From 2f3d92c916d9a72f7e7b44afdb6f66b8e0fe07ba Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Thu, 14 Aug 2025 17:37:19 +0200
Subject: [PATCH 01/14] adds https://github.com/palukku/jabref/issues/23 adds
 https://github.com/palukku/jabref/issues/38 adds
 https://github.com/palukku/jabref/issues/42

---
 jabgui/build.gradle.kts                       |  1 +
 jabgui/src/main/java/module-info.java         |  1 +
 .../main/java/org/jabref/gui/JabRefGUI.java   | 14 ++++
 .../gui/preferences/general/GeneralTab.java   |  7 ++
 .../general/GeneralTabViewModel.java          | 54 ++++++++++++++
 .../gui/preferences/general/GeneralTab.fxml   |  6 ++
 .../preferences/JabRefCliPreferences.java     | 10 ++-
 .../logic/remote/RemotePreferences.java       | 35 ++++++++-
 .../logic/remote/RemotePreferencesTest.java   |  2 +-
 jabls/src/main/java/module-info.java          |  2 +-
 .../BibtexTextDocumentService.java            | 74 ++++++++++++++++---
 .../jabref/languageserver/LSPLauncher.java    | 12 ++-
 .../manager/LanguageServerManager.java        | 46 ++++++++++++
 .../manager/LanguageServerThread.java         | 49 ++++++++++++
 .../languageserver/manager/package-info.java  |  2 +
 jabsrv/src/main/java/module-info.java         |  4 -
 16 files changed, 295 insertions(+), 24 deletions(-)
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerManager.java
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerThread.java
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/manager/package-info.java

diff --git a/jabgui/build.gradle.kts b/jabgui/build.gradle.kts
index d8762e73053..b837855f4ff 100644
--- a/jabgui/build.gradle.kts
+++ b/jabgui/build.gradle.kts
@@ -24,6 +24,7 @@ dependencies {
     implementation("org.openjfx:javafx-web")
 
     implementation(project(":jabsrv"))
+    implementation(project(":jabls"))
 
     implementation("com.pixelduke:fxthemes")
 
diff --git a/jabgui/src/main/java/module-info.java b/jabgui/src/main/java/module-info.java
index 5b62ad2acc4..a79dd369c83 100644
--- a/jabgui/src/main/java/module-info.java
+++ b/jabgui/src/main/java/module-info.java
@@ -2,6 +2,7 @@
     requires org.jabref.jablib;
 
     requires org.jabref.jabsrv;
+    requires org.jabref.jabls;
 
     // Swing
     requires java.desktop;
diff --git a/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java b/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
index 348fa9c41b3..aec9ae84d15 100644
--- a/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
+++ b/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -32,6 +32,7 @@
 import org.jabref.gui.util.UiTaskExecutor;
 import org.jabref.gui.util.WebViewStore;
 import org.jabref.http.manager.HttpServerManager;
+import org.jabref.languageserver.manager.LanguageServerManager;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.ai.AiService;
 import org.jabref.logic.citation.SearchCitationsRelationsService;
@@ -85,6 +86,7 @@ public class JabRefGUI extends Application {
 
     private static RemoteListenerServerManager remoteListenerServerManager;
     private static HttpServerManager httpServerManager;
+    private static LanguageServerManager languageServerManager;
 
     private Stage mainStage;
 
@@ -167,6 +169,9 @@ public void initialize() {
         JabRefGUI.httpServerManager = new HttpServerManager();
         Injector.setModelOrService(HttpServerManager.class, JabRefGUI.httpServerManager);
 
+        JabRefGUI.languageServerManager = new LanguageServerManager();
+        Injector.setModelOrService(LanguageServerManager.class, JabRefGUI.languageServerManager);
+
         JabRefGUI.stateManager = new JabRefGuiStateManager();
         Injector.setModelOrService(StateManager.class, stateManager);
 
@@ -422,6 +427,9 @@ public void startBackgroundTasks() {
         if (remotePreferences.enableHttpServer()) {
             httpServerManager.start(stateManager, remotePreferences.getHttpServerUri());
         }
+        if (remotePreferences.enableLanguageServer()) {
+            languageServerManager.start(preferences, Injector.instantiateModelOrService(JournalAbbreviationRepository.class), remotePreferences.getLanguageServerPort());
+        }
     }
 
     @Override
@@ -465,6 +473,12 @@ public void stop() {
                 LOGGER.trace("HttpServerManager shut down");
             });
 
+            executor.submit(() -> {
+                LOGGER.trace("Shutting down language server manager");
+                languageServerManager.stop();
+                LOGGER.trace("LanguageServerManager shut down");
+            });
+
             executor.submit(() -> {
                 LOGGER.trace("Stopping background tasks");
                 Unirest.shutDown();
diff --git a/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTab.java b/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTab.java
index 28a224ba2ca..839e1ba0976 100644
--- a/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTab.java
+++ b/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTab.java
@@ -59,6 +59,8 @@ public class GeneralTab extends AbstractPreferenceTabView<GeneralTabViewModel> i
     @FXML private TextField remotePort;
     @FXML private CheckBox enableHttpServer;
     @FXML private TextField httpServerPort;
+    @FXML private CheckBox enableLanguageServer;
+    @FXML private TextField languageServerPort;
     @FXML private Button remoteHelp;
     @Inject private FileUpdateMonitor fileUpdateMonitor;
     @Inject private BibEntryTypesManager entryTypesManager;
@@ -145,6 +147,7 @@ public void initialize() {
         Platform.runLater(() -> {
             validationVisualizer.initVisualization(viewModel.remotePortValidationStatus(), remotePort);
             validationVisualizer.initVisualization(viewModel.httpPortValidationStatus(), httpServerPort);
+            validationVisualizer.initVisualization(viewModel.languageServerPortValidationStatus(), languageServerPort);
             validationVisualizer.initVisualization(viewModel.fontSizeValidationStatus(), fontSize);
             validationVisualizer.initVisualization(viewModel.customPathToThemeValidationStatus(), customThemePath);
         });
@@ -156,6 +159,10 @@ public void initialize() {
         enableHttpServer.selectedProperty().bindBidirectional(viewModel.enableHttpServerProperty());
         httpServerPort.textProperty().bindBidirectional(viewModel.httpPortProperty());
         httpServerPort.disableProperty().bind(enableHttpServer.selectedProperty().not());
+
+        enableLanguageServer.selectedProperty().bindBidirectional(viewModel.enableLanguageServerProperty());
+        languageServerPort.textProperty().bindBidirectional(viewModel.languageServerPortProperty());
+        languageServerPort.disableProperty().bind(enableLanguageServer.selectedProperty().not());
     }
 
     @FXML
diff --git a/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java b/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
index fb753d849c8..dd14af1f6f5 100644
--- a/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
+++ b/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
@@ -33,8 +33,10 @@
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.http.manager.HttpServerManager;
+import org.jabref.languageserver.manager.LanguageServerManager;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.LibraryPreferences;
+import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Language;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.ssl.TrustStoreManager;
@@ -111,6 +113,9 @@ public class GeneralTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty enableHttpServerProperty = new SimpleBooleanProperty();
     private final StringProperty httpPortProperty = new SimpleStringProperty("");
     private final Validator httpPortValidator;
+    private final Validator languageServerPortValidator;
+    private final BooleanProperty enableLanguageServerProperty = new SimpleBooleanProperty();
+    private final StringProperty languageServerPortProperty = new SimpleStringProperty("");
     private final TrustStoreManager trustStoreManager;
 
     private final FileUpdateMonitor fileUpdateMonitor;
@@ -171,6 +176,19 @@ public GeneralTabViewModel(DialogService dialogService, GuiPreferences preferenc
                     }
                 },
                 ValidationMessage.error("%s".formatted(Localization.lang("You must enter an integer value in the interval 1025-65535"))));
+
+        languageServerPortValidator = new FunctionBasedValidator<>(
+                languageServerPortProperty,
+                input -> {
+                    try {
+                        int portNumber = Integer.parseInt(languageServerPortProperty().getValue());
+                        return RemoteUtil.isUserPort(portNumber);
+                    } catch (NumberFormatException ex) {
+                        return false;
+                    }
+                },
+                ValidationMessage.error("%s".formatted(Localization.lang("You must enter an integer value in the interval 1025-65535"))));
+
         this.trustStoreManager = new TrustStoreManager(Path.of(preferences.getSSLPreferences().getTruststorePath()));
     }
 
@@ -182,6 +200,10 @@ public ValidationStatus httpPortValidationStatus() {
         return httpPortValidator.getValidationStatus();
     }
 
+    public ValidationStatus languageServerPortValidationStatus() {
+        return languageServerPortValidator.getValidationStatus();
+    }
+
     @Override
     public void setValues() {
         selectedLanguageProperty.setValue(workspacePreferences.getLanguage());
@@ -225,6 +247,9 @@ public void setValues() {
 
         enableHttpServerProperty.setValue(remotePreferences.enableHttpServer());
         httpPortProperty.setValue(String.valueOf(remotePreferences.getHttpPort()));
+
+        enableLanguageServerProperty.setValue(remotePreferences.enableLanguageServer());
+        languageServerPortProperty.setValue(String.valueOf(remotePreferences.getLanguageServerPort()));
     }
 
     @Override
@@ -297,6 +322,12 @@ public void storeSettings() {
             }
         });
 
+        getPortAsInt(languageServerPortProperty.getValue()).ifPresent(newPort -> {
+            if (remotePreferences.isDifferentLanguageServerPort(newPort)) {
+                remotePreferences.setLanguageServerPort(newPort);
+            }
+        });
+
         HttpServerManager httpServerManager = Injector.instantiateModelOrService(HttpServerManager.class);
         // stop in all cases, because the port might have changed
         httpServerManager.stop();
@@ -309,6 +340,17 @@ public void storeSettings() {
             httpServerManager.stop();
         }
 
+        LanguageServerManager languageServerManager = Injector.instantiateModelOrService(LanguageServerManager.class);
+        // stop in all cases, because the port might have changed
+        languageServerManager.stop();
+        if (enableLanguageServerProperty.getValue()) {
+            remotePreferences.setEnableLanguageServer(true);
+            languageServerManager.start(preferences, Injector.instantiateModelOrService(JournalAbbreviationRepository.class), remotePreferences.getLanguageServerPort());
+        } else {
+            remotePreferences.setEnableLanguageServer(false);
+            languageServerManager.stop();
+        }
+
         trustStoreManager.flush();
     }
 
@@ -332,6 +374,10 @@ public boolean validateSettings() {
             validator.addValidators(httpPortValidator);
         }
 
+        if (enableLanguageServerProperty.getValue()) {
+            validator.addValidators(languageServerPortValidator);
+        }
+
         if (fontOverrideProperty.getValue()) {
             validator.addValidators(fontSizeValidator);
         }
@@ -470,6 +516,14 @@ public StringProperty httpPortProperty() {
         return httpPortProperty;
     }
 
+    public BooleanProperty enableLanguageServerProperty() {
+        return enableLanguageServerProperty;
+    }
+
+    public StringProperty languageServerPortProperty() {
+        return languageServerPortProperty;
+    }
+
     public void openBrowser() {
         String url = "https://themes.jabref.org";
         try {
diff --git a/jabgui/src/main/resources/org/jabref/gui/preferences/general/GeneralTab.fxml b/jabgui/src/main/resources/org/jabref/gui/preferences/general/GeneralTab.fxml
index cab859b9ac9..4929d113058 100644
--- a/jabgui/src/main/resources/org/jabref/gui/preferences/general/GeneralTab.fxml
+++ b/jabgui/src/main/resources/org/jabref/gui/preferences/general/GeneralTab.fxml
@@ -88,6 +88,12 @@
         <TextField fx:id="httpServerPort" maxWidth="100.0" HBox.hgrow="ALWAYS" />
     </HBox>
 
+    <Label styleClass="sectionHeader" text="%Language Server" />
+    <HBox alignment="CENTER_LEFT" spacing="10.0">
+        <CheckBox fx:id="enableLanguageServer" text="%Enable Language Server on port" />
+        <TextField fx:id="languageServerPort" maxWidth="100.0" HBox.hgrow="ALWAYS" />
+    </HBox>
+
     <Label styleClass="sectionHeader" text="%Libraries"/>
     <GridPane hgap="10.0" vgap="4.0">
         <columnConstraints>
diff --git a/jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java b/jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java
index 5d7edac82a9..69ba38e69fb 100644
--- a/jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java
+++ b/jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java
@@ -371,6 +371,8 @@ public class JabRefCliPreferences implements CliPreferences {
     private static final String REMOTE_SERVER_PORT = "remoteServerPort";
     private static final String HTTP_SERVER_PORT = "httpServerPort";
     private static final String ENABLE_HTTP_SERVER = "enableHttpServer";
+    private static final String ENABLE_LANGUAGE_SERVER = "enableLanguageServer";
+    private static final String LANGUAGE_SERVER_PORT = "languageServerPort";
 
     private static final String AI_ENABLED = "aiEnabled";
     private static final String AI_AUTO_GENERATE_EMBEDDINGS = "aiAutoGenerateEmbeddings";
@@ -662,6 +664,8 @@ public JabRefCliPreferences() {
         defaults.put(REMOTE_SERVER_PORT, 6050);
         defaults.put(ENABLE_HTTP_SERVER, Boolean.FALSE);
         defaults.put(HTTP_SERVER_PORT, 23119);
+        defaults.put(ENABLE_LANGUAGE_SERVER, Boolean.FALSE);
+        defaults.put(LANGUAGE_SERVER_PORT, 2087);
 
         defaults.put(EXTERNAL_JOURNAL_LISTS, "");
         defaults.put(USE_AMS_FJOURNAL, true);
@@ -1366,12 +1370,16 @@ public RemotePreferences getRemotePreferences() {
                 getInt(REMOTE_SERVER_PORT),
                 getBoolean(USE_REMOTE_SERVER),
                 getInt(HTTP_SERVER_PORT),
-                getBoolean(ENABLE_HTTP_SERVER));
+                getBoolean(ENABLE_HTTP_SERVER),
+                getBoolean(ENABLE_LANGUAGE_SERVER),
+                getInt(LANGUAGE_SERVER_PORT));
 
         EasyBind.listen(remotePreferences.portProperty(), (_, _, newValue) -> putInt(REMOTE_SERVER_PORT, newValue));
         EasyBind.listen(remotePreferences.useRemoteServerProperty(), (_, _, newValue) -> putBoolean(USE_REMOTE_SERVER, newValue));
         EasyBind.listen(remotePreferences.httpPortProperty(), (_, _, newValue) -> putInt(HTTP_SERVER_PORT, newValue));
         EasyBind.listen(remotePreferences.enableHttpServerProperty(), (_, _, newValue) -> putBoolean(ENABLE_HTTP_SERVER, newValue));
+        EasyBind.listen(remotePreferences.languageServerPortProperty(), (_, _, newValue) -> putInt(LANGUAGE_SERVER_PORT, newValue));
+        EasyBind.listen(remotePreferences.enableLanguageServerProperty(), (_, _, newValue) -> putBoolean(ENABLE_LANGUAGE_SERVER, newValue));
 
         return remotePreferences;
     }
diff --git a/jablib/src/main/java/org/jabref/logic/remote/RemotePreferences.java b/jablib/src/main/java/org/jabref/logic/remote/RemotePreferences.java
index cb228f327e6..72eeb9f9dbc 100644
--- a/jablib/src/main/java/org/jabref/logic/remote/RemotePreferences.java
+++ b/jablib/src/main/java/org/jabref/logic/remote/RemotePreferences.java
@@ -27,11 +27,16 @@ public class RemotePreferences {
     private final IntegerProperty httpPort;
     private final BooleanProperty enableHttpServer;
 
-    public RemotePreferences(int port, boolean useRemoteServer, int httpPort, boolean enableHttpServer) {
+    private final BooleanProperty enableLanguageServer;
+    private final IntegerProperty languageServerPort;
+
+    public RemotePreferences(int port, boolean useRemoteServer, int httpPort, boolean enableHttpServer, boolean enableLanguageServer, int languageServerPort) {
         this.port = new SimpleIntegerProperty(port);
         this.useRemoteServer = new SimpleBooleanProperty(useRemoteServer);
         this.httpPort = new SimpleIntegerProperty(httpPort);
         this.enableHttpServer = new SimpleBooleanProperty(enableHttpServer);
+        this.enableLanguageServer = new SimpleBooleanProperty(enableLanguageServer);
+        this.languageServerPort = new SimpleIntegerProperty(languageServerPort);
     }
 
     public int getPort() {
@@ -90,6 +95,34 @@ public void setEnableHttpServer(boolean enableHttpServer) {
         this.enableHttpServer.setValue(enableHttpServer);
     }
 
+    public int getLanguageServerPort() {
+        return languageServerPort.getValue();
+    }
+
+    public IntegerProperty languageServerPortProperty() {
+        return languageServerPort;
+    }
+
+    public void setLanguageServerPort(int languageServerPort) {
+        this.languageServerPort.setValue(languageServerPort);
+    }
+
+    public boolean isDifferentLanguageServerPort(int otherLanguageServerPort) {
+        return getLanguageServerPort() != otherLanguageServerPort;
+    }
+
+    public boolean enableLanguageServer() {
+        return enableLanguageServer.getValue();
+    }
+
+    public BooleanProperty enableLanguageServerProperty() {
+        return enableLanguageServer;
+    }
+
+    public void setEnableLanguageServer(boolean enableLanguageServer) {
+        this.enableLanguageServer.setValue(enableLanguageServer);
+    }
+
     /// Gets the IP address where both the remote server and the http server are listening.
     public static InetAddress getIpAddress() throws UnknownHostException {
         return InetAddress.getByName("localhost");
diff --git a/jablib/src/test/java/org/jabref/logic/remote/RemotePreferencesTest.java b/jablib/src/test/java/org/jabref/logic/remote/RemotePreferencesTest.java
index ad0c8a0e70c..d33626f3696 100644
--- a/jablib/src/test/java/org/jabref/logic/remote/RemotePreferencesTest.java
+++ b/jablib/src/test/java/org/jabref/logic/remote/RemotePreferencesTest.java
@@ -13,7 +13,7 @@ class RemotePreferencesTest {
 
     @BeforeEach
     void setUp() {
-        preferences = new RemotePreferences(1000, true, 3000, false);
+        preferences = new RemotePreferences(1000, true, 3000, false, false, 2087);
     }
 
     @Test
diff --git a/jabls/src/main/java/module-info.java b/jabls/src/main/java/module-info.java
index 1d16730351d..3ecd8b83352 100644
--- a/jabls/src/main/java/module-info.java
+++ b/jabls/src/main/java/module-info.java
@@ -1,6 +1,7 @@
 module org.jabref.jabls {
     exports org.jabref.languageserver;
     opens org.jabref.languageserver to lsp4j, lsp4j.jsonrpc;
+    exports org.jabref.languageserver.manager;
 
     requires org.jabref.jablib;
 
@@ -9,5 +10,4 @@
     requires lsp4j;
     requires lsp4j.jsonrpc;
     requires lsp4j.websocket;
-    requires lsp4j.websocket.jakarta;
 }
diff --git a/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java b/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
index 37377bfd991..13cc91bb4b1 100644
--- a/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
+++ b/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
@@ -1,14 +1,25 @@
 package org.jabref.languageserver;
 
 import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
+import java.util.Optional;
+import java.util.Set;
 import java.util.concurrent.CompletableFuture;
+import java.util.stream.Collectors;
 
 import org.jabref.logic.importer.fileformat.BibtexParser;
 import org.jabref.logic.integrity.IntegrityCheck;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
+import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibEntryType;
+import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.field.Field;
 
 import org.eclipse.lsp4j.CompletionItem;
 import org.eclipse.lsp4j.CompletionList;
@@ -29,6 +40,7 @@
 public class BibtexTextDocumentService implements TextDocumentService {
 
     private static final Range NULL_RANGE = new Range(new Position(0, 0), new Position(0, 0));
+    private static final String DIAGNOSTIC_SOURCE = "JabRef";
     private final CliPreferences jabRefCliPreferences;
     private final JournalAbbreviationRepository abbreviationRepository;
     private LanguageClient client;
@@ -75,12 +87,47 @@ private void handleDiagnostics(String uri, String content, int version) {
                     NULL_RANGE,
                     "Parse error: " + e.getMessage(),
                     DiagnosticSeverity.Error,
-                    "JabRef"
+                    DIAGNOSTIC_SOURCE
             );
             client.publishDiagnostics(new PublishDiagnosticsParams(uri, List.of(parseDiagnostic), version));
             return;
         }
 
+        List<Diagnostic> diagnostics = new ArrayList<>();
+
+        diagnostics.addAll(integrityCheck(bibDatabaseContext, content));
+        diagnostics.addAll(consistencyCheck(bibDatabaseContext, content));
+
+        client.publishDiagnostics(new PublishDiagnosticsParams(uri, diagnostics, version));
+    }
+
+    private List<Diagnostic> consistencyCheck(BibDatabaseContext bibDatabaseContext, String content) {
+        List<Diagnostic> diagnostics = new ArrayList<>();
+        BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
+        BibliographyConsistencyCheck.Result result = consistencyCheck.check(bibDatabaseContext.getEntries(), (_, _) -> { });
+
+        result.entryTypeToResultMap().forEach((entryType, entryTypeResult) -> {
+            Optional<BibEntryType> bibEntryType = new BibEntryTypesManager().enrich(entryType, bibDatabaseContext.getMode());
+            Set<Field> requiredFields = bibEntryType
+                    .map(BibEntryType::getRequiredFields)
+                    .stream()
+                    .flatMap(Collection::stream)
+                    .flatMap(orFields -> orFields.getFields().stream())
+                    .collect(Collectors.toSet());
+
+            entryTypeResult.sortedEntries().forEach(entry -> {
+                requiredFields.forEach(requiredField -> {
+                    if (!entry.hasField(requiredField)) {
+                        diagnostics.add(createGeneralDiagnostic(Localization.lang("required field '%0' is missing", requiredField.getName()), content, entry));
+                    }
+                });
+            });
+        });
+
+        return diagnostics;
+    }
+
+    private List<Diagnostic> integrityCheck(BibDatabaseContext bibDatabaseContext, String content) {
         IntegrityCheck integrityCheck = new IntegrityCheck(
                 bibDatabaseContext,
                 jabRefCliPreferences.getFilePreferences(),
@@ -89,18 +136,21 @@ private void handleDiagnostics(String uri, String content, int version) {
                 true
         );
 
-        List<Diagnostic> diagnostics = bibDatabaseContext.getEntries().stream()
-                                                         .flatMap(entry -> integrityCheck.checkEntry(entry).stream()
-                                                                                         .map(message -> new Diagnostic(
-                                                                                                 findTextRange(content, entry.getParsedSerialization()),
-                                                                                                 message.message(),
-                                                                                                 DiagnosticSeverity.Warning,
-                                                                                                 "JabRef"
-                                                                                         ))
-                                                         )
-                                                         .toList();
+        return bibDatabaseContext.getEntries().stream().flatMap(entry -> integrityCheck.checkEntry(entry).stream().map(message -> {
+            if (entry.getField(message.field()).isPresent()) {
+                return createFieldDiagnostic(message.message(), message.field(), content, entry);
+            } else {
+                return createGeneralDiagnostic(message.message(), content, entry);
+            }
+        })).toList();
+    }
 
-        client.publishDiagnostics(new PublishDiagnosticsParams(uri, diagnostics, version));
+    private Diagnostic createFieldDiagnostic(String message, Field field, String content, BibEntry entry) {
+        return new Diagnostic(findTextRange(content, entry.getField(field).get()), message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
+    }
+
+    private Diagnostic createGeneralDiagnostic(String message, String content, BibEntry entry) {
+        return new Diagnostic(findTextRange(content, entry.getCitationKey().orElse("")), message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
     }
 
     private static Range findTextRange(String content, String searchText) {
diff --git a/jabls/src/main/java/org/jabref/languageserver/LSPLauncher.java b/jabls/src/main/java/org/jabref/languageserver/LSPLauncher.java
index 1fa997a443b..c576b500f85 100644
--- a/jabls/src/main/java/org/jabref/languageserver/LSPLauncher.java
+++ b/jabls/src/main/java/org/jabref/languageserver/LSPLauncher.java
@@ -28,13 +28,13 @@ public class LSPLauncher {
     private JournalAbbreviationRepository abbreviationRepository;
 
     public void run(CliPreferences cliPreferences) {
-        run(cliPreferences, new JournalAbbreviationRepository());
+        run(cliPreferences, new JournalAbbreviationRepository(), 2087);
     }
 
-    public void run(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
+    public void run(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository, int port) {
         this.cliPreferences = cliPreferences;
         this.abbreviationRepository = abbreviationRepository;
-        start(2087);
+        start(port);
     }
 
     public void start(int port) {
@@ -83,7 +83,6 @@ private void handleClient(Socket socket) {
     }
 
     public void shutdown() {
-        running = false;
         try {
             if (serverSocket != null && !serverSocket.isClosed()) {
                 serverSocket.close();
@@ -94,6 +93,11 @@ public void shutdown() {
         } catch (IOException e) {
             LOGGER.error("Error during LSP shutdown", e);
         }
+        running = false;
         LOGGER.info("LSP Server shutdown.");
     }
+
+    public boolean isRunning() {
+        return running;
+    }
 }
diff --git a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerManager.java b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerManager.java
new file mode 100644
index 00000000000..2d61caa9c72
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerManager.java
@@ -0,0 +1,46 @@
+package org.jabref.languageserver.manager;
+
+import org.jabref.logic.journals.JournalAbbreviationRepository;
+import org.jabref.logic.preferences.CliPreferences;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/// Manages the LanguageServerThread through typical life cycle methods.
+public class LanguageServerManager implements AutoCloseable {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(LanguageServerManager.class);
+
+    private LanguageServerThread languageServerThread;
+
+    public synchronized void start(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository, int port) {
+        if (languageServerThread != null) {
+            LOGGER.warn("Language server manager already started, cannot start again.");
+            return;
+        }
+
+        languageServerThread = new LanguageServerThread(cliPreferences, abbreviationRepository, port);
+        // This enqueues the thread to run in the background
+        // The JVM will take care of running it at some point in time in the future
+        // Thus, we cannot check directly if it really runs
+        languageServerThread.start();
+        LOGGER.debug("Triggered language server start up.");
+    }
+
+    public synchronized void stop() {
+        LOGGER.debug("Stopping language server manager...");
+        if (languageServerThread != null) {
+            languageServerThread.interrupt();
+            languageServerThread = null;
+            LOGGER.debug("Language server stopped successfully.");
+        } else {
+            LOGGER.debug("Language server is not started, nothing to stop.");
+        }
+    }
+
+    @Override
+    public void close() {
+        LOGGER.debug("Closing Language server manager...");
+        stop();
+    }
+}
diff --git a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerThread.java b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerThread.java
new file mode 100644
index 00000000000..73c2304a2a1
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerThread.java
@@ -0,0 +1,49 @@
+package org.jabref.languageserver.manager;
+
+import org.jabref.languageserver.LSPLauncher;
+import org.jabref.logic.journals.JournalAbbreviationRepository;
+import org.jabref.logic.preferences.CliPreferences;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * This thread wrapper is required to be able to interrupt the language server, e.g. when JabRef is closing down the language server should shutdown as well.
+ */
+public class LanguageServerThread extends Thread {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(LanguageServerThread.class);
+
+    private final CliPreferences cliPreferences;
+    private final JournalAbbreviationRepository abbreviationRepository;
+    private LSPLauncher lspLauncher;
+    private int port;
+
+    public LanguageServerThread(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository, int port) {
+        this.cliPreferences = cliPreferences;
+        this.abbreviationRepository = abbreviationRepository;
+        this.lspLauncher = new LSPLauncher();
+        this.port = port;
+        this.setName("JabLs - JabRef Language Server on :" + port);
+    }
+
+    @Override
+    public void run() {
+        this.lspLauncher.run(cliPreferences, abbreviationRepository, port);
+    }
+
+    @Override
+    public void interrupt() {
+        LOGGER.debug("Interrupting {}", this.getName());
+        if (this.lspLauncher == null) {
+            LOGGER.warn("LSPLauncher is null, cannot shutdown.");
+        } else {
+            this.lspLauncher.shutdown();
+        }
+        super.interrupt();
+    }
+
+    public boolean started() {
+        return lspLauncher != null && lspLauncher.isRunning();
+    }
+}
diff --git a/jabls/src/main/java/org/jabref/languageserver/manager/package-info.java b/jabls/src/main/java/org/jabref/languageserver/manager/package-info.java
new file mode 100644
index 00000000000..e61d6ce7087
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/manager/package-info.java
@@ -0,0 +1,2 @@
+/// Implemented similar to package org.jabref.logic.remote.server;
+package org.jabref.languageserver.manager;
diff --git a/jabsrv/src/main/java/module-info.java b/jabsrv/src/main/java/module-info.java
index 4031ddff5e7..5f9b180b771 100644
--- a/jabsrv/src/main/java/module-info.java
+++ b/jabsrv/src/main/java/module-info.java
@@ -59,8 +59,4 @@
     requires com.fasterxml.jackson.annotation;
     requires com.fasterxml.jackson.databind;
 
-    requires lsp4j;
-    requires lsp4j.jsonrpc;
-    requires lsp4j.websocket;
-    requires lsp4j.websocket.jakarta;
 }

From bf259a0084755e69a6d6c4df6b23eaad5ff2ab57 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Fri, 15 Aug 2025 12:49:27 +0200
Subject: [PATCH 02/14] fix localization

---
 jablib/src/main/resources/l10n/JabRef_en.properties | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/jablib/src/main/resources/l10n/JabRef_en.properties b/jablib/src/main/resources/l10n/JabRef_en.properties
index 4bfe86d2053..f359335afa6 100644
--- a/jablib/src/main/resources/l10n/JabRef_en.properties
+++ b/jablib/src/main/resources/l10n/JabRef_en.properties
@@ -1848,6 +1848,9 @@ Cannot\ use\ port\ %0\ for\ remote\ operation;\ another\ application\ may\ be\ u
 Enable\ HTTP\ Server\ (e.g.,\ for\ JabMap)\ on\ port=Enable HTTP Server (e.g., for JabMap) on port
 HTTP\ Server=HTTP Server
 
+Enable\ Language\ Server\ on\ port=Enable Language Server on port
+Language\ Server=Language Server
+
 Grobid\ URL=Grobid URL
 Allow\ sending\ PDF\ files\ and\ raw\ citation\ strings\ to\ a\ JabRef\ online\ service\ (Grobid)\ to\ determine\ Metadata.\ This\ produces\ better\ results.=Allow sending PDF files and raw citation strings to a JabRef online service (Grobid) to determine Metadata. This produces better results.
 Send\ to\ Grobid=Send to Grobid

From d4d222a37fb9d9b79d579a2725c5c2144a72d90f Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Fri, 22 Aug 2025 16:59:16 +0200
Subject: [PATCH 03/14] Changes according to review comments Remove unnecessary
 classes and renaming

---
 .../main/java/org/jabref/gui/JabRefGUI.java   | 15 +++---
 .../general/GeneralTabViewModel.java          | 43 ++++------------
 .../org/jabref/logic/remote/RemoteUtil.java   |  9 ++++
 .../main/resources/l10n/JabRef_en.properties  |  1 +
 .../jabref/languageserver/cli/ServerCli.java  |  9 ++--
 .../src/main/resources/tinylog.properties     |  2 +-
 .../BibtexTextDocumentService.java            | 35 +++++++++++--
 .../{LSPServer.java => LspClientHandler.java} |  6 +--
 .../{LSPLauncher.java => LspLauncher.java}    | 51 ++++++++++---------
 ...ger.java => LanguageServerController.java} | 29 +++++++----
 .../manager/LanguageServerThread.java         | 49 ------------------
 11 files changed, 116 insertions(+), 133 deletions(-)
 rename jabls/src/main/java/org/jabref/languageserver/{LSPServer.java => LspClientHandler.java} (92%)
 rename jabls/src/main/java/org/jabref/languageserver/{LSPLauncher.java => LspLauncher.java} (66%)
 rename jabls/src/main/java/org/jabref/languageserver/manager/{LanguageServerManager.java => LanguageServerController.java} (56%)
 delete mode 100644 jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerThread.java

diff --git a/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java b/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
index b3b8922c05b..ef74648cd35 100644
--- a/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
+++ b/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -33,7 +33,7 @@
 import org.jabref.gui.util.UiTaskExecutor;
 import org.jabref.gui.util.WebViewStore;
 import org.jabref.http.manager.HttpServerManager;
-import org.jabref.languageserver.manager.LanguageServerManager;
+import org.jabref.languageserver.manager.LanguageServerController;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.ai.AiService;
 import org.jabref.logic.citation.SearchCitationsRelationsService;
@@ -87,7 +87,7 @@ public class JabRefGUI extends Application {
 
     private static RemoteListenerServerManager remoteListenerServerManager;
     private static HttpServerManager httpServerManager;
-    private static LanguageServerManager languageServerManager;
+    private static LanguageServerController languageServerController;
 
     private Stage mainStage;
 
@@ -158,8 +158,9 @@ public void initialize() {
         Injector.setModelOrService(DirectoryMonitor.class, directoryMonitor);
 
         BibEntryTypesManager entryTypesManager = preferences.getCustomEntryTypesRepository();
+        JournalAbbreviationRepository journalAbbreviationRepository = JournalAbbreviationLoader.loadRepository(preferences.getJournalAbbreviationPreferences());
         Injector.setModelOrService(BibEntryTypesManager.class, entryTypesManager);
-        Injector.setModelOrService(JournalAbbreviationRepository.class, JournalAbbreviationLoader.loadRepository(preferences.getJournalAbbreviationPreferences()));
+        Injector.setModelOrService(JournalAbbreviationRepository.class, journalAbbreviationRepository);
         Injector.setModelOrService(ProtectedTermsLoader.class, new ProtectedTermsLoader(preferences.getProtectedTermsPreferences()));
 
         IndexManager.clearOldSearchIndices();
@@ -170,8 +171,8 @@ public void initialize() {
         JabRefGUI.httpServerManager = new HttpServerManager();
         Injector.setModelOrService(HttpServerManager.class, JabRefGUI.httpServerManager);
 
-        JabRefGUI.languageServerManager = new LanguageServerManager();
-        Injector.setModelOrService(LanguageServerManager.class, JabRefGUI.languageServerManager);
+        JabRefGUI.languageServerController = new LanguageServerController(preferences, journalAbbreviationRepository);
+        Injector.setModelOrService(LanguageServerController.class, JabRefGUI.languageServerController);
 
         JabRefGUI.stateManager = new JabRefGuiStateManager();
         Injector.setModelOrService(StateManager.class, stateManager);
@@ -430,7 +431,7 @@ public void startBackgroundTasks() {
             httpServerManager.start(stateManager, remotePreferences.getHttpServerUri());
         }
         if (remotePreferences.enableLanguageServer()) {
-            languageServerManager.start(preferences, Injector.instantiateModelOrService(JournalAbbreviationRepository.class), remotePreferences.getLanguageServerPort());
+            languageServerController.start(remotePreferences.getLanguageServerPort());
         }
     }
 
@@ -477,7 +478,7 @@ public void stop() {
 
             executor.submit(() -> {
                 LOGGER.trace("Shutting down language server manager");
-                languageServerManager.stop();
+                languageServerController.stop();
                 LOGGER.trace("LanguageServerManager shut down");
             });
 
diff --git a/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java b/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
index dd14af1f6f5..51125c69a2e 100644
--- a/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
+++ b/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
@@ -33,10 +33,9 @@
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.http.manager.HttpServerManager;
-import org.jabref.languageserver.manager.LanguageServerManager;
+import org.jabref.languageserver.manager.LanguageServerController;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.LibraryPreferences;
-import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Language;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.ssl.TrustStoreManager;
@@ -153,41 +152,21 @@ public GeneralTabViewModel(DialogService dialogService, GuiPreferences preferenc
 
         remotePortValidator = new FunctionBasedValidator<>(
                 remotePortProperty,
-                input -> {
-                    try {
-                        int portNumber = Integer.parseInt(remotePortProperty().getValue());
-                        return RemoteUtil.isUserPort(portNumber);
-                    } catch (NumberFormatException ex) {
-                        return false;
-                    }
-                },
+                RemoteUtil::isStringUserPort,
                 ValidationMessage.error("%s > %s %n %n %s".formatted(
                         Localization.lang("Network"),
                         Localization.lang("Remote operation"),
                         Localization.lang("You must enter an integer value in the interval 1025-65535"))));
+
         httpPortValidator = new FunctionBasedValidator<>(
                 httpPortProperty,
-                input -> {
-                    try {
-                        int portNumber = Integer.parseInt(httpPortProperty().getValue());
-                        return RemoteUtil.isUserPort(portNumber);
-                    } catch (NumberFormatException ex) {
-                        return false;
-                    }
-                },
+                RemoteUtil::isStringUserPort,
                 ValidationMessage.error("%s".formatted(Localization.lang("You must enter an integer value in the interval 1025-65535"))));
 
         languageServerPortValidator = new FunctionBasedValidator<>(
                 languageServerPortProperty,
-                input -> {
-                    try {
-                        int portNumber = Integer.parseInt(languageServerPortProperty().getValue());
-                        return RemoteUtil.isUserPort(portNumber);
-                    } catch (NumberFormatException ex) {
-                        return false;
-                    }
-                },
-                ValidationMessage.error("%s".formatted(Localization.lang("You must enter an integer value in the interval 1025-65535"))));
+                RemoteUtil::isStringUserPort,
+                ValidationMessage.error(Localization.lang("You must enter an integer value in the interval 1025-65535")));
 
         this.trustStoreManager = new TrustStoreManager(Path.of(preferences.getSSLPreferences().getTruststorePath()));
     }
@@ -340,15 +319,15 @@ public void storeSettings() {
             httpServerManager.stop();
         }
 
-        LanguageServerManager languageServerManager = Injector.instantiateModelOrService(LanguageServerManager.class);
-        // stop in all cases, because the port might have changed
-        languageServerManager.stop();
+        LanguageServerController languageServerController = Injector.instantiateModelOrService(LanguageServerController.class);
+        // stop in all cases, because the port might have changed (or other settings that can't be easily tracked https://github.com/JabRef/jabref/pull/13697#discussion_r2285997003)
+        languageServerController.stop();
         if (enableLanguageServerProperty.getValue()) {
             remotePreferences.setEnableLanguageServer(true);
-            languageServerManager.start(preferences, Injector.instantiateModelOrService(JournalAbbreviationRepository.class), remotePreferences.getLanguageServerPort());
+            languageServerController.start(remotePreferences.getLanguageServerPort());
         } else {
             remotePreferences.setEnableLanguageServer(false);
-            languageServerManager.stop();
+            languageServerController.stop();
         }
 
         trustStoreManager.flush();
diff --git a/jablib/src/main/java/org/jabref/logic/remote/RemoteUtil.java b/jablib/src/main/java/org/jabref/logic/remote/RemoteUtil.java
index 66e3a543c65..042f18f0d32 100644
--- a/jablib/src/main/java/org/jabref/logic/remote/RemoteUtil.java
+++ b/jablib/src/main/java/org/jabref/logic/remote/RemoteUtil.java
@@ -8,4 +8,13 @@ private RemoteUtil() {
     public static boolean isUserPort(int portNumber) {
         return (portNumber >= 1024) && (portNumber <= 65535);
     }
+
+    public static boolean isStringUserPort(String portString) {
+        try {
+            int portNumber = Integer.parseInt(portString);
+            return isUserPort(portNumber);
+        } catch (NumberFormatException numberFormatException) {
+            return false;
+        }
+    }
 }
diff --git a/jablib/src/main/resources/l10n/JabRef_en.properties b/jablib/src/main/resources/l10n/JabRef_en.properties
index f359335afa6..a1789d26e6d 100644
--- a/jablib/src/main/resources/l10n/JabRef_en.properties
+++ b/jablib/src/main/resources/l10n/JabRef_en.properties
@@ -1814,6 +1814,7 @@ Connect=Connect
 Connection\ error=Connection error
 Connection\ to\ %0\ server\ established.=Connection to %0 server established.
 Required\ field\ "%0"\ is\ empty.=Required field "%0" is empty.
+Optional\ field\ "%0"\ is\ empty.=Optional field "%0" is empty.
 %0\ driver\ not\ available.=%0 driver not available.
 The\ connection\ to\ the\ server\ has\ been\ terminated.=The connection to the server has been terminated.
 Reconnect=Reconnect
diff --git a/jabls-cli/src/main/java/org/jabref/languageserver/cli/ServerCli.java b/jabls-cli/src/main/java/org/jabref/languageserver/cli/ServerCli.java
index e55c084d411..b1a7515d3db 100644
--- a/jabls-cli/src/main/java/org/jabref/languageserver/cli/ServerCli.java
+++ b/jabls-cli/src/main/java/org/jabref/languageserver/cli/ServerCli.java
@@ -3,7 +3,7 @@
 import java.util.concurrent.Callable;
 
 import org.jabref.architecture.AllowedToUseStandardStreams;
-import org.jabref.languageserver.LSPLauncher;
+import org.jabref.languageserver.LspLauncher;
 import org.jabref.logic.preferences.JabRefCliPreferences;
 
 import org.slf4j.Logger;
@@ -16,6 +16,9 @@
 public class ServerCli implements Callable<Void> {
     private static final Logger LOGGER = LoggerFactory.getLogger(ServerCli.class);
 
+    @CommandLine.Option(names = {"-p", "--port"}, description = "the port")
+    private Integer port = 2087;
+
     public static void main(final String[] args) throws InterruptedException {
         SLF4JBridgeHandler.removeHandlersForRootLogger();
         SLF4JBridgeHandler.install();
@@ -25,8 +28,8 @@ public static void main(final String[] args) throws InterruptedException {
 
     @Override
     public Void call() throws InterruptedException {
-        LSPLauncher lspLauncher = new LSPLauncher();
-        lspLauncher.run(JabRefCliPreferences.getInstance());
+        LspLauncher lspLauncher = new LspLauncher(JabRefCliPreferences.getInstance(), port);
+        lspLauncher.run();
 
         // Keep the server running until user kills the process (e.g., presses Ctrl+C)
         Thread.currentThread().join();
diff --git a/jabls-cli/src/main/resources/tinylog.properties b/jabls-cli/src/main/resources/tinylog.properties
index c10c6ac62fd..9b0e192d38e 100644
--- a/jabls-cli/src/main/resources/tinylog.properties
+++ b/jabls-cli/src/main/resources/tinylog.properties
@@ -4,7 +4,7 @@ writerConsole = console
 # More shrunk exception logs. See https://tinylog.org/v2/configuration/#strip-stack-trace-elements for details
 exception = strip: jdk.internal
 
-level@org.jabref.languageserver.LSPLauncher = debug
+level@org.jabref.languageserver.LspLauncher = debug
 level@org.jabref.languageserver.cli.ServerCli = debug
 
 level@org.apache.pdfbox.pdmodel.font = error
diff --git a/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java b/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
index 13cc91bb4b1..49d1454943d 100644
--- a/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
+++ b/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
@@ -19,6 +19,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryType;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.field.BibField;
 import org.jabref.model.entry.field.Field;
 
 import org.eclipse.lsp4j.CompletionItem;
@@ -41,9 +42,12 @@ public class BibtexTextDocumentService implements TextDocumentService {
 
     private static final Range NULL_RANGE = new Range(new Position(0, 0), new Position(0, 0));
     private static final String DIAGNOSTIC_SOURCE = "JabRef";
+
     private final CliPreferences jabRefCliPreferences;
     private final JournalAbbreviationRepository abbreviationRepository;
+
     private LanguageClient client;
+    private boolean checkConsistency = true;
 
     public BibtexTextDocumentService(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
         this.jabRefCliPreferences = cliPreferences;
@@ -85,7 +89,9 @@ private void handleDiagnostics(String uri, String content, int version) {
         } catch (Exception e) {
             Diagnostic parseDiagnostic = new Diagnostic(
                     NULL_RANGE,
-                    "Parse error: " + e.getMessage(),
+                    Localization.lang(
+                            "Failed to parse entries.\nThe following error was encountered:\n%0",
+                            e.getMessage()),
                     DiagnosticSeverity.Error,
                     DIAGNOSTIC_SOURCE
             );
@@ -96,7 +102,10 @@ private void handleDiagnostics(String uri, String content, int version) {
         List<Diagnostic> diagnostics = new ArrayList<>();
 
         diagnostics.addAll(integrityCheck(bibDatabaseContext, content));
-        diagnostics.addAll(consistencyCheck(bibDatabaseContext, content));
+
+        if (checkConsistency) {
+            diagnostics.addAll(consistencyCheck(bibDatabaseContext, content));
+        }
 
         client.publishDiagnostics(new PublishDiagnosticsParams(uri, diagnostics, version));
     }
@@ -104,7 +113,8 @@ private void handleDiagnostics(String uri, String content, int version) {
     private List<Diagnostic> consistencyCheck(BibDatabaseContext bibDatabaseContext, String content) {
         List<Diagnostic> diagnostics = new ArrayList<>();
         BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
-        BibliographyConsistencyCheck.Result result = consistencyCheck.check(bibDatabaseContext.getEntries(), (_, _) -> { });
+        BibliographyConsistencyCheck.Result result = consistencyCheck.check(bibDatabaseContext.getEntries(), (_, _) -> {
+        });
 
         result.entryTypeToResultMap().forEach((entryType, entryTypeResult) -> {
             Optional<BibEntryType> bibEntryType = new BibEntryTypesManager().enrich(entryType, bibDatabaseContext.getMode());
@@ -117,8 +127,23 @@ private List<Diagnostic> consistencyCheck(BibDatabaseContext bibDatabaseContext,
 
             entryTypeResult.sortedEntries().forEach(entry -> {
                 requiredFields.forEach(requiredField -> {
-                    if (!entry.hasField(requiredField)) {
-                        diagnostics.add(createGeneralDiagnostic(Localization.lang("required field '%0' is missing", requiredField.getName()), content, entry));
+                    if (entry.getFieldOrAlias(requiredField).isEmpty()) {
+                        diagnostics.add(createGeneralDiagnostic(Localization.lang("Required field \"%0\" is empty.", requiredField.getName()), content, entry));
+                    }
+                });
+            });
+
+            Set<Field> optionalFields = bibEntryType
+                    .map(BibEntryType::getOptionalFields)
+                    .stream()
+                    .flatMap(Collection::stream)
+                    .map(BibField::field)
+                    .collect(Collectors.toSet());
+
+            entryTypeResult.sortedEntries().forEach(entry -> {
+                optionalFields.forEach(optionalField -> {
+                    if (entry.getFieldOrAlias(optionalField).isEmpty()) {
+                        diagnostics.add(createGeneralDiagnostic(Localization.lang("Optional field \"%0\" is empty.", optionalField.getName()), content, entry));
                     }
                 });
             });
diff --git a/jabls/src/main/java/org/jabref/languageserver/LSPServer.java b/jabls/src/main/java/org/jabref/languageserver/LspClientHandler.java
similarity index 92%
rename from jabls/src/main/java/org/jabref/languageserver/LSPServer.java
rename to jabls/src/main/java/org/jabref/languageserver/LspClientHandler.java
index 91caba54b3e..2ef2e972c15 100644
--- a/jabls/src/main/java/org/jabref/languageserver/LSPServer.java
+++ b/jabls/src/main/java/org/jabref/languageserver/LspClientHandler.java
@@ -20,15 +20,15 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class LSPServer implements LanguageServer, LanguageClientAware {
+public class LspClientHandler implements LanguageServer, LanguageClientAware {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(LSPServer.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(LspClientHandler.class);
 
     private LanguageClient client;
     private BibtexWorkspaceService workspaceService;
     private BibtexTextDocumentService textDocumentService;
 
-    public LSPServer(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
+    public LspClientHandler(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
         this.workspaceService = new BibtexWorkspaceService();
         this.textDocumentService = new BibtexTextDocumentService(cliPreferences, abbreviationRepository);
     }
diff --git a/jabls/src/main/java/org/jabref/languageserver/LSPLauncher.java b/jabls/src/main/java/org/jabref/languageserver/LspLauncher.java
similarity index 66%
rename from jabls/src/main/java/org/jabref/languageserver/LSPLauncher.java
rename to jabls/src/main/java/org/jabref/languageserver/LspLauncher.java
index c576b500f85..207f3e83087 100644
--- a/jabls/src/main/java/org/jabref/languageserver/LSPLauncher.java
+++ b/jabls/src/main/java/org/jabref/languageserver/LspLauncher.java
@@ -9,6 +9,7 @@
 import java.util.concurrent.Executors;
 import java.util.function.Function;
 
+import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.preferences.CliPreferences;
 
@@ -17,32 +18,35 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class LSPLauncher {
+public class LspLauncher extends Thread {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(LSPLauncher.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(LspLauncher.class);
 
-    private ServerSocket serverSocket;
-    private ExecutorService threadPool;
-    private volatile boolean running;
-    private CliPreferences cliPreferences;
-    private JournalAbbreviationRepository abbreviationRepository;
+    private final CliPreferences cliPreferences;
+    private final JournalAbbreviationRepository abbreviationRepository;
+    private final ExecutorService threadPool;
 
-    public void run(CliPreferences cliPreferences) {
-        run(cliPreferences, new JournalAbbreviationRepository(), 2087);
-    }
+    private final int port;
+    private volatile boolean running;
+    private ServerSocket serverSocket;
 
-    public void run(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository, int port) {
+    public LspLauncher(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository, int port) {
         this.cliPreferences = cliPreferences;
         this.abbreviationRepository = abbreviationRepository;
-        start(port);
+        this.threadPool = Executors.newCachedThreadPool();
+        this.port = port;
+        this.setName("JabLs - JabRef Language Server on: " + port);
+    }
+
+    public LspLauncher(CliPreferences cliPreferences, int port) {
+        this(cliPreferences, JournalAbbreviationLoader.loadRepository(cliPreferences.getJournalAbbreviationPreferences()), port);
     }
 
-    public void start(int port) {
+    @Override
+    public void run() {
+        running = true;
         try {
             serverSocket = new ServerSocket(port);
-            threadPool = Executors.newCachedThreadPool();
-            running = true;
-
             threadPool.execute(() -> {
                 LOGGER.info("LSP Server listening on port {}...", port);
                 while (running) {
@@ -65,15 +69,15 @@ public void start(int port) {
     }
 
     private void handleClient(Socket socket) {
-        LSPServer server = new LSPServer(cliPreferences, abbreviationRepository);
-        LOGGER.debug("LSP server started.");
+        LspClientHandler clientHandler = new LspClientHandler(cliPreferences, abbreviationRepository);
+        LOGGER.debug("LSP clientHandler started.");
         try (socket; // socket should be closed on error
              InputStream in = socket.getInputStream();
              OutputStream out = socket.getOutputStream()) {
-            Launcher<LanguageClient> launcher = org.eclipse.lsp4j.launch.LSPLauncher.createServerLauncher(server, in, out, Executors.newCachedThreadPool(), Function.identity());
-            LOGGER.debug("LSP server launched.");
-            server.connect(launcher.getRemoteProxy());
-            LOGGER.debug("LSP server connected.");
+            Launcher<LanguageClient> launcher = org.eclipse.lsp4j.launch.LSPLauncher.createServerLauncher(clientHandler, in, out, Executors.newCachedThreadPool(), Function.identity());
+            LOGGER.debug("LSP clientHandler launched.");
+            clientHandler.connect(launcher.getRemoteProxy());
+            LOGGER.debug("LSP clientHandler connected.");
             launcher.startListening().get();
         } catch (Throwable e) {
             LOGGER.error("Error in handleClient", e);
@@ -82,7 +86,8 @@ private void handleClient(Socket socket) {
         }
     }
 
-    public void shutdown() {
+    @Override
+    public void interrupt() {
         try {
             if (serverSocket != null && !serverSocket.isClosed()) {
                 serverSocket.close();
diff --git a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerManager.java b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java
similarity index 56%
rename from jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerManager.java
rename to jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java
index 2d61caa9c72..f5e0f733b90 100644
--- a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerManager.java
+++ b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java
@@ -1,5 +1,6 @@
 package org.jabref.languageserver.manager;
 
+import org.jabref.languageserver.LspLauncher;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.preferences.CliPreferences;
 
@@ -7,31 +8,39 @@
 import org.slf4j.LoggerFactory;
 
 /// Manages the LanguageServerThread through typical life cycle methods.
-public class LanguageServerManager implements AutoCloseable {
+public class LanguageServerController implements AutoCloseable {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(LanguageServerManager.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(LanguageServerController.class);
 
-    private LanguageServerThread languageServerThread;
+    private LspLauncher lspLauncher;
+    private final CliPreferences cliPreferences;
+    private final JournalAbbreviationRepository abbreviationRepository;
 
-    public synchronized void start(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository, int port) {
-        if (languageServerThread != null) {
+    public LanguageServerController(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
+        this.cliPreferences = cliPreferences;
+        this.abbreviationRepository = abbreviationRepository;
+        LOGGER.debug("LanguageServerManager initialized.");
+    }
+
+    public synchronized void start(int port) {
+        if (lspLauncher != null) {
             LOGGER.warn("Language server manager already started, cannot start again.");
             return;
         }
 
-        languageServerThread = new LanguageServerThread(cliPreferences, abbreviationRepository, port);
+        lspLauncher = new LspLauncher(cliPreferences, abbreviationRepository, port);
         // This enqueues the thread to run in the background
         // The JVM will take care of running it at some point in time in the future
         // Thus, we cannot check directly if it really runs
-        languageServerThread.start();
+        lspLauncher.start();
         LOGGER.debug("Triggered language server start up.");
     }
 
     public synchronized void stop() {
         LOGGER.debug("Stopping language server manager...");
-        if (languageServerThread != null) {
-            languageServerThread.interrupt();
-            languageServerThread = null;
+        if (lspLauncher != null) {
+            lspLauncher.interrupt();
+            lspLauncher = null;
             LOGGER.debug("Language server stopped successfully.");
         } else {
             LOGGER.debug("Language server is not started, nothing to stop.");
diff --git a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerThread.java b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerThread.java
deleted file mode 100644
index 73c2304a2a1..00000000000
--- a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerThread.java
+++ /dev/null
@@ -1,49 +0,0 @@
-package org.jabref.languageserver.manager;
-
-import org.jabref.languageserver.LSPLauncher;
-import org.jabref.logic.journals.JournalAbbreviationRepository;
-import org.jabref.logic.preferences.CliPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This thread wrapper is required to be able to interrupt the language server, e.g. when JabRef is closing down the language server should shutdown as well.
- */
-public class LanguageServerThread extends Thread {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(LanguageServerThread.class);
-
-    private final CliPreferences cliPreferences;
-    private final JournalAbbreviationRepository abbreviationRepository;
-    private LSPLauncher lspLauncher;
-    private int port;
-
-    public LanguageServerThread(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository, int port) {
-        this.cliPreferences = cliPreferences;
-        this.abbreviationRepository = abbreviationRepository;
-        this.lspLauncher = new LSPLauncher();
-        this.port = port;
-        this.setName("JabLs - JabRef Language Server on :" + port);
-    }
-
-    @Override
-    public void run() {
-        this.lspLauncher.run(cliPreferences, abbreviationRepository, port);
-    }
-
-    @Override
-    public void interrupt() {
-        LOGGER.debug("Interrupting {}", this.getName());
-        if (this.lspLauncher == null) {
-            LOGGER.warn("LSPLauncher is null, cannot shutdown.");
-        } else {
-            this.lspLauncher.shutdown();
-        }
-        super.interrupt();
-    }
-
-    public boolean started() {
-        return lspLauncher != null && lspLauncher.isRunning();
-    }
-}

From 4b32019bb4fcc7667be7b24f8b68e2d19ed56885 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Sat, 23 Aug 2025 22:14:56 +0200
Subject: [PATCH 04/14] modify CHANGELOG and split checks to other classes

---
 CHANGELOG.md                                  |   1 +
 .../BibtexTextDocumentService.java            | 130 ++----------------
 .../util/LspConsistencyCheck.java             |  71 ++++++++++
 .../util/LspDiagnosticUtil.java               |  56 ++++++++
 .../util/LspIntegrityCheck.java               |  39 ++++++
 5 files changed, 179 insertions(+), 118 deletions(-)
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticUtil.java
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ee187579b5d..2639da7107a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added the Option to enable the language server in the preferences. [#13697](https://github.com/JabRef/jabref/pull/13697)
 - We added tooltips (on hover) for 'Library-specific file directory', 'User-specific file directory' and 'LaTeX file directory' fields of the library properties window. [#12269](https://github.com/JabRef/jabref/issues/12269)
 - A space is now added by default after citations inserted via the Libre/OpenOffice integration. [#13559](https://github.com/JabRef/jabref/issues/13559)
 - We added the option to configure 'Add space after citation' in Libre/OpenOffice panel settings. [#13559](https://github.com/JabRef/jabref/issues/13559)
diff --git a/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java b/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
index 9bdfc305a05..e8eadf4f38b 100644
--- a/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
+++ b/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
@@ -1,48 +1,36 @@
 package org.jabref.languageserver;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
-import java.util.Optional;
-import java.util.Set;
 import java.util.concurrent.CompletableFuture;
-import java.util.stream.Collectors;
 
-import org.jabref.logic.integrity.IntegrityCheck;
+import org.jabref.languageserver.util.LspConsistencyCheck;
+import org.jabref.languageserver.util.LspDiagnosticUtil;
+import org.jabref.languageserver.util.LspIntegrityCheck;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.CliPreferences;
-import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.BibEntryType;
-import org.jabref.model.entry.BibEntryTypesManager;
-import org.jabref.model.entry.field.BibField;
-import org.jabref.model.entry.field.Field;
 
 import org.eclipse.lsp4j.CompletionItem;
 import org.eclipse.lsp4j.CompletionList;
 import org.eclipse.lsp4j.CompletionParams;
 import org.eclipse.lsp4j.Diagnostic;
-import org.eclipse.lsp4j.DiagnosticSeverity;
 import org.eclipse.lsp4j.DidChangeTextDocumentParams;
 import org.eclipse.lsp4j.DidCloseTextDocumentParams;
 import org.eclipse.lsp4j.DidOpenTextDocumentParams;
 import org.eclipse.lsp4j.DidSaveTextDocumentParams;
-import org.eclipse.lsp4j.Position;
 import org.eclipse.lsp4j.PublishDiagnosticsParams;
-import org.eclipse.lsp4j.Range;
 import org.eclipse.lsp4j.jsonrpc.messages.Either;
 import org.eclipse.lsp4j.services.LanguageClient;
 import org.eclipse.lsp4j.services.TextDocumentService;
 
 public class BibtexTextDocumentService implements TextDocumentService {
 
-    private static final Range NULL_RANGE = new Range(new Position(0, 0), new Position(0, 0));
-    private static final String DIAGNOSTIC_SOURCE = "JabRef";
-
     private final CliPreferences jabRefCliPreferences;
     private final JournalAbbreviationRepository abbreviationRepository;
+    private final LspIntegrityCheck lspIntegrityCheck;
+    private final LspConsistencyCheck lspConsistencyCheck;
 
     private LanguageClient client;
     private boolean checkConsistency = true;
@@ -50,6 +38,8 @@ public class BibtexTextDocumentService implements TextDocumentService {
     public BibtexTextDocumentService(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
         this.jabRefCliPreferences = cliPreferences;
         this.abbreviationRepository = abbreviationRepository;
+        this.lspIntegrityCheck = new LspIntegrityCheck(cliPreferences, abbreviationRepository);
+        this.lspConsistencyCheck = new LspConsistencyCheck();
     }
 
     public void setClient(LanguageClient client) {
@@ -85,117 +75,21 @@ private void handleDiagnostics(String uri, String content, int version) {
         try {
             bibDatabaseContext = BibDatabaseContext.of(content, jabRefCliPreferences.getImportFormatPreferences());
         } catch (Exception e) {
-            Diagnostic parseDiagnostic = new Diagnostic(
-                    NULL_RANGE,
-                    Localization.lang(
-                            "Failed to parse entries.\nThe following error was encountered:\n%0",
-                            e.getMessage()),
-                    DiagnosticSeverity.Error,
-                    DIAGNOSTIC_SOURCE
-            );
+            Diagnostic parseDiagnostic = LspDiagnosticUtil.createGeneralDiagnostic(Localization.lang(
+                    "Failed to parse entries.\nThe following error was encountered:\n%0",
+                    e.getMessage()));
             client.publishDiagnostics(new PublishDiagnosticsParams(uri, List.of(parseDiagnostic), version));
             return;
         }
 
         List<Diagnostic> diagnostics = new ArrayList<>();
 
-        diagnostics.addAll(integrityCheck(bibDatabaseContext, content));
+        diagnostics.addAll(lspIntegrityCheck.check(bibDatabaseContext, content));
 
         if (checkConsistency) {
-            diagnostics.addAll(consistencyCheck(bibDatabaseContext, content));
+            diagnostics.addAll(lspConsistencyCheck.check(bibDatabaseContext, content));
         }
 
         client.publishDiagnostics(new PublishDiagnosticsParams(uri, diagnostics, version));
     }
-
-    private List<Diagnostic> consistencyCheck(BibDatabaseContext bibDatabaseContext, String content) {
-        List<Diagnostic> diagnostics = new ArrayList<>();
-        BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
-        BibliographyConsistencyCheck.Result result = consistencyCheck.check(bibDatabaseContext.getEntries(), (_, _) -> {
-        });
-
-        result.entryTypeToResultMap().forEach((entryType, entryTypeResult) -> {
-            Optional<BibEntryType> bibEntryType = new BibEntryTypesManager().enrich(entryType, bibDatabaseContext.getMode());
-            Set<Field> requiredFields = bibEntryType
-                    .map(BibEntryType::getRequiredFields)
-                    .stream()
-                    .flatMap(Collection::stream)
-                    .flatMap(orFields -> orFields.getFields().stream())
-                    .collect(Collectors.toSet());
-
-            entryTypeResult.sortedEntries().forEach(entry -> {
-                requiredFields.forEach(requiredField -> {
-                    if (entry.getFieldOrAlias(requiredField).isEmpty()) {
-                        diagnostics.add(createGeneralDiagnostic(Localization.lang("Required field \"%0\" is empty.", requiredField.getName()), content, entry));
-                    }
-                });
-            });
-
-            Set<Field> optionalFields = bibEntryType
-                    .map(BibEntryType::getOptionalFields)
-                    .stream()
-                    .flatMap(Collection::stream)
-                    .map(BibField::field)
-                    .collect(Collectors.toSet());
-
-            entryTypeResult.sortedEntries().forEach(entry -> {
-                optionalFields.forEach(optionalField -> {
-                    if (entry.getFieldOrAlias(optionalField).isEmpty()) {
-                        diagnostics.add(createGeneralDiagnostic(Localization.lang("Optional field \"%0\" is empty.", optionalField.getName()), content, entry));
-                    }
-                });
-            });
-        });
-
-        return diagnostics;
-    }
-
-    private List<Diagnostic> integrityCheck(BibDatabaseContext bibDatabaseContext, String content) {
-        IntegrityCheck integrityCheck = new IntegrityCheck(
-                bibDatabaseContext,
-                jabRefCliPreferences.getFilePreferences(),
-                jabRefCliPreferences.getCitationKeyPatternPreferences(),
-                abbreviationRepository,
-                true
-        );
-
-        return bibDatabaseContext.getEntries().stream().flatMap(entry -> integrityCheck.checkEntry(entry).stream().map(message -> {
-            if (entry.getField(message.field()).isPresent()) {
-                return createFieldDiagnostic(message.message(), message.field(), content, entry);
-            } else {
-                return createGeneralDiagnostic(message.message(), content, entry);
-            }
-        })).toList();
-    }
-
-    private Diagnostic createFieldDiagnostic(String message, Field field, String content, BibEntry entry) {
-        return new Diagnostic(findTextRange(content, entry.getField(field).get()), message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
-    }
-
-    private Diagnostic createGeneralDiagnostic(String message, String content, BibEntry entry) {
-        return new Diagnostic(findTextRange(content, entry.getCitationKey().orElse("")), message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
-    }
-
-    private static Range findTextRange(String content, String searchText) {
-        int startOffset = content.indexOf(searchText);
-        if (startOffset == -1) {
-            return NULL_RANGE;
-        }
-        int endOffset = startOffset + searchText.length();
-        return new Range(offsetToPosition(content, startOffset), offsetToPosition(content, endOffset));
-    }
-
-    private static Position offsetToPosition(String content, int offset) {
-        int line = 0;
-        int col = 0;
-        for (int i = 0; i < offset; i++) {
-            if (content.charAt(i) == '\n') {
-                line++;
-                col = 0;
-            } else {
-                col++;
-            }
-        }
-        return new Position(line, col);
-    }
 }
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java b/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
new file mode 100644
index 00000000000..9564f295e79
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
@@ -0,0 +1,71 @@
+package org.jabref.languageserver.util;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntryType;
+import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.field.BibField;
+import org.jabref.model.entry.field.Field;
+
+import org.eclipse.lsp4j.Diagnostic;
+
+public class LspConsistencyCheck {
+
+    public List<Diagnostic> check(BibDatabaseContext bibDatabaseContext, String content) {
+        List<Diagnostic> diagnostics = new ArrayList<>();
+        BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
+        BibliographyConsistencyCheck.Result result = consistencyCheck.check(bibDatabaseContext.getEntries(), (_, _) -> {
+        });
+
+        List<Field> allReportedFields = result.entryTypeToResultMap().values().stream()
+                                              .flatMap(entryTypeResult -> entryTypeResult.fields().stream())
+                                              .sorted(Comparator.comparing(Field::getName))
+                                              .distinct()
+                                              .toList();
+
+        result.entryTypeToResultMap().forEach((entryType, entryTypeResult) -> {
+            Optional<BibEntryType> bibEntryType = new BibEntryTypesManager().enrich(entryType, bibDatabaseContext.getMode());
+            Set<Field> requiredFields = bibEntryType
+                    .map(BibEntryType::getRequiredFields)
+                    .stream()
+                    .flatMap(Collection::stream)
+                    .flatMap(orFields -> orFields.getFields().stream())
+                    .collect(Collectors.toSet());
+
+            entryTypeResult.sortedEntries().forEach(entry -> {
+                requiredFields.forEach(requiredField -> {
+                    if (entry.getFieldOrAlias(requiredField).isEmpty()) {
+                        diagnostics.add(LspDiagnosticUtil.createGeneralEntryDiagnostic(Localization.lang("Required field \"%0\" is empty.", requiredField.getName()), content, entry));
+                    }
+                });
+            });
+
+            Set<Field> optionalFields = bibEntryType
+                    .map(BibEntryType::getOptionalFields)
+                    .stream()
+                    .flatMap(Collection::stream)
+                    .map(BibField::field)
+                    .filter(allReportedFields::contains)
+                    .collect(Collectors.toSet());
+
+            optionalFields.forEach(requiredField -> {
+                entryTypeResult.sortedEntries().forEach(entry -> {
+                    if (entry.getFieldOrAlias(requiredField).isEmpty()) {
+                        diagnostics.add(LspDiagnosticUtil.createGeneralEntryDiagnostic(Localization.lang("Optional field \"%0\" is empty.", requiredField.getName()), content, entry));
+                    }
+                });
+            });
+        });
+
+        return diagnostics;
+    }
+}
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticUtil.java b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticUtil.java
new file mode 100644
index 00000000000..749895e8c82
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticUtil.java
@@ -0,0 +1,56 @@
+package org.jabref.languageserver.util;
+
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.Field;
+
+import org.eclipse.lsp4j.Diagnostic;
+import org.eclipse.lsp4j.DiagnosticSeverity;
+import org.eclipse.lsp4j.Position;
+import org.eclipse.lsp4j.Range;
+
+public class LspDiagnosticUtil {
+
+    private static final Range NULL_RANGE = new Range(new Position(0, 0), new Position(0, 0));
+    private static final String DIAGNOSTIC_SOURCE = "JabRef";
+
+    public static Diagnostic createFieldDiagnostic(String message, Field field, String content, BibEntry entry) {
+        if (entry.getFieldOrAlias(field).isEmpty()) {
+            return createGeneralEntryDiagnostic(message, content, entry);
+        }
+        return new Diagnostic(findTextRange(content, entry.getFieldOrAlias(field).get()), message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
+    }
+
+    public static Diagnostic createGeneralEntryDiagnostic(String message, String content, BibEntry entry) {
+        if (entry.getCitationKey().isEmpty()) {
+            return createGeneralDiagnostic(message);
+        }
+        return new Diagnostic(findTextRange(content, entry.getCitationKey().get()), message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
+    }
+
+    public static Diagnostic createGeneralDiagnostic(String message) {
+        return new Diagnostic(NULL_RANGE, message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
+    }
+
+    private static Range findTextRange(String content, String searchText) {
+        int startOffset = content.indexOf(searchText);
+        if (startOffset == -1) {
+            return NULL_RANGE;
+        }
+        int endOffset = startOffset + searchText.length();
+        return new Range(offsetToPosition(content, startOffset), offsetToPosition(content, endOffset));
+    }
+
+    private static Position offsetToPosition(String content, int offset) {
+        int line = 0;
+        int col = 0;
+        for (int i = 0; i < offset; i++) {
+            if (content.charAt(i) == '\n') {
+                line++;
+                col = 0;
+            } else {
+                col++;
+            }
+        }
+        return new Position(line, col);
+    }
+}
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java b/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
new file mode 100644
index 00000000000..25a105a38ec
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
@@ -0,0 +1,39 @@
+package org.jabref.languageserver.util;
+
+import java.util.List;
+
+import org.jabref.logic.integrity.IntegrityCheck;
+import org.jabref.logic.journals.JournalAbbreviationRepository;
+import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.model.database.BibDatabaseContext;
+
+import org.eclipse.lsp4j.Diagnostic;
+
+public class LspIntegrityCheck {
+
+    private final CliPreferences cliPreferences;
+    private final JournalAbbreviationRepository abbreviationRepository;
+
+    public LspIntegrityCheck(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
+        this.cliPreferences = cliPreferences;
+        this.abbreviationRepository = abbreviationRepository;
+    }
+
+    public List<Diagnostic> check(BibDatabaseContext bibDatabaseContext, String content) {
+        IntegrityCheck integrityCheck = new IntegrityCheck(
+                bibDatabaseContext,
+                cliPreferences.getFilePreferences(),
+                cliPreferences.getCitationKeyPatternPreferences(),
+                abbreviationRepository,
+                true
+        );
+
+        return bibDatabaseContext.getEntries().stream().flatMap(entry -> integrityCheck.checkEntry(entry).stream().map(message -> {
+            if (entry.getField(message.field()).isPresent()) {
+                return LspDiagnosticUtil.createFieldDiagnostic(message.message(), message.field(), content, entry);
+            } else {
+                return LspDiagnosticUtil.createGeneralEntryDiagnostic(message.message(), content, entry);
+            }
+        })).toList();
+    }
+}

From 76bb0d7265219b2185f249fbb0fdc2ec1db82b76 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Sat, 23 Aug 2025 22:18:13 +0200
Subject: [PATCH 05/14] rename variable

---
 .../org/jabref/languageserver/util/LspConsistencyCheck.java | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java b/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
index 9564f295e79..07c0b172602 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
@@ -57,10 +57,10 @@ public List<Diagnostic> check(BibDatabaseContext bibDatabaseContext, String cont
                     .filter(allReportedFields::contains)
                     .collect(Collectors.toSet());
 
-            optionalFields.forEach(requiredField -> {
+            optionalFields.forEach(optionalField -> {
                 entryTypeResult.sortedEntries().forEach(entry -> {
-                    if (entry.getFieldOrAlias(requiredField).isEmpty()) {
-                        diagnostics.add(LspDiagnosticUtil.createGeneralEntryDiagnostic(Localization.lang("Optional field \"%0\" is empty.", requiredField.getName()), content, entry));
+                    if (entry.getFieldOrAlias(optionalField).isEmpty()) {
+                        diagnostics.add(LspDiagnosticUtil.createGeneralEntryDiagnostic(Localization.lang("Optional field \"%0\" is empty.", optionalField.getName()), content, entry));
                     }
                 });
             });

From fa574f9bbb0add78d10e096a060bb4a196698758 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Mon, 25 Aug 2025 01:21:52 +0200
Subject: [PATCH 06/14] add settings support and fix comments

---
 CHANGELOG.md                                  |   2 +-
 .../main/java/org/jabref/gui/JabRefGUI.java   |   4 +-
 .../src/main/resources/tinylog.properties     |   4 +-
 jabls/src/main/java/module-info.java          |   4 +-
 .../BibtexTextDocumentService.java            |  59 ++-------
 .../BibtexWorkspaceService.java               |  17 +++
 .../languageserver/ExtensionSettings.java     |  56 ++++++++
 .../languageserver/LspClientHandler.java      |  20 ++-
 .../manager/LanguageServerController.java     |  10 +-
 .../util/LspConsistencyCheck.java             |  32 +++--
 .../util/LspDiagnosticBuilder.java            | 122 ++++++++++++++++++
 .../util/LspDiagnosticHandler.java            | 100 ++++++++++++++
 .../util/LspDiagnosticUtil.java               |  56 --------
 .../util/LspIntegrityCheck.java               |   8 +-
 14 files changed, 356 insertions(+), 138 deletions(-)
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticBuilder.java
 create mode 100644 jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
 delete mode 100644 jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticUtil.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2639da7107a..d9dee5852cb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,7 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
-- We added the Option to enable the language server in the preferences. [#13697](https://github.com/JabRef/jabref/pull/13697)
+- We added the option to enable the language server in the preferences. [#13697](https://github.com/JabRef/jabref/pull/13697)
 - We added tooltips (on hover) for 'Library-specific file directory', 'User-specific file directory' and 'LaTeX file directory' fields of the library properties window. [#12269](https://github.com/JabRef/jabref/issues/12269)
 - A space is now added by default after citations inserted via the Libre/OpenOffice integration. [#13559](https://github.com/JabRef/jabref/issues/13559)
 - We added the option to configure 'Add space after citation' in Libre/OpenOffice panel settings. [#13559](https://github.com/JabRef/jabref/issues/13559)
diff --git a/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java b/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
index ef74648cd35..eb6eedb16fb 100644
--- a/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
+++ b/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -477,9 +477,9 @@ public void stop() {
             });
 
             executor.submit(() -> {
-                LOGGER.trace("Shutting down language server manager");
+                LOGGER.trace("Shutting down language server controller");
                 languageServerController.stop();
-                LOGGER.trace("LanguageServerManager shut down");
+                LOGGER.trace("LanguageServerController shut down");
             });
 
             executor.submit(() -> {
diff --git a/jabls-cli/src/main/resources/tinylog.properties b/jabls-cli/src/main/resources/tinylog.properties
index 9b0e192d38e..28f5cdc77b3 100644
--- a/jabls-cli/src/main/resources/tinylog.properties
+++ b/jabls-cli/src/main/resources/tinylog.properties
@@ -4,8 +4,8 @@ writerConsole = console
 # More shrunk exception logs. See https://tinylog.org/v2/configuration/#strip-stack-trace-elements for details
 exception = strip: jdk.internal
 
-level@org.jabref.languageserver.LspLauncher = debug
-level@org.jabref.languageserver.cli.ServerCli = debug
+level@org.jabref.languageserver = debug
+level@org.jabref.languageserver.util = debug
 
 level@org.apache.pdfbox.pdmodel.font = error
 level@org.apache.pdfbox.pdmodel.PDSimpleFont = error
diff --git a/jabls/src/main/java/module-info.java b/jabls/src/main/java/module-info.java
index 3ecd8b83352..873c35e7706 100644
--- a/jabls/src/main/java/module-info.java
+++ b/jabls/src/main/java/module-info.java
@@ -1,7 +1,8 @@
 module org.jabref.jabls {
     exports org.jabref.languageserver;
-    opens org.jabref.languageserver to lsp4j, lsp4j.jsonrpc;
+    opens org.jabref.languageserver to lsp4j, lsp4j.jsonrpc, com.google.gson;
     exports org.jabref.languageserver.manager;
+    exports org.jabref.languageserver.util;
 
     requires org.jabref.jablib;
 
@@ -10,4 +11,5 @@
     requires lsp4j;
     requires lsp4j.jsonrpc;
     requires lsp4j.websocket;
+    requires com.google.gson;
 }
diff --git a/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java b/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
index e8eadf4f38b..10cd45abb1a 100644
--- a/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
+++ b/jabls/src/main/java/org/jabref/languageserver/BibtexTextDocumentService.java
@@ -1,45 +1,30 @@
 package org.jabref.languageserver;
 
-import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 import java.util.concurrent.CompletableFuture;
 
-import org.jabref.languageserver.util.LspConsistencyCheck;
-import org.jabref.languageserver.util.LspDiagnosticUtil;
-import org.jabref.languageserver.util.LspIntegrityCheck;
-import org.jabref.logic.journals.JournalAbbreviationRepository;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.preferences.CliPreferences;
-import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.languageserver.util.LspDiagnosticHandler;
 
 import org.eclipse.lsp4j.CompletionItem;
 import org.eclipse.lsp4j.CompletionList;
 import org.eclipse.lsp4j.CompletionParams;
-import org.eclipse.lsp4j.Diagnostic;
 import org.eclipse.lsp4j.DidChangeTextDocumentParams;
 import org.eclipse.lsp4j.DidCloseTextDocumentParams;
 import org.eclipse.lsp4j.DidOpenTextDocumentParams;
 import org.eclipse.lsp4j.DidSaveTextDocumentParams;
-import org.eclipse.lsp4j.PublishDiagnosticsParams;
 import org.eclipse.lsp4j.jsonrpc.messages.Either;
 import org.eclipse.lsp4j.services.LanguageClient;
 import org.eclipse.lsp4j.services.TextDocumentService;
 
 public class BibtexTextDocumentService implements TextDocumentService {
 
-    private final CliPreferences jabRefCliPreferences;
-    private final JournalAbbreviationRepository abbreviationRepository;
-    private final LspIntegrityCheck lspIntegrityCheck;
-    private final LspConsistencyCheck lspConsistencyCheck;
+    private final LspDiagnosticHandler diagnosticHandler;
 
     private LanguageClient client;
-    private boolean checkConsistency = true;
 
-    public BibtexTextDocumentService(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
-        this.jabRefCliPreferences = cliPreferences;
-        this.abbreviationRepository = abbreviationRepository;
-        this.lspIntegrityCheck = new LspIntegrityCheck(cliPreferences, abbreviationRepository);
-        this.lspConsistencyCheck = new LspConsistencyCheck();
+    public BibtexTextDocumentService(LspDiagnosticHandler diagnosticHandler) {
+        this.diagnosticHandler = Objects.requireNonNull(diagnosticHandler);
     }
 
     public void setClient(LanguageClient client) {
@@ -48,48 +33,22 @@ public void setClient(LanguageClient client) {
 
     @Override
     public void didOpen(DidOpenTextDocumentParams params) {
-        handleDiagnostics(params.getTextDocument().getUri(), params.getTextDocument().getText(), params.getTextDocument().getVersion());
+        diagnosticHandler.computeAndPublishDiagnostics(client, params.getTextDocument().getUri(), params.getTextDocument().getText(), params.getTextDocument().getVersion());
     }
 
     @Override
     public void didChange(DidChangeTextDocumentParams params) {
-        handleDiagnostics(params.getTextDocument().getUri(), params.getContentChanges().getFirst().getText(), params.getTextDocument().getVersion());
+        diagnosticHandler.computeAndPublishDiagnostics(client, params.getTextDocument().getUri(), params.getContentChanges().getFirst().getText(), params.getTextDocument().getVersion());
     }
 
     @Override
-    public void didClose(DidCloseTextDocumentParams params) {
-        client.publishDiagnostics(new PublishDiagnosticsParams(params.getTextDocument().getUri(), List.of()));
-    }
+    public void didClose(DidCloseTextDocumentParams params) { }
 
     @Override
-    public void didSave(DidSaveTextDocumentParams params) {
-    }
+    public void didSave(DidSaveTextDocumentParams params) { }
 
     @Override
     public CompletableFuture<Either<List<CompletionItem>, CompletionList>> completion(CompletionParams position) {
         return TextDocumentService.super.completion(position);
     }
-
-    private void handleDiagnostics(String uri, String content, int version) {
-        BibDatabaseContext bibDatabaseContext;
-        try {
-            bibDatabaseContext = BibDatabaseContext.of(content, jabRefCliPreferences.getImportFormatPreferences());
-        } catch (Exception e) {
-            Diagnostic parseDiagnostic = LspDiagnosticUtil.createGeneralDiagnostic(Localization.lang(
-                    "Failed to parse entries.\nThe following error was encountered:\n%0",
-                    e.getMessage()));
-            client.publishDiagnostics(new PublishDiagnosticsParams(uri, List.of(parseDiagnostic), version));
-            return;
-        }
-
-        List<Diagnostic> diagnostics = new ArrayList<>();
-
-        diagnostics.addAll(lspIntegrityCheck.check(bibDatabaseContext, content));
-
-        if (checkConsistency) {
-            diagnostics.addAll(lspConsistencyCheck.check(bibDatabaseContext, content));
-        }
-
-        client.publishDiagnostics(new PublishDiagnosticsParams(uri, diagnostics, version));
-    }
 }
diff --git a/jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java b/jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java
index 3c81c3534ae..0956dfa6f3d 100644
--- a/jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java
+++ b/jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java
@@ -1,5 +1,8 @@
 package org.jabref.languageserver;
 
+import org.jabref.languageserver.util.LspDiagnosticHandler;
+
+import com.google.gson.JsonObject;
 import org.eclipse.lsp4j.DidChangeConfigurationParams;
 import org.eclipse.lsp4j.DidChangeWatchedFilesParams;
 import org.eclipse.lsp4j.services.LanguageClient;
@@ -11,11 +14,25 @@ public class BibtexWorkspaceService implements WorkspaceService {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(BibtexWorkspaceService.class);
 
+    private final LspClientHandler clientHandler;
+    private final LspDiagnosticHandler diagnosticHandler;
+
     private LanguageClient client;
 
+    public BibtexWorkspaceService(LspClientHandler clientHandler, LspDiagnosticHandler lspClientHandler) {
+        this.clientHandler = clientHandler;
+        this.diagnosticHandler = lspClientHandler;
+    }
+
     // Todo: handle event
     @Override
     public void didChangeConfiguration(DidChangeConfigurationParams didChangeConfigurationParams) {
+        if (didChangeConfigurationParams.getSettings() instanceof JsonObject settings) {
+            clientHandler.getSettings().copyFromJsonObject(settings);
+            LOGGER.info("Updated settings: {}", clientHandler.getSettings());
+            diagnosticHandler.refreshDiagnostics(client);
+            LOGGER.debug("Refreshed diagnostics.");
+        }
         LOGGER.debug("DidChangeConfigurationParams: {}", didChangeConfigurationParams);
     }
 
diff --git a/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java b/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
new file mode 100644
index 00000000000..ddc352813d9
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
@@ -0,0 +1,56 @@
+package org.jabref.languageserver;
+
+public class ExtensionSettings {
+    private boolean consistencyCheck;
+    private boolean integrityCheck;
+
+    private ExtensionSettings() {
+        this.consistencyCheck = true;
+        this.integrityCheck = true;
+    }
+
+    public static ExtensionSettings getDefaultSettings() {
+        return new ExtensionSettings();
+    }
+
+    public void setConsistencyCheck(boolean consistencyCheck) {
+        this.consistencyCheck = consistencyCheck;
+    }
+
+    public boolean isConsistencyCheck() {
+        return consistencyCheck;
+    }
+
+    public void setIntegrityCheck(boolean integrityCheck) {
+        this.integrityCheck = integrityCheck;
+    }
+
+    public boolean isIntegrityCheck() {
+        return integrityCheck;
+    }
+
+    public void copyFromOther(ExtensionSettings other) {
+        this.consistencyCheck = other.consistencyCheck;
+        this.integrityCheck = other.integrityCheck;
+    }
+
+    public void copyFromJsonObject(com.google.gson.JsonObject json) {
+        if (json.has("jabref") && json.get("jabref").isJsonObject()) {
+            json = json.getAsJsonObject("jabref");
+        }
+        if (json.has("consistencyCheck") && json.get("consistencyCheck").isJsonPrimitive()) {
+            this.consistencyCheck = json.get("consistencyCheck").getAsBoolean();
+        }
+        if (json.has("integrityCheck") && json.get("integrityCheck").isJsonPrimitive()) {
+            this.integrityCheck = json.get("integrityCheck").getAsBoolean();
+        }
+    }
+
+    @Override
+    public String toString() {
+        return "ExtensionSettings{" +
+                "consistencyCheck=" + consistencyCheck +
+                ", integrityCheck=" + integrityCheck +
+                '}';
+    }
+}
diff --git a/jabls/src/main/java/org/jabref/languageserver/LspClientHandler.java b/jabls/src/main/java/org/jabref/languageserver/LspClientHandler.java
index 2ef2e972c15..01b719b3132 100644
--- a/jabls/src/main/java/org/jabref/languageserver/LspClientHandler.java
+++ b/jabls/src/main/java/org/jabref/languageserver/LspClientHandler.java
@@ -2,6 +2,7 @@
 
 import java.util.concurrent.CompletableFuture;
 
+import org.jabref.languageserver.util.LspDiagnosticHandler;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.preferences.CliPreferences;
 
@@ -12,6 +13,7 @@
 import org.eclipse.lsp4j.ServerCapabilities;
 import org.eclipse.lsp4j.TextDocumentSyncKind;
 import org.eclipse.lsp4j.TextDocumentSyncOptions;
+import org.eclipse.lsp4j.WorkspaceServerCapabilities;
 import org.eclipse.lsp4j.services.LanguageClient;
 import org.eclipse.lsp4j.services.LanguageClientAware;
 import org.eclipse.lsp4j.services.LanguageServer;
@@ -24,13 +26,18 @@ public class LspClientHandler implements LanguageServer, LanguageClientAware {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(LspClientHandler.class);
 
+    private final LspDiagnosticHandler diagnosticHandler;
+    private final BibtexWorkspaceService workspaceService;
+    private final BibtexTextDocumentService textDocumentService;
+    private final ExtensionSettings settings;
+
     private LanguageClient client;
-    private BibtexWorkspaceService workspaceService;
-    private BibtexTextDocumentService textDocumentService;
 
     public LspClientHandler(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
-        this.workspaceService = new BibtexWorkspaceService();
-        this.textDocumentService = new BibtexTextDocumentService(cliPreferences, abbreviationRepository);
+        this.settings = ExtensionSettings.getDefaultSettings();
+        this.diagnosticHandler = new LspDiagnosticHandler(this, cliPreferences, abbreviationRepository);
+        this.workspaceService = new BibtexWorkspaceService(this, diagnosticHandler);
+        this.textDocumentService = new BibtexTextDocumentService(diagnosticHandler);
     }
 
     @Override
@@ -43,6 +50,7 @@ public CompletableFuture<InitializeResult> initialize(InitializeParams params) {
         syncOptions.setOpenClose(true);
 
         capabilities.setTextDocumentSync(syncOptions);
+        capabilities.setWorkspace(new WorkspaceServerCapabilities());
 
         return CompletableFuture.completedFuture(new InitializeResult(capabilities));
     }
@@ -69,6 +77,10 @@ public WorkspaceService getWorkspaceService() {
         return this.workspaceService;
     }
 
+    public ExtensionSettings getSettings() {
+        return settings;
+    }
+
     @Override
     public void connect(LanguageClient client) {
         this.client = client;
diff --git a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java
index f5e0f733b90..49d852bda24 100644
--- a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java
+++ b/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java
@@ -7,7 +7,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-/// Manages the LanguageServerThread through typical life cycle methods.
+/// Manages the LspLauncher through typical life cycle methods.
 public class LanguageServerController implements AutoCloseable {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(LanguageServerController.class);
@@ -19,12 +19,12 @@ public class LanguageServerController implements AutoCloseable {
     public LanguageServerController(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
         this.cliPreferences = cliPreferences;
         this.abbreviationRepository = abbreviationRepository;
-        LOGGER.debug("LanguageServerManager initialized.");
+        LOGGER.debug("LanguageServerController initialized.");
     }
 
     public synchronized void start(int port) {
         if (lspLauncher != null) {
-            LOGGER.warn("Language server manager already started, cannot start again.");
+            LOGGER.warn("Language server controller already started, cannot start again.");
             return;
         }
 
@@ -37,7 +37,7 @@ public synchronized void start(int port) {
     }
 
     public synchronized void stop() {
-        LOGGER.debug("Stopping language server manager...");
+        LOGGER.debug("Stopping language server controller...");
         if (lspLauncher != null) {
             lspLauncher.interrupt();
             lspLauncher = null;
@@ -49,7 +49,7 @@ public synchronized void stop() {
 
     @Override
     public void close() {
-        LOGGER.debug("Closing Language server manager...");
+        LOGGER.debug("Closing Language server controller...");
         stop();
     }
 }
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java b/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
index 07c0b172602..eb3315c8bd8 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
@@ -17,6 +17,7 @@
 import org.jabref.model.entry.field.Field;
 
 import org.eclipse.lsp4j.Diagnostic;
+import org.eclipse.lsp4j.DiagnosticSeverity;
 
 public class LspConsistencyCheck {
 
@@ -41,13 +42,15 @@ public List<Diagnostic> check(BibDatabaseContext bibDatabaseContext, String cont
                     .flatMap(orFields -> orFields.getFields().stream())
                     .collect(Collectors.toSet());
 
-            entryTypeResult.sortedEntries().forEach(entry -> {
-                requiredFields.forEach(requiredField -> {
-                    if (entry.getFieldOrAlias(requiredField).isEmpty()) {
-                        diagnostics.add(LspDiagnosticUtil.createGeneralEntryDiagnostic(Localization.lang("Required field \"%0\" is empty.", requiredField.getName()), content, entry));
-                    }
-                });
-            });
+            entryTypeResult.sortedEntries().forEach(entry -> requiredFields.forEach(requiredField -> {
+                if (entry.getFieldOrAlias(requiredField).isEmpty()) {
+                    LspDiagnosticBuilder diagnosticBuilder = LspDiagnosticBuilder.create(Localization.lang("Required field \"%0\" is empty.", requiredField.getName()));
+                    diagnosticBuilder.setSeverity(DiagnosticSeverity.Error);
+                    diagnosticBuilder.setContent(content);
+                    diagnosticBuilder.setEntry(entry);
+                    diagnostics.add(diagnosticBuilder.build());
+                }
+            }));
 
             Set<Field> optionalFields = bibEntryType
                     .map(BibEntryType::getOptionalFields)
@@ -57,13 +60,14 @@ public List<Diagnostic> check(BibDatabaseContext bibDatabaseContext, String cont
                     .filter(allReportedFields::contains)
                     .collect(Collectors.toSet());
 
-            optionalFields.forEach(optionalField -> {
-                entryTypeResult.sortedEntries().forEach(entry -> {
-                    if (entry.getFieldOrAlias(optionalField).isEmpty()) {
-                        diagnostics.add(LspDiagnosticUtil.createGeneralEntryDiagnostic(Localization.lang("Optional field \"%0\" is empty.", optionalField.getName()), content, entry));
-                    }
-                });
-            });
+            optionalFields.forEach(optionalField -> entryTypeResult.sortedEntries().forEach(entry -> {
+                if (entry.getFieldOrAlias(optionalField).isEmpty()) {
+                    LspDiagnosticBuilder diagnosticBuilder = LspDiagnosticBuilder.create(Localization.lang("Required field \"%0\" is empty.", optionalField.getName()));
+                    diagnosticBuilder.setContent(content);
+                    diagnosticBuilder.setEntry(entry);
+                    diagnostics.add(diagnosticBuilder.build());
+                }
+            }));
         });
 
         return diagnostics;
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticBuilder.java b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticBuilder.java
new file mode 100644
index 00000000000..8ebc0b7f47f
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticBuilder.java
@@ -0,0 +1,122 @@
+package org.jabref.languageserver.util;
+
+import java.util.Objects;
+import java.util.Optional;
+
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.Field;
+
+import org.eclipse.lsp4j.Diagnostic;
+import org.eclipse.lsp4j.DiagnosticSeverity;
+import org.eclipse.lsp4j.Position;
+import org.eclipse.lsp4j.Range;
+
+public final class LspDiagnosticBuilder {
+
+    private static final Range NULL_RANGE = new Range(new Position(0, 0), new Position(0, 0));
+    private static final String DEFAULT_SOURCE = "JabRef";
+
+    private String message;
+    private DiagnosticSeverity severity = DiagnosticSeverity.Warning;
+    private String source = DEFAULT_SOURCE;
+
+    private String content;
+    private BibEntry entry;
+    private Field field;
+    private Range explicitRange;
+
+    private LspDiagnosticBuilder() { }
+
+    public static LspDiagnosticBuilder create(String message) {
+        return new LspDiagnosticBuilder().setMessage(message);
+    }
+
+    public LspDiagnosticBuilder setMessage(String message) {
+        this.message = Objects.requireNonNull(message, "message must not be null");
+        return this;
+    }
+
+    public LspDiagnosticBuilder setSeverity(DiagnosticSeverity severity) {
+        this.severity = Objects.requireNonNull(severity, "severity must not be null");
+        return this;
+    }
+
+    public LspDiagnosticBuilder setSource(String source) {
+        this.source = Objects.requireNonNull(source, "source must not be null");
+        return this;
+    }
+
+    public LspDiagnosticBuilder setContent(String content) {
+        this.content = content;
+        return this;
+    }
+
+    public LspDiagnosticBuilder setEntry(BibEntry entry) {
+        this.entry = entry;
+        return this;
+    }
+
+    public LspDiagnosticBuilder setField(Field field) {
+        this.field = field;
+        return this;
+    }
+
+    public LspDiagnosticBuilder setRange(Range range) {
+        this.explicitRange = range;
+        return this;
+    }
+
+    public Diagnostic build() {
+        Objects.requireNonNull(message, "message must be set");
+
+        Range range = computeRange();
+        return new Diagnostic(range, message, severity, source);
+    }
+
+    private Range computeRange() {
+        if (explicitRange != null) {
+            return explicitRange;
+        }
+
+        if (content == null || entry == null) {
+            return NULL_RANGE;
+        }
+
+        if (field != null) {
+            Optional<String> entryField = entry.getFieldOrAlias(field);
+            if (entryField.isPresent()) {
+                return findTextRange(content, entryField.get());
+            }
+            return entry.getCitationKey()
+                        .map(key -> findTextRange(content, key))
+                        .orElse(NULL_RANGE);
+        }
+
+        return entry.getCitationKey()
+                    .map(key -> findTextRange(content, key))
+                    .orElse(NULL_RANGE);
+    }
+
+    private static Range findTextRange(String content, String searchText) {
+        int startOffset = content.indexOf(searchText);
+        if (startOffset == -1) {
+            return NULL_RANGE;
+        }
+        int endOffset = startOffset + searchText.length();
+        return new Range(offsetToPosition(content, startOffset), offsetToPosition(content, endOffset));
+    }
+
+    private static Position offsetToPosition(String content, int offset) {
+        int line = 0;
+        int col = 0;
+        for (int i = 0; i < offset; i++) {
+            if (content.charAt(i) == '\n') {
+                line++;
+                col = 0;
+            } else {
+                col++;
+            }
+        }
+        return new Position(line, col);
+    }
+}
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
new file mode 100644
index 00000000000..fdfca50ef74
--- /dev/null
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
@@ -0,0 +1,100 @@
+package org.jabref.languageserver.util;
+
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.stream.Stream;
+
+import org.jabref.languageserver.ExtensionSettings;
+import org.jabref.languageserver.LspClientHandler;
+import org.jabref.logic.journals.JournalAbbreviationRepository;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.model.database.BibDatabaseContext;
+
+import org.eclipse.lsp4j.Diagnostic;
+import org.eclipse.lsp4j.DiagnosticSeverity;
+import org.eclipse.lsp4j.PublishDiagnosticsParams;
+import org.eclipse.lsp4j.services.LanguageClient;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class LspDiagnosticHandler {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(LspDiagnosticHandler.class);
+
+    private final CliPreferences jabRefCliPreferences;
+    private final LspIntegrityCheck lspIntegrityCheck;
+    private final LspConsistencyCheck lspConsistencyCheck;
+    private final LspClientHandler clientHandler;
+
+    private LanguageClient client;
+
+    private final Map<String, List<Diagnostic>> integrityDiagnosticsCache;
+    private final Map<String, List<Diagnostic>> consistencyDiagnosticsCache;
+
+    public LspDiagnosticHandler(LspClientHandler clientHandler, CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
+        this.clientHandler = clientHandler;
+        this.jabRefCliPreferences = cliPreferences;
+        this.lspIntegrityCheck = new LspIntegrityCheck(cliPreferences, abbreviationRepository);
+        this.lspConsistencyCheck = new LspConsistencyCheck();
+        this.integrityDiagnosticsCache = new ConcurrentHashMap<>();
+        this.consistencyDiagnosticsCache = new ConcurrentHashMap<>();
+    }
+
+    public void computeAndPublishDiagnostics(LanguageClient client, String uri, String content, Integer version) {
+        List<Diagnostic> diagnostics = computeDiagnostics(content, uri);
+        publishDiagnostics(client, uri, version, diagnostics);
+    }
+
+    public void publishDiagnostics(LanguageClient client, String uri, Integer version, List<Diagnostic> diagnostics) {
+        PublishDiagnosticsParams params = new PublishDiagnosticsParams();
+        params.setUri(uri);
+        params.setVersion(version);
+        params.setDiagnostics(diagnostics);
+        client.publishDiagnostics(params);
+    }
+
+    public void publishDiagnostics(LanguageClient client, String uri, List<Diagnostic> diagnostics) {
+        publishDiagnostics(client, uri, -1, diagnostics);
+    }
+
+    private List<Diagnostic> computeDiagnostics(String content, String uri) {
+        BibDatabaseContext bibDatabaseContext;
+        try {
+            bibDatabaseContext = BibDatabaseContext.of(content, jabRefCliPreferences.getImportFormatPreferences());
+        } catch (Exception e) {
+            Diagnostic parseDiagnostic = LspDiagnosticBuilder.create(Localization.lang(
+                    "Failed to parse entries.\nThe following error was encountered:\n%0",
+                    e.getMessage())).setSeverity(DiagnosticSeverity.Error).build();
+            return List.of(parseDiagnostic);
+        }
+
+        if (clientHandler.getSettings().isIntegrityCheck()) {
+            integrityDiagnosticsCache.put(uri, lspIntegrityCheck.check(bibDatabaseContext, content));
+            LOGGER.debug("Cached integrity diagnostics for {}", uri);
+        }
+
+        if (clientHandler.getSettings().isConsistencyCheck()) {
+            consistencyDiagnosticsCache.put(uri, lspConsistencyCheck.check(bibDatabaseContext, content));
+            LOGGER.debug("Cached consistency diagnostics for {}", uri);
+        }
+
+        return getFinalDiagnosticsList(uri);
+    }
+
+    private List<Diagnostic> getFinalDiagnosticsList(String uri) {
+        ExtensionSettings settings = clientHandler.getSettings();
+        return Stream.concat(
+                settings.isIntegrityCheck() ? integrityDiagnosticsCache.getOrDefault(uri, List.of()).stream() : Stream.empty(),
+                settings.isConsistencyCheck() ? consistencyDiagnosticsCache.getOrDefault(uri, List.of()).stream() : Stream.empty()
+        ).toList();
+    }
+
+    public void refreshDiagnostics(LanguageClient client) {
+        for (String uri : Stream.concat(integrityDiagnosticsCache.keySet().stream(), consistencyDiagnosticsCache.keySet().stream()).distinct().toList()) {
+            List<Diagnostic> diagnostics = getFinalDiagnosticsList(uri);
+            publishDiagnostics(client, uri, diagnostics);
+        }
+    }
+}
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticUtil.java b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticUtil.java
deleted file mode 100644
index 749895e8c82..00000000000
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticUtil.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package org.jabref.languageserver.util;
-
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.field.Field;
-
-import org.eclipse.lsp4j.Diagnostic;
-import org.eclipse.lsp4j.DiagnosticSeverity;
-import org.eclipse.lsp4j.Position;
-import org.eclipse.lsp4j.Range;
-
-public class LspDiagnosticUtil {
-
-    private static final Range NULL_RANGE = new Range(new Position(0, 0), new Position(0, 0));
-    private static final String DIAGNOSTIC_SOURCE = "JabRef";
-
-    public static Diagnostic createFieldDiagnostic(String message, Field field, String content, BibEntry entry) {
-        if (entry.getFieldOrAlias(field).isEmpty()) {
-            return createGeneralEntryDiagnostic(message, content, entry);
-        }
-        return new Diagnostic(findTextRange(content, entry.getFieldOrAlias(field).get()), message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
-    }
-
-    public static Diagnostic createGeneralEntryDiagnostic(String message, String content, BibEntry entry) {
-        if (entry.getCitationKey().isEmpty()) {
-            return createGeneralDiagnostic(message);
-        }
-        return new Diagnostic(findTextRange(content, entry.getCitationKey().get()), message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
-    }
-
-    public static Diagnostic createGeneralDiagnostic(String message) {
-        return new Diagnostic(NULL_RANGE, message, DiagnosticSeverity.Warning, DIAGNOSTIC_SOURCE);
-    }
-
-    private static Range findTextRange(String content, String searchText) {
-        int startOffset = content.indexOf(searchText);
-        if (startOffset == -1) {
-            return NULL_RANGE;
-        }
-        int endOffset = startOffset + searchText.length();
-        return new Range(offsetToPosition(content, startOffset), offsetToPosition(content, endOffset));
-    }
-
-    private static Position offsetToPosition(String content, int offset) {
-        int line = 0;
-        int col = 0;
-        for (int i = 0; i < offset; i++) {
-            if (content.charAt(i) == '\n') {
-                line++;
-                col = 0;
-            } else {
-                col++;
-            }
-        }
-        return new Position(line, col);
-    }
-}
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java b/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
index 25a105a38ec..e08d7745c83 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
@@ -11,6 +11,8 @@
 
 public class LspIntegrityCheck {
 
+    private static final boolean ALLOWINTEGEREDITION = true;
+
     private final CliPreferences cliPreferences;
     private final JournalAbbreviationRepository abbreviationRepository;
 
@@ -25,14 +27,14 @@ public List<Diagnostic> check(BibDatabaseContext bibDatabaseContext, String cont
                 cliPreferences.getFilePreferences(),
                 cliPreferences.getCitationKeyPatternPreferences(),
                 abbreviationRepository,
-                true
+                ALLOWINTEGEREDITION
         );
 
         return bibDatabaseContext.getEntries().stream().flatMap(entry -> integrityCheck.checkEntry(entry).stream().map(message -> {
             if (entry.getField(message.field()).isPresent()) {
-                return LspDiagnosticUtil.createFieldDiagnostic(message.message(), message.field(), content, entry);
+                return LspDiagnosticBuilder.create(message.message()).setField(message.field()).setContent(content).setEntry(entry).build();
             } else {
-                return LspDiagnosticUtil.createGeneralEntryDiagnostic(message.message(), content, entry);
+                return LspDiagnosticBuilder.create(message.message()).setContent(content).setEntry(entry).build();
             }
         })).toList();
     }

From edc616dc500ec2fbc1694711813845143e5fe296 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Mon, 25 Aug 2025 01:31:57 +0200
Subject: [PATCH 07/14] Update
 jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java

Co-authored-by: Subhramit Basu <subhramit.bb@live.in>
---
 .../java/org/jabref/languageserver/util/LspIntegrityCheck.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java b/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
index e08d7745c83..734376abe07 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
@@ -11,7 +11,7 @@
 
 public class LspIntegrityCheck {
 
-    private static final boolean ALLOWINTEGEREDITION = true;
+    private static final boolean ALLOW_INTEGER_EDITION = true;
 
     private final CliPreferences cliPreferences;
     private final JournalAbbreviationRepository abbreviationRepository;

From cbd9b3031e8702132a8545dd8eea04cb1a93fa1c Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Mon, 25 Aug 2025 01:32:43 +0200
Subject: [PATCH 08/14] rename parameter

---
 .../org/jabref/languageserver/BibtexWorkspaceService.java     | 4 ++--
 .../org/jabref/languageserver/util/LspIntegrityCheck.java     | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java b/jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java
index 0956dfa6f3d..d0a3a6d10a6 100644
--- a/jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java
+++ b/jabls/src/main/java/org/jabref/languageserver/BibtexWorkspaceService.java
@@ -19,9 +19,9 @@ public class BibtexWorkspaceService implements WorkspaceService {
 
     private LanguageClient client;
 
-    public BibtexWorkspaceService(LspClientHandler clientHandler, LspDiagnosticHandler lspClientHandler) {
+    public BibtexWorkspaceService(LspClientHandler clientHandler, LspDiagnosticHandler diagnosticHandler) {
         this.clientHandler = clientHandler;
-        this.diagnosticHandler = lspClientHandler;
+        this.diagnosticHandler = diagnosticHandler;
     }
 
     // Todo: handle event
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java b/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
index 734376abe07..a5600feb079 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspIntegrityCheck.java
@@ -27,7 +27,7 @@ public List<Diagnostic> check(BibDatabaseContext bibDatabaseContext, String cont
                 cliPreferences.getFilePreferences(),
                 cliPreferences.getCitationKeyPatternPreferences(),
                 abbreviationRepository,
-                ALLOWINTEGEREDITION
+                ALLOW_INTEGER_EDITION
         );
 
         return bibDatabaseContext.getEntries().stream().flatMap(entry -> integrityCheck.checkEntry(entry).stream().map(message -> {

From 30ed0608df7e9347f081499d0757e5953ceb1ae5 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Mon, 25 Aug 2025 01:37:16 +0200
Subject: [PATCH 09/14] remove package and add import

---
 .../java/org/jabref/languageserver/ExtensionSettings.java     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java b/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
index ddc352813d9..46b0da656e9 100644
--- a/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
+++ b/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
@@ -1,5 +1,7 @@
 package org.jabref.languageserver;
 
+import com.google.gson.JsonObject;
+
 public class ExtensionSettings {
     private boolean consistencyCheck;
     private boolean integrityCheck;
@@ -34,7 +36,7 @@ public void copyFromOther(ExtensionSettings other) {
         this.integrityCheck = other.integrityCheck;
     }
 
-    public void copyFromJsonObject(com.google.gson.JsonObject json) {
+    public void copyFromJsonObject(JsonObject json) {
         if (json.has("jabref") && json.get("jabref").isJsonObject()) {
             json = json.getAsJsonObject("jabref");
         }

From 4f34afce311e83749f259dab950a4891b9d35307 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Mon, 25 Aug 2025 01:39:33 +0200
Subject: [PATCH 10/14] rename package from manager to controller

---
 jabgui/src/main/java/org/jabref/gui/JabRefGUI.java              | 2 +-
 .../org/jabref/gui/preferences/general/GeneralTabViewModel.java | 2 +-
 jabls/src/main/java/module-info.java                            | 2 +-
 .../{manager => controller}/LanguageServerController.java       | 2 +-
 .../languageserver/{manager => controller}/package-info.java    | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)
 rename jabls/src/main/java/org/jabref/languageserver/{manager => controller}/LanguageServerController.java (97%)
 rename jabls/src/main/java/org/jabref/languageserver/{manager => controller}/package-info.java (59%)

diff --git a/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java b/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
index eb6eedb16fb..47e191d7b80 100644
--- a/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
+++ b/jabgui/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -33,7 +33,7 @@
 import org.jabref.gui.util.UiTaskExecutor;
 import org.jabref.gui.util.WebViewStore;
 import org.jabref.http.manager.HttpServerManager;
-import org.jabref.languageserver.manager.LanguageServerController;
+import org.jabref.languageserver.controller.LanguageServerController;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.ai.AiService;
 import org.jabref.logic.citation.SearchCitationsRelationsService;
diff --git a/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java b/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
index 51125c69a2e..2de265144f5 100644
--- a/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
+++ b/jabgui/src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java
@@ -33,7 +33,7 @@
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.http.manager.HttpServerManager;
-import org.jabref.languageserver.manager.LanguageServerController;
+import org.jabref.languageserver.controller.LanguageServerController;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.LibraryPreferences;
 import org.jabref.logic.l10n.Language;
diff --git a/jabls/src/main/java/module-info.java b/jabls/src/main/java/module-info.java
index 873c35e7706..aa072e5194e 100644
--- a/jabls/src/main/java/module-info.java
+++ b/jabls/src/main/java/module-info.java
@@ -1,7 +1,7 @@
 module org.jabref.jabls {
     exports org.jabref.languageserver;
     opens org.jabref.languageserver to lsp4j, lsp4j.jsonrpc, com.google.gson;
-    exports org.jabref.languageserver.manager;
+    exports org.jabref.languageserver.controller;
     exports org.jabref.languageserver.util;
 
     requires org.jabref.jablib;
diff --git a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java b/jabls/src/main/java/org/jabref/languageserver/controller/LanguageServerController.java
similarity index 97%
rename from jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java
rename to jabls/src/main/java/org/jabref/languageserver/controller/LanguageServerController.java
index 49d852bda24..97980089fee 100644
--- a/jabls/src/main/java/org/jabref/languageserver/manager/LanguageServerController.java
+++ b/jabls/src/main/java/org/jabref/languageserver/controller/LanguageServerController.java
@@ -1,4 +1,4 @@
-package org.jabref.languageserver.manager;
+package org.jabref.languageserver.controller;
 
 import org.jabref.languageserver.LspLauncher;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
diff --git a/jabls/src/main/java/org/jabref/languageserver/manager/package-info.java b/jabls/src/main/java/org/jabref/languageserver/controller/package-info.java
similarity index 59%
rename from jabls/src/main/java/org/jabref/languageserver/manager/package-info.java
rename to jabls/src/main/java/org/jabref/languageserver/controller/package-info.java
index e61d6ce7087..2f1a1cdf1b5 100644
--- a/jabls/src/main/java/org/jabref/languageserver/manager/package-info.java
+++ b/jabls/src/main/java/org/jabref/languageserver/controller/package-info.java
@@ -1,2 +1,2 @@
 /// Implemented similar to package org.jabref.logic.remote.server;
-package org.jabref.languageserver.manager;
+package org.jabref.languageserver.controller;

From d98ba47f58961f74e27e255e88f4dd3d5243dfda Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Mon, 25 Aug 2025 01:55:07 +0200
Subject: [PATCH 11/14] address review comments

Co-authored-by: Subhramit Basu <subhramit.bb@live.in>
---
 .../org/jabref/logic/remote/RemoteUtil.java   |  2 +-
 .../util/LspConsistencyCheck.java             |  2 +-
 .../util/LspDiagnosticHandler.java            | 19 ++++++++++++-------
 3 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/jablib/src/main/java/org/jabref/logic/remote/RemoteUtil.java b/jablib/src/main/java/org/jabref/logic/remote/RemoteUtil.java
index 042f18f0d32..964b372f207 100644
--- a/jablib/src/main/java/org/jabref/logic/remote/RemoteUtil.java
+++ b/jablib/src/main/java/org/jabref/logic/remote/RemoteUtil.java
@@ -13,7 +13,7 @@ public static boolean isStringUserPort(String portString) {
         try {
             int portNumber = Integer.parseInt(portString);
             return isUserPort(portNumber);
-        } catch (NumberFormatException numberFormatException) {
+        } catch (NumberFormatException e) {
             return false;
         }
     }
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java b/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
index eb3315c8bd8..75358fbb601 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspConsistencyCheck.java
@@ -62,7 +62,7 @@ public List<Diagnostic> check(BibDatabaseContext bibDatabaseContext, String cont
 
             optionalFields.forEach(optionalField -> entryTypeResult.sortedEntries().forEach(entry -> {
                 if (entry.getFieldOrAlias(optionalField).isEmpty()) {
-                    LspDiagnosticBuilder diagnosticBuilder = LspDiagnosticBuilder.create(Localization.lang("Required field \"%0\" is empty.", optionalField.getName()));
+                    LspDiagnosticBuilder diagnosticBuilder = LspDiagnosticBuilder.create(Localization.lang("Optional field \"%0\" is empty.", optionalField.getName()));
                     diagnosticBuilder.setContent(content);
                     diagnosticBuilder.setEntry(entry);
                     diagnostics.add(diagnosticBuilder.build());
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
index fdfca50ef74..fbed3ec03e8 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
@@ -1,12 +1,15 @@
 package org.jabref.languageserver.util;
 
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.stream.Stream;
 
 import org.jabref.languageserver.ExtensionSettings;
 import org.jabref.languageserver.LspClientHandler;
+import org.jabref.logic.JabRefException;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.CliPreferences;
@@ -22,17 +25,17 @@
 public class LspDiagnosticHandler {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(LspDiagnosticHandler.class);
+    private static final int NO_VERSION = -1;
 
     private final CliPreferences jabRefCliPreferences;
     private final LspIntegrityCheck lspIntegrityCheck;
     private final LspConsistencyCheck lspConsistencyCheck;
     private final LspClientHandler clientHandler;
-
-    private LanguageClient client;
-
     private final Map<String, List<Diagnostic>> integrityDiagnosticsCache;
     private final Map<String, List<Diagnostic>> consistencyDiagnosticsCache;
 
+    private LanguageClient client;
+
     public LspDiagnosticHandler(LspClientHandler clientHandler, CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
         this.clientHandler = clientHandler;
         this.jabRefCliPreferences = cliPreferences;
@@ -56,14 +59,14 @@ public void publishDiagnostics(LanguageClient client, String uri, Integer versio
     }
 
     public void publishDiagnostics(LanguageClient client, String uri, List<Diagnostic> diagnostics) {
-        publishDiagnostics(client, uri, -1, diagnostics);
+        publishDiagnostics(client, uri, NO_VERSION, diagnostics);
     }
 
     private List<Diagnostic> computeDiagnostics(String content, String uri) {
         BibDatabaseContext bibDatabaseContext;
         try {
             bibDatabaseContext = BibDatabaseContext.of(content, jabRefCliPreferences.getImportFormatPreferences());
-        } catch (Exception e) {
+        } catch (JabRefException e) {
             Diagnostic parseDiagnostic = LspDiagnosticBuilder.create(Localization.lang(
                     "Failed to parse entries.\nThe following error was encountered:\n%0",
                     e.getMessage())).setSeverity(DiagnosticSeverity.Error).build();
@@ -92,9 +95,11 @@ private List<Diagnostic> getFinalDiagnosticsList(String uri) {
     }
 
     public void refreshDiagnostics(LanguageClient client) {
-        for (String uri : Stream.concat(integrityDiagnosticsCache.keySet().stream(), consistencyDiagnosticsCache.keySet().stream()).distinct().toList()) {
+        Set<String> allUris = new HashSet<>(integrityDiagnosticsCache.keySet());
+        allUris.addAll(consistencyDiagnosticsCache.keySet());
+        allUris.forEach(uri -> {
             List<Diagnostic> diagnostics = getFinalDiagnosticsList(uri);
             publishDiagnostics(client, uri, diagnostics);
-        }
+        });
     }
 }

From 89399b1856b9b266c2f238429e61aad3a902216a Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Mon, 25 Aug 2025 14:46:03 +0200
Subject: [PATCH 12/14] fix tests and minor changes

---
 jabgui/build.gradle.kts                                     | 6 +++---
 jabgui/src/main/java/module-info.java                       | 3 +--
 .../test/java/org/jabref/logic/l10n/LocalizationParser.java | 4 ++--
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/jabgui/build.gradle.kts b/jabgui/build.gradle.kts
index b837855f4ff..2e14ae5af1d 100644
--- a/jabgui/build.gradle.kts
+++ b/jabgui/build.gradle.kts
@@ -20,12 +20,12 @@ dependencies {
     // implementation("org.openjfx:javafx-fxml")
     // implementation("org.openjfx:javafx-graphics")
 
+    implementation(project(":jabls"))
+    implementation(project(":jabsrv"))
+
     implementation("org.openjfx:javafx-swing")
     implementation("org.openjfx:javafx-web")
 
-    implementation(project(":jabsrv"))
-    implementation(project(":jabls"))
-
     implementation("com.pixelduke:fxthemes")
 
     // From JavaFX25 onwards
diff --git a/jabgui/src/main/java/module-info.java b/jabgui/src/main/java/module-info.java
index a79dd369c83..09b87d8b53f 100644
--- a/jabgui/src/main/java/module-info.java
+++ b/jabgui/src/main/java/module-info.java
@@ -1,8 +1,7 @@
 open module org.jabref {
     requires org.jabref.jablib;
-
-    requires org.jabref.jabsrv;
     requires org.jabref.jabls;
+    requires org.jabref.jabsrv;
 
     // Swing
     requires java.desktop;
diff --git a/jablib/src/test/java/org/jabref/logic/l10n/LocalizationParser.java b/jablib/src/test/java/org/jabref/logic/l10n/LocalizationParser.java
index 076fb63ea0d..5f1b541f17b 100644
--- a/jablib/src/test/java/org/jabref/logic/l10n/LocalizationParser.java
+++ b/jablib/src/test/java/org/jabref/logic/l10n/LocalizationParser.java
@@ -90,7 +90,7 @@ public static Set<LocalizationEntry> findLocalizationParametersStringsInJavaFile
 
     private static Set<LocalizationEntry> findLocalizationEntriesInJavaFiles(LocalizationBundleForTest type) throws IOException {
         try {
-            return List.of("jablib", "jabkit", "jabsrv", "jabgui")
+            return List.of("jablib", "jabkit", "jabsrv", "jabgui", "jabls")
                        .stream()
                        .map(path -> Path.of("..", path, "src", "main", "java").normalize())
                        .flatMap(Unchecked.function(path -> Files.walk(path)))
@@ -104,7 +104,7 @@ private static Set<LocalizationEntry> findLocalizationEntriesInJavaFiles(Localiz
 
     private static Set<LocalizationEntry> findLocalizationEntriesInFxmlFiles(LocalizationBundleForTest type) throws IOException {
         try {
-            return List.of("jablib", "jabkit", "jabsrv", "jabgui")
+            return List.of("jablib", "jabkit", "jabsrv", "jabgui", "jabls")
                        .stream()
                        .map(path -> Path.of("..", path, "src", "main", "resources").normalize())
                        .filter(Files::isDirectory)

From 950c55657406cb6027ffaab363c90a2254d22435 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Tue, 26 Aug 2025 00:12:28 +0200
Subject: [PATCH 13/14] address comments

---
 .../java/org/jabref/languageserver/ExtensionSettings.java    | 5 -----
 .../languageserver/controller/LanguageServerController.java  | 4 +++-
 .../org/jabref/languageserver/util/LspDiagnosticHandler.java | 4 ++--
 3 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java b/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
index 46b0da656e9..c1b41b2a94b 100644
--- a/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
+++ b/jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java
@@ -31,11 +31,6 @@ public boolean isIntegrityCheck() {
         return integrityCheck;
     }
 
-    public void copyFromOther(ExtensionSettings other) {
-        this.consistencyCheck = other.consistencyCheck;
-        this.integrityCheck = other.integrityCheck;
-    }
-
     public void copyFromJsonObject(JsonObject json) {
         if (json.has("jabref") && json.get("jabref").isJsonObject()) {
             json = json.getAsJsonObject("jabref");
diff --git a/jabls/src/main/java/org/jabref/languageserver/controller/LanguageServerController.java b/jabls/src/main/java/org/jabref/languageserver/controller/LanguageServerController.java
index 97980089fee..84a4992bded 100644
--- a/jabls/src/main/java/org/jabref/languageserver/controller/LanguageServerController.java
+++ b/jabls/src/main/java/org/jabref/languageserver/controller/LanguageServerController.java
@@ -4,6 +4,7 @@
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.preferences.CliPreferences;
 
+import org.jspecify.annotations.Nullable;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -12,10 +13,11 @@ public class LanguageServerController implements AutoCloseable {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(LanguageServerController.class);
 
-    private LspLauncher lspLauncher;
     private final CliPreferences cliPreferences;
     private final JournalAbbreviationRepository abbreviationRepository;
 
+    @Nullable private LspLauncher lspLauncher;
+
     public LanguageServerController(CliPreferences cliPreferences, JournalAbbreviationRepository abbreviationRepository) {
         this.cliPreferences = cliPreferences;
         this.abbreviationRepository = abbreviationRepository;
diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
index fbed3ec03e8..b3de7149dd2 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
@@ -31,8 +31,8 @@ public class LspDiagnosticHandler {
     private final LspIntegrityCheck lspIntegrityCheck;
     private final LspConsistencyCheck lspConsistencyCheck;
     private final LspClientHandler clientHandler;
-    private final Map<String, List<Diagnostic>> integrityDiagnosticsCache;
-    private final Map<String, List<Diagnostic>> consistencyDiagnosticsCache;
+    private final Map<String, List<Diagnostic>> integrityDiagnosticsCache; // Maps file URIs to the according list of integrity diagnostics
+    private final Map<String, List<Diagnostic>> consistencyDiagnosticsCache; // Maps file URIs to the according list of consistency diagnostics
 
     private LanguageClient client;
 

From 5ac29fc404be954d5c296c6cd304c167ab3343c5 Mon Sep 17 00:00:00 2001
From: Philip <37398281+palukku@users.noreply.github.com>
Date: Wed, 27 Aug 2025 12:12:35 +0200
Subject: [PATCH 14/14] fix typo

---
 .../org/jabref/languageserver/util/LspDiagnosticHandler.java  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
index b3de7149dd2..77397cb90a1 100644
--- a/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
+++ b/jabls/src/main/java/org/jabref/languageserver/util/LspDiagnosticHandler.java
@@ -31,8 +31,8 @@ public class LspDiagnosticHandler {
     private final LspIntegrityCheck lspIntegrityCheck;
     private final LspConsistencyCheck lspConsistencyCheck;
     private final LspClientHandler clientHandler;
-    private final Map<String, List<Diagnostic>> integrityDiagnosticsCache; // Maps file URIs to the according list of integrity diagnostics
-    private final Map<String, List<Diagnostic>> consistencyDiagnosticsCache; // Maps file URIs to the according list of consistency diagnostics
+    private final Map<String, List<Diagnostic>> integrityDiagnosticsCache; // Maps file URIs to the corresponding list of integrity diagnostics
+    private final Map<String, List<Diagnostic>> consistencyDiagnosticsCache; // Maps file URIs to the corresponding list of consistency diagnostics
 
     private LanguageClient client;