diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/FixDotProjectPathResourceListener.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/FixDotProjectPathResourceListener.java
new file mode 100644
index 0000000000..48efb92a05
--- /dev/null
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/FixDotProjectPathResourceListener.java
@@ -0,0 +1,103 @@
+/*******************************************************************************
+ * Copyright (c) 2023 Red Hat Inc. and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License 2.0
+ * which accompanies this distribution, and is available at
+ * https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ *******************************************************************************/
+package org.eclipse.jdt.ls.core.internal;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributeView;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.time.Instant;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.eclipse.core.internal.events.ILifecycleListener;
+import org.eclipse.core.internal.events.LifecycleEvent;
+import org.eclipse.core.resources.IFile;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IProjectDescription;
+import org.eclipse.core.resources.IResource;
+import org.eclipse.core.resources.IResourceChangeEvent;
+import org.eclipse.core.resources.IResourceChangeListener;
+import org.eclipse.core.resources.WorkspaceJob;
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.ICoreRunnable;
+import org.eclipse.jdt.ls.core.internal.managers.ProjectsManager;
+
+public class FixDotProjectPathResourceListener implements IResourceChangeListener, ILifecycleListener {
+
+	private Map<IProject, Instant> createdProjects = new HashMap<>();
+
+	@Override
+	public void resourceChanged(IResourceChangeEvent event) {
+		if (ProjectsManager.generatesMetadataFilesAtProjectRoot() || event.getDelta() == null) {
+			return;
+		}
+		try {
+			event.getDelta().accept(delta -> {
+				if (delta.getResource() instanceof IProject project && //
+					project.isOpen() && //
+					createdProjects.containsKey(project)) {
+					Instant projectCreation = createdProjects.remove(project);
+					Path dotProjectOnDisk = project.getLocation().append(IProjectDescription.DESCRIPTION_FILE_NAME).toPath();
+					try {
+						BasicFileAttributes attributes = Files.getFileAttributeView(dotProjectOnDisk, BasicFileAttributeView.class).readAttributes();
+						if (attributes.creationTime().toInstant().isAfter(projectCreation)) {
+							// cannot link to resource in current workspace task, plan it next
+							WorkspaceJob.createSystem("Use linked .project for " + project, (ICoreRunnable) (monitor -> {
+								ProjectsManager.linkDotProject(project);
+								ProjectsManager.linkResources(project);
+							})).schedule();
+						}
+					} catch (IOException ex) {
+						JavaLanguageServerPlugin.logException(ex);
+					}
+				}
+				return delta.getResource().getType() == IResource.ROOT;
+			});
+		} catch (CoreException e) {
+			JavaLanguageServerPlugin.logException(e);
+		}
+	}
+
+	@Override
+	public void handleEvent(LifecycleEvent event) throws CoreException {
+		if (event.kind == LifecycleEvent.PRE_PROJECT_CREATE) {
+			if (event.resource instanceof IProject project) {
+				createdProjects.put(project, Instant.now());
+			}
+		} else if (event.kind == LifecycleEvent.PRE_REFRESH) {
+			unlinkIfLocal(event.resource);
+		}
+	}
+
+	private void unlinkIfLocal(IResource resource) {
+		if (resource instanceof IProject project && project.isOpen()) { 
+			try {
+				Arrays.stream(project.members())
+					.filter(IFile.class::isInstance)
+					.map(IFile.class::cast)
+					.filter(IFile::isLinked)
+					.filter(file -> file.getProject().getLocation().append(file.getProjectRelativePath()).toFile().isFile())
+					.forEach(file -> {
+						try {
+							file.delete(false, false, null);
+						} catch (CoreException e) {
+							JavaLanguageServerPlugin.logException(e);
+						}
+					});
+			} catch (CoreException e) {
+				JavaLanguageServerPlugin.logException(e);
+			}
+		}
+	}
+
+}
diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/JavaLanguageServerPlugin.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/JavaLanguageServerPlugin.java
index 95973f0e73..374167e212 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/JavaLanguageServerPlugin.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/JavaLanguageServerPlugin.java
@@ -28,8 +28,10 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.eclipse.core.internal.net.ProxySelector;
+import org.eclipse.core.internal.resources.Workspace;
 import org.eclipse.core.net.proxy.IProxyData;
 import org.eclipse.core.net.proxy.IProxyService;
+import org.eclipse.core.resources.IResourceChangeEvent;
 import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IStatus;
@@ -113,7 +115,7 @@ public class JavaLanguageServerPlugin extends Plugin {
 	private ProjectsManager projectsManager;
 	private DigestStore digestStore;
 	private ContentProviderManager contentProviderManager;
-
+	private FixDotProjectPathResourceListener fixDotProjectListener;
 	private BaseJDTLanguageServer protocol;
 
 	private PreferenceManager preferenceManager;
@@ -155,6 +157,9 @@ public void start(BundleContext bundleContext) throws Exception {
 			preferenceManager = new StandardPreferenceManager();
 			projectsManager = new StandardProjectsManager(preferenceManager);
 		}
+		fixDotProjectListener = new FixDotProjectPathResourceListener();
+		ResourcesPlugin.getWorkspace().addResourceChangeListener(fixDotProjectListener, IResourceChangeEvent.POST_CHANGE);
+		((Workspace)ResourcesPlugin.getWorkspace()).addLifecycleListener(fixDotProjectListener);
 		digestStore = new DigestStore(getStateLocation().toFile());
 		try {
 			ResourcesPlugin.getWorkspace().addSaveParticipant(IConstants.PLUGIN_ID, projectsManager);
@@ -365,6 +370,7 @@ public void stop(BundleContext bundleContext) throws Exception {
 		JavaLanguageServerPlugin.pluginInstance = null;
 		JavaLanguageServerPlugin.context = null;
 		ResourcesPlugin.getWorkspace().removeSaveParticipant(IConstants.PLUGIN_ID);
+		ResourcesPlugin.getWorkspace().removeResourceChangeListener(fixDotProjectListener);
 		projectsManager = null;
 		contentProviderManager = null;
 		languageServer = null;
diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/ProjectsManager.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/ProjectsManager.java
index a52eff6d77..b01d7e01bf 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/ProjectsManager.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/ProjectsManager.java
@@ -19,6 +19,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
+import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -486,6 +487,25 @@ public static void linkResources(IProject project) throws CoreException {
 		}
 	}
 
+	public static void linkDotProject(IProject project) throws CoreException {
+		IFile dotProject = project.getFile(IProjectDescription.DESCRIPTION_FILE_NAME);
+		if (dotProject.isLinked()) {
+			return;
+		}
+		File targetDiskFile = getMetaDataFilePath(project.getName(), dotProject.getProjectRelativePath()).toFile();
+		if (!targetDiskFile.exists()) {
+			try {
+				targetDiskFile.getParentFile().mkdirs();
+				Files.copy(dotProject.getLocation().toPath(), targetDiskFile.toPath());
+			} catch (Exception ex) {
+				throw new CoreException(Status.error(targetDiskFile + " cannot be created", ex)); //$NON-NLS-1$
+			}
+		}
+		File sourceDiskFile = dotProject.getLocation().toFile();
+		dotProject.createLink(IPath.fromFile(targetDiskFile), IResource.FORCE | IResource.REPLACE, null);
+		sourceDiskFile.delete();
+	}
+
 	@Override
 	public Job updateProject(IProject project, boolean force) {
 		if (project == null || ProjectUtils.isInternalBuildSupport(BuildSupportManager.find(project).orElse(null))) {
diff --git a/org.eclipse.jdt.ls.filesystem/.classpath b/org.eclipse.jdt.ls.filesystem/.classpath
deleted file mode 100644
index 5508535a40..0000000000
--- a/org.eclipse.jdt.ls.filesystem/.classpath
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-17"/>
-	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
-	<classpathentry kind="src" path="src/"/>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
diff --git a/org.eclipse.jdt.ls.filesystem/.project b/org.eclipse.jdt.ls.filesystem/.project
deleted file mode 100644
index d34fd35ec5..0000000000
--- a/org.eclipse.jdt.ls.filesystem/.project
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>org.eclipse.jdt.ls.filesystem</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.ManifestBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.SchemaBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.m2e.core.maven2Builder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.m2e.core.maven2Nature</nature>
-		<nature>org.eclipse.pde.PluginNature</nature>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-	</natures>
-	<filteredResources>
-		<filter>
-			<id>1675270185050</id>
-			<name></name>
-			<type>30</type>
-			<matcher>
-				<id>org.eclipse.core.resources.regexFilterMatcher</id>
-				<arguments>node_modules|\.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
-			</matcher>
-		</filter>
-	</filteredResources>
-</projectDescription>
diff --git a/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.core.resources.prefs b/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.core.resources.prefs
deleted file mode 100644
index 99f26c0203..0000000000
--- a/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.core.resources.prefs
+++ /dev/null
@@ -1,2 +0,0 @@
-eclipse.preferences.version=1
-encoding/<project>=UTF-8
diff --git a/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.jdt.core.prefs
deleted file mode 100644
index 62ef3488cc..0000000000
--- a/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.jdt.core.prefs
+++ /dev/null
@@ -1,9 +0,0 @@
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=17
-org.eclipse.jdt.core.compiler.compliance=17
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
-org.eclipse.jdt.core.compiler.release=enabled
-org.eclipse.jdt.core.compiler.source=17
diff --git a/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.m2e.core.prefs b/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.m2e.core.prefs
deleted file mode 100644
index f897a7f1cb..0000000000
--- a/org.eclipse.jdt.ls.filesystem/.settings/org.eclipse.m2e.core.prefs
+++ /dev/null
@@ -1,4 +0,0 @@
-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1
diff --git a/org.eclipse.jdt.ls.filesystem/META-INF/MANIFEST.MF b/org.eclipse.jdt.ls.filesystem/META-INF/MANIFEST.MF
deleted file mode 100644
index 6fed55d678..0000000000
--- a/org.eclipse.jdt.ls.filesystem/META-INF/MANIFEST.MF
+++ /dev/null
@@ -1,16 +0,0 @@
-Manifest-Version: 1.0
-Bundle-ManifestVersion: 2
-Bundle-SymbolicName: org.eclipse.jdt.ls.filesystem;singleton:=true
-Bundle-Name: %Bundle-Name
-Bundle-Version: 1.25.0.qualifier
-Export-Package: org.eclipse.jdt.ls.core.internal.filesystem;x-friends:="org.eclipse.jdt.ls.tests"
-Bundle-Localization: plugin
-Bundle-Activator: org.eclipse.jdt.ls.core.internal.filesystem.JDTLSFilesystemActivator
-Bundle-Vendor: %Bundle-Vendor
-Require-Bundle: org.eclipse.core.runtime,
- org.eclipse.core.filesystem;bundle-version="1.9.500",
- org.eclipse.core.resources;bundle-version="3.18.100",
- org.eclipse.jdt.core;bundle-version="3.32.0"
-Bundle-RequiredExecutionEnvironment: JavaSE-17
-Automatic-Module-Name: org.eclipse.jdt.ls.application
-Bundle-ActivationPolicy: lazy
diff --git a/org.eclipse.jdt.ls.filesystem/build.properties b/org.eclipse.jdt.ls.filesystem/build.properties
deleted file mode 100644
index 0dc34f7833..0000000000
--- a/org.eclipse.jdt.ls.filesystem/build.properties
+++ /dev/null
@@ -1,6 +0,0 @@
-source.. = src/
-output.. = bin/
-bin.includes = META-INF/,\
-               .,\
-               plugin.xml,\
-               plugin.properties
diff --git a/org.eclipse.jdt.ls.filesystem/plugin.properties b/org.eclipse.jdt.ls.filesystem/plugin.properties
deleted file mode 100644
index 1f57838980..0000000000
--- a/org.eclipse.jdt.ls.filesystem/plugin.properties
+++ /dev/null
@@ -1,14 +0,0 @@
-###############################################################################
-# Copyright (c) 2016-2017 Red Hat Inc. and others.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the Eclipse Public License 2.0
-# which accompanies this distribution, and is available at
-# https://www.eclipse.org/legal/epl-2.0/
-#
-# SPDX-License-Identifier: EPL-2.0
-#
-# Contributors:
-#     Red Hat Inc. - initial API and implementation
-###############################################################################
-Bundle-Vendor = Eclipse.org
-Bundle-Name = JDT Language Server - Core
\ No newline at end of file
diff --git a/org.eclipse.jdt.ls.filesystem/plugin.xml b/org.eclipse.jdt.ls.filesystem/plugin.xml
deleted file mode 100644
index 986a53bee5..0000000000
--- a/org.eclipse.jdt.ls.filesystem/plugin.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?eclipse version="3.4"?>
-<plugin>
-   <extension id="org.eclipse.jdt.ls.filesystem" name="JDT LS File System" point="org.eclipse.core.filesystem.filesystems">
-      <filesystem scheme="file">
-         <run class="org.eclipse.jdt.ls.core.internal.filesystem.JLSFileSystem"/>
-      </filesystem>
-   </extension>
-
-</plugin>
diff --git a/org.eclipse.jdt.ls.filesystem/pom.xml b/org.eclipse.jdt.ls.filesystem/pom.xml
deleted file mode 100644
index 5fdd7cb065..0000000000
--- a/org.eclipse.jdt.ls.filesystem/pom.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<groupId>org.eclipse.jdt.ls</groupId>
-		<artifactId>parent</artifactId>
-		<version>1.25.0-SNAPSHOT</version>
-	</parent>
-	<artifactId>org.eclipse.jdt.ls.filesystem</artifactId>
-	<packaging>eclipse-plugin</packaging>
-	<name>${base.name} :: Filesystem</name>
-</project>
diff --git a/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JDTLSFilesystemActivator.java b/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JDTLSFilesystemActivator.java
deleted file mode 100644
index 6b930e88fc..0000000000
--- a/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JDTLSFilesystemActivator.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package org.eclipse.jdt.ls.core.internal.filesystem;
-
-import org.osgi.framework.BundleActivator;
-import org.osgi.framework.BundleContext;
-
-/*******************************************************************************
- * Copyright (c) 2022 Red Hat Inc. and others.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License 2.0
- * which accompanies this distribution, and is available at
- * https://www.eclipse.org/legal/epl-2.0/
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-public class JDTLSFilesystemActivator implements BundleActivator {
-
-	private static BundleContext context;
-
-	static BundleContext getContext() {
-		return context;
-	}
-
-	public void start(BundleContext bundleContext) throws Exception {
-		JDTLSFilesystemActivator.context = bundleContext;
-	}
-
-	public void stop(BundleContext bundleContext) throws Exception {
-		JDTLSFilesystemActivator.context = null;
-	}
-
-}
diff --git a/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFile.java b/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFile.java
deleted file mode 100644
index 4875bc6c7f..0000000000
--- a/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFile.java
+++ /dev/null
@@ -1,103 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2021 Microsoft Corporation and others.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License 2.0
- * which accompanies this distribution, and is available at
- * https://www.eclipse.org/legal/epl-2.0/
- *
- * SPDX-License-Identifier: EPL-2.0
- *
- * Contributors:
- *     Microsoft Corporation
- *******************************************************************************/
-
-package org.eclipse.jdt.ls.core.internal.filesystem;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.LinkedHashSet;
-import java.util.Set;
-
-import org.eclipse.core.filesystem.IFileStore;
-import org.eclipse.core.internal.filesystem.local.LocalFile;
-import org.eclipse.core.resources.IProjectDescription;
-import org.eclipse.core.runtime.IPath;
-import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.Path;
-
-/**
- * JDT.LS's own implementation of files in the local operating system's file system.
- * The instance of this class will be returned by {@link JLSFileSystem}.
- */
-public class JLSFile extends LocalFile {
-
-    public JLSFile(File file) {
-        super(file);
-    }
-
-    /**
-     * {@inheritDoc}
-     * 
-     * <p>
-     * Since the metadata files may be redirected into the workspace,
-     * we override the method to make sure those files are not missed.
-     * </p>
-     */
-    @Override
-    public String[] childNames(int options, IProgressMonitor monitor) {
-        String[] childNames = super.childNames(options, monitor);
-        if (JLSFsUtils.generatesMetadataFilesAtProjectRoot()) {
-            return childNames;
-        }
-
-        IPath filePath = new Path(this.filePath);
-        String projectName = JLSFsUtils.getProjectNameIfLocationIsProjectRoot(filePath);
-        if (projectName == null) {
-            return childNames;
-        }
-
-        Set<String> childNameSet = new LinkedHashSet<>(Arrays.asList(childNames));
-        if (!childNameSet.contains(IProjectDescription.DESCRIPTION_FILE_NAME) &&
-                JLSFsUtils.METADATA_FOLDER_PATH.append(projectName).append(IProjectDescription.DESCRIPTION_FILE_NAME).toFile().exists()) {
-            childNameSet.add(IProjectDescription.DESCRIPTION_FILE_NAME);
-        }
-
-        return childNameSet.toArray(String[]::new);
-    }
-
-    @Override
-    public IFileStore getChild(String name) {
-        IPath path = new Path(this.filePath).append(name);
-        if (JLSFsUtils.shouldStoreInMetadataArea(path)) {
-            IPath containerPath = JLSFsUtils.getContainerPath(path);
-            String projectName = JLSFsUtils.getProjectNameIfLocationIsProjectRoot(containerPath);
-            if (projectName == null) {
-                return new JLSFile(new File(file, name));
-            }
-            IPath redirectedPath = JLSFsUtils.getMetaDataFilePath(projectName, new Path(name));
-            if (redirectedPath != null) {
-                return new JLSFile(redirectedPath.toFile());
-            }
-        }
-
-        return new JLSFile(new File(file, name));
-    }
-
-    @Override
-    public IFileStore getFileStore(IPath path) {
-        IPath fullPath = new Path(this.filePath).append(path);
-        if (JLSFsUtils.shouldStoreInMetadataArea(fullPath)) {
-            IPath containerPath = JLSFsUtils.getContainerPath(fullPath);
-            String projectName = JLSFsUtils.getProjectNameIfLocationIsProjectRoot(containerPath);
-            if (projectName == null) {
-                return new JLSFile(fullPath.toFile());
-            }
-            IPath redirectedPath = JLSFsUtils.getMetaDataFilePath(projectName, path);
-            if (redirectedPath != null) {
-                return new JLSFile(redirectedPath.toFile());
-            }
-        }
-
-        return new JLSFile(fullPath.toFile());
-    }
-}
diff --git a/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFileSystem.java b/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFileSystem.java
deleted file mode 100644
index 96562c19d2..0000000000
--- a/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFileSystem.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2021 Microsoft Corporation and others.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License 2.0
- * which accompanies this distribution, and is available at
- * https://www.eclipse.org/legal/epl-2.0/
- *
- * SPDX-License-Identifier: EPL-2.0
- *
- * Contributors:
- *     Microsoft Corporation
- *******************************************************************************/
-
-package org.eclipse.jdt.ls.core.internal.filesystem;
-
-import java.net.URI;
-import java.nio.file.Paths;
-
-import org.eclipse.core.filesystem.IFileStore;
-import org.eclipse.core.internal.filesystem.local.LocalFileSystem;
-import org.eclipse.core.runtime.IPath;
-import org.eclipse.core.runtime.Path;
-
-/**
- * JDT.LS's own implementation of file system to handle the 'file' scheme uri.
- * The purpose of this implementation is to allow the .project files can be
- * persisted out of the project root, since for the moment using linked resources
- * seem not possible.
- */
-public class JLSFileSystem extends LocalFileSystem {
-
-    @Override
-    public IFileStore getStore(IPath path) {
-        if (JLSFsUtils.shouldStoreInMetadataArea(path)) {
-            IPath containerPath = JLSFsUtils.getContainerPath(path);
-            String projectName = JLSFsUtils.getProjectNameIfLocationIsProjectRoot(containerPath);
-            if (projectName == null) {
-                return new JLSFile(path.toFile());
-            }
-            IPath redirectedPath = JLSFsUtils.getMetaDataFilePath(projectName, path);
-            if (redirectedPath != null) {
-                return new JLSFile(redirectedPath.toFile()); 
-            }
-        }
-        return new JLSFile(path.toFile());
-    }
-
-    @Override
-    public IFileStore getStore(URI uri) {
-        IPath path = filePathFromURI(uri.toString());
-        return path == null ? super.getStore(uri) : getStore(path);
-    }
-
-	public static IPath filePathFromURI(String uriStr) {
-		URI uri = URI.create(uriStr);
-		return "file".equals(uri.getScheme()) ?
-			Path.fromOSString(Paths.get(uri).toString()) :
-			null;
-	}
-
-}
diff --git a/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFsUtils.java b/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFsUtils.java
deleted file mode 100644
index 8831e4621b..0000000000
--- a/org.eclipse.jdt.ls.filesystem/src/org/eclipse/jdt/ls/core/internal/filesystem/JLSFsUtils.java
+++ /dev/null
@@ -1,143 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2021-2022 Microsoft Corporation and others.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License 2.0
- * which accompanies this distribution, and is available at
- * https://www.eclipse.org/legal/epl-2.0/
- *
- * SPDX-License-Identifier: EPL-2.0
- *
- * Contributors:
- *     Microsoft Corporation
- *******************************************************************************/
-
-package org.eclipse.jdt.ls.core.internal.filesystem;
-
-import java.util.Objects;
-
-import org.eclipse.core.resources.IContainer;
-import org.eclipse.core.resources.IProject;
-import org.eclipse.core.resources.IProjectDescription;
-import org.eclipse.core.resources.ResourcesPlugin;
-import org.eclipse.core.runtime.IPath;
-
-/**
- * Utilities of the file system implementation.
- */
-public class JLSFsUtils {
-    private JLSFsUtils() {}
-
-    /**
-	 * ⚠ This value is duplicated in ProjectsManager as both bundles must remain independent,
-	 * but the same dir should be used for .project or .settings/.classpath.
-	 * So when updating one, think about updating the other.
-	 **/
-    static final IPath METADATA_FOLDER_PATH = ResourcesPlugin.getWorkspace().getRoot().getLocation().append(".projects");;
-    /**
-     * The system property key to specify the file system mode.
-	 * 
-	 * This value is duplicated in ProjectsManager as both bundles must remain independent,
-	 * but the same dir should be used for .project or .settings/.classpath.
-	 * So when updating one, think about updating the other.
-     */
-    static final String GENERATES_METADATA_FILES_AT_PROJECT_ROOT = "java.import.generatesMetadataFilesAtProjectRoot";
-
-    /**
-     * Determine whether the resource should be stored in workspace's metadata folder.
-     * <p>
-     * The file will be stored in workspace's metadata folder when following conditions meet:
-     * <ul>
-     *   <li>The system property shows that it's allowed to store them in workspace.</li>
-     *   <li>The file belongs to the metadata file defined in {@link JLSFsUtils#METADATA_NAMES}.</li>
-     *   <li>The project's root path does not contain the metadata file with the same name.</li>
-     * </ul>
-     * </p>
-     *
-     * @param location the path of the resource.
-     * @return whether the resource needs to be stored in workspace's metadata folder.
-     */
-    static boolean shouldStoreInMetadataArea(IPath location) {
-        if (generatesMetadataFilesAtProjectRoot()) {
-            return false;
-        }
-
-        if (!isProjectMetadataFile(location)) {
-            return false;
-        }
-
-        // do not redirect if the file already exists on disk
-        if (location.toFile().exists()) {
-            return false;
-        }
-
-        return true;
-    }
-
-    /**
-     * Check whether the given location points to a metadata file.
-     * @param location file location.
-     * @return whether the given location points to a metadata file.
-     */
-    static boolean isProjectMetadataFile(IPath location) {
-        return location != null && //
-            location.segmentCount() != 2 && //
-            IProjectDescription.DESCRIPTION_FILE_NAME.equals(location.lastSegment());
-    }
-
-    /**
-     * Get the container path of the given file path.
-     * If the file path is a preferences file, the grand-parent container will be returned.
-     * @param filePath the file path.
-     */
-    static IPath getContainerPath(IPath filePath) {
-        return filePath.removeLastSegments(1);
-    }
-
-    /**
-     * Get the project name if the given path is a project root, or <code>null</code> if
-     * no project root can match the path.
-     * @param location the location path.
-     * @return The project name
-     */
-    static String getProjectNameIfLocationIsProjectRoot(IPath location) {
-        IProject[] projects = ResourcesPlugin.getWorkspace().getRoot().getProjects(IContainer.INCLUDE_HIDDEN);
-        for (IProject project : projects) {
-            IPath projectLocation = project.getLocation();
-            if (Objects.equals(projectLocation, location)) {
-                return project.getName();
-            }
-        }
-        return null;
-    }
-
-    /**
-     * Get the redirected path of the input path. The path will be redirected to
-     * the workspace's metadata folder ({@link JLSFsUtils#METADATA_FOLDER_PATH}).
-     * @param projectName name of the project.
-     * @param path path needs to be redirected.
-     * @return the redirected path.
-     */
-    static IPath getMetaDataFilePath(String projectName, IPath path) {
-        if (path.segmentCount() == 1) {
-            return METADATA_FOLDER_PATH.append(projectName).append(path);
-        }
-
-        String lastSegment = path.lastSegment();
-        if (IProjectDescription.DESCRIPTION_FILE_NAME.equals(lastSegment)) {
-            return METADATA_FOLDER_PATH.append(projectName).append(lastSegment);
-        }
-
-        return null;
-    }
-
-    /**
-     * Check whether the metadata files needs to be generated at project root.
-     */
-    public static boolean generatesMetadataFilesAtProjectRoot() {
-        String property = System.getProperty(GENERATES_METADATA_FILES_AT_PROJECT_ROOT);
-        if (property == null) {
-            return true;
-        }
-        return Boolean.parseBoolean(property);
-    }
-}
diff --git a/org.eclipse.jdt.ls.product/languageServer.product b/org.eclipse.jdt.ls.product/languageServer.product
index 71edf46a64..36c4b06b4f 100644
--- a/org.eclipse.jdt.ls.product/languageServer.product
+++ b/org.eclipse.jdt.ls.product/languageServer.product
@@ -53,7 +53,6 @@
       <plugin id="org.eclipse.jdt.launching"/>
       <plugin id="org.eclipse.jdt.launching.macosx"/>
       <plugin id="org.eclipse.jdt.ls.core"/>
-      <plugin id="org.eclipse.jdt.ls.filesystem"/>
       <plugin id="org.eclipse.jdt.ls.logback.appender" fragment="true"/>
       <plugin id="org.eclipse.m2e.apt.core"/>
       <plugin id="org.eclipse.m2e.core"/>
diff --git a/org.eclipse.jdt.ls.product/syntaxServer.product b/org.eclipse.jdt.ls.product/syntaxServer.product
index b4eed3bd6d..5dbaa8eb8c 100644
--- a/org.eclipse.jdt.ls.product/syntaxServer.product
+++ b/org.eclipse.jdt.ls.product/syntaxServer.product
@@ -27,7 +27,6 @@
       <plugin id="org.eclipse.core.commands"/>
       <plugin id="org.eclipse.core.contenttype"/>
       <plugin id="org.eclipse.core.expressions"/>
-      <plugin id="org.eclipse.core.filesystem"/>
       <plugin id="org.eclipse.core.jobs"/>
       <plugin id="org.eclipse.core.net"/>
       <plugin id="org.eclipse.core.net.linux" fragment="true"/>
diff --git a/org.eclipse.jdt.ls.tests/META-INF/MANIFEST.MF b/org.eclipse.jdt.ls.tests/META-INF/MANIFEST.MF
index 96aca4c458..fb9f941e17 100644
--- a/org.eclipse.jdt.ls.tests/META-INF/MANIFEST.MF
+++ b/org.eclipse.jdt.ls.tests/META-INF/MANIFEST.MF
@@ -33,7 +33,6 @@ Require-Bundle: org.eclipse.jdt.ls.core,
  org.eclipse.jdt.apt.pluggable.core,
  org.eclipse.m2e.apt.core,
  org.eclipse.buildship.core,
- org.mockito.mockito-core;bundle-version="4.3.1",
- org.eclipse.jdt.ls.filesystem;bundle-version="1.0.0"
+ org.mockito.mockito-core;bundle-version="4.3.1"
 Bundle-Vendor: %Bundle-Vendor
 Bundle-Activator: org.eclipse.jdt.ls.core.internal.JavaLanguageServerTestPlugin
diff --git a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/filesystem/GradleProjectMetadataFileTest.java b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/filesystem/GradleProjectMetadataFileTest.java
index 62b1df32e8..2b5556d35a 100644
--- a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/filesystem/GradleProjectMetadataFileTest.java
+++ b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/filesystem/GradleProjectMetadataFileTest.java
@@ -15,6 +15,7 @@
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
@@ -23,6 +24,7 @@
 import java.io.InputStream;
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
 
 import org.eclipse.buildship.core.internal.CorePlugin;
@@ -88,10 +90,10 @@ public void testMetadataFileLocation() throws Exception {
 		// then we check the sub-module
 		project = WorkspaceHelper.getProject("app");
 		projectDescription = project.getFile(IProjectDescription.DESCRIPTION_FILE_NAME);
-		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
-		projectDescriptionPath = FileUtil.toPath(projectDescription.getLocationURI());
+		projectDescriptionPath = projectDescription.getLocation();
 		assertTrue(projectDescriptionPath.toFile().exists());
 		assertEquals(project.getLocation().isPrefixOf(projectDescriptionPath), ProjectsManager.generatesMetadataFilesAtProjectRoot());
+		assertEquals(project.getLocation().append(IProjectDescription.DESCRIPTION_FILE_NAME).toFile().exists(), ProjectsManager.generatesMetadataFilesAtProjectRoot());
 
 		IFile classpath = project.getFile(IJavaProject.CLASSPATH_FILE_NAME);
 		IPath classpathPath = classpath.getLocation();
@@ -113,7 +115,7 @@ public void testMetadataFileLocation2() throws Exception {
 		waitForBackgroundJobs();
 
 		List<IMarker> markers = ResourceUtils.findMarkers(project, IMarker.SEVERITY_ERROR);
-		assertTrue(markers.isEmpty());
+		assertEquals(Collections.emptyList(), markers);
 	}
 
 	@Test
diff --git a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/filesystem/MavenProjectMetadataFileTest.java b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/filesystem/MavenProjectMetadataFileTest.java
index 853c8e6ecc..ddf9ceeb78 100644
--- a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/filesystem/MavenProjectMetadataFileTest.java
+++ b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/filesystem/MavenProjectMetadataFileTest.java
@@ -16,6 +16,7 @@
 import static org.eclipse.jdt.ls.core.internal.WorkspaceHelper.getProject;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
@@ -25,7 +26,6 @@
 
 import org.apache.commons.io.FileUtils;
 import org.eclipse.core.internal.preferences.EclipsePreferences;
-import org.eclipse.core.internal.utils.FileUtil;
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.IProjectDescription;
@@ -72,9 +72,10 @@ public void testMetadataFileLocation() throws Exception {
 
 		IFile projectDescription = project.getFile(IProjectDescription.DESCRIPTION_FILE_NAME);
 		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
-		IPath projectDescriptionPath = FileUtil.toPath(projectDescription.getLocationURI());
+		IPath projectDescriptionPath = projectDescription.getLocation();
 		assertTrue(projectDescriptionPath.toFile().exists());
 		assertEquals(project.getLocation().isPrefixOf(projectDescriptionPath), ProjectsManager.generatesMetadataFilesAtProjectRoot());
+		assertEquals(project.getLocation().append(IProjectDescription.DESCRIPTION_FILE_NAME).toFile().exists(), ProjectsManager.generatesMetadataFilesAtProjectRoot());
 
 		IFile classpath = project.getFile(IJavaProject.CLASSPATH_FILE_NAME);
 		IPath classpathPath = classpath.getLocation();
@@ -116,7 +117,7 @@ public void testInvalidProject() throws Exception {
 		IFile projectFile = invalid.getFile(IProjectDescription.DESCRIPTION_FILE_NAME);
 		assertTrue(projectFile.exists());
 		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
-		File file = FileUtil.toPath(projectFile.getLocationURI()).toFile();
+		File file = projectFile.getLocation().toFile();
 		invalid.close(new NullProgressMonitor());
 		assertTrue(file.exists());
 		file.delete();
@@ -135,7 +136,6 @@ public void testDeleteClasspath() throws Exception {
 		assertIsJavaProject(project);
 		assertIsMavenProject(project);
 		IFile dotClasspath = project.getFile(IJavaProject.CLASSPATH_FILE_NAME);
-		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
 		File file = dotClasspath.getLocation().toFile();
 		assertTrue(file.exists());
 		file.delete();
@@ -155,24 +155,21 @@ public void testFactoryPathFileLocation() throws Exception {
 
 		IFile projectDescription = project.getFile(IProjectDescription.DESCRIPTION_FILE_NAME);
 		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
-		IPath projectDescriptionPath = FileUtil.toPath(projectDescription.getLocationURI());
+		IPath projectDescriptionPath = projectDescription.getLocation();
 		assertTrue(projectDescriptionPath.toFile().exists());
 		assertEquals(project.getLocation().isPrefixOf(projectDescriptionPath), ProjectsManager.generatesMetadataFilesAtProjectRoot());
 
 		IFile classpath = project.getFile(IJavaProject.CLASSPATH_FILE_NAME);
-		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
 		IPath classpathPath = classpath.getLocation();
 		assertTrue(classpathPath.toFile().exists());
 		assertEquals(project.getLocation().isPrefixOf(classpathPath), ProjectsManager.generatesMetadataFilesAtProjectRoot());
 
 		IFile preferencesFile = project.getFile(EclipsePreferences.DEFAULT_PREFERENCES_DIRNAME);
-		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
 		IPath preferencesPath = preferencesFile.getLocation();
 		assertTrue(preferencesPath.toFile().exists());
 		assertEquals(project.getLocation().isPrefixOf(preferencesPath), ProjectsManager.generatesMetadataFilesAtProjectRoot());
 
 		IFile factoryPathFile = project.getFile(".factorypath");
-		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
 		IPath factoryPathFilePath = factoryPathFile.getLocation();
 		assertTrue(factoryPathFilePath.toFile().exists());
 		assertEquals(project.getLocation().isPrefixOf(factoryPathFilePath), ProjectsManager.generatesMetadataFilesAtProjectRoot());
@@ -187,13 +184,10 @@ public void testMultipleMetadataFile() throws Exception {
 		importProjects("maven/" + name);
 		IProject project = getProject(name);
 		IFile projectDescription = project.getFile(IProjectDescription.DESCRIPTION_FILE_NAME);
-		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
 		File projectDescriptionFile = projectDescription.getLocation().toFile();
 		IFile classpath = project.getFile(IJavaProject.CLASSPATH_FILE_NAME);
-		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
 		File classpathPathFile = classpath.getLocation().toFile();
 		IFile preferencesFile = project.getFile(EclipsePreferences.DEFAULT_PREFERENCES_DIRNAME);
-		// workaround to get the correct path, see: https://github.com/eclipse/eclipse.jdt.ls/pull/1900
 		File preferencesPathFile = preferencesFile.getLocation().toFile();
 		FileUtils.copyFile(projectDescriptionFile, project.getLocation().append(IProjectDescription.DESCRIPTION_FILE_NAME).toFile());
 		FileUtils.copyFile(classpathPathFile, project.getLocation().append(IJavaProject.CLASSPATH_FILE_NAME).toFile());
diff --git a/pom.xml b/pom.xml
index 778c33bf19..e187ed7d10 100644
--- a/pom.xml
+++ b/pom.xml
@@ -35,7 +35,6 @@
 	<modules>
 		<module>org.eclipse.jdt.ls.target</module>
 		<module>org.eclipse.jdt.ls.core</module>
-		<module>org.eclipse.jdt.ls.filesystem</module>
 		<module>org.eclipse.jdt.ls.tests</module>
 		<module>org.eclipse.jdt.ls.logback.appender</module>
 		<module>org.eclipse.jdt.ls.tests.syntaxserver</module>