumbs.db
 Thumbs.db:encryptable
 ehthumbs.db
 ehthumbs_vista.db
-data.tsv
 # Dump file
 *.stackdump
 
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
index fe1b4774eed..073655373ec 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
@@ -11,6 +11,8 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import org.jabref.logic.util.io.FileUtil;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -18,6 +20,7 @@ public class FileFilterUtils {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(FileFilterUtils.class);
     private static Set<String> FILEIGNORESET = null;
+
     /* Returns the last edited time of a file as LocalDateTime. */
     public static LocalDateTime getFileTime(Path path) {
         FileTime lastEditedTime = null;
@@ -80,12 +83,8 @@ public static boolean filterByDate(Path path, DateRange filter) {
     public static boolean filterForUnlinkedFiles(Path path, FileIgnoreUnlinkedFiles unlinkedFileFilter) {
         if (unlinkedFileFilter.equals(FileIgnoreUnlinkedFiles.DEFAULT)) {
             try {
-                FILEIGNORESET = FileIgnoreUnlinkedFiles.getIgnoreFileSet();
-                String fileExtension = "";
-                int i = path.toString().lastIndexOf('.');
-                if (i > 0) {
-                    fileExtension = path.toString().substring(i + 1);
-                }
+                FILEIGNORESET = UnlinkedFilesDialogViewModel.getIgnoreFileSet();
+                String fileExtension = FileUtil.getFileExtension(path).orElse("");
                 if (!fileExtension.equals("") && FILEIGNORESET.contains(fileExtension)) {
                     return false;
                 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java b/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
index 7e3d26671fa..8779bfe47fe 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
@@ -1,27 +1,13 @@
 package org.jabref.gui.externalfiles;
 
-import java.io.BufferedReader;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.HashSet;
-import java.util.Set;
-
 import org.jabref.logic.l10n.Localization;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 public enum FileIgnoreUnlinkedFiles {
     DEFAULT(Localization.lang("Default")),
     INCLUDE_ALL(Localization.lang("Include All Files"));
 
-    private static FileIgnoreUnlinkedFiles instance;
-    private static String gitIgnorePath = ".gitignore";
-    private static Set<String> IgnoreFileSet = new HashSet<>();
-    private static final Logger LOGGER = LoggerFactory.getLogger(FileIgnoreUnlinkedFiles.class);
-
     private final String fileIgnoreOption;
+
     FileIgnoreUnlinkedFiles(String fileIgnoreOption) {
         this.fileIgnoreOption = fileIgnoreOption;
     }
@@ -29,25 +15,4 @@ public enum FileIgnoreUnlinkedFiles {
     public String getFileIgnoreOption() {
         return fileIgnoreOption;
     }
-
-    public static Set<String> getIgnoreFileSet() {
-        try (BufferedReader br = new BufferedReader(new InputStreamReader(
-                new FileInputStream(gitIgnorePath)
-        ))) {
-            String line = br.readLine();
-            while (line != null) {
-                line = br.readLine();
-                if (line != null && line.length() > 2 && line.charAt(0) == '*') {
-                    IgnoreFileSet.add(line.substring(2));
-                } else if (line != null && line.length() > 1 && line.charAt(0) == '.') {
-                    IgnoreFileSet.add(line.substring(1));
-                } else if (line != null && line.length() > 1 && (!line.contains("/"))) {
-                    IgnoreFileSet.add(line);
-                }
-            }
-        } catch (IOException e) {
-            LOGGER.error("No such file.");
-        }
-        return IgnoreFileSet;
-    }
 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
index 15155694716..6e74f41d62e 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
@@ -52,7 +52,7 @@
 
                 <Label text="%File type" GridPane.columnIndex="0" GridPane.rowIndex="1"/>
                 <ComboBox fx:id="fileTypeCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="1"/>
-                <Label text="%Ignore Unlinked Files" GridPane.columnIndex="0" GridPane.rowIndex="2"/>
+                <Label text="%Ignore File Extensions" GridPane.columnIndex="0" GridPane.rowIndex="2"/>
                 <ComboBox fx:id="unlinkedFileCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="2"/>
                 <Label text="%Last edited:" GridPane.columnIndex="0" GridPane.rowIndex="3"/>
                 <ComboBox fx:id="fileDateCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="3"/>
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
index e1e40d3909b..069a33e2e58 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
@@ -1,14 +1,20 @@
 package org.jabref.gui.externalfiles;
 
+import java.io.BufferedReader;
 import java.io.BufferedWriter;
+import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.DirectoryStream.Filter;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Optional;
+import java.util.Set;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
 
@@ -302,4 +308,25 @@ public BooleanProperty taskActiveProperty() {
     public SimpleListProperty<TreeItem<FileNodeViewModel>> checkedFileListProperty() {
         return checkedFileListProperty;
     }
+
+    public static Set<String> getIgnoreFileSet() {
+        String gitIgnorePath = ".gitignore";
+        Set<String> IgnoreFileSet = new HashSet<>();
+        try (BufferedReader br = new BufferedReader(new InputStreamReader(
+                new FileInputStream(gitIgnorePath)
+        ))) {
+            String line = br.readLine();
+            while (line != null) {
+                line = br.readLine();
+                if (line != null && line.length() > 2 && line.charAt(0) == '*') {
+                    IgnoreFileSet.add(line.substring(2).toLowerCase(Locale.ROOT));
+                } else if (line != null && line.length() > 1 && !line.contains("/")) {
+                    IgnoreFileSet.add(line);
+                }
+            }
+        } catch (IOException e) {
+            LOGGER.error("No such file.");
+        }
+        return IgnoreFileSet;
+    }
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 7df1c85b9e6..45dfcee2484 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2487,5 +2487,5 @@ Success\!\ Finished\ writing\ metadata.=Success! Finished writing metadata.
 
 Custom\ API\ key=Custom API key
 Check\ %0\ API\ Key\ Setting=Check %0 API Key Setting
-Ignore\ Unlinked\ Files=Ignore Unlinked Files
+Ignore\ File\ Extensions=Ignore File Extensions
 Include\ All\ Files=Include All Files

From 68bdca8caf3ac1116b3e65b8019ef59ce720cf2b Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Tue, 17 May 2022 15:27:17 +0930
Subject: [PATCH 09/20] Update CHANGELOG.md

Co-authored-by: Christoph <siedlerkiller@gmail.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ee828522a9b..bd5421dde46 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,7 +13,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We added a fetcher for [Biodiversity Heritage Library)](https://www.biodiversitylibrary.org/) [8539](https://github.com/JabRef/jabref/issues/8539)
 - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
-- We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [#373](https://github.com/koppor/jabref/issues/373)
+- We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [koppor#373](https://github.com/koppor/jabref/issues/373)
 - JabRef now writes log files. Linux: `$home/.cache/jabref/logs/version`, Windows: `%APPDATA%\..\Local\harawata\jabref\version\logs`, Mac: `Users/.../Library/Logs/jabref/version`
 
 ### Changed

From 79be853b2b5bcc342c26ba15746f28b6ea8ffcf1 Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Tue, 17 May 2022 15:36:22 +0930
Subject: [PATCH 10/20] remove any modification from JabRef_Main.xml

---
 .idea/runConfigurations/JabRef_Main.xml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/.idea/runConfigurations/JabRef_Main.xml b/.idea/runConfigurations/JabRef_Main.xml
index dfced3eec6c..731578b5c75 100644
--- a/.idea/runConfigurations/JabRef_Main.xml
+++ b/.idea/runConfigurations/JabRef_Main.xml
@@ -1,14 +1,14 @@
 <component name="ProjectRunConfigurationManager">
-    <configuration default="false" name="JabRef Main" type="Application" factoryName="Application" singleton="true">
-        <option name="MAIN_CLASS_NAME" value="org.jabref.gui.JabRefMain" />
-        <module name="JabRef.main" />
-        <option name="VM_PARAMETERS" value="--patch-module org.jabref=build/resources/main --add-exports javafx.controls/com.sun.javafx.scene.control=org.jabref --add-exports org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref --add-opens javafx.controls/javafx.scene.control=org.jabref --add-opens org.controlsfx.controls/org.controlsfx.control.textfield=org.jabref --add-exports javafx.graphics/com.sun.javafx.scene=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.scene.traversal=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control.inputmap=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.event=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.collections=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.runtime=org.controlsfx.controls --add-exports javafx.web/com.sun.webkit=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls --add-opens javafx.controls/javafx.scene.control.skin=org.controlsfx.controls --add-opens javafx.graphics/javafx.scene=org.controlsfx.controls --add-exports com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle --add-exports javafx.graphics/com.sun.javafx.stage=com.jfoenix --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix" />
-        <option name="WORKING_DIRECTORY" value="$MODULE_WORKING_DIR$" />
-        <RunnerSettings RunnerId="Profile ">
-            <option name="myExternalizedOptions" value="additional-options2=onexit\=snapshot,_no_java_version_check&#13;&#10;startup=12" />
-        </RunnerSettings>
-        <method v="2">
-            <option name="Make" enabled="true" />
-        </method>
-    </configuration>
+  <configuration default="false" name="JabRef Main" type="Application" factoryName="Application" singleton="true">
+    <option name="MAIN_CLASS_NAME" value="org.jabref.gui.JabRefMain" />
+    <module name="JabRef.main" />
+    <option name="VM_PARAMETERS" value="--patch-module org.jabref=build/resources/main --add-exports javafx.controls/com.sun.javafx.scene.control=org.jabref --add-exports org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref --add-opens javafx.controls/javafx.scene.control=org.jabref --add-opens org.controlsfx.controls/org.controlsfx.control.textfield=org.jabref --add-exports javafx.graphics/com.sun.javafx.scene=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.scene.traversal=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control=org.controlsfx.controls --add-exports javafx.controls/com.sun.javafx.scene.control.inputmap=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.event=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.collections=org.controlsfx.controls --add-exports javafx.base/com.sun.javafx.runtime=org.controlsfx.controls --add-exports javafx.web/com.sun.webkit=org.controlsfx.controls --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls --add-opens javafx.controls/javafx.scene.control.skin=org.controlsfx.controls --add-opens javafx.graphics/javafx.scene=org.controlsfx.controls --add-exports com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle --add-exports javafx.graphics/com.sun.javafx.stage=com.jfoenix --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix" />
+    <option name="WORKING_DIRECTORY" value="$MODULE_WORKING_DIR$" />
+    <RunnerSettings RunnerId="Profile ">
+      <option name="myExternalizedOptions" value="additional-options2=onexit\=snapshot,_no_java_version_check&#13;&#10;startup=12" />
+    </RunnerSettings>
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
 </component>

From a10916e73b5a9a21e4a46f874b217e61b49646dd Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Thu, 19 May 2022 19:51:31 +0200
Subject: [PATCH 11/20] Rrefactor and move Check for existing files before
 reading

---
 .../gui/externalfiles/FileFilterUtils.java    |  9 +++--
 .../externalfiles/UnlinkedFilesCrawler.java   | 33 +++++++++++++++++--
 .../UnlinkedFilesDialogViewModel.java         | 27 ---------------
 3 files changed, 35 insertions(+), 34 deletions(-)

diff --git a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
index 073655373ec..2f0c7182982 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
@@ -19,7 +19,6 @@
 public class FileFilterUtils {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(FileFilterUtils.class);
-    private static Set<String> FILEIGNORESET = null;
 
     /* Returns the last edited time of a file as LocalDateTime. */
     public static LocalDateTime getFileTime(Path path) {
@@ -80,18 +79,18 @@ public static boolean filterByDate(Path path, DateRange filter) {
     }
 
     /* Returns true if a file should be ignored by .gitignore */
-    public static boolean filterForUnlinkedFiles(Path path, FileIgnoreUnlinkedFiles unlinkedFileFilter) {
+    public static boolean filterForUnlinkedFiles(Path path, FileIgnoreUnlinkedFiles unlinkedFileFilter, Set<String> ignoreFileSet ) {
         if (unlinkedFileFilter.equals(FileIgnoreUnlinkedFiles.DEFAULT)) {
             try {
-                FILEIGNORESET = UnlinkedFilesDialogViewModel.getIgnoreFileSet();
+
                 String fileExtension = FileUtil.getFileExtension(path).orElse("");
-                if (!fileExtension.equals("") && FILEIGNORESET.contains(fileExtension)) {
+                if (!fileExtension.equals("") && ignoreFileSet.contains(fileExtension)) {
                     return false;
                 }
             } catch (Exception e) {
                 LOGGER.info("Not file");
             }
-            return !FILEIGNORESET.contains(path.getFileName().toString());
+            return !ignoreFileSet.contains(path.getFileName().toString());
         }
         return true;
     }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index ada85a29f8c..94d48bc9c6c 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -1,13 +1,17 @@
 package org.jabref.gui.externalfiles;
 
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.DirectoryStream.Filter;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
+import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 import java.util.stream.StreamSupport;
@@ -102,9 +106,9 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
             }
         }
         // filter files according to last edited date.
-        List<Path> filteredFiles = new ArrayList<Path>();
+        List<Path> filteredFiles = new ArrayList<>();
         for (Path path : files) {
-            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterForUnlinkedFiles(path, unlinkedFileFilter)) {
+            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterForUnlinkedFiles(path, unlinkedFileFilter, getIgnoreFileSet(path))) {
                 filteredFiles.add(path);
             }
         }
@@ -116,4 +120,29 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
                 .collect(Collectors.toList()));
         return parent;
     }
+
+
+    private Set<String> getIgnoreFileSet(Path directory) {
+        String gitIgnorePath = ".gitignore";
+        Set<String> IgnoreFileSet = new HashSet<>();
+
+        Path ignoreFile = directory.resolve(gitIgnorePath);
+
+        if (Files.exists(ignoreFile)) {
+            try (BufferedReader br = Files.newBufferedReader(ignoreFile)) {
+                String line = br.readLine();
+                while (line != null) {
+                    line = br.readLine();
+                    if ((line != null) && (line.length() > 2) && (line.charAt(0) == '*')) {
+                        IgnoreFileSet.add(line.substring(2).toLowerCase(Locale.ROOT));
+                    } else if ((line != null) && (line.length() > 1) && !line.contains("/")) {
+                        IgnoreFileSet.add(line);
+                    }
+                }
+            } catch (IOException e) {
+                LOGGER.error("Error reading file.", e);
+            }
+        }
+        return IgnoreFileSet;
+    }
 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
index 069a33e2e58..e1e40d3909b 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
@@ -1,20 +1,14 @@
 package org.jabref.gui.externalfiles;
 
-import java.io.BufferedReader;
 import java.io.BufferedWriter;
-import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStreamReader;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.DirectoryStream.Filter;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Locale;
 import java.util.Optional;
-import java.util.Set;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
 
@@ -308,25 +302,4 @@ public BooleanProperty taskActiveProperty() {
     public SimpleListProperty<TreeItem<FileNodeViewModel>> checkedFileListProperty() {
         return checkedFileListProperty;
     }
-
-    public static Set<String> getIgnoreFileSet() {
-        String gitIgnorePath = ".gitignore";
-        Set<String> IgnoreFileSet = new HashSet<>();
-        try (BufferedReader br = new BufferedReader(new InputStreamReader(
-                new FileInputStream(gitIgnorePath)
-        ))) {
-            String line = br.readLine();
-            while (line != null) {
-                line = br.readLine();
-                if (line != null && line.length() > 2 && line.charAt(0) == '*') {
-                    IgnoreFileSet.add(line.substring(2).toLowerCase(Locale.ROOT));
-                } else if (line != null && line.length() > 1 && !line.contains("/")) {
-                    IgnoreFileSet.add(line);
-                }
-            }
-        } catch (IOException e) {
-            LOGGER.error("No such file.");
-        }
-        return IgnoreFileSet;
-    }
 }

From 2dae7de65d58c07e3cc1071a793896fb8bde492a Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Thu, 19 May 2022 20:02:37 +0200
Subject: [PATCH 12/20] checkstyle

---
 .../gui/externalfiles/FileFilterUtils.java    |  2 +-
 .../externalfiles/UnlinkedFilesCrawler.java   |  1 -
 .../externalfiles/FileFilterUtilsTest.java    | 22 +++++++++----------
 3 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
index 2f0c7182982..b93e4f962b9 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
@@ -79,7 +79,7 @@ public static boolean filterByDate(Path path, DateRange filter) {
     }
 
     /* Returns true if a file should be ignored by .gitignore */
-    public static boolean filterForUnlinkedFiles(Path path, FileIgnoreUnlinkedFiles unlinkedFileFilter, Set<String> ignoreFileSet ) {
+    public static boolean filterForUnlinkedFiles(Path path, FileIgnoreUnlinkedFiles unlinkedFileFilter, Set<String> ignoreFileSet) {
         if (unlinkedFileFilter.equals(FileIgnoreUnlinkedFiles.DEFAULT)) {
             try {
 
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index 94d48bc9c6c..627ae44d6f0 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -121,7 +121,6 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
         return parent;
     }
 
-
     private Set<String> getIgnoreFileSet(Path directory) {
         String gitIgnorePath = ".gitignore";
         Set<String> IgnoreFileSet = new HashSet<>();
diff --git a/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java b/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
index a6888ab8d3a..ec491bee2c8 100755
--- a/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
+++ b/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
@@ -64,20 +64,20 @@ public void isDuringLastYearPositiveTest() {
     @Nested
     class SortingTests {
 
-        private List<Path> files = new ArrayList<Path>();
-        private List<String> expectedSortByDateAscending = new ArrayList<String>();
-        private List<String> expectedSortByDateDescending = new ArrayList<String>();
-        private List<String> wrongOrder = new ArrayList<String>();
+        private final List<Path> files = new ArrayList<>();
+        private final List<String> expectedSortByDateAscending = new ArrayList<>();
+        private final List<String> expectedSortByDateDescending = new ArrayList<>();
+        private final List<String> wrongOrder = new ArrayList<>();
 
         /* Initialize the directory and files used in the sorting tests, and change their last edited dates. */
         @BeforeEach
         public void setUp(@TempDir Path tempDir) throws Exception {
-            
+
             Path firstPath = tempDir.resolve("firstFile.pdf");
             Path secondPath = tempDir.resolve("secondFile.pdf");
             Path thirdPath = tempDir.resolve("thirdFile.pdf");
             Path fourthPath = tempDir.resolve("fourthFile.pdf");
-    
+
             Files.createFile(firstPath);
             Files.createFile(secondPath);
             Files.createFile(thirdPath);
@@ -88,19 +88,19 @@ public void setUp(@TempDir Path tempDir) throws Exception {
             Files.setLastModifiedTime(secondPath, FileTime.fromMillis(5));
             Files.setLastModifiedTime(thirdPath, FileTime.fromMillis(1));
             Files.setLastModifiedTime(fourthPath, FileTime.fromMillis(2));
-            
+
             // fill the list to be sorted by the tests.
             files.add(firstPath);
             files.add(secondPath);
             files.add(thirdPath);
             files.add(fourthPath);
-    
+
             // fill the expected values lists.
             expectedSortByDateAscending.add(thirdPath.toString());
             expectedSortByDateAscending.add(fourthPath.toString());
             expectedSortByDateAscending.add(secondPath.toString());
             expectedSortByDateAscending.add(firstPath.toString());
-    
+
             expectedSortByDateDescending.add(firstPath.toString());
             expectedSortByDateDescending.add(secondPath.toString());
             expectedSortByDateDescending.add(fourthPath.toString());
@@ -111,7 +111,7 @@ public void setUp(@TempDir Path tempDir) throws Exception {
             wrongOrder.add(thirdPath.toString());
             wrongOrder.add(fourthPath.toString());
         }
-    
+
         @Test
         public void sortByDateAscendingPositiveTest() {
             List<String> sortedPaths = fileFilterUtils
@@ -131,7 +131,7 @@ public void sortByDateAscendingNegativeTest() {
                 .collect(Collectors.toList());
             assertNotEquals(sortedPaths, wrongOrder);
         }
-    
+
         @Test
         public void sortByDateDescendingPositiveTest() {
             List<String> sortedPaths = fileFilterUtils

From 663f1b47f941795dd7bbf5a880410ca7228ab1cf Mon Sep 17 00:00:00 2001
From: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
Date: Thu, 19 May 2022 20:39:48 +0200
Subject: [PATCH 13/20] Update .gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 97619dbff5e..fd187d3f735 100644
--- a/.gitignore
+++ b/.gitignore
@@ -418,6 +418,7 @@ Thumbs.db
 Thumbs.db:encryptable
 ehthumbs.db
 ehthumbs_vista.db
+
 # Dump file
 *.stackdump
 

From dfefd35a84393182c2a3dc953d8c83b71c567763 Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Sat, 21 May 2022 19:22:59 +0930
Subject: [PATCH 14/20] changing to read .gitignore from source directory of
 JabRef

---
 .../org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java     | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index 627ae44d6f0..bfd7d366b10 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -6,6 +6,7 @@
 import java.nio.file.DirectoryStream.Filter;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -108,7 +109,7 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
         // filter files according to last edited date.
         List<Path> filteredFiles = new ArrayList<>();
         for (Path path : files) {
-            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterForUnlinkedFiles(path, unlinkedFileFilter, getIgnoreFileSet(path))) {
+            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterForUnlinkedFiles(path, unlinkedFileFilter, getIgnoreFileSet(Paths.get("")))) {
                 filteredFiles.add(path);
             }
         }

From a78b739a633770d80c284b5b7cdcc11ac8de4c84 Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Sat, 21 May 2022 19:41:45 +0930
Subject: [PATCH 15/20] using Path.of instead Paths

---
 .../org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java     | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index bfd7d366b10..7e9395ee16c 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -6,7 +6,6 @@
 import java.nio.file.DirectoryStream.Filter;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -109,7 +108,7 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
         // filter files according to last edited date.
         List<Path> filteredFiles = new ArrayList<>();
         for (Path path : files) {
-            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterForUnlinkedFiles(path, unlinkedFileFilter, getIgnoreFileSet(Paths.get("")))) {
+            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterForUnlinkedFiles(path, unlinkedFileFilter, getIgnoreFileSet(Path.of("")))) {
                 filteredFiles.add(path);
             }
         }

From 81e8d9d9dfbc58cd971c8543a6d125d6bb879619 Mon Sep 17 00:00:00 2001
From: Prashant Singh <prashantsingh.sp@gmail.com>
Date: Sun, 22 May 2022 18:51:27 +0930
Subject: [PATCH 16/20] adding test for filterForUnlinkedFiles

---
 .../externalfiles/FileFilterUtilsTest.java    | 67 +++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java b/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
index ec491bee2c8..45c7726b6a0 100755
--- a/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
+++ b/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
@@ -5,7 +5,9 @@
 import java.nio.file.attribute.FileTime;
 import java.time.LocalDateTime;
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.junit.jupiter.api.BeforeEach;
@@ -152,4 +154,69 @@ public void testSortByDateDescendingNegativeTest() {
             assertNotEquals(sortedPaths, wrongOrder);
         }
     }
+
+    @Nested
+    class filteringTests {
+        private final List<Path> files = new ArrayList<>();
+        private final List<Path> targetFiles = new ArrayList<>();
+        private final Set<String> ignoreFileSet = new HashSet<>();
+
+        @BeforeEach
+        public void setUp(@TempDir Path tempDir) throws Exception {
+
+            ignoreFileSet.add(".DS_Store");
+            ignoreFileSet.add("Thumbs.db");
+
+            Path firstPath = tempDir.resolve("firstFile.pdf");
+            Path secondPath = tempDir.resolve("secondFile.pdf");
+            Path thirdPath = tempDir.resolve("thirdFile.pdf");
+            Path fourthPath = tempDir.resolve("fourthFile.pdf");
+            Path fifthPath = tempDir.resolve(".DS_Store");
+            Path sixthPath = tempDir.resolve("Thumbs.db");
+
+            Files.createFile(firstPath);
+            Files.createFile(secondPath);
+            Files.createFile(thirdPath);
+            Files.createFile(fourthPath);
+            Files.createFile(fifthPath);
+            Files.createFile(sixthPath);
+
+            files.add(firstPath);
+            files.add(secondPath);
+            files.add(thirdPath);
+            files.add(fourthPath);
+            files.add(fifthPath);
+            files.add(sixthPath);
+
+            targetFiles.add(firstPath);
+            targetFiles.add(secondPath);
+            targetFiles.add(thirdPath);
+            targetFiles.add(fourthPath);
+        }
+
+        @Test
+        public void filteringByGitIgnore() {
+            ArrayList<Path> filteredFiles = new ArrayList<>();
+            for (Path path : files) {
+                if (FileFilterUtils.filterForUnlinkedFiles(path, FileIgnoreUnlinkedFiles.DEFAULT,
+                        ignoreFileSet)) {
+                    filteredFiles.add(path);
+                }
+            }
+            assertEquals(true, compareTwoPathList(filteredFiles, targetFiles));
+        }
+
+        public boolean compareTwoPathList(List<Path> list1, List<Path> list2) {
+            if (list1.size() != list2.size()) {
+                return false;
+            }
+            int cnt = 0;
+            for (Path path : list1) {
+                if (list2.contains(path)) {
+                    cnt++;
+                }
+            }
+            return cnt == list2.size();
+        }
+    }
 }

From 0a066ea065bb7c170f698db6fd284efb0f15200b Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 20 Jun 2022 23:27:02 +0200
Subject: [PATCH 17/20] Rewrote .gitignore logic

Co-authored-by: Christoph <siedlerkiller@gmail.com>
Co-authored-by: Carl Christian Snethlage <50491877
Co-authored-by: ThiloteE <73715071+ThiloteE@users.noreply.github.com>
---
 .../gui/externalfiles/ChainedFilters.java     | 35 +++++++
 .../gui/externalfiles/FileFilterUtils.java    | 37 +++----
 .../FileIgnoreUnlinkedFiles.java              | 18 ----
 .../externalfiles/GitIgnoreFileFilter.java    | 67 +++++++++++++
 .../externalfiles/UnlinkedFilesCrawler.java   | 96 +++++++++----------
 .../externalfiles/UnlinkedFilesDialog.fxml    | 12 +--
 .../UnlinkedFilesDialogView.java              |  7 --
 .../UnlinkedFilesDialogViewModel.java         | 15 +--
 .../externalfiles/UnlinkedPDFFileFilter.java  |  1 -
 src/main/resources/l10n/JabRef_en.properties  |  2 -
 .../externalfiles/FileFilterUtilsTest.java    | 26 -----
 .../GitIgnoreFileFilterTest.java              | 30 ++++++
 .../UnlinkedFilesCrawlerTest.java             | 38 ++++++++
 13 files changed, 236 insertions(+), 148 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/externalfiles/ChainedFilters.java
 delete mode 100644 src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
 create mode 100644 src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
 create mode 100644 src/test/java/org/jabref/gui/externalfiles/GitIgnoreFileFilterTest.java
 create mode 100644 src/test/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawlerTest.java

diff --git a/src/main/java/org/jabref/gui/externalfiles/ChainedFilters.java b/src/main/java/org/jabref/gui/externalfiles/ChainedFilters.java
new file mode 100644
index 00000000000..4162c9c674f
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiles/ChainedFilters.java
@@ -0,0 +1,35 @@
+package org.jabref.gui.externalfiles;
+
+import java.io.IOException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Path;
+import java.util.Arrays;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Chains the given filters - if ALL of them accept, the result is also accepted
+ */
+public class ChainedFilters implements DirectoryStream.Filter<Path> {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(ChainedFilters.class);
+
+    private DirectoryStream.Filter<Path>[] filters;
+
+    public ChainedFilters(DirectoryStream.Filter<Path>... filters) {
+        this.filters = filters;
+    }
+
+    @Override
+    public boolean accept(Path entry) throws IOException {
+        return Arrays.stream(filters).allMatch(filter -> {
+            try {
+                return filter.accept(entry);
+            } catch (IOException e) {
+                LOGGER.error("Could not apply filter", e);
+                return true;
+            }
+        });
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
index b93e4f962b9..2050a71f336 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
@@ -22,7 +22,7 @@ public class FileFilterUtils {
 
     /* Returns the last edited time of a file as LocalDateTime. */
     public static LocalDateTime getFileTime(Path path) {
-        FileTime lastEditedTime = null;
+        FileTime lastEditedTime;
         try {
             lastEditedTime = Files.getLastModifiedTime(path);
         } catch (IOException e) {
@@ -78,25 +78,10 @@ public static boolean filterByDate(Path path, DateRange filter) {
         return isInDateRange;
     }
 
-    /* Returns true if a file should be ignored by .gitignore */
-    public static boolean filterForUnlinkedFiles(Path path, FileIgnoreUnlinkedFiles unlinkedFileFilter, Set<String> ignoreFileSet) {
-        if (unlinkedFileFilter.equals(FileIgnoreUnlinkedFiles.DEFAULT)) {
-            try {
-
-                String fileExtension = FileUtil.getFileExtension(path).orElse("");
-                if (!fileExtension.equals("") && ignoreFileSet.contains(fileExtension)) {
-                    return false;
-                }
-            } catch (Exception e) {
-                LOGGER.info("Not file");
-            }
-            return !ignoreFileSet.contains(path.getFileName().toString());
-        }
-        return true;
-    }
-
-    /* Sorts a list of Path objects according to the last edited date
-     * of their corresponding files, from newest to oldest. */
+    /**
+     * Sorts a list of Path objects according to the last edited date
+     * of their corresponding files, from newest to oldest.
+     */
     public List<Path> sortByDateAscending(List<Path> files) {
         return files.stream()
                 .sorted(Comparator.comparingLong(file -> FileFilterUtils.getFileTime(file)
@@ -106,8 +91,10 @@ public List<Path> sortByDateAscending(List<Path> files) {
                 .collect(Collectors.toList());
     }
 
-    /* Sorts a list of Path objects according to the last edited date
-     * of their corresponding files, from oldest to newest. */
+    /**
+     * Sorts a list of Path objects according to the last edited date
+     * of their corresponding files, from oldest to newest.
+     */
     public List<Path> sortByDateDescending(List<Path> files) {
         return files.stream()
                 .sorted(Comparator.comparingLong(file -> -FileFilterUtils.getFileTime(file)
@@ -117,8 +104,10 @@ public List<Path> sortByDateDescending(List<Path> files) {
                 .collect(Collectors.toList());
     }
 
-    /* Sorts a list of Path objects according to the last edited date
-     * the order depends on the specified sorter type. */
+    /**
+     * Sorts a list of Path objects according to the last edited date
+     * the order depends on the specified sorter type.
+     */
     public static List<Path> sortByDate(List<Path> files, ExternalFileSorter sortType) {
         FileFilterUtils fileFilter = new FileFilterUtils();
         List<Path> sortedFiles = switch (sortType) {
diff --git a/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java b/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
deleted file mode 100644
index 8779bfe47fe..00000000000
--- a/src/main/java/org/jabref/gui/externalfiles/FileIgnoreUnlinkedFiles.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package org.jabref.gui.externalfiles;
-
-import org.jabref.logic.l10n.Localization;
-
-public enum FileIgnoreUnlinkedFiles {
-    DEFAULT(Localization.lang("Default")),
-    INCLUDE_ALL(Localization.lang("Include All Files"));
-
-    private final String fileIgnoreOption;
-
-    FileIgnoreUnlinkedFiles(String fileIgnoreOption) {
-        this.fileIgnoreOption = fileIgnoreOption;
-    }
-
-    public String getFileIgnoreOption() {
-        return fileIgnoreOption;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java b/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
new file mode 100644
index 00000000000..23d9be182e8
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
@@ -0,0 +1,67 @@
+package org.jabref.gui.externalfiles;
+
+import java.io.IOException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.FileSystems;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.PathMatcher;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.function.Predicate;
+import java.util.stream.Collectors;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static java.util.function.Predicate.not;
+
+public class GitIgnoreFileFilter implements DirectoryStream.Filter<Path> {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(GitIgnoreFileFilter.class);
+
+    private Set<PathMatcher> gitIgnorePatterns;
+
+    public GitIgnoreFileFilter(Path path) {
+        Path currentPath = path;
+        while ((currentPath != null) && !Files.exists(currentPath.resolve(".gitignore"))) {
+            currentPath = currentPath.getParent();
+        }
+        if (currentPath == null) {
+            // we did not find any gitignore, lets use the default
+            gitIgnorePatterns = Set.of(".git", ".DS_Store", "desktop.ini", "Thumbs.db").stream()
+                                   // duplicate code as below
+                                   .map(line -> "glob:" + line)
+                                   .map(matcherString -> FileSystems.getDefault().getPathMatcher(matcherString))
+                                   .collect(Collectors.toSet());
+        } else {
+            Path gitIgnore = currentPath.resolve(".gitignore");
+            try {
+                Set<PathMatcher> plainGitIgnorePatternsFromGitIgnoreFile = Files.readAllLines(gitIgnore).stream()
+                                                                                .map(line -> line.trim())
+                                                                                .filter(not(String::isEmpty))
+                                                                                .filter(line -> !line.startsWith("#"))
+                                                                                // convert to Java syntax for Glob patterns
+                                                                                .map(line -> "glob:" + line)
+                                                                                .map(matcherString -> FileSystems.getDefault().getPathMatcher(matcherString))
+                                                                                .collect(Collectors.toSet());
+                gitIgnorePatterns = new HashSet<>(plainGitIgnorePatternsFromGitIgnoreFile);
+                // we want to ignore ".gitignore" itself
+                gitIgnorePatterns.add(FileSystems.getDefault().getPathMatcher("glob:.gitignore"));
+            } catch (IOException e) {
+                LOGGER.info("Could not read .gitignore from {}", gitIgnore, e);
+                gitIgnorePatterns = Set.of();
+            }
+        }
+    }
+
+    @Override
+    public boolean accept(Path path) throws IOException {
+        // We assume that git does not stop at a patern, but tries all. We implement that behavior
+        return gitIgnorePatterns.stream().noneMatch(filter ->
+                // we need this one for "*.png"
+                filter.matches(path.getFileName()) ||
+                // we need this one for "**/*.png"
+                filter.matches(path));
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index 7e9395ee16c..2e7ffcdda3e 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -40,16 +40,14 @@ public class UnlinkedFilesCrawler extends BackgroundTask<FileNodeViewModel> {
     private final ExternalFileSorter sorter;
     private final BibDatabaseContext databaseContext;
     private final FilePreferences filePreferences;
-    private final FileIgnoreUnlinkedFiles unlinkedFileFilter;
 
-    public UnlinkedFilesCrawler(Path directory, Filter<Path> fileFilter, DateRange dateFilter, ExternalFileSorter sorter, BibDatabaseContext databaseContext, FilePreferences filePreferences, FileIgnoreUnlinkedFiles unlinkedFileFilter) {
+    public UnlinkedFilesCrawler(Path directory, Filter<Path> fileFilter, DateRange dateFilter, ExternalFileSorter sorter, BibDatabaseContext databaseContext, FilePreferences filePreferences) {
         this.directory = directory;
         this.fileFilter = fileFilter;
         this.dateFilter = dateFilter;
         this.sorter = sorter;
         this.databaseContext = databaseContext;
         this.filePreferences = filePreferences;
-        this.unlinkedFileFilter = unlinkedFileFilter;
     }
 
     @Override
@@ -72,76 +70,76 @@ protected FileNodeViewModel call() throws IOException {
      * 'state' must be set to 1, to keep the recursion running. When the states value changes, the method will resolve
      * its recursion and return what it has saved so far.
      * <br>
-     * The files are filtered according to the {@link DateRange} filter value & the {@link FileIgnoreUnlinkedFiles} filter value
+     * The files are filtered according to the {@link DateRange} filter value
      * and then sorted according to the {@link ExternalFileSorter} value.
      *
+     * @param unlinkedPDFFileFilter contains a BibDatabaseContext which is used to determine whether the file is linked
+     *
+     * @return FileNodeViewModel containing the data of the current directory and all subdirectories
      * @throws IOException if directory is not a directory or empty
      */
-    private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter fileFilter) throws IOException {
+    FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter unlinkedPDFFileFilter) throws IOException {
         // Return null if the directory is not valid.
         if ((directory == null) || !Files.isDirectory(directory)) {
             throw new IOException(String.format("Invalid directory for searching: %s", directory));
         }
 
-        FileNodeViewModel parent = new FileNodeViewModel(directory);
-        Map<Boolean, List<Path>> fileListPartition;
-
-        try (Stream<Path> filesStream = StreamSupport.stream(Files.newDirectoryStream(directory, fileFilter).spliterator(), false)) {
-            fileListPartition = filesStream.collect(Collectors.partitioningBy(Files::isDirectory));
+        FileNodeViewModel fileNodeViewModelForCurrentDirectory = new FileNodeViewModel(directory);
+
+        // Map from isDirectory (true/false) to full path
+        // Result: Contains only files not matching the filter (i.e., PDFs not linked and files not ignored)
+        // Filters:
+        //   1. UnlinkedPDFFileFilter
+        //   2. GitIgnoreFilter
+        ChainedFilters filters = new ChainedFilters(unlinkedPDFFileFilter, new GitIgnoreFileFilter(directory));
+        Map<Boolean, List<Path>> directoryAndFilePartition;
+        try (Stream<Path> filesStream = StreamSupport.stream(Files.newDirectoryStream(directory, filters).spliterator(), false)) {
+            directoryAndFilePartition = filesStream.collect(Collectors.partitioningBy(Files::isDirectory));
         } catch (IOException e) {
-            LOGGER.error(String.format("%s while searching files: %s", e.getClass().getName(), e.getMessage()));
-            return parent;
+            LOGGER.error("Error while searching files", e);
+            return fileNodeViewModelForCurrentDirectory;
         }
+        List<Path> subDirectories = directoryAndFilePartition.get(true);
+        List<Path> files = directoryAndFilePartition.get(false);
 
-        List<Path> subDirectories = fileListPartition.get(true);
-        List<Path> files = new ArrayList<>(fileListPartition.get(false));
-        int fileCount = 0;
+        // at this point, only unlinked PDFs AND unignored files are contained
 
-        for (Path subDirectory : subDirectories) {
-            FileNodeViewModel subRoot = searchDirectory(subDirectory, fileFilter);
+        // initially, we find no files at all
+        int fileCountOfSubdirectories = 0;
 
+        // now we crawl into the found subdirectories first (!)
+        for (Path subDirectory : subDirectories) {
+            FileNodeViewModel subRoot = searchDirectory(subDirectory, unlinkedPDFFileFilter);
             if (!subRoot.getChildren().isEmpty()) {
-                fileCount += subRoot.getFileCount();
-                parent.getChildren().add(subRoot);
+                fileCountOfSubdirectories += subRoot.getFileCount();
+                fileNodeViewModelForCurrentDirectory.getChildren().add(subRoot);
             }
         }
+        // now we have the data of all subdirectories
+        // it is stored in fileNodeViewModelForCurrentDirectory.getChildren()
+
+        // now we handle the files in the current directory
+
         // filter files according to last edited date.
-        List<Path> filteredFiles = new ArrayList<>();
+        // Note that we do not use the "StreamSupport.stream" filtering functionality, because refactoring the code to that would lead to more code
+        List<Path> resultingFiles = new ArrayList<>();
         for (Path path : files) {
-            if (FileFilterUtils.filterByDate(path, dateFilter) && FileFilterUtils.filterForUnlinkedFiles(path, unlinkedFileFilter, getIgnoreFileSet(Path.of("")))) {
-                filteredFiles.add(path);
+            if (FileFilterUtils.filterByDate(path, dateFilter)) {
+                resultingFiles.add(path);
             }
         }
+
         // sort files according to last edited date.
-        filteredFiles = FileFilterUtils.sortByDate(filteredFiles, sorter);
-        parent.setFileCount(filteredFiles.size() + fileCount);
-        parent.getChildren().addAll(filteredFiles.stream()
+        resultingFiles = FileFilterUtils.sortByDate(resultingFiles, sorter);
+
+        // the count of all files is the count of the found files in current directory plus the count of all files in the subdirectories
+        fileNodeViewModelForCurrentDirectory.setFileCount(resultingFiles.size() + fileCountOfSubdirectories);
+
+        // create and add FileNodeViewModel to the FileNodeViewModel for the current directory
+        fileNodeViewModelForCurrentDirectory.getChildren().addAll(resultingFiles.stream()
                 .map(FileNodeViewModel::new)
                 .collect(Collectors.toList()));
-        return parent;
-    }
 
-    private Set<String> getIgnoreFileSet(Path directory) {
-        String gitIgnorePath = ".gitignore";
-        Set<String> IgnoreFileSet = new HashSet<>();
-
-        Path ignoreFile = directory.resolve(gitIgnorePath);
-
-        if (Files.exists(ignoreFile)) {
-            try (BufferedReader br = Files.newBufferedReader(ignoreFile)) {
-                String line = br.readLine();
-                while (line != null) {
-                    line = br.readLine();
-                    if ((line != null) && (line.length() > 2) && (line.charAt(0) == '*')) {
-                        IgnoreFileSet.add(line.substring(2).toLowerCase(Locale.ROOT));
-                    } else if ((line != null) && (line.length() > 1) && !line.contains("/")) {
-                        IgnoreFileSet.add(line);
-                    }
-                }
-            } catch (IOException e) {
-                LOGGER.error("Error reading file.", e);
-            }
-        }
-        return IgnoreFileSet;
+        return fileNodeViewModelForCurrentDirectory;
     }
 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
index 6e74f41d62e..e3d2b8b9133 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
@@ -52,14 +52,12 @@
 
                 <Label text="%File type" GridPane.columnIndex="0" GridPane.rowIndex="1"/>
                 <ComboBox fx:id="fileTypeCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="1"/>
-                <Label text="%Ignore File Extensions" GridPane.columnIndex="0" GridPane.rowIndex="2"/>
-                <ComboBox fx:id="unlinkedFileCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="2"/>
-                <Label text="%Last edited:" GridPane.columnIndex="0" GridPane.rowIndex="3"/>
-                <ComboBox fx:id="fileDateCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="3"/>
-                <Label text="%Sort by:" GridPane.columnIndex="0" GridPane.rowIndex="4"/>
-                <ComboBox fx:id="fileSortCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="4"/>
+                <Label text="%Last edited:" GridPane.columnIndex="0" GridPane.rowIndex="2"/>
+                <ComboBox fx:id="fileDateCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="2"/>
+                <Label text="%Sort by:" GridPane.columnIndex="0" GridPane.rowIndex="3"/>
+                <ComboBox fx:id="fileSortCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="3"/>
                 <Button fx:id="scanButton" onAction="#scanFiles" text="%Search"
-                        GridPane.columnIndex="2" GridPane.rowIndex="4">
+                        GridPane.columnIndex="2" GridPane.rowIndex="3">
                     <tooltip>
                         <Tooltip text="%Searches the selected directory for unlinked files."/>
                     </tooltip>
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
index 14f8728024b..2d1af899d12 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
@@ -55,7 +55,6 @@ public class UnlinkedFilesDialogView extends BaseDialog<Void> {
 
     @FXML private TextField directoryPathField;
     @FXML private ComboBox<FileExtensionViewModel> fileTypeCombo;
-    @FXML private ComboBox<FileIgnoreUnlinkedFiles> unlinkedFileCombo;
     @FXML private ComboBox<DateRange> fileDateCombo;
     @FXML private ComboBox<ExternalFileSorter> fileSortCombo;
     @FXML private CheckTreeView<FileNodeViewModel> unlinkedFilesList;
@@ -160,12 +159,6 @@ private void initDirectorySelection() {
         fileSortCombo.setItems(viewModel.getSorters());
         fileSortCombo.valueProperty().bindBidirectional(viewModel.selectedSortProperty());
         fileSortCombo.getSelectionModel().selectFirst();
-        new ViewModelListCellFactory<FileIgnoreUnlinkedFiles>()
-                .withText(FileIgnoreUnlinkedFiles::getFileIgnoreOption)
-                .install(unlinkedFileCombo);
-        unlinkedFileCombo.setItems(viewModel.unlinkedFileFilter());
-        unlinkedFileCombo.valueProperty().bindBidirectional(viewModel.selectedFileIgnoreProperty());
-        unlinkedFileCombo.getSelectionModel().selectFirst();
     }
 
     private void initUnlinkedFilesList() {
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
index e1e40d3909b..7d19b2bdc98 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
@@ -55,7 +55,6 @@ public class UnlinkedFilesDialogViewModel {
     private final ImportHandler importHandler;
     private final StringProperty directoryPath = new SimpleStringProperty("");
     private final ObjectProperty<FileExtensionViewModel> selectedExtension = new SimpleObjectProperty<>();
-    private final ObjectProperty<FileIgnoreUnlinkedFiles> selectedFileIgnore = new SimpleObjectProperty<>();
     private final ObjectProperty<DateRange> selectedDate = new SimpleObjectProperty<>();
     private final ObjectProperty<ExternalFileSorter> selectedSort = new SimpleObjectProperty<>();
 
@@ -70,7 +69,6 @@ public class UnlinkedFilesDialogViewModel {
     private final ObservableList<FileExtensionViewModel> fileFilterList;
     private final ObservableList<DateRange> dateFilterList;
     private final ObservableList<ExternalFileSorter> fileSortList;
-    private final ObservableList<FileIgnoreUnlinkedFiles> unlinkedFileFilter;
 
     private final DialogService dialogService;
     private final PreferencesService preferences;
@@ -107,8 +105,6 @@ public UnlinkedFilesDialogViewModel(DialogService dialogService,
                 new FileExtensionViewModel(StandardFileType.BIBTEX_DB, externalFileTypes),
                 new FileExtensionViewModel(StandardFileType.PDF, externalFileTypes));
 
-        this.unlinkedFileFilter = FXCollections.observableArrayList(FileIgnoreUnlinkedFiles.values());
-
         this.dateFilterList = FXCollections.observableArrayList(DateRange.values());
 
         this.fileSortList = FXCollections.observableArrayList(ExternalFileSorter.values());
@@ -123,13 +119,12 @@ public UnlinkedFilesDialogViewModel(DialogService dialogService,
     public void startSearch() {
         Path directory = this.getSearchDirectory();
         Filter<Path> selectedFileFilter = selectedExtension.getValue().dirFilter();
-        FileIgnoreUnlinkedFiles selectedUnlinkedFileIgnoreFilter = selectedFileIgnore.getValue();
         DateRange selectedDateFilter = selectedDate.getValue();
         ExternalFileSorter selectedSortFilter = selectedSort.getValue();
         progressValueProperty.unbind();
         progressTextProperty.unbind();
 
-        findUnlinkedFilesTask = new UnlinkedFilesCrawler(directory, selectedFileFilter, selectedDateFilter, selectedSortFilter, bibDatabase, preferences.getFilePreferences(), selectedUnlinkedFileIgnoreFilter)
+        findUnlinkedFilesTask = new UnlinkedFilesCrawler(directory, selectedFileFilter, selectedDateFilter, selectedSortFilter, bibDatabase, preferences.getFilePreferences())
                 .onRunning(() -> {
                     progressValueProperty.set(ProgressIndicator.INDETERMINATE_PROGRESS);
                     progressTextProperty.setValue(Localization.lang("Searching file system..."));
@@ -210,10 +205,6 @@ public ObservableList<FileExtensionViewModel> getFileFilters() {
         return this.fileFilterList;
     }
 
-    public ObservableList<FileIgnoreUnlinkedFiles> unlinkedFileFilter() {
-        return this.unlinkedFileFilter;
-    }
-
     public ObservableList<DateRange> getDateFilters() {
         return this.dateFilterList;
     }
@@ -275,10 +266,6 @@ public ObjectProperty<ExternalFileSorter> selectedSortProperty() {
         return this.selectedSort;
     }
 
-    public ObjectProperty<FileIgnoreUnlinkedFiles> selectedFileIgnoreProperty() {
-        return this.selectedFileIgnore;
-    }
-
     public StringProperty directoryPathProperty() {
         return this.directoryPath;
     }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java
index 0cdb7263263..0532801d222 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java
@@ -32,7 +32,6 @@ public UnlinkedPDFFileFilter(DirectoryStream.Filter<Path> fileFilter, BibDatabas
 
     @Override
     public boolean accept(Path pathname) throws IOException {
-
         if (Files.isDirectory(pathname)) {
             return true;
         } else {
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 0ff8e56e7f9..1cc2c330268 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2502,5 +2502,3 @@ Success\!\ Finished\ writing\ metadata.=Success! Finished writing metadata.
 
 Custom\ API\ key=Custom API key
 Check\ %0\ API\ Key\ Setting=Check %0 API Key Setting
-Ignore\ File\ Extensions=Ignore File Extensions
-Include\ All\ Files=Include All Files
diff --git a/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java b/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
index 45c7726b6a0..9af4b1364bb 100755
--- a/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
+++ b/src/test/java/org/jabref/gui/externalfiles/FileFilterUtilsTest.java
@@ -163,7 +163,6 @@ class filteringTests {
 
         @BeforeEach
         public void setUp(@TempDir Path tempDir) throws Exception {
-
             ignoreFileSet.add(".DS_Store");
             ignoreFileSet.add("Thumbs.db");
 
@@ -193,30 +192,5 @@ public void setUp(@TempDir Path tempDir) throws Exception {
             targetFiles.add(thirdPath);
             targetFiles.add(fourthPath);
         }
-
-        @Test
-        public void filteringByGitIgnore() {
-            ArrayList<Path> filteredFiles = new ArrayList<>();
-            for (Path path : files) {
-                if (FileFilterUtils.filterForUnlinkedFiles(path, FileIgnoreUnlinkedFiles.DEFAULT,
-                        ignoreFileSet)) {
-                    filteredFiles.add(path);
-                }
-            }
-            assertEquals(true, compareTwoPathList(filteredFiles, targetFiles));
-        }
-
-        public boolean compareTwoPathList(List<Path> list1, List<Path> list2) {
-            if (list1.size() != list2.size()) {
-                return false;
-            }
-            int cnt = 0;
-            for (Path path : list1) {
-                if (list2.contains(path)) {
-                    cnt++;
-                }
-            }
-            return cnt == list2.size();
-        }
     }
 }
diff --git a/src/test/java/org/jabref/gui/externalfiles/GitIgnoreFileFilterTest.java b/src/test/java/org/jabref/gui/externalfiles/GitIgnoreFileFilterTest.java
new file mode 100644
index 00000000000..a5922bbe9c6
--- /dev/null
+++ b/src/test/java/org/jabref/gui/externalfiles/GitIgnoreFileFilterTest.java
@@ -0,0 +1,30 @@
+package org.jabref.gui.externalfiles;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class GitIgnoreFileFilterTest {
+
+    @Test
+    public void checkSimpleGitIgnore(@TempDir Path dir) throws Exception {
+        Files.writeString(dir.resolve(".gitignore"), """
+                *.png
+                """);
+        GitIgnoreFileFilter gitIgnoreFileFilter = new GitIgnoreFileFilter(dir);
+        assertFalse(gitIgnoreFileFilter.accept(dir.resolve("test.png")));
+    }
+
+    @Test
+    public void checkDirectoryGitIgnore(@TempDir Path dir) throws Exception {
+        Files.writeString(dir.resolve(".gitignore"), """
+                **/*.png
+                """);
+        GitIgnoreFileFilter gitIgnoreFileFilter = new GitIgnoreFileFilter(dir);
+        assertFalse(gitIgnoreFileFilter.accept(dir.resolve("test.png")));
+    }
+}
diff --git a/src/test/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawlerTest.java b/src/test/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawlerTest.java
new file mode 100644
index 00000000000..3d53ae3ef59
--- /dev/null
+++ b/src/test/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawlerTest.java
@@ -0,0 +1,38 @@
+package org.jabref.gui.externalfiles;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.jabref.gui.util.FileNodeViewModel;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.preferences.FilePreferences;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+class UnlinkedFilesCrawlerTest {
+
+    @Test
+    public void minimalGitIgnore(@TempDir Path testRoot) throws Exception {
+        Files.writeString(testRoot.resolve(".gitignore"), """
+                *.png
+                """);
+        Path subDir = testRoot.resolve("subdir");
+        Files.createDirectories(subDir);
+        Files.createFile(subDir.resolve("test.png"));
+
+        UnlinkedPDFFileFilter unlinkedPDFFileFilter = mock(UnlinkedPDFFileFilter.class);
+        when(unlinkedPDFFileFilter.accept(any(Path.class))).thenReturn(true);
+
+        UnlinkedFilesCrawler unlinkedFilesCrawler = new UnlinkedFilesCrawler(testRoot, unlinkedPDFFileFilter, DateRange.ALL_TIME, ExternalFileSorter.DEFAULT, mock(BibDatabaseContext.class), mock(FilePreferences.class));
+
+        FileNodeViewModel fileNodeViewModel = unlinkedFilesCrawler.searchDirectory(testRoot, unlinkedPDFFileFilter);
+
+        assertEquals(new FileNodeViewModel(testRoot), fileNodeViewModel);
+    }
+}

From 27d021f134405fd2d0de23ee37ca1ae8108e1bdd Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 27 Jun 2022 22:33:28 +0200
Subject: [PATCH 18/20] Fix tests by adding hashcode and equals add some more
 tests Fix checsktyle

---
 .../gui/externalfiles/FileFilterUtils.java    |  3 ---
 .../externalfiles/GitIgnoreFileFilter.java    |  9 ++++----
 .../externalfiles/UnlinkedFilesCrawler.java   |  4 ----
 .../jabref/gui/util/FileNodeViewModel.java    | 19 ++++++++++++++++
 .../GitIgnoreFileFilterTest.java              | 22 ++++++++++++++++++-
 5 files changed, 44 insertions(+), 13 deletions(-)

diff --git a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
index 2050a71f336..6c9e48d13e3 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileFilterUtils.java
@@ -8,11 +8,8 @@
 import java.time.ZoneId;
 import java.util.Comparator;
 import java.util.List;
-import java.util.Set;
 import java.util.stream.Collectors;
 
-import org.jabref.logic.util.io.FileUtil;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java b/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
index 23d9be182e8..eb99ee3f425 100644
--- a/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
+++ b/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
@@ -8,7 +8,6 @@
 import java.nio.file.PathMatcher;
 import java.util.HashSet;
 import java.util.Set;
-import java.util.function.Predicate;
 import java.util.stream.Collectors;
 
 import org.slf4j.Logger;
@@ -59,9 +58,9 @@ public GitIgnoreFileFilter(Path path) {
     public boolean accept(Path path) throws IOException {
         // We assume that git does not stop at a patern, but tries all. We implement that behavior
         return gitIgnorePatterns.stream().noneMatch(filter ->
-                // we need this one for "*.png"
-                filter.matches(path.getFileName()) ||
-                // we need this one for "**/*.png"
-                filter.matches(path));
+        // we need this one for "*.png"
+        filter.matches(path.getFileName()) ||
+        // we need this one for "**/*.png"
+                                                              filter.matches(path));
     }
 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index 2e7ffcdda3e..ef26c177a25 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -1,17 +1,13 @@
 package org.jabref.gui.externalfiles;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.DirectoryStream.Filter;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Locale;
 import java.util.Map;
-import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 import java.util.stream.StreamSupport;
diff --git a/src/main/java/org/jabref/gui/util/FileNodeViewModel.java b/src/main/java/org/jabref/gui/util/FileNodeViewModel.java
index 2c7d4e1a103..cf4ff7196a6 100644
--- a/src/main/java/org/jabref/gui/util/FileNodeViewModel.java
+++ b/src/main/java/org/jabref/gui/util/FileNodeViewModel.java
@@ -7,6 +7,7 @@
 import java.time.LocalDateTime;
 import java.time.ZoneId;
 import java.time.format.DateTimeFormatter;
+import java.util.Objects;
 
 import javafx.beans.property.ReadOnlyListWrapper;
 import javafx.collections.FXCollections;
@@ -94,4 +95,22 @@ public String toString() {
                 this.children,
                 this.fileCount);
     }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(children, fileCount, path);
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (this == obj) {
+            return true;
+        }
+        if (!(obj instanceof FileNodeViewModel)) {
+            return false;
+        }
+        FileNodeViewModel other = (FileNodeViewModel) obj;
+        return Objects.equals(children, other.children) && (fileCount == other.fileCount) && Objects.equals(path, other.path);
+    }
+
 }
diff --git a/src/test/java/org/jabref/gui/externalfiles/GitIgnoreFileFilterTest.java b/src/test/java/org/jabref/gui/externalfiles/GitIgnoreFileFilterTest.java
index a5922bbe9c6..2504ffb55b7 100644
--- a/src/test/java/org/jabref/gui/externalfiles/GitIgnoreFileFilterTest.java
+++ b/src/test/java/org/jabref/gui/externalfiles/GitIgnoreFileFilterTest.java
@@ -6,7 +6,8 @@
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.io.TempDir;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 class GitIgnoreFileFilterTest {
 
@@ -19,6 +20,25 @@ public void checkSimpleGitIgnore(@TempDir Path dir) throws Exception {
         assertFalse(gitIgnoreFileFilter.accept(dir.resolve("test.png")));
     }
 
+    @Test
+    public void checkSimpleGitIgnoreWithAllowing(@TempDir Path dir) throws Exception {
+        Files.writeString(dir.resolve(".gitignore"), """
+                !*.png
+                """);
+        GitIgnoreFileFilter gitIgnoreFileFilter = new GitIgnoreFileFilter(dir);
+        assertTrue(gitIgnoreFileFilter.accept(dir.resolve("test.png")));
+    }
+
+    @Test
+    public void checkSimpleGitIgnoreWithOverwritingDefs(@TempDir Path dir) throws Exception {
+        Files.writeString(dir.resolve(".gitignore"), """
+                !*.png
+                *.png
+                """);
+        GitIgnoreFileFilter gitIgnoreFileFilter = new GitIgnoreFileFilter(dir);
+        assertFalse(gitIgnoreFileFilter.accept(dir.resolve("test.png")));
+    }
+
     @Test
     public void checkDirectoryGitIgnore(@TempDir Path dir) throws Exception {
         Files.writeString(dir.resolve(".gitignore"), """

From 9ede81d272aaab830289e2b4a8d817e7511885e6 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <1366654+koppor@users.noreply.github.com>
Date: Mon, 27 Jun 2022 22:41:28 +0200
Subject: [PATCH 19/20] Update FileNodeViewModel.java

---
 src/main/java/org/jabref/gui/util/FileNodeViewModel.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/util/FileNodeViewModel.java b/src/main/java/org/jabref/gui/util/FileNodeViewModel.java
index cf4ff7196a6..2410ad4b67c 100644
--- a/src/main/java/org/jabref/gui/util/FileNodeViewModel.java
+++ b/src/main/java/org/jabref/gui/util/FileNodeViewModel.java
@@ -112,5 +112,4 @@ public boolean equals(Object obj) {
         FileNodeViewModel other = (FileNodeViewModel) obj;
         return Objects.equals(children, other.children) && (fileCount == other.fileCount) && Objects.equals(path, other.path);
     }
-
 }

From 17ef36fca3e501d436fd65db10e5340fee003b3f Mon Sep 17 00:00:00 2001
From: Oliver Kopp <1366654+koppor@users.noreply.github.com>
Date: Mon, 27 Jun 2022 23:07:23 +0200
Subject: [PATCH 20/20] Fix indent

---
 .../org/jabref/gui/externalfiles/GitIgnoreFileFilter.java | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java b/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
index eb99ee3f425..64f01de977b 100644
--- a/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
+++ b/src/main/java/org/jabref/gui/externalfiles/GitIgnoreFileFilter.java
@@ -58,9 +58,9 @@ public GitIgnoreFileFilter(Path path) {
     public boolean accept(Path path) throws IOException {
         // We assume that git does not stop at a patern, but tries all. We implement that behavior
         return gitIgnorePatterns.stream().noneMatch(filter ->
-        // we need this one for "*.png"
-        filter.matches(path.getFileName()) ||
-        // we need this one for "**/*.png"
-                                                              filter.matches(path));
+                // we need this one for "*.png"
+                filter.matches(path.getFileName()) ||
+                // we need this one for "**/*.png"
+                filter.matches(path));
     }
 }