diff --git a/app/src/main/assets/data/common/tooling-api-all.jar b/app/src/main/assets/data/common/tooling-api-all.jar
index 2aa15b4fa..4397b7c88 100644
Binary files a/app/src/main/assets/data/common/tooling-api-all.jar and b/app/src/main/assets/data/common/tooling-api-all.jar differ
diff --git a/shared/src/main/java/com/itsaky/androidide/utils/ClassTrie.kt b/shared/src/main/java/com/itsaky/androidide/utils/ClassTrie.kt
index 01f1b80c5..5249f33c1 100644
--- a/shared/src/main/java/com/itsaky/androidide/utils/ClassTrie.kt
+++ b/shared/src/main/java/com/itsaky/androidide/utils/ClassTrie.kt
@@ -220,6 +220,10 @@ open class ClassTrie(val root: Node = Node()) {
       return children.computeIfAbsent(name) { Node(it, qualifiedName, this) }
     }
 
+    open fun removeChild(child: Node) {
+      this.children.remove(child.name)
+    }
+
     open fun allClassNames(): Set<String> {
       return this.allClassNodes().map { it.qualifiedName }.toSet()
     }
diff --git a/subprojects/projects/src/main/java/com/itsaky/androidide/projects/ProjectManager.kt b/subprojects/projects/src/main/java/com/itsaky/androidide/projects/ProjectManager.kt
index 6e21af10e..973098fc9 100644
--- a/subprojects/projects/src/main/java/com/itsaky/androidide/projects/ProjectManager.kt
+++ b/subprojects/projects/src/main/java/com/itsaky/androidide/projects/ProjectManager.kt
@@ -32,9 +32,11 @@ import com.itsaky.androidide.projects.util.ProjectTransformer
 import com.itsaky.androidide.tasks.executeAsync
 import com.itsaky.androidide.tooling.api.IProject
 import com.itsaky.androidide.tooling.api.messages.result.InitializeResult
+import com.itsaky.androidide.utils.DocumentUtils
 import com.itsaky.androidide.utils.ILogger
 import com.itsaky.androidide.utils.flashError
 import java.io.File
+import java.nio.file.Files
 import java.nio.file.Path
 import kotlin.io.path.extension
 import kotlin.io.path.isDirectory
@@ -148,10 +150,6 @@ object ProjectManager : EventReceiver {
     return app
   }
 
-  fun getApplicationResDirectories(): Set<File> {
-    return getApplicationModule()?.getResourceDirectories() ?: emptySet()
-  }
-
   fun notifyProjectUpdate() {
 
     executeAsync {
@@ -170,16 +168,18 @@ object ProjectManager : EventReceiver {
     }
   }
 
-  fun findModuleForFile(file: File): ModuleProject? {
+  @JvmOverloads
+  fun findModuleForFile(file: File, checkExistance: Boolean = false): ModuleProject? {
     if (!checkInit()) {
       return null
     }
 
-    return this.rootProject!!.findModuleForFile(file)
+    return this.rootProject!!.findModuleForFile(file, checkExistance)
   }
 
-  fun findModuleForFile(file: Path): ModuleProject? {
-    return findModuleForFile(file.toFile())
+  @JvmOverloads
+  fun findModuleForFile(file: Path, checkExistance: Boolean = false): ModuleProject? {
+    return findModuleForFile(file.toFile(), checkExistance)
   }
 
   fun containsSourceFile(file: Path): Boolean {
@@ -187,6 +187,10 @@ object ProjectManager : EventReceiver {
       return false
     }
 
+    if (!Files.exists(file)) {
+      return false
+    }
+
     for (module in this.rootProject!!.subModules) {
       if (module !is ModuleProject) {
         continue
@@ -245,18 +249,55 @@ object ProjectManager : EventReceiver {
   @Subscribe(threadMode = BACKGROUND)
   fun onFileCreated(event: FileCreationEvent) {
     generateSourcesIfNecessary(event)
+
+    if (DocumentUtils.isJavaFile(event.file.toPath())) {
+      findModuleForFile(event.file)?.let {
+        val sourceRoot = it.findSourceRoot(event.file) ?: return@let
+
+        // add the source node entry
+        it.compileJavaSourceClasses.append(event.file.toPath(), sourceRoot)
+      }
+    }
   }
 
   @Suppress("unused")
   @Subscribe(threadMode = BACKGROUND)
   fun onFileDeleted(event: FileDeletionEvent) {
     generateSourcesIfNecessary(event)
+
+    // Remove the source node entry
+    // Do not check for Java file DocumentUtils.isJavaFile(...) as it checks for file existence as
+    // well. As the file is already deleted, it will always return false
+    if (event.file.extension == "java") {
+      findModuleForFile(event.file)
+        ?.compileJavaSourceClasses
+        ?.findSource(event.file.toPath())
+        ?.let { it.parent?.removeChild(it) }
+    }
   }
 
   @Suppress("unused")
   @Subscribe(threadMode = BACKGROUND)
   fun onFileRenamed(event: FileRenameEvent) {
     generateSourcesIfNecessary(event)
+
+    // Do not check for Java file DocumentUtils.isJavaFile(...) as it checks for file existence as
+    // well. As the file is already renamed to another filename, it will always return false
+    if (event.file.extension == "java") {
+      // remove the source node entry
+      findModuleForFile(event.file)
+        ?.compileJavaSourceClasses
+        ?.findSource(event.file.toPath())
+        ?.let { it.parent?.removeChild(it) }
+    }
+
+    if (DocumentUtils.isJavaFile(event.newFile.toPath())) {
+      findModuleForFile(event.newFile)?.let {
+        val sourceRoot = it.findSourceRoot(event.newFile) ?: return@let
+        // add the new source node entry
+        it.compileJavaSourceClasses.append(event.newFile.toPath(), sourceRoot)
+      }
+    }
   }
 
   private fun generateSourcesIfNecessary(event: FileEvent) {
@@ -269,6 +310,10 @@ object ProjectManager : EventReceiver {
     generateSources(builder)
   }
 
+  private fun ModuleProject.findSourceRoot(file: File): Path? {
+    return getCompileSourceDirectories().find { file.path.startsWith(it.path) }?.toPath()
+  }
+
   private fun isResource(file: File): Boolean {
     val module = findModuleForFile(file) ?: return false
     if (module is AndroidModule) {
diff --git a/subprojects/projects/src/main/java/com/itsaky/androidide/projects/api/Project.kt b/subprojects/projects/src/main/java/com/itsaky/androidide/projects/api/Project.kt
index 1485cd856..44dba1bc2 100644
--- a/subprojects/projects/src/main/java/com/itsaky/androidide/projects/api/Project.kt
+++ b/subprojects/projects/src/main/java/com/itsaky/androidide/projects/api/Project.kt
@@ -33,7 +33,7 @@ import java.util.concurrent.*
  * @param name The display name of the project.
  * @param description The project description.
  * @param path The project path (same as Gradle project paths). For example, `:app`,
- * `:module:submodule`, etc. Root project is always represented by path `:`.
+ *   `:module:submodule`, etc. Root project is always represented by path `:`.
  * @param projectDir The project directory.
  * @param buildDir The build directory of the project.
  * @param buildScript The Gradle buildscript file of the project.
@@ -124,7 +124,13 @@ open class Project(
     return findModuleForFile(file.toFile())
   }
 
-  fun findModuleForFile(file: File): ModuleProject? {
+  @JvmOverloads
+  fun findModuleForFile(file: File, checkExistance: Boolean = false): ModuleProject? {
+
+    if (!file.exists() && checkExistance) {
+      return null
+    }
+
     val path = file.path
     var longestPath = ""
     var moduleWithLongestPath: ModuleProject? = null
diff --git a/subprojects/projects/src/test/java/com/itsaky/androidide/projects/api/ModuleProjectTest.kt b/subprojects/projects/src/test/java/com/itsaky/androidide/projects/api/ModuleProjectTest.kt
index 86f383ccb..d583bfeed 100644
--- a/subprojects/projects/src/test/java/com/itsaky/androidide/projects/api/ModuleProjectTest.kt
+++ b/subprojects/projects/src/test/java/com/itsaky/androidide/projects/api/ModuleProjectTest.kt
@@ -18,18 +18,23 @@
 package com.itsaky.androidide.projects.api
 
 import com.google.common.truth.Truth.assertThat
+import com.itsaky.androidide.eventbus.events.file.FileCreationEvent
+import com.itsaky.androidide.eventbus.events.file.FileDeletionEvent
+import com.itsaky.androidide.eventbus.events.file.FileRenameEvent
 import com.itsaky.androidide.lookup.Lookup
 import com.itsaky.androidide.projects.ProjectManager
 import com.itsaky.androidide.projects.builder.BuildService
 import com.itsaky.androidide.tooling.api.messages.InitializeProjectMessage
 import com.itsaky.androidide.tooling.testing.ToolingApiTestLauncher
 import com.itsaky.androidide.utils.SourceClassTrie.SourceNode
-import java.io.File
-import java.nio.file.Files
 import org.junit.Test
 import org.junit.runner.RunWith
 import org.robolectric.RobolectricTestRunner
 import org.robolectric.annotation.Config
+import java.io.File
+import java.nio.file.Files
+import java.nio.file.Paths
+import kotlin.io.path.writeText
 
 /** @author Akash Yadav */
 @RunWith(RobolectricTestRunner::class)
@@ -40,9 +45,8 @@ class ModuleProjectTest {
   fun test() {
     val (server, project) = ToolingApiTestLauncher().launchServer()
     server.initialize(InitializeProjectMessage(File("../../tests/test-project").absolutePath)).get()
-    
+
     Lookup.DEFAULT.register(BuildService.KEY_PROJECT_PROXY, project)
-    ProjectManager.setupProject()
 
     verifyProjectManagerAPIs()
 
@@ -177,18 +181,35 @@ class ModuleProjectTest {
   }
 
   private fun verifyProjectManagerAPIs() {
+
+    val testCls =
+      Paths.get("../../tests/test-project/app/src/main/java/com/itsaky/test/app/Test.java")
+        .toAbsolutePath()
+        .normalize()
+    val testCls_renamed = testCls.parent!!.resolve("TestRenamed.java")
+
+    if (Files.exists(testCls)) {
+      Files.delete(testCls)
+    }
+
+    if (Files.exists(testCls_renamed)) {
+      Files.delete(testCls_renamed)
+    }
+
+    ProjectManager.setupProject()
+
     val root = ProjectManager.rootProject
     assertThat(root).isNotNull()
     assertThat(root!!.path).isEqualTo(":")
 
     val source =
       root.projectDir.toPath().resolve("app/src/main/java/com/itsaky/test/app/MainActivity.java")
-    val moduleForFile = root.findModuleForFile(source)
-    assertThat(moduleForFile).isNotNull()
-    assertThat(moduleForFile!!.path).isEqualTo(":app")
-    assertThat(moduleForFile.projectDir.path).isEqualTo(File(root.projectDir, "app").path)
+    val module = root.findModuleForFile(source)
+    assertThat(module).isNotNull()
+    assertThat(module!!.path).isEqualTo(":app")
+    assertThat(module.projectDir.path).isEqualTo(File(root.projectDir, "app").path)
 
-    val sourceNode = moduleForFile.compileJavaSourceClasses.findSource(source)
+    val sourceNode = module.compileJavaSourceClasses.findSource(source)
     assertThat(sourceNode).isNotNull()
     assertThat(sourceNode!!.isClass).isTrue()
     assertThat(sourceNode.name).isEqualTo("MainActivity")
@@ -196,5 +217,30 @@ class ModuleProjectTest {
     assertThat(sourceNode.qualifiedName).isEqualTo("com.itsaky.test.app.MainActivity")
     assertThat(sourceNode.children).isEmpty()
     assertThat(Files.isSameFile(source, sourceNode.file)).isTrue()
+
+    // make sure the files are not indexed
+    assertThat(ProjectManager.containsSourceFile(testCls)).isFalse()
+    assertThat(ProjectManager.containsSourceFile(testCls_renamed)).isFalse()
+
+    testCls.writeText("public class Test {  }")
+    ProjectManager.onFileCreated(FileCreationEvent(testCls.toFile()))
+    assertThat(ProjectManager.containsSourceFile(testCls)).isTrue()
+    assertThat(ProjectManager.containsSourceFile(testCls_renamed)).isFalse()
+    assertThat(ProjectManager.findModuleForFile(testCls, true)).isEqualTo(module)
+    assertThat(ProjectManager.findModuleForFile(testCls_renamed, true)).isNull()
+
+    Files.move(testCls, testCls_renamed)
+    ProjectManager.onFileRenamed(FileRenameEvent(testCls.toFile(), testCls_renamed.toFile()))
+    assertThat(ProjectManager.containsSourceFile(testCls)).isFalse()
+    assertThat(ProjectManager.containsSourceFile(testCls_renamed)).isTrue()
+    assertThat(ProjectManager.findModuleForFile(testCls, true)).isNull()
+    assertThat(ProjectManager.findModuleForFile(testCls_renamed, true)).isEqualTo(module)
+
+    Files.delete(testCls_renamed)
+    ProjectManager.onFileDeleted(FileDeletionEvent(testCls_renamed.toFile()))
+    assertThat(ProjectManager.containsSourceFile(testCls)).isFalse()
+    assertThat(ProjectManager.containsSourceFile(testCls_renamed)).isFalse()
+    assertThat(ProjectManager.findModuleForFile(testCls, true)).isNull()
+    assertThat(ProjectManager.findModuleForFile(testCls_renamed, true)).isNull()
   }
 }
diff --git a/tests/test-project/app/src/main/java/com/itsaky/test/app/Test.java b/tests/test-project/app/src/main/java/com/itsaky/test/app/Test.java
new file mode 100644
index 000000000..96154701e
--- /dev/null
+++ b/tests/test-project/app/src/main/java/com/itsaky/test/app/Test.java
@@ -0,0 +1 @@
+public class Test {  }
\ No newline at end of file