fix(project-tree): list a re-installed SNAPSHOT's entries after reloading the project

A SNAPSHOT installed again replaces its jar in place, which no file watcher
reports, so folders already expanded inside it under External Libraries kept
the old entries, even after collapsing and expanding them again. The project
view now re-reads its loaded folders inside archives when project roots change
(a build tool sync); the backend's archive listing already follows the jar's
modification time and size.

crates/ide-host/src/ops/build.rs

@@ -15,6 +15,7 @@ use ide_build::{BuildModel, BuildTool, SyncOptions, SyncProgress};
 use ide_core::settings::Settings;
 use ide_core::{DocId, FileEdit, IdeError, IdeEvent, IdeResult, Location, Pos, Range, RequestId, WorkspaceEdit};
 use std::path::Path;
+use std::sync::Arc;
 
 fn join_err(e: tokio::task::JoinError) -> IdeError {
     IdeError::internal(e.to_string())
@@ -330,21 +331,61 @@ pub async fn build_sync(
     // holds for Gradle: it reuses its cached classpath on restart, so a
     // dependency added to `build.gradle` stays unresolved until told to sync.
     let lsp = project.lsp.clone();
+    let documents = project.documents.clone();
     tokio::spawn(async move {
         if profiles_changed {
             // jdtls takes the profiles from its Maven settings (see `ide_sdk::maven_profiles`).
             lsp.reconfigure().await;
         }
+        let first = updates.first().cloned();
         for file in updates {
             let uri = ide_lsp::path_to_uri_string(&file);
             if let Err(e) = lsp.java_update_project_configs(&file, vec![uri]).await {
                 tracing::debug!("java/projectConfigurationsUpdate: {e}");
             }
         }
+        let changed = {
+            let lsp = lsp.clone();
+            tokio::task::spawn_blocking(move || lsp.changed_library_archives()).await.unwrap_or_default()
+        };
+        if let Some(file) = first
+            && let Err(e) = lsp.java_refresh_archives(&file, &changed).await
+        {
+            tracing::debug!("openidea.java.refreshArchives: {e}");
+        }
+        refresh_library_classes(&lsp, &documents).await;
     });
     Ok(model)
 }
 
+/// Open library classes whose jar was replaced in place (a SNAPSHOT installed
+/// again keeps its path) show the new contents, like a reopened one.
+async fn refresh_library_classes(lsp: &Arc<ide_lsp::LspManager>, documents: &Arc<ide_workspace::Documents>) {
+    let changed = {
+        let (lsp, documents) = (lsp.clone(), documents.clone());
+        tokio::task::spawn_blocking(move || {
+            documents
+                .open_documents()
+                .into_iter()
+                .filter_map(|doc| Some((doc, documents.virtual_uri(doc).ok().flatten()?)))
+                .filter(|(_, uri)| lsp.library_class_changed(uri))
+                .collect::<Vec<_>>()
+        })
+        .await
+        .unwrap_or_default()
+    };
+    for (doc, uri) in changed {
+        match lsp.virtual_document(&uri).await {
+            Ok(vd) => {
+                if let Err(e) = documents.replace_virtual(doc, &vd.text, &vd.encoding, vd.has_bom) {
+                    tracing::debug!("refreshing {uri}: {e}");
+                }
+            }
+            Err(e) => tracing::debug!("refreshing {uri}: {e}"),
+        }
+    }
+}
+
 /// The POM declaring `dependency` for the Maven module `pom` (project-relative): the
 /// module's own, else its nearest parent in the project; its path, text and declaration.
 fn declaring_pom(
@@ -1051,7 +1092,6 @@ mod maven_completion_tests {
     use ide_build::maven::completion::PomCompletionKind;
     use ide_core::CancellationToken;
     use ide_workspace::dependencies::DependencyVersionSource;
-    use std::sync::Arc;
 
     /// Cache answers the test plants before completing, so the op's Central
     /// lookups hit the session cache and the network is never reached.

crates/ide-lsp/src/jdtls.rs

@@ -809,6 +809,21 @@ impl LspManager {
             .map_err(|e| crate::rpc_err(&server.name, "java/projectConfigurationsUpdate", e))
     }
 
+    /// Asks jdtls to re-read library archives replaced in place (`openidea.java.refreshArchives`):
+    /// a SNAPSHOT installed again keeps its path, and JDT would keep showing the classes it read
+    /// from the old archive. Best-effort: skipped while jdtls is not already running.
+    pub async fn java_refresh_archives(&self, path: &Path, archives: &[PathBuf]) -> IdeResult<()> {
+        let java = LanguageId::new("java");
+        let Some(server) = self.servers_for(&java, path).into_iter().find(|s| s.name == SERVER) else {
+            return Ok(());
+        };
+        if server.running().is_none() {
+            return Ok(());
+        }
+        let archives = archives.iter().map(|a| Value::String(a.to_string_lossy().into_owned())).collect();
+        self.jdtls_command(path, "openidea.java.refreshArchives", archives).await.map(|_| ())
+    }
+
     /// Pause autobuild before resolving the launch classpath. That query takes the
     /// Java project's workspace scheduling rule, draining the interrupted autobuild.
     /// Keep this guard until Maven outputs have been copied out of JDT's reach.

crates/ide-lsp/src/lib.rs

@@ -241,6 +241,9 @@ pub struct LspManager {
     virtual_origins: Mutex<HashMap<String, ide_core::ServerId>>,
     /// Contents fetched for virtual URIs.
     virtual_docs: Mutex<HashMap<String, VirtualDocument>>,
+    /// Modification time of the archive behind a cached library class, so a jar
+    /// replaced in place (a SNAPSHOT installed again) is read again.
+    virtual_stamps: Mutex<HashMap<String, std::time::SystemTime>>,
     injections: injections::State,
     /// Open notebooks by path. Locked before `docs` when both are.
     notebooks: Mutex<HashMap<PathBuf, notebook::NotebookState>>,
@@ -508,6 +511,7 @@ impl LspManager {
             go_mod_checked: Mutex::new(HashSet::new()),
             virtual_origins: Mutex::new(HashMap::new()),
             virtual_docs: Mutex::new(HashMap::new()),
+            virtual_stamps: Mutex::new(HashMap::new()),
             injections: injections::State::default(),
             notebooks: Mutex::new(HashMap::new()),
         })
@@ -3202,14 +3206,44 @@ impl LspManager {
         Ok(found)
     }
 
+    /// Whether the archive behind a cached library class changed since it was read.
+    /// Stats the archive: call from a blocking worker.
+    pub fn library_class_changed(&self, uri: &str) -> bool {
+        let Some(stamp) = self.virtual_stamps.lock().get(uri).copied() else { return false };
+        virtual_doc::archive_modified(uri) != Some(stamp)
+    }
+
+    /// Archives behind cached library classes that changed since they were read.
+    /// Stats each archive: call from a blocking worker.
+    pub fn changed_library_archives(&self) -> Vec<PathBuf> {
+        let uris: Vec<String> = self.virtual_stamps.lock().keys().cloned().collect();
+        let mut archives: Vec<PathBuf> = uris
+            .iter()
+            .filter(|uri| self.library_class_changed(uri))
+            .filter_map(|uri| virtual_doc::archive(uri))
+            .collect();
+        archives.sort();
+        archives.dedup();
+        archives
+    }
+
     /// Contents of a virtual document, from the server that owns `uri`:
     /// `workspace/textDocumentContent` (LSP 3.18) when the server serves the
     /// scheme, jdtls' `java/classFileContents` for `jdt:` URIs. A `jar:` entry
     /// is read from its archive, a `jar:` class shown as its library source
     /// (see [`library_source`]) or else decompiled by the server. Cached.
     pub async fn virtual_document(&self, uri: &str) -> IdeResult<VirtualDocument> {
-        if let Some(d) = self.virtual_docs.lock().get(uri) {
-            return Ok(d.clone());
+        let cached = self.virtual_docs.lock().get(uri).cloned();
+        if let Some(d) = cached {
+            let stamp = self.virtual_stamps.lock().get(uri).copied();
+            let current = {
+                let uri = uri.to_owned();
+                tokio::task::spawn_blocking(move || virtual_doc::archive_modified(&uri)).await.ok().flatten()
+            };
+            if stamp.is_none() || stamp == current {
+                return Ok(d);
+            }
+            self.virtual_docs.lock().remove(uri);
         }
         let scheme = virtual_doc::scheme(uri).to_owned();
         let jar_class = scheme == "jar" && library_source::parse(uri).is_some_and(|e| e.entry.ends_with(".class"));
@@ -3353,11 +3387,18 @@ impl LspManager {
         if let Some(server) = server {
             self.virtual_origins.lock().entry(uri.to_owned()).or_insert(server);
         }
+        let stamp = virtual_doc::archive_modified(uri);
         let mut cache = self.virtual_docs.lock();
+        let mut stamps = self.virtual_stamps.lock();
         if cache.len() >= VIRTUAL_CACHE_LIMIT {
             cache.clear();
+            stamps.clear();
         }
         cache.insert(uri.to_owned(), doc.clone());
+        match stamp {
+            Some(stamp) => stamps.insert(uri.to_owned(), stamp),
+            None => stamps.remove(uri),
+        };
         doc
     }
 

crates/ide-lsp/src/virtual_doc.rs

@@ -172,6 +172,20 @@ pub fn description(uri: &str) -> Option<String> {
     }
 }
 
+/// The archive a `jar:` or `jdt:` library class comes from.
+pub(crate) fn archive(uri: &str) -> Option<std::path::PathBuf> {
+    match scheme(uri) {
+        "jar" => Some(crate::library_source::parse(uri)?.jar),
+        "jdt" => description(uri).filter(|p| p.ends_with(".jar") || p.ends_with(".jmod")).map(Into::into),
+        _ => None,
+    }
+}
+
+/// Modification time of the archive a `jar:` or `jdt:` library class comes from.
+pub(crate) fn archive_modified(uri: &str) -> Option<std::time::SystemTime> {
+    std::fs::metadata(archive(uri)?).and_then(|m| m.modified()).ok()
+}
+
 /// Check both the package and actual archive, so duplicate type names never pick another jar.
 pub(crate) fn matches_class(uri: &str, jar: &std::path::Path, package: &str, name: &str) -> bool {
     let segs = segments(uri);
@@ -304,6 +318,29 @@ mod tests {
         assert_eq!(description("foo://x/y"), None);
     }
 
+    #[test]
+    fn finds_the_archive_behind_a_library_class() {
+        assert_eq!(archive(JDT), Some("/Users/me/.m2/repository/spring-boot-4.1.1.jar".into()));
+        assert_eq!(
+            archive("jdt://contents/java.base/java.lang/String.class?=p/%5C/jdk%5C/lib%5C/jrt-fs.jar%60java.base=x"),
+            None
+        );
+        assert_eq!(archive("jdt://contents/a.jar/p/C.class"), None);
+        assert_eq!(archive("file:///a/C.java"), None);
+
+        let dir = tempfile::tempdir().unwrap();
+        let jar = dir.path().join("lib-1.0-SNAPSHOT.jar");
+        std::fs::write(&jar, b"PK").unwrap();
+        let uri = format!("jar:file://{}!/p/C.class", jar.display());
+        assert_eq!(archive(&uri), Some(jar.clone()));
+        let before = archive_modified(&uri).unwrap();
+        let file = std::fs::File::options().write(true).open(&jar).unwrap();
+        file.set_modified(before + std::time::Duration::from_secs(5)).unwrap();
+        assert_ne!(archive_modified(&uri), Some(before));
+        std::fs::remove_file(&jar).unwrap();
+        assert_eq!(archive_modified(&uri), None);
+    }
+
     #[test]
     fn detects_generated_code() {
         assert!(is_decompiled(

crates/ide-sdk/src/java.rs

@@ -1547,7 +1547,7 @@ pub fn usages_bundle(data_dir: &Path) -> Option<PathBuf> {
     install_bundle(
         data_dir,
         "java-usages",
-        "1.13.0",
+        "1.14.0",
         include_bytes!("../../../java/java-usages/openidea-java-usages.jar"),
     )
 }

java/java-usages/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: OpenIDEA Java usages
 Bundle-SymbolicName: ai.openidea.usages;singleton:=true
-Bundle-Version: 1.13.0
+Bundle-Version: 1.14.0
 Bundle-RequiredExecutionEnvironment: JavaSE-21
 Require-Bundle: org.eclipse.jdt.ls.core,org.eclipse.jdt.core,
  org.eclipse.jdt.core.manipulation,org.eclipse.core.runtime,

java/java-usages/plugin.xml

@@ -17,6 +17,9 @@
     <delegateCommandHandler class="ai.openidea.implementations.ImplementationsCommand">
       <command id="openidea.java.implementations"/>
     </delegateCommandHandler>
+    <delegateCommandHandler class="ai.openidea.archives.RefreshArchivesCommand">
+      <command id="openidea.java.refreshArchives"/>
+    </delegateCommandHandler>
     <delegateCommandHandler class="ai.openidea.hierarchy.HierarchyCommand">
       <command id="openidea.java.hierarchy.members"/>
       <command id="openidea.java.hierarchy.refactor"/>

java/java-usages/src/ai/openidea/archives/RefreshArchivesCommand.java

@@ -0,0 +1,68 @@
+package ai.openidea.archives;
+
+import java.lang.reflect.Field;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.OperationCanceledException;
+import org.eclipse.core.runtime.Path;
+import org.eclipse.jdt.core.IJavaModel;
+import org.eclipse.jdt.core.IJavaProject;
+import org.eclipse.jdt.core.IPackageFragmentRoot;
+import org.eclipse.jdt.core.JavaCore;
+import org.eclipse.jdt.ls.core.internal.IDelegateCommandHandler;
+import org.eclipse.jdt.ls.core.internal.JavaLanguageServerPlugin;
+
+/**
+ * Re-reads library archives replaced in place (a SNAPSHOT installed again keeps its path). The
+ * arguments are the archives' file system paths. Their package fragment roots are closed, which
+ * drops the class files read from the old archive, and jdtls' decompiled sources (cached by class
+ * handle, which a replaced archive keeps) are dropped, so the classes are read again.
+ */
+public final class RefreshArchivesCommand implements IDelegateCommandHandler {
+    @Override
+    public Object executeCommand(String command, List<Object> arguments, IProgressMonitor monitor) throws Exception {
+        IJavaModel model = JavaCore.create(ResourcesPlugin.getWorkspace().getRoot());
+        model.refreshExternalArchives(null, monitor);
+        Set<IPath> archives = new HashSet<>();
+        for (Object argument : arguments) {
+            if (argument instanceof String path) archives.add(Path.fromOSString(path));
+        }
+        int closed = 0;
+        if (archives.isEmpty()) return closed;
+        clearDecompilerCache();
+        for (IJavaProject project : model.getJavaProjects()) {
+            for (IPackageFragmentRoot root : project.getPackageFragmentRoots()) {
+                if (monitor.isCanceled()) throw new OperationCanceledException();
+                if (root.isArchive() && root.isExternal() && archives.contains(root.getPath()) && root.isOpen()) {
+                    root.close();
+                    closed++;
+                }
+            }
+        }
+        return closed;
+    }
+
+    /** jdtls keeps decompiled sources in a static per-decompiler LRU with no API to drop them. */
+    private static void clearDecompilerCache() {
+        try {
+            Class<?> impl = IDelegateCommandHandler.class.getClassLoader()
+                    .loadClass("org.eclipse.jdt.ls.core.internal.decompiler.DecompilerImpl");
+            Field field = impl.getDeclaredField("decompilerCache");
+            field.setAccessible(true);
+            if (field.get(null) instanceof Map<?, ?> caches) {
+                synchronized (caches) {
+                    for (Object cache : caches.values()) {
+                        if (cache instanceof Map<?, ?> map) map.clear();
+                    }
+                }
+            }
+        } catch (ReflectiveOperationException | RuntimeException e) {
+            JavaLanguageServerPlugin.logException("Clearing decompiled sources", e);
+        }
+    }
+}

src/editor/core/librarySources.ts

@@ -1,10 +1,10 @@
 import { useEffect, useState } from "react";
 import { create } from "zustand";
 import { registerActions } from "@/platform/actions";
-import { call, commands, isCancelled, nextRequestId, type RequestId } from "@/platform/ipc";
+import { call, commands, isCancelled, nextRequestId, onIdeEvent, type RequestId } from "@/platform/ipc";
 import { tx } from "@/platform/i18n";
 import { useProject } from "@/platform/project";
-import { invalidateVirtualDocument } from "@/platform/virtualDocs";
+import { invalidateVirtualDocument, invalidateVirtualDocuments } from "@/platform/virtualDocs";
 import { maybeEditorService, notifications } from "@/workbench/contributions";
 
 interface SourceState {
@@ -82,6 +82,9 @@ export function registerLibrarySourcesActions(): () => void {
   const offProject = useProject.subscribe((state, previous) => {
     if (state.project !== previous.project) clear();
   });
+  // A reload may have replaced a library jar in place (a SNAPSHOT installed again): reopened
+  // classes fetch their contents again (the backend refreshes the open ones).
+  const offRoots = onIdeEvent("projectRootsChanged", () => invalidateVirtualDocuments());
   const offActions = registerActions([
     {
       id: "editor.downloadSources",
@@ -118,6 +121,7 @@ export function registerLibrarySourcesActions(): () => void {
   return () => {
     offActions();
     offProject();
+    offRoots();
     clear();
   };
 }

src/features/project-tree/index.ts

@@ -34,6 +34,7 @@ import {
   initProjectTree,
   leadSelection,
   reloadAll,
+  reloadArchiveDirs,
   reloadLoadedDirs,
   setChangedFiles,
   setOpenFiles,
@@ -253,6 +254,7 @@ export function activate(): () => void {
     initProjectTypes(),
     onIdeEvent("fsChanged", (e) => void applyFsChange(e)),
     onIdeEvent("excludedDirsChanged", (e) => void reloadLoadedDirs(e.dirs)),
+    onIdeEvent("projectRootsChanged", () => void reloadArchiveDirs()),
   ];
   return () => {
     disposers.reverse().forEach((d) => d());

src/features/project-tree/store.test.ts

@@ -3,6 +3,7 @@ import { MemoryFs, setProjectFsForTests } from "./fs";
 import { visibleInfo } from "./model";
 import {
   applyFsChange,
+  reloadArchiveDirs,
   reloadLoadedDirs,
   currentModel,
   expandAll,
@@ -114,6 +115,28 @@ describe("refresh of excluded folders", () => {
   });
 });
 
+describe("refresh of library archives", () => {
+  it("re-reads the loaded folders inside archives only", async () => {
+    await fs.createFile("/m2/lib.jar!/p/A.class");
+    await loadDir(ROOT);
+    await loadDir("/m2/lib.jar!");
+    await loadDir("/m2/lib.jar!/p");
+    await fs.createFile("/m2/lib.jar!/p/B.class");
+    const spy = vi.spyOn(fs, "readDir");
+
+    await reloadArchiveDirs();
+
+    expect(spy.mock.calls.map(([p]) => p).sort()).toEqual(["/m2/lib.jar!", "/m2/lib.jar!/p"]);
+    expect(
+      useProjectTree
+        .getState()
+        .listings.get("/m2/lib.jar!/p")
+        ?.map((e) => e.name),
+    ).toEqual(["A.class", "B.class"]);
+    spy.mockRestore();
+  });
+});
+
 describe("refresh on ignore-rule changes", () => {
   it("refreshes loaded descendants once, preserving selection and unrelated folders", async () => {
     await fs.createFile("/p/docs/sub/note.md");

src/features/project-tree/store.ts

@@ -565,6 +565,16 @@ export async function reloadLoadedDirs(dirs: readonly string[]) {
   await Promise.all(dirs.filter((p) => listings.has(p)).map((p) => loadDir(p, true)));
 }
 
+/**
+ * Re-reads the loaded folders inside archives (`<archive>!…`): a build tool sync may have replaced
+ * a library jar in place (a SNAPSHOT installed again), which no file watcher reports.
+ */
+export async function reloadArchiveDirs() {
+  const { listings } = get();
+  const inArchive = (p: string) => p.endsWith("!") || p.includes("!/") || p.includes("!\\");
+  await Promise.all([...listings.keys()].filter(inArchive).map((p) => loadDir(p, true)));
+}
+
 /** Re-reads every loaded folder (View › Reload from Disk). */
 export async function reloadAll() {
   const { listings } = get();

src/platform/virtualDocs.ts

@@ -73,6 +73,11 @@ export function invalidateVirtualDocument(uri: string): void {
   cache.delete(uri);
 }
 
+/** Forgets every cached document: a build tool reload may have replaced library jars in place. */
+export function invalidateVirtualDocuments(): void {
+  cache.clear();
+}
+
 /** Contents of a virtual document (cached; failures are retried on the next call). */
 export function virtualDocument(uri: string): Promise<VirtualDocument> {
   let p = cache.get(uri);

src/ui/Menu.tsx

@@ -344,6 +344,9 @@ export function MenuList({
       aria-label={aria["aria-label"]}
       className={styles.menu}
       onKeyDown={onKeyDown}
+      // A right-click in an open menu does nothing; without this it reaches whatever is under the
+      // menu in the component tree, e.g. the title bar's toolbar menu behind File › Open Recent.
+      onContextMenu={(e) => e.preventDefault()}
       onPointerMove={(e) => {
         if (e.currentTarget.contains(e.target as Node)) pointerMove({ x: e.clientX, y: e.clientY });
       }}

src/ui/Popup.test.tsx

@@ -283,6 +283,17 @@ describe("Menu action enablement", () => {
     expect(open).toHaveFocus();
   });
 
+  it("keeps a right-click in a menu from reaching the components behind it", () => {
+    const behind = vi.fn((e: { defaultPrevented: boolean }) => e.defaultPrevented);
+    render(
+      <div onContextMenu={(e) => behind(e)}>
+        <MenuList items={[{ label: "Recent", run: () => undefined }]} onDone={() => {}} />
+      </div>,
+    );
+    fireEvent.contextMenu(screen.getByRole("menuitem", { name: "Recent" }));
+    expect(behind).toHaveReturnedWith(true);
+  });
+
   it("reports a hovered row once and lets the keyboard continue from it", () => {
     const active: string[] = [];
     const item = (label: string) => ({ label, onActive: () => active.push(label), run: () => undefined });