Add workspace indexing progress notifications

Implement LSP $/progress notifications during workspace file indexing
to provide visual feedback in editors/clients.

- Add progress callback parameter to ASTNodeCache.update()
- Report per-file progress using AtomicInteger for thread-safe counting
- Create ProgressNotification in LanguageService.update0() for multi-file updates
- Show progress when indexing > 1 file (initial scan or batch updates)
- Use workspace-specific token to support multiple workspaces

Closes #148

Author: ewels

src/main/java/nextflow/lsp/ast/ASTNodeCache.java

@@ -25,6 +25,8 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.function.BiConsumer;
 import java.util.stream.Collectors;
 
 import nextflow.lsp.compiler.LanguageServerCompiler;
@@ -86,8 +88,9 @@ public void clear() {
      *
      * @param uris
      * @param fileCache
+     * @param progress optional callback to report progress as (current, total)
      */
-    public Set<URI> update(Set<URI> uris, FileCache fileCache) {
+    public Set<URI> update(Set<URI> uris, FileCache fileCache, BiConsumer<Integer, Integer> progress) {
         // invalidate cache for each source file
         for( var uri : uris ) {
             var nodes = nodesByURI.remove(uri);
@@ -101,12 +104,17 @@ public Set<URI> update(Set<URI> uris, FileCache fileCache) {
         }
 
         // parse source files
+        var counter = new AtomicInteger(0);
+        var total = uris.size();
         var sources = uris.parallelStream()
             .map(uri -> compiler.createSourceUnit(uri, fileCache))
             .filter(sourceUnit -> sourceUnit != null)
             .map(sourceUnit -> {
                 compiler.addSource(sourceUnit);
                 compiler.compile(sourceUnit);
+                if( progress != null ) {
+                    progress.accept(counter.incrementAndGet(), total);
+                }
                 return sourceUnit;
             })
             .sequential()

src/main/java/nextflow/lsp/services/LanguageService.java

@@ -38,6 +38,7 @@
 import nextflow.lsp.util.DebouncingExecutor;
 import nextflow.lsp.util.LanguageServerUtils;
 import nextflow.lsp.util.Logger;
+import nextflow.lsp.util.ProgressNotification;
 import nextflow.lsp.util.Positions;
 import nextflow.script.control.ParanoidWarning;
 import nextflow.script.control.RelatedInformationAware;
@@ -363,14 +364,34 @@ private void update0() {
             log.debug(builder.toString());
         }
 
+        // Create progress notification for multi-file updates
+        ProgressNotification progress = null;
+        if( uris.size() > 1 && client != null ) {
+            var token = "indexing-" + (rootUri != null ? rootUri.hashCode() : "default");
+            progress = new ProgressNotification(client, token);
+            progress.create();
+            progress.begin(String.format("Indexing %d files...", uris.size()));
+        }
+
         try {
-            var changedUris = astCache.update(uris, fileCache);
+            final var progressNotification = progress;
+            var changedUris = astCache.update(uris, fileCache,
+                progressNotification != null
+                    ? (current, total) -> progressNotification.update(
+                        String.format("Indexing: %d / %d files", current, total),
+                        current * 100 / total)
+                    : null);
             publishDiagnostics(changedUris);
         }
         catch( Throwable e ) {
             System.err.println(e);
             e.printStackTrace();
         }
+        finally {
+            if( progress != null ) {
+                progress.end();
+            }
+        }
     }
 
     /**