From 5429aec0f161e7da1e191131ef1713c9ec69bba7 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Tue, 1 Jul 2025 15:58:36 +0200
Subject: [PATCH 01/18] Log LSP messages

---
 apps/lsp/src/config.ts          |  11 +-
 apps/lsp/src/index.ts           |  34 +++--
 apps/lsp/src/logging.ts         | 211 +++++++++++++++++---------------
 apps/lsp/src/service/logging.ts |  12 ++
 4 files changed, 160 insertions(+), 108 deletions(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index a51cf1a2..4cc81397 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -24,7 +24,8 @@ import {
   IncludeWorkspaceHeaderCompletions,
   LsConfiguration,
   defaultLsConfiguration,
-  PreferredMdPathExtensionStyle
+  PreferredMdPathExtensionStyle,
+  ILogger
 } from './service';
 
 export type ValidateEnabled = 'ignore' | 'warning' | 'error' | 'hint';
@@ -131,9 +132,14 @@ export class ConfigurationManager extends Disposable {
   public readonly onDidChangeConfiguration = this._onDidChangeConfiguration.event;
 
   private _settings: Settings;
+  private _logger: ILogger;
 
-  constructor(private readonly connection_: Connection) {
+  constructor(
+    private readonly connection_: Connection,
+    logger: ILogger,
+  ) {
     super();
+    this._logger = logger;
     this._settings = defaultSettings();
   }
 
@@ -163,6 +169,7 @@ export class ConfigurationManager extends Disposable {
       undefined
     );
     this.connection_.onDidChangeConfiguration(() => {
+      this._logger.logNotification('didChangeConfiguration');
       this.update();
     });
   }
diff --git a/apps/lsp/src/index.ts b/apps/lsp/src/index.ts
index 19cf7448..3db6e020 100644
--- a/apps/lsp/src/index.ts
+++ b/apps/lsp/src/index.ts
@@ -52,12 +52,17 @@ import { registerDiagnostics } from "./diagnostics";
 // Also include all preview / proposed LSP features.
 const connection = createConnection(ProposedFeatures.all);
 
+// Initialize logger
+const logger = new LogFunctionLogger(
+  console.log.bind(console),
+);
+
 // Create text document manager
 const documents: TextDocuments<Document> = new TextDocuments(TextDocument);
 documents.listen(connection);
 
 // Configuration
-const configManager = new ConfigurationManager(connection);
+const configManager = new ConfigurationManager(connection, logger);
 const config = lsConfiguration(configManager);
 
 // Capabilities
@@ -76,6 +81,8 @@ connection.onInitialize((params: InitializeParams) => {
   capabilities = params.capabilities;
 
   connection.onCompletion(async (params, token): Promise<CompletionItem[]> => {
+    logger.logRequest('completion');
+
     const document = documents.get(params.textDocument.uri);
     if (!document) {
       return [];
@@ -85,6 +92,8 @@ connection.onInitialize((params: InitializeParams) => {
   })
 
   connection.onHover(async (params, token): Promise<Hover | null | undefined> => {
+    logger.logRequest('hover');
+
     const document = documents.get(params.textDocument.uri);
     if (!document) {
       return null;
@@ -94,6 +103,8 @@ connection.onInitialize((params: InitializeParams) => {
 
 
   connection.onDocumentLinks(async (params, token): Promise<DocumentLink[]> => {
+    logger.logRequest('documentLinks');
+
     const document = documents.get(params.textDocument.uri);
     if (!document) {
       return [];
@@ -102,10 +113,13 @@ connection.onInitialize((params: InitializeParams) => {
   });
 
   connection.onDocumentLinkResolve(async (link, token): Promise<DocumentLink | undefined> => {
+    logger.logRequest('documentLinksResolve');
     return mdLs?.resolveDocumentLink(link, token);
   });
 
   connection.onDocumentSymbol(async (params, token): Promise<DocumentSymbol[]> => {
+    logger.logRequest('documentSymbol');
+
     const document = documents.get(params.textDocument.uri);
     if (!document) {
       return [];
@@ -114,6 +128,8 @@ connection.onInitialize((params: InitializeParams) => {
   });
 
   connection.onFoldingRanges(async (params, token): Promise<FoldingRange[]> => {
+    logger.logRequest('foldingRanges');
+
     const document = documents.get(params.textDocument.uri);
     if (!document) {
       return [];
@@ -122,6 +138,8 @@ connection.onInitialize((params: InitializeParams) => {
   });
 
   connection.onSelectionRanges(async (params, token): Promise<SelectionRange[] | undefined> => {
+    logger.logRequest('selectionRanges');
+
     const document = documents.get(params.textDocument.uri);
     if (!document) {
       return [];
@@ -130,10 +148,13 @@ connection.onInitialize((params: InitializeParams) => {
   });
 
   connection.onWorkspaceSymbol(async (params, token): Promise<WorkspaceSymbol[]> => {
+    logger.logRequest('workspaceSymbol');
     return mdLs?.getWorkspaceSymbols(params.query, token) || [];
   });
 
   connection.onReferences(async (params, token): Promise<Location[]> => {
+    logger.logRequest('references');
+
     const document = documents.get(params.textDocument.uri);
     if (!document) {
       return [];
@@ -142,6 +163,8 @@ connection.onInitialize((params: InitializeParams) => {
   });
 
   connection.onDefinition(async (params, token): Promise<Definition | undefined> => {
+    logger.logRequest('definition');
+
     const document = documents.get(params.textDocument.uri);
     if (!document) {
       return undefined;
@@ -182,10 +205,12 @@ connection.onInitialize((params: InitializeParams) => {
 
 // further config dependent initialization
 connection.onInitialized(async () => {
+  logger.logNotification('initialized');
 
   // sync config if possible
   if (capabilities?.workspace?.configuration) {
     await configManager.subscribe();
+    logger.setConfigurationManager(configManager);
   }
 
   // initialize connection to quarto
@@ -207,12 +232,6 @@ connection.onInitialized(async () => {
   );
   const quarto = await initializeQuarto(quartoContext);
 
-  // initialize logger
-  const logger = new LogFunctionLogger(
-    console.log.bind(console),
-    configManager
-  );
-
   // initialize workspace
   const workspace = languageServiceWorkspace(
     workspaceFolders?.map(value => URI.parse(value.uri)) || [],
@@ -255,7 +274,6 @@ connection.onInitialized(async () => {
 
   // register custom methods
   registerCustomMethods(quarto, lspConnection, documents);
-
 });
 
 
diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 7bc2bf86..e7c866a5 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -1,98 +1,113 @@
-/*
- * logging.ts
- *
- * Copyright (C) 2023 by Posit Software, PBC
- * Copyright (c) Microsoft Corporation. All rights reserved.
- *
- * Unless you have received this program directly from Posit Software pursuant
- * to the terms of a commercial license agreement with Posit Software, then
- * this program is licensed to you under the terms of version 3 of the
- * GNU Affero General Public License. This program is distributed WITHOUT
- * ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING THOSE OF NON-INFRINGEMENT,
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Please refer to the
- * AGPL (http://www.gnu.org/licenses/agpl-3.0.txt) for more details.
- *
- */
-
-// based on:
-// https://github.com/microsoft/vscode/blob/main/extensions/markdown-language-features/server/src/logging.ts
-
-
-import { Disposable } from 'core';
-
-import { ILogger, LogLevel } from "./service";
-
-import { ConfigurationManager } from './config';
-
-export class LogFunctionLogger extends Disposable implements ILogger {
-
-  private static now(): string {
-    const now = new Date();
-    return String(now.getUTCHours()).padStart(2, '0')
-      + ':' + String(now.getMinutes()).padStart(2, '0')
-      + ':' + String(now.getUTCSeconds()).padStart(2, '0') + '.' + String(now.getMilliseconds()).padStart(3, '0');
-  }
-
-  private static data2String(data: unknown): string {
-    if (data instanceof Error) {
-      if (typeof data.stack === 'string') {
-        return data.stack;
-      }
-      return data.message;
-    }
-    if (typeof data === 'string') {
-      return data;
-    }
-    return JSON.stringify(data, undefined, 2);
-  }
-
-  private _logLevel: LogLevel;
-
-  constructor(
-    private readonly _logFn: typeof console.log,
-    private readonly _config: ConfigurationManager,
-  ) {
-    super();
-
-    this._register(this._config.onDidChangeConfiguration(() => {
-      this._logLevel = LogFunctionLogger.readLogLevel(this._config);
-    }));
-
-    this._logLevel = LogFunctionLogger.readLogLevel(this._config);
-  }
-
-  private static readLogLevel(config: ConfigurationManager): LogLevel {
-    switch (config.getSettings().markdown.server.log) {
-      case 'trace': return LogLevel.Trace;
-      case 'debug': return LogLevel.Debug;
-      case 'off':
-      default:
-        return LogLevel.Off;
-    }
-  }
-
-  get level(): LogLevel { return this._logLevel; }
-
-  public log(level: LogLevel, message: string, data?: unknown): void {
-    if (this.level < level) {
-      return;
-    }
-
-    this.appendLine(`[${this.toLevelLabel(level)} ${LogFunctionLogger.now()}] ${message}`);
-    if (data) {
-      this.appendLine(LogFunctionLogger.data2String(data));
-    }
-  }
-
-  private toLevelLabel(level: LogLevel): string {
-    switch (level) {
-      case LogLevel.Off: return 'Off';
-      case LogLevel.Debug: return 'Debug';
-      case LogLevel.Trace: return 'Trace';
-    }
-  }
-
-  private appendLine(value: string): void {
-    this._logFn(value);
-  }
-}
+/*
+ * logging.ts
+ *
+ * Copyright (C) 2023 by Posit Software, PBC
+ * Copyright (c) Microsoft Corporation. All rights reserved.
+ *
+ * Unless you have received this program directly from Posit Software pursuant
+ * to the terms of a commercial license agreement with Posit Software, then
+ * this program is licensed to you under the terms of version 3 of the
+ * GNU Affero General Public License. This program is distributed WITHOUT
+ * ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING THOSE OF NON-INFRINGEMENT,
+ * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Please refer to the
+ * AGPL (http://www.gnu.org/licenses/agpl-3.0.txt) for more details.
+ *
+ */
+
+// based on:
+// https://github.com/microsoft/vscode/blob/main/extensions/markdown-language-features/server/src/logging.ts
+
+
+import { Disposable } from 'core';
+
+import { ILogger, LogLevel } from "./service";
+
+import { ConfigurationManager } from './config';
+
+export class LogFunctionLogger extends Disposable implements ILogger {
+
+  private static now(): string {
+    const now = new Date();
+    return String(now.getUTCHours()).padStart(2, '0')
+      + ':' + String(now.getMinutes()).padStart(2, '0')
+      + ':' + String(now.getUTCSeconds()).padStart(2, '0') + '.' + String(now.getMilliseconds()).padStart(3, '0');
+  }
+
+  private static data2String(data: unknown): string {
+    if (data instanceof Error) {
+      if (typeof data.stack === 'string') {
+        return data.stack;
+      }
+      return data.message;
+    }
+    if (typeof data === 'string') {
+      return data;
+    }
+    return JSON.stringify(data, undefined, 2);
+  }
+
+  private _logLevel: LogLevel;
+  private _config?: ConfigurationManager;
+
+  constructor(
+    private readonly _logFn: typeof console.log,
+  ) {
+    super();
+
+    // Be verbose during init until we have a chance to get the user configuration
+    this._logLevel = LogLevel.Debug;
+  }
+
+  setConfigurationManager(config: ConfigurationManager) {
+    this._config = config;
+
+    this._register(this._config.onDidChangeConfiguration(() => {
+      this._logLevel = LogFunctionLogger.readLogLevel(this._config!);
+    }));
+
+    this._logLevel = LogFunctionLogger.readLogLevel(this._config);
+  }
+
+  private static readLogLevel(config: ConfigurationManager): LogLevel {
+    switch (config.getSettings().markdown.server.log) {
+      case 'trace': return LogLevel.Trace;
+      case 'debug': return LogLevel.Debug;
+      case 'off':
+      default:
+        return LogLevel.Off;
+    }
+  }
+
+  get level(): LogLevel { return this._logLevel; }
+
+  public log(level: LogLevel, message: string, data?: unknown): void {
+    if (this.level < level) {
+      return;
+    }
+
+    this.appendLine(`[${this.toLevelLabel(level)} ${LogFunctionLogger.now()}] ${message}`);
+    if (data) {
+      this.appendLine(LogFunctionLogger.data2String(data));
+    }
+  }
+
+  public logNotification(method: string) {
+    this.log(LogLevel.Trace, `Got notification: '${method}'`);
+  }
+
+  public logRequest(method: string) {
+    this.log(LogLevel.Trace, `Got request: '${method}'`);
+  }
+
+  private toLevelLabel(level: LogLevel): string {
+    switch (level) {
+      case LogLevel.Off: return 'off';
+      case LogLevel.Debug: return 'debug';
+      case LogLevel.Trace: return 'trace';
+    }
+  }
+
+  private appendLine(value: string): void {
+    this._logFn(value);
+  }
+}
diff --git a/apps/lsp/src/service/logging.ts b/apps/lsp/src/service/logging.ts
index a44b47ef..198ea5ca 100644
--- a/apps/lsp/src/service/logging.ts
+++ b/apps/lsp/src/service/logging.ts
@@ -45,4 +45,16 @@ export interface ILogger {
    * @param data Additional information about what is being logged.
    */
   log(level: LogLevel, message: string, data?: Record<string, unknown>): void;
+
+  /**
+   * Log notification at Trace level.
+   * @param method Message type name.
+   */
+  logNotification(method: string): void;
+
+  /**
+   * Log request at Trace level.
+   * @param method Message type name.
+   */
+  logRequest(method: string): void;
 }

From 08fe7c941afe66b593973b659467b134c86100a3 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Tue, 1 Jul 2025 16:29:45 +0200
Subject: [PATCH 02/18] Log via LSP once we're connected

---
 apps/lsp/src/index.ts   |  8 ++++----
 apps/lsp/src/logging.ts | 15 +++++++++++++--
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/apps/lsp/src/index.ts b/apps/lsp/src/index.ts
index 3db6e020..cb0212e1 100644
--- a/apps/lsp/src/index.ts
+++ b/apps/lsp/src/index.ts
@@ -53,9 +53,7 @@ import { registerDiagnostics } from "./diagnostics";
 const connection = createConnection(ProposedFeatures.all);
 
 // Initialize logger
-const logger = new LogFunctionLogger(
-  console.log.bind(console),
-);
+const logger = new LogFunctionLogger(console.log.bind(console));
 
 // Create text document manager
 const documents: TextDocuments<Document> = new TextDocuments(TextDocument);
@@ -71,10 +69,12 @@ let capabilities: ClientCapabilities | undefined;
 // Initialization options
 let initializationOptions: LspInitializationOptions | undefined;
 
-// Markdowdn language service
+// Markdown language service
 let mdLs: IMdLanguageService | undefined;
 
 connection.onInitialize((params: InitializeParams) => {
+  // We're connected, log messages via LSP
+  logger.setConnection(connection);
 
   // alias options and capabilities
   initializationOptions = params.initializationOptions;
diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index e7c866a5..56d18e93 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -23,6 +23,7 @@ import { Disposable } from 'core';
 import { ILogger, LogLevel } from "./service";
 
 import { ConfigurationManager } from './config';
+import { Connection } from 'vscode-languageserver';
 
 export class LogFunctionLogger extends Disposable implements ILogger {
 
@@ -47,6 +48,7 @@ export class LogFunctionLogger extends Disposable implements ILogger {
   }
 
   private _logLevel: LogLevel;
+  private _connection?: Connection;
   private _config?: ConfigurationManager;
 
   constructor(
@@ -58,6 +60,10 @@ export class LogFunctionLogger extends Disposable implements ILogger {
     this._logLevel = LogLevel.Debug;
   }
 
+  setConnection(connection: Connection) {
+    this._connection = connection;
+  }
+
   setConfigurationManager(config: ConfigurationManager) {
     this._config = config;
 
@@ -85,7 +91,7 @@ export class LogFunctionLogger extends Disposable implements ILogger {
       return;
     }
 
-    this.appendLine(`[${this.toLevelLabel(level)} ${LogFunctionLogger.now()}] ${message}`);
+    this.appendLine(`[lsp-${this.toLevelLabel(level)} ${LogFunctionLogger.now()}] ${message}`);
     if (data) {
       this.appendLine(LogFunctionLogger.data2String(data));
     }
@@ -108,6 +114,11 @@ export class LogFunctionLogger extends Disposable implements ILogger {
   }
 
   private appendLine(value: string): void {
-    this._logFn(value);
+    // If we're connected, send log messages to client as LSP notifications
+    if (this._connection) {
+      this._connection.console.log(value);
+    } else {
+      this._logFn(value);
+    }
   }
 }

From 045cf913aa53f5d14c59ee21d656c89464d985a8 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Tue, 1 Jul 2025 17:09:48 +0200
Subject: [PATCH 03/18] Don't log time twice now that time is added on the
 frontend side

---
 apps/lsp/src/logging.ts | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 56d18e93..69ab9410 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -62,6 +62,7 @@ export class LogFunctionLogger extends Disposable implements ILogger {
 
   setConnection(connection: Connection) {
     this._connection = connection;
+    this.log(LogLevel.Debug, 'LSP is now connected');
   }
 
   setConfigurationManager(config: ConfigurationManager) {
@@ -91,7 +92,7 @@ export class LogFunctionLogger extends Disposable implements ILogger {
       return;
     }
 
-    this.appendLine(`[lsp-${this.toLevelLabel(level)} ${LogFunctionLogger.now()}] ${message}`);
+    this.appendLine(`[lsp-${this.toLevelLabel(level)}] ${message}`);
     if (data) {
       this.appendLine(LogFunctionLogger.data2String(data));
     }

From 78b4dc272d9c5dad64303e5421c32f906eee5a00 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Mon, 30 Jun 2025 12:58:57 +0200
Subject: [PATCH 04/18] Add `justfile` for CLI shortcuts

---
 apps/vscode/justfile | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 apps/vscode/justfile

diff --git a/apps/vscode/justfile b/apps/vscode/justfile
new file mode 100644
index 00000000..a5f5e7e4
--- /dev/null
+++ b/apps/vscode/justfile
@@ -0,0 +1,8 @@
+install:
+  rm -rf *.vsix && vsce package && code --install-extension *.vsix && positron --install-extension *.vsix
+
+install-vscode:
+  rm -rf *.vsix && vsce package && code --install-extension *.vsix
+
+install-positron:
+  rm -rf *.vsix && vsce package && positron --install-extension *.vsix

From 13fa25c01c9405e19255213679f21763a7fa4d1c Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Wed, 2 Jul 2025 07:01:53 +0200
Subject: [PATCH 05/18] Finish plumbing configuration change notifications

---
 apps/lsp/.eslintrc.js         |  3 +++
 apps/lsp/src/config.ts        | 20 ++++++++++++++------
 apps/lsp/src/index.ts         |  1 +
 apps/vscode/src/lsp/client.ts | 11 +++++++++++
 4 files changed, 29 insertions(+), 6 deletions(-)

diff --git a/apps/lsp/.eslintrc.js b/apps/lsp/.eslintrc.js
index 2308ff96..f00ad881 100644
--- a/apps/lsp/.eslintrc.js
+++ b/apps/lsp/.eslintrc.js
@@ -1,4 +1,7 @@
 module.exports = {
   root: true,
   extends: ["custom-server"],
+  rules: {
+    '@typescript-eslint/no-unused-vars': ['error', { argsIgnorePattern: '^_' }],
+  },
 };
diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index 4cc81397..d6513ea8 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -25,7 +25,8 @@ import {
   LsConfiguration,
   defaultLsConfiguration,
   PreferredMdPathExtensionStyle,
-  ILogger
+  ILogger,
+  LogLevel
 } from './service';
 
 export type ValidateEnabled = 'ignore' | 'warning' | 'error' | 'hint';
@@ -144,6 +145,7 @@ export class ConfigurationManager extends Disposable {
   }
 
   public async update() {
+    this._logger.log(LogLevel.Trace, 'Sending \'configuration\' request');
     const settings = await this.connection_.workspace.getConfiguration();
 
     this._settings = {
@@ -163,15 +165,21 @@ export class ConfigurationManager extends Disposable {
   }
 
   public async subscribe() {
-    await this.update();
+    // Ignore the settings in parameters, the modern usage is to fetch the settings
+    // when we get this notification
+    this.connection_.onDidChangeConfiguration((_params) => {
+      this._logger.logNotification('didChangeConfiguration');
+      this.update();
+    });
+
+    // Get notified of configuration changes by client
     await this.connection_.client.register(
       DidChangeConfigurationNotification.type,
       undefined
     );
-    this.connection_.onDidChangeConfiguration(() => {
-      this._logger.logNotification('didChangeConfiguration');
-      this.update();
-    });
+
+    // Retrieve initial values for settings of interest
+    await this.update();
   }
 
   public getSettings(): Settings {
diff --git a/apps/lsp/src/index.ts b/apps/lsp/src/index.ts
index cb0212e1..82eafb44 100644
--- a/apps/lsp/src/index.ts
+++ b/apps/lsp/src/index.ts
@@ -75,6 +75,7 @@ let mdLs: IMdLanguageService | undefined;
 connection.onInitialize((params: InitializeParams) => {
   // We're connected, log messages via LSP
   logger.setConnection(connection);
+  logger.logRequest('initialize');
 
   // alias options and capabilities
   initializationOptions = params.initializationOptions;
diff --git a/apps/vscode/src/lsp/client.ts b/apps/vscode/src/lsp/client.ts
index 0799d3d8..74451a53 100644
--- a/apps/vscode/src/lsp/client.ts
+++ b/apps/vscode/src/lsp/client.ts
@@ -146,6 +146,17 @@ export async function activateLsp(
     clientOptions
   );
 
+  // Notify LSP of quarto setting changes
+  context.subscriptions.push(workspace.onDidChangeConfiguration(e => {
+    if (client.state !== State.Running) {
+      return;
+    }
+
+    if (e.affectsConfiguration("quarto")) {
+      client.sendNotification("workspace/didChangeConfiguration", {});
+    }
+  }));
+
   // return once the server is running
   return new Promise<LanguageClient>((resolve, reject) => {
 

From d7c69405d984e168703dcd49f50b1993c4066545 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Wed, 2 Jul 2025 07:16:32 +0200
Subject: [PATCH 06/18] Make log level a quarto setting

---
 apps/lsp/src/config.ts         | 11 ++++-------
 apps/lsp/src/logging.ts        | 12 ++++++++----
 apps/lsp/src/service/config.ts |  9 ++++++---
 apps/vscode/package.json       | 11 +++++++++++
 4 files changed, 29 insertions(+), 14 deletions(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index d6513ea8..8e0d3d0a 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -28,6 +28,7 @@ import {
   ILogger,
   LogLevel
 } from './service';
+import { LogFunctionLogger } from './logging';
 
 export type ValidateEnabled = 'ignore' | 'warning' | 'error' | 'hint';
 
@@ -36,6 +37,7 @@ export interface Settings {
     readonly colorTheme: string;
   };
   readonly quarto: {
+    readonly logLevel: LogLevel;
     readonly path: string;
     readonly mathjax: {
       readonly scale: number;
@@ -43,10 +45,6 @@ export interface Settings {
     }
   };
   readonly markdown: {
-    readonly server: {
-      readonly log: 'off' | 'debug' | 'trace';
-    };
-
     readonly preferredMdPathExtensionStyle: 'auto' | 'includeExtension' | 'removeExtension';
 
     readonly suggest: {
@@ -85,6 +83,7 @@ function defaultSettings(): Settings {
       colorTheme: 'Dark+'
     },
     quarto: {
+      logLevel: LogLevel.Trace,
       path: "",
       mathjax: {
         scale: 1,
@@ -92,9 +91,6 @@ function defaultSettings(): Settings {
       }
     },
     markdown: {
-      server: {
-        log: 'off'
-      },
       preferredMdPathExtensionStyle: 'auto',
       suggest: {
         paths: {
@@ -154,6 +150,7 @@ export class ConfigurationManager extends Disposable {
         colorTheme: settings.workbench.colorTheme
       },
       quarto: {
+        logLevel: LogFunctionLogger.parseLogLevel(settings.quarto.server.logLevel),
         path: settings.quarto.path,
         mathjax: {
           scale: settings.quarto.mathjax.scale,
diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 69ab9410..31dda9ed 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -69,14 +69,18 @@ export class LogFunctionLogger extends Disposable implements ILogger {
     this._config = config;
 
     this._register(this._config.onDidChangeConfiguration(() => {
-      this._logLevel = LogFunctionLogger.readLogLevel(this._config!);
+      this._logLevel = LogFunctionLogger.currentLogLevel(this._config!);
     }));
 
-    this._logLevel = LogFunctionLogger.readLogLevel(this._config);
+    this._logLevel = LogFunctionLogger.currentLogLevel(this._config);
   }
 
-  private static readLogLevel(config: ConfigurationManager): LogLevel {
-    switch (config.getSettings().markdown.server.log) {
+  private static currentLogLevel(config: ConfigurationManager): LogLevel {
+    return config.getSettings().quarto.logLevel;
+  }
+
+  public static parseLogLevel(logLevel: string): LogLevel {
+    switch (logLevel) {
       case 'trace': return LogLevel.Trace;
       case 'debug': return LogLevel.Debug;
       case 'off':
diff --git a/apps/lsp/src/service/config.ts b/apps/lsp/src/service/config.ts
index 3f3f2281..f0b88031 100644
--- a/apps/lsp/src/service/config.ts
+++ b/apps/lsp/src/service/config.ts
@@ -17,6 +17,7 @@
 import * as picomatch from 'picomatch';
 import { URI } from 'vscode-uri';
 import { MathjaxSupportedExtension } from 'editor-types';
+import { LogLevel } from './logging';
 
 /**
  * Preferred style for file paths to {@link markdownFileExtensions markdown files}.
@@ -39,6 +40,8 @@ export enum PreferredMdPathExtensionStyle {
 }
 
 export interface LsConfiguration {
+  readonly logLevel: LogLevel;
+
   /**
    * List of file extensions should be considered markdown.
    *
@@ -73,15 +76,15 @@ export interface LsConfiguration {
 
   readonly includeWorkspaceHeaderCompletions: 'never' | 'onSingleOrDoubleHash' | 'onDoubleHash';
 
-  readonly colorTheme: "light" | "dark";
+  readonly colorTheme: 'light' | 'dark';
   readonly mathjaxScale: number;
   readonly mathjaxExtensions: readonly MathjaxSupportedExtension[];
-
 }
 
 export const defaultMarkdownFileExtension = 'qmd';
 
 const defaultConfig: LsConfiguration = {
+  logLevel: LogLevel.Trace,
   markdownFileExtensions: [defaultMarkdownFileExtension, 'md'],
   knownLinkedToFileExtensions: [
     'jpg',
@@ -104,7 +107,7 @@ const defaultConfig: LsConfiguration = {
     "**/env/**"
   ],
   includeWorkspaceHeaderCompletions: 'never',
-  colorTheme: "light",
+  colorTheme: 'light',
   mathjaxScale: 1,
   mathjaxExtensions: []
 };
diff --git a/apps/vscode/package.json b/apps/vscode/package.json
index 83c30344..02730b2f 100644
--- a/apps/vscode/package.json
+++ b/apps/vscode/package.json
@@ -1306,6 +1306,17 @@
             "type": "string"
           },
           "uniqueItems": true
+        },
+        "quarto.server.logLevel": {
+          "scope": "window",
+          "type": "string",
+          "default": "warn",
+          "enum": [
+            "trace",
+            "debug",
+            "off"
+          ],
+          "markdownDescription": "Log level for the Quarto language server."
         }
       }
     },

From ad8be1ae77ed32580be25462956c12459487afe1 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 07:49:24 +0200
Subject: [PATCH 07/18] Take info, warn, and error log levels

---
 apps/lsp/src/config.ts          |  2 +-
 apps/lsp/src/logging.ts         | 14 +++++++++-----
 apps/lsp/src/service/logging.ts | 14 ++++++++++----
 apps/vscode/package.json        |  4 +++-
 4 files changed, 23 insertions(+), 11 deletions(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index 8e0d3d0a..98b4a104 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -83,7 +83,7 @@ function defaultSettings(): Settings {
       colorTheme: 'Dark+'
     },
     quarto: {
-      logLevel: LogLevel.Trace,
+      logLevel: LogLevel.Info,
       path: "",
       mathjax: {
         scale: 1,
diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 31dda9ed..6f453da4 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -83,16 +83,18 @@ export class LogFunctionLogger extends Disposable implements ILogger {
     switch (logLevel) {
       case 'trace': return LogLevel.Trace;
       case 'debug': return LogLevel.Debug;
-      case 'off':
+      case 'info': return LogLevel.Info;
+      case 'warn': return LogLevel.Warn;
+      case 'error': return LogLevel.Error;
       default:
-        return LogLevel.Off;
+        return LogLevel.Warn;
     }
   }
 
   get level(): LogLevel { return this._logLevel; }
 
   public log(level: LogLevel, message: string, data?: unknown): void {
-    if (this.level < level) {
+    if (level < this.level) {
       return;
     }
 
@@ -112,9 +114,11 @@ export class LogFunctionLogger extends Disposable implements ILogger {
 
   private toLevelLabel(level: LogLevel): string {
     switch (level) {
-      case LogLevel.Off: return 'off';
-      case LogLevel.Debug: return 'debug';
       case LogLevel.Trace: return 'trace';
+      case LogLevel.Debug: return 'debug';
+      case LogLevel.Info: return 'info';
+      case LogLevel.Warn: return 'warn';
+      case LogLevel.Error: return 'error';
     }
   }
 
diff --git a/apps/lsp/src/service/logging.ts b/apps/lsp/src/service/logging.ts
index 198ea5ca..44f3fe26 100644
--- a/apps/lsp/src/service/logging.ts
+++ b/apps/lsp/src/service/logging.ts
@@ -18,14 +18,20 @@
  * The level of verbosity that the language service logs at.
  */
 export enum LogLevel {
-  /** Disable logging */
-  Off,
+  /** Log extremely verbose info about language server operation, such as calls into the file system */
+  Trace,
 
   /** Log verbose info about language server operation, such as when references are re-computed for a md file. */
   Debug,
 
-  /** Log extremely verbose info about language server operation, such as calls into the file system */
-  Trace,
+  /** Informational messages that highlight the progress of the application at coarse-grained level. */
+  Info,
+
+  /** Potentially harmful situations which still allow the application to continue running. */
+  Warn,
+
+  /** Error events that might still allow the application to continue running. */
+  Error,
 }
 
 /**
diff --git a/apps/vscode/package.json b/apps/vscode/package.json
index 02730b2f..1a69d34e 100644
--- a/apps/vscode/package.json
+++ b/apps/vscode/package.json
@@ -1314,7 +1314,9 @@
           "enum": [
             "trace",
             "debug",
-            "off"
+            "info",
+            "warn",
+            "error"
           ],
           "markdownDescription": "Log level for the Quarto language server."
         }

From acfda25cb9d54db1047008b4b0d5e9c815dc8e38 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 07:51:56 +0200
Subject: [PATCH 08/18] Add `log()` wrappers

---
 apps/lsp/src/config.ts                        |  2 +-
 apps/lsp/src/diagnostics.ts                   |  3 +--
 apps/lsp/src/logging.ts                       | 25 +++++++++++++++----
 apps/lsp/src/service/logging.ts               | 10 ++++++--
 apps/lsp/src/service/providers/diagnostics.ts |  8 +++---
 .../src/service/providers/document-links.ts   |  2 +-
 .../src/service/providers/document-symbols.ts |  2 +-
 apps/lsp/src/service/providers/folding.ts     |  2 +-
 apps/lsp/src/service/providers/references.ts  |  4 +--
 .../lsp/src/service/providers/smart-select.ts |  2 +-
 apps/lsp/src/service/toc.ts                   |  2 +-
 apps/lsp/src/workspace.ts                     | 19 +++++++-------
 12 files changed, 50 insertions(+), 31 deletions(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index 98b4a104..e3d2ebf1 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -141,7 +141,7 @@ export class ConfigurationManager extends Disposable {
   }
 
   public async update() {
-    this._logger.log(LogLevel.Trace, 'Sending \'configuration\' request');
+    this._logger.logTrace('Sending \'configuration\' request');
     const settings = await this.connection_.workspace.getConfiguration();
 
     this._settings = {
diff --git a/apps/lsp/src/diagnostics.ts b/apps/lsp/src/diagnostics.ts
index 4a9ce14d..725eb54f 100644
--- a/apps/lsp/src/diagnostics.ts
+++ b/apps/lsp/src/diagnostics.ts
@@ -35,7 +35,6 @@ import {
   ILogger,
   IMdLanguageService,
   IWorkspace,
-  LogLevel,
 } from "./service";
 import {
   ConfigurationManager,
@@ -130,7 +129,7 @@ export async function registerDiagnostics(
         FullDocumentDiagnosticReport | UnchangedDocumentDiagnosticReport
       > => {
 
-        logger.log(LogLevel.Debug, "connection.languages.diagnostics.on", {
+        logger.logDebug("connection.languages.diagnostics.on", {
           document: params.textDocument.uri,
         });
 
diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 6f453da4..26d67ca7 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -62,7 +62,7 @@ export class LogFunctionLogger extends Disposable implements ILogger {
 
   setConnection(connection: Connection) {
     this._connection = connection;
-    this.log(LogLevel.Debug, 'LSP is now connected');
+    this.logInfo('LSP is now connected');
   }
 
   setConfigurationManager(config: ConfigurationManager) {
@@ -104,12 +104,27 @@ export class LogFunctionLogger extends Disposable implements ILogger {
     }
   }
 
-  public logNotification(method: string) {
-    this.log(LogLevel.Trace, `Got notification: '${method}'`);
+  public logTrace(message: string, data?: Record<string, unknown>): void {
+    this.log(LogLevel.Trace, message, data);
+  }
+  public logDebug(message: string, data?: Record<string, unknown>): void {
+    this.log(LogLevel.Debug, message, data);
+  }
+  public logInfo(message: string, data?: Record<string, unknown>): void {
+    this.log(LogLevel.Info, message, data);
+  }
+  public logWarn(message: string, data?: Record<string, unknown>): void {
+    this.log(LogLevel.Warn, message, data);
+  }
+  public logError(message: string, data?: Record<string, unknown>): void {
+    this.log(LogLevel.Error, message, data);
   }
 
-  public logRequest(method: string) {
-    this.log(LogLevel.Trace, `Got request: '${method}'`);
+  public logNotification(method: string, data?: Record<string, unknown>) {
+    this.logTrace(`Got notification: '${method}'`, data);
+  }
+  public logRequest(method: string, data?: Record<string, unknown>) {
+    this.logTrace(`Got request: '${method}'`, data);
   }
 
   private toLevelLabel(level: LogLevel): string {
diff --git a/apps/lsp/src/service/logging.ts b/apps/lsp/src/service/logging.ts
index 44f3fe26..973ca2a9 100644
--- a/apps/lsp/src/service/logging.ts
+++ b/apps/lsp/src/service/logging.ts
@@ -52,15 +52,21 @@ export interface ILogger {
    */
   log(level: LogLevel, message: string, data?: Record<string, unknown>): void;
 
+  logTrace(message: string, data?: Record<string, unknown>): void;
+  logDebug(message: string, data?: Record<string, unknown>): void;
+  logInfo(message: string, data?: Record<string, unknown>): void;
+  logWarn(message: string, data?: Record<string, unknown>): void;
+  logError(message: string, data?: Record<string, unknown>): void;
+
   /**
    * Log notification at Trace level.
    * @param method Message type name.
    */
-  logNotification(method: string): void;
+  logNotification(method: string, data?: Record<string, unknown>): void;
 
   /**
    * Log request at Trace level.
    * @param method Message type name.
    */
-  logRequest(method: string): void;
+  logRequest(method: string, data?: Record<string, unknown>): void;
 }
diff --git a/apps/lsp/src/service/providers/diagnostics.ts b/apps/lsp/src/service/providers/diagnostics.ts
index 6cd33afa..ca21ea99 100644
--- a/apps/lsp/src/service/providers/diagnostics.ts
+++ b/apps/lsp/src/service/providers/diagnostics.ts
@@ -210,7 +210,7 @@ export class DiagnosticComputer {
     readonly links: readonly MdLink[];
     readonly statCache: ResourceMap<{ readonly exists: boolean }>;
   }> {
-    this.#logger.log(LogLevel.Debug, 'DiagnosticComputer.compute', { document: doc.uri, version: doc.version });
+    this.#logger.logDebug('DiagnosticComputer.compute', { document: doc.uri, version: doc.version });
 
     const { links, definitions } = await this.#linkProvider.getLinks(doc);
     const statCache = new ResourceMap<{ readonly exists: boolean }>();
@@ -235,7 +235,7 @@ export class DiagnosticComputer {
       ])).flat());
     }
 
-    this.#logger.log(LogLevel.Trace, 'DiagnosticComputer.compute finished', { document: doc.uri, version: doc.version, diagnostics });
+    this.#logger.logTrace('DiagnosticComputer.compute finished', { document: doc.uri, version: doc.version, diagnostics });
 
     return {
       links: links,
@@ -612,7 +612,7 @@ class FileLinkState extends Disposable {
   }
 
   #onLinkedResourceChanged(resource: URI, exists: boolean) {
-    this.#logger.log(LogLevel.Trace, 'FileLinkState.onLinkedResourceChanged', { resource, exists });
+    this.#logger.logTrace('FileLinkState.onLinkedResourceChanged', { resource, exists });
 
     const entry = this.#linkedToFile.get(resource);
     if (entry) {
@@ -650,7 +650,7 @@ export class DiagnosticsManager extends Disposable implements IPullDiagnosticsMa
     this.#linkWatcher = this._register(linkWatcher);
 
     this._register(this.#linkWatcher.onDidChangeLinkedToFile(e => {
-      logger.log(LogLevel.Trace, 'DiagnosticsManager.onDidChangeLinkedToFile', { resource: e.changedResource });
+      logger.logTrace('DiagnosticsManager.onDidChangeLinkedToFile', { resource: e.changedResource });
 
       this.#onLinkedToFileChanged.fire({
         changedResource: e.changedResource,
diff --git a/apps/lsp/src/service/providers/document-links.ts b/apps/lsp/src/service/providers/document-links.ts
index 54f8d14e..d62869de 100644
--- a/apps/lsp/src/service/providers/document-links.ts
+++ b/apps/lsp/src/service/providers/document-links.ts
@@ -779,7 +779,7 @@ export class MdLinkProvider extends Disposable {
 
     this.#linkComputer = new MdLinkComputer(parser, this.#workspace);
     this.#linkCache = this._register(new MdDocumentInfoCache(this.#workspace, async (doc, token) => {
-      logger.log(LogLevel.Debug, 'LinkProvider.compute', { document: doc.uri, version: doc.version });
+      logger.logDebug('LinkProvider.compute', { document: doc.uri, version: doc.version });
 
       const links = await this.#linkComputer.getAllLinks(doc, token);
       return {
diff --git a/apps/lsp/src/service/providers/document-symbols.ts b/apps/lsp/src/service/providers/document-symbols.ts
index ddd6e047..678a8a1a 100644
--- a/apps/lsp/src/service/providers/document-symbols.ts
+++ b/apps/lsp/src/service/providers/document-symbols.ts
@@ -48,7 +48,7 @@ export class MdDocumentSymbolProvider {
   }
 
   public async provideDocumentSymbols(document: Document, options: ProvideDocumentSymbolOptions, token: CancellationToken): Promise<lsp.DocumentSymbol[]> {
-    this.#logger.log(LogLevel.Debug, 'DocumentSymbolProvider.provideDocumentSymbols', { document: document.uri, version: document.version });
+    this.#logger.logDebug('DocumentSymbolProvider.provideDocumentSymbols', { document: document.uri, version: document.version });
 
     if (token.isCancellationRequested) {
       return [];
diff --git a/apps/lsp/src/service/providers/folding.ts b/apps/lsp/src/service/providers/folding.ts
index d6a9e6c2..6add2efa 100644
--- a/apps/lsp/src/service/providers/folding.ts
+++ b/apps/lsp/src/service/providers/folding.ts
@@ -45,7 +45,7 @@ export class MdFoldingProvider {
   }
 
   public async provideFoldingRanges(document: Document, token: CancellationToken): Promise<lsp.FoldingRange[]> {
-    this.#logger.log(LogLevel.Debug, 'MdFoldingProvider.provideFoldingRanges', { document: document.uri, version: document.version });
+    this.#logger.logDebug('MdFoldingProvider.provideFoldingRanges', { document: document.uri, version: document.version });
 
     if (token.isCancellationRequested) {
       return [];
diff --git a/apps/lsp/src/service/providers/references.ts b/apps/lsp/src/service/providers/references.ts
index d87341ba..0119f439 100644
--- a/apps/lsp/src/service/providers/references.ts
+++ b/apps/lsp/src/service/providers/references.ts
@@ -119,7 +119,7 @@ export class MdReferencesProvider extends Disposable {
   }
 
   public async getReferencesAtPosition(document: Document, position: lsp.Position, token: CancellationToken): Promise<MdReference[]> {
-    this.#logger.log(LogLevel.Debug, 'ReferencesProvider.getReferencesAtPosition', { document: document.uri, version: document.version });
+    this.#logger.logDebug('ReferencesProvider.getReferencesAtPosition', { document: document.uri, version: document.version });
 
     const toc = await this.#tocProvider.getForDocument(document);
     if (token.isCancellationRequested) {
@@ -135,7 +135,7 @@ export class MdReferencesProvider extends Disposable {
   }
 
   public async getReferencesToFileInWorkspace(resource: URI, token: CancellationToken): Promise<MdReference[]> {
-    this.#logger.log(LogLevel.Debug, 'ReferencesProvider.getAllReferencesToFileInWorkspace', { resource });
+    this.#logger.logDebug('ReferencesProvider.getAllReferencesToFileInWorkspace', { resource });
 
     if (token.isCancellationRequested) {
       return [];
diff --git a/apps/lsp/src/service/providers/smart-select.ts b/apps/lsp/src/service/providers/smart-select.ts
index ab3b374f..6758beeb 100644
--- a/apps/lsp/src/service/providers/smart-select.ts
+++ b/apps/lsp/src/service/providers/smart-select.ts
@@ -41,7 +41,7 @@ export class MdSelectionRangeProvider {
   }
 
   public async provideSelectionRanges(document: Document, positions: readonly Position[], token: CancellationToken): Promise<lsp.SelectionRange[] | undefined> {
-    this.#logger.log(LogLevel.Debug, 'MdSelectionRangeProvider.provideSelectionRanges', { document: document.uri, version: document.version });
+    this.#logger.logDebug('MdSelectionRangeProvider.provideSelectionRanges', { document: document.uri, version: document.version });
 
     if (token.isCancellationRequested) {
       return undefined;
diff --git a/apps/lsp/src/service/toc.ts b/apps/lsp/src/service/toc.ts
index 8ffe3fd4..1df0f731 100644
--- a/apps/lsp/src/service/toc.ts
+++ b/apps/lsp/src/service/toc.ts
@@ -299,7 +299,7 @@ export class MdTableOfContentsProvider extends Disposable {
     this.#logger = logger;
 
     this.#cache = this._register(new MdDocumentInfoCache<TableOfContents>(workspace, (doc, token) => {
-      this.#logger.log(LogLevel.Debug, 'TableOfContentsProvider.create', { document: doc.uri, version: doc.version });
+      this.#logger.logDebug('TableOfContentsProvider.create', { document: doc.uri, version: doc.version });
       return TableOfContents.create(parser, doc, token);
     }));
   }
diff --git a/apps/lsp/src/workspace.ts b/apps/lsp/src/workspace.ts
index 69c4b82f..d310fcb0 100644
--- a/apps/lsp/src/workspace.ts
+++ b/apps/lsp/src/workspace.ts
@@ -33,7 +33,6 @@ import { Document, isQuartoDoc } from "quarto-core";
 import {
   FileStat,
   ILogger,
-  LogLevel,
   LsConfiguration,
   IWorkspace,
   IWorkspaceWithWatching,
@@ -98,7 +97,7 @@ export function languageServiceWorkspace(
   const onDidDeleteMarkdownDocument = new Emitter<URI>();
 
   const doDeleteDocument = (uri: URI) => {
-    logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.deleteDocument', { document: uri.toString() });
+    logger.logTrace('VsCodeClientWorkspace.deleteDocument', { document: uri.toString() });
     documentCache.delete(uri);
     onDidDeleteMarkdownDocument.fire(uri);
   }
@@ -107,7 +106,7 @@ export function languageServiceWorkspace(
     if (!isRelevantMarkdownDocument(e.document)) {
       return;
     }
-    logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.TextDocument.onDidOpen', { document: e.document.uri });
+    logger.logNotification('onDidOpen', { document: e.document.uri });
 
     const uri = URI.parse(e.document.uri);
     const doc = documentCache.get(uri);
@@ -132,7 +131,7 @@ export function languageServiceWorkspace(
       return;
     }
 
-    logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.TextDocument.onDidChanceContent', { document: e.document.uri });
+    logger.logNotification('onDidChangeContent', { document: e.document.uri });
 
     const uri = URI.parse(e.document.uri);
     const entry = documentCache.get(uri);
@@ -147,7 +146,7 @@ export function languageServiceWorkspace(
       return;
     }
 
-    logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.TextDocument.onDidClose', { document: e.document.uri });
+    logger.logNotification('onDidClose', { document: e.document.uri });
 
     const uri = URI.parse(e.document.uri);
     const doc = documentCache.get(uri);
@@ -254,7 +253,7 @@ export function languageServiceWorkspace(
     },
 
     async stat(resource: URI): Promise<FileStat | undefined> {
-      logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.stat', { resource: resource.toString() });
+      logger.logTrace('VsCodeClientWorkspace.stat', { resource: resource.toString() });
       if (documentCache.has(resource)) {
         return { isDirectory: false };
       }
@@ -262,7 +261,7 @@ export function languageServiceWorkspace(
     },
 
     async readDirectory(resource: URI): Promise<Iterable<readonly [string, FileStat]>> {
-      logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.readDirectory', { resource: resource.toString() });
+      logger.logTrace('VsCodeClientWorkspace.readDirectory', { resource: resource.toString() });
       const result = await fspromises.readdir(resource.fsPath, { withFileTypes: true });
       return result.map(value => [value.name, { isDirectory: value.isDirectory() }]);
     },
@@ -313,7 +312,7 @@ export function languageServiceWorkspace(
       // keep document cache up to date and notify clients
       for (const change of changes) {
         const resource = URI.parse(change.uri);
-        logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.onDidChangeWatchedFiles', { type: change.type, resource: resource.toString() });
+        logger.logTrace('VsCodeClientWorkspace.onDidChangeWatchedFiles', { type: change.type, resource: resource.toString() });
         switch (change.type) {
           case FileChangeType.Changed: {
             const entry = documentCache.get(resource);
@@ -356,7 +355,7 @@ export function languageServiceWorkspace(
     const fsWorkspace: IWorkspaceWithWatching = {
       ...workspace,
       watchFile(resource, options) {
-        logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.watchFile', { resource: resource.toString() });
+        logger.logTrace('VsCodeClientWorkspace.watchFile', { resource: resource.toString() });
 
         const entry = {
           resource,
@@ -371,7 +370,7 @@ export function languageServiceWorkspace(
           onDidChange: entry.onDidChange.event,
           onDidDelete: entry.onDidDelete.event,
           dispose: () => {
-            logger.log(LogLevel.Trace, 'VsCodeClientWorkspace.disposeWatcher', { resource: resource.toString() });
+            logger.logTrace('VsCodeClientWorkspace.disposeWatcher', { resource: resource.toString() });
             watchers.delete(entry.resource.toString());
           }
         };

From 41ced6e905c38f14475e14fd5a2045c416f53472 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 09:06:19 +0200
Subject: [PATCH 09/18] Pass `logLevel` via init options

---
 apps/lsp/src/config.ts          | 14 ++++++++++++++
 apps/lsp/src/index.ts           |  4 ++++
 apps/lsp/src/logging.ts         |  3 ---
 apps/vscode/src/lsp/client.ts   |  3 ++-
 packages/quarto-core/src/lsp.ts |  3 ++-
 5 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index e3d2ebf1..7d1da492 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -140,6 +140,20 @@ export class ConfigurationManager extends Disposable {
     this._settings = defaultSettings();
   }
 
+  public init(logLevel?: string) {
+    const initLogLevel = LogFunctionLogger.parseLogLevel(
+      logLevel ?? "warn"
+    );
+
+    this._settings = {
+      ...this._settings,
+      quarto: {
+        ...this._settings.quarto,
+        logLevel: initLogLevel,
+      }
+    };
+  }
+
   public async update() {
     this._logger.logTrace('Sending \'configuration\' request');
     const settings = await this.connection_.workspace.getConfiguration();
diff --git a/apps/lsp/src/index.ts b/apps/lsp/src/index.ts
index 82eafb44..f64db03f 100644
--- a/apps/lsp/src/index.ts
+++ b/apps/lsp/src/index.ts
@@ -73,6 +73,10 @@ let initializationOptions: LspInitializationOptions | undefined;
 let mdLs: IMdLanguageService | undefined;
 
 connection.onInitialize((params: InitializeParams) => {
+  // Set log level from initialization options if provided so that we use the
+  // expected level as soon as possible
+  configManager.init(params.initializationOptions?.logLevel);
+
   // We're connected, log messages via LSP
   logger.setConnection(connection);
   logger.logRequest('initialize');
diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 26d67ca7..dbf4a356 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -55,9 +55,6 @@ export class LogFunctionLogger extends Disposable implements ILogger {
     private readonly _logFn: typeof console.log,
   ) {
     super();
-
-    // Be verbose during init until we have a chance to get the user configuration
-    this._logLevel = LogLevel.Debug;
   }
 
   setConnection(connection: Connection) {
diff --git a/apps/vscode/src/lsp/client.ts b/apps/vscode/src/lsp/client.ts
index 74451a53..f70cccd7 100644
--- a/apps/vscode/src/lsp/client.ts
+++ b/apps/vscode/src/lsp/client.ts
@@ -117,7 +117,8 @@ export async function activateLsp(
 
   // create client options
   const initializationOptions: LspInitializationOptions = {
-    quartoBinPath: quartoContext.binPath
+    quartoBinPath: quartoContext.binPath,
+    logLevel: config.get("server.logLevel"),
   };
 
   const documentSelectorPattern = semver.gte(quartoContext.version, "1.6.24") ?
diff --git a/packages/quarto-core/src/lsp.ts b/packages/quarto-core/src/lsp.ts
index 4a7c6009..09b58d65 100644
--- a/packages/quarto-core/src/lsp.ts
+++ b/packages/quarto-core/src/lsp.ts
@@ -15,4 +15,5 @@
 
 export interface LspInitializationOptions {
   quartoBinPath?: string;
-}
\ No newline at end of file
+  logLevel?: 'trace' | 'debug' | 'info' | 'warn' | 'error';
+}

From dd5d0b50e2b74441ebb1f61a939e576bb4ffb83c Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 09:24:59 +0200
Subject: [PATCH 10/18] Pass log level to client

---
 apps/lsp/src/logging.ts | 29 +++++++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index dbf4a356..c777d814 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -95,9 +95,12 @@ export class LogFunctionLogger extends Disposable implements ILogger {
       return;
     }
 
-    this.appendLine(`[lsp-${this.toLevelLabel(level)}] ${message}`);
+    // Mention log level because until we switch to languageclient 10.x, the
+    // output channel will use the `info` level for all our messages.
+    // See https://github.com/microsoft/vscode-languageserver-node/issues/1116.
+    this.appendLine(level, `[lsp-${this.toLevelLabel(level)}] ${message}`);
     if (data) {
-      this.appendLine(LogFunctionLogger.data2String(data));
+      this.appendLine(level, LogFunctionLogger.data2String(data));
     }
   }
 
@@ -134,10 +137,28 @@ export class LogFunctionLogger extends Disposable implements ILogger {
     }
   }
 
-  private appendLine(value: string): void {
+  private appendLine(level: LogLevel, value: string): void {
     // If we're connected, send log messages to client as LSP notifications
     if (this._connection) {
-      this._connection.console.log(value);
+      // The log level is not currently forwarded to our `LogOutputChannel` on
+      // the client side. We'll need to update to languageclient 10.x for this,
+      // see https://github.com/microsoft/vscode-languageserver-node/issues/1116.
+      switch (level) {
+        case LogLevel.Error:
+          this._connection.console.error(value);
+          break;
+        case LogLevel.Warn:
+          this._connection.console.warn(value);
+          break;
+        case LogLevel.Info:
+          this._connection.console.info(value);
+          break;
+        case LogLevel.Debug:
+        case LogLevel.Trace:
+        default:
+          this._connection.console.log(value);
+          break;
+      }
     } else {
       this._logFn(value);
     }

From 48c8b28135f890e7e99449800e2f5627f834af6c Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 09:34:30 +0200
Subject: [PATCH 11/18] Ignore format commit in git blame

---
 .git-blame-ignore-revs | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 .git-blame-ignore-revs

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
new file mode 100644
index 00000000..ba1235f3
--- /dev/null
+++ b/.git-blame-ignore-revs
@@ -0,0 +1,8 @@
+# This file lists revisions of large-scale formatting/style changes so that
+# they can be excluded from git blame results.
+#
+# To set this file as the default ignore file for git blame, run:
+#   $ git config blame.ignoreRevsFile .git-blame-ignore-revs
+
+# Format vscode extention and LSP files consistently (#748)
+a1513effc913e6e59651256d79295da37134dbbf

From 7840fb9baf151a580dc875d9ad516a56cdce0989 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 09:45:42 +0200
Subject: [PATCH 12/18] Fix default setting

---
 apps/lsp/src/config.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index 7d1da492..e285fc4b 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -83,7 +83,7 @@ function defaultSettings(): Settings {
       colorTheme: 'Dark+'
     },
     quarto: {
-      logLevel: LogLevel.Info,
+      logLevel: LogLevel.Warn,
       path: "",
       mathjax: {
         scale: 1,

From d2a66b333be79e59970a7d437b2c488d9d42f1f3 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 09:51:15 +0200
Subject: [PATCH 13/18] Revert propagation of log level to client

---
 apps/lsp/src/logging.ts | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index c777d814..0b5afcde 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -143,18 +143,8 @@ export class LogFunctionLogger extends Disposable implements ILogger {
       // The log level is not currently forwarded to our `LogOutputChannel` on
       // the client side. We'll need to update to languageclient 10.x for this,
       // see https://github.com/microsoft/vscode-languageserver-node/issues/1116.
+      // So just emit everything via `log` for now.
       switch (level) {
-        case LogLevel.Error:
-          this._connection.console.error(value);
-          break;
-        case LogLevel.Warn:
-          this._connection.console.warn(value);
-          break;
-        case LogLevel.Info:
-          this._connection.console.info(value);
-          break;
-        case LogLevel.Debug:
-        case LogLevel.Trace:
         default:
           this._connection.console.log(value);
           break;

From 0c0e710b738ac2366a743530898bce4169a571a0 Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 14:03:42 +0200
Subject: [PATCH 14/18] Rename `LogFunctionLogger` to `Logger`

---
 apps/lsp/src/config.ts  | 6 +++---
 apps/lsp/src/index.ts   | 4 ++--
 apps/lsp/src/logging.ts | 9 ++++-----
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index e285fc4b..cc0e78f7 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -28,7 +28,7 @@ import {
   ILogger,
   LogLevel
 } from './service';
-import { LogFunctionLogger } from './logging';
+import { Logger } from './logging';
 
 export type ValidateEnabled = 'ignore' | 'warning' | 'error' | 'hint';
 
@@ -141,7 +141,7 @@ export class ConfigurationManager extends Disposable {
   }
 
   public init(logLevel?: string) {
-    const initLogLevel = LogFunctionLogger.parseLogLevel(
+    const initLogLevel = Logger.parseLogLevel(
       logLevel ?? "warn"
     );
 
@@ -164,7 +164,7 @@ export class ConfigurationManager extends Disposable {
         colorTheme: settings.workbench.colorTheme
       },
       quarto: {
-        logLevel: LogFunctionLogger.parseLogLevel(settings.quarto.server.logLevel),
+        logLevel: Logger.parseLogLevel(settings.quarto.server.logLevel),
         path: settings.quarto.path,
         mathjax: {
           scale: settings.quarto.mathjax.scale,
diff --git a/apps/lsp/src/index.ts b/apps/lsp/src/index.ts
index f64db03f..8b9599e7 100644
--- a/apps/lsp/src/index.ts
+++ b/apps/lsp/src/index.ts
@@ -40,7 +40,7 @@ import { registerCustomMethods } from "./custom";
 import { isWindows, LspConnection } from "core-node";
 import { initQuartoContext, Document, markdownitParser, LspInitializationOptions } from "quarto-core";
 import { ConfigurationManager, lsConfiguration } from "./config";
-import { LogFunctionLogger } from "./logging";
+import { Logger } from "./logging";
 import { languageServiceWorkspace } from "./workspace";
 import { middlewareCapabilities, middlewareRegister } from "./middleware";
 import { createLanguageService, IMdLanguageService } from "./service";
@@ -53,7 +53,7 @@ import { registerDiagnostics } from "./diagnostics";
 const connection = createConnection(ProposedFeatures.all);
 
 // Initialize logger
-const logger = new LogFunctionLogger(console.log.bind(console));
+const logger = new Logger(console.log.bind(console));
 
 // Create text document manager
 const documents: TextDocuments<Document> = new TextDocuments(TextDocument);
diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 0b5afcde..81812f55 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -25,8 +25,7 @@ import { ILogger, LogLevel } from "./service";
 import { ConfigurationManager } from './config';
 import { Connection } from 'vscode-languageserver';
 
-export class LogFunctionLogger extends Disposable implements ILogger {
-
+export class Logger extends Disposable implements ILogger {
   private static now(): string {
     const now = new Date();
     return String(now.getUTCHours()).padStart(2, '0')
@@ -66,10 +65,10 @@ export class LogFunctionLogger extends Disposable implements ILogger {
     this._config = config;
 
     this._register(this._config.onDidChangeConfiguration(() => {
-      this._logLevel = LogFunctionLogger.currentLogLevel(this._config!);
+      this._logLevel = Logger.currentLogLevel(this._config!);
     }));
 
-    this._logLevel = LogFunctionLogger.currentLogLevel(this._config);
+    this._logLevel = Logger.currentLogLevel(this._config);
   }
 
   private static currentLogLevel(config: ConfigurationManager): LogLevel {
@@ -100,7 +99,7 @@ export class LogFunctionLogger extends Disposable implements ILogger {
     // See https://github.com/microsoft/vscode-languageserver-node/issues/1116.
     this.appendLine(level, `[lsp-${this.toLevelLabel(level)}] ${message}`);
     if (data) {
-      this.appendLine(level, LogFunctionLogger.data2String(data));
+      this.appendLine(level, Logger.data2String(data));
     }
   }
 

From b1f1dd7ce9d779123a746d24a7e77bfc2216267c Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Thu, 3 Jul 2025 14:16:42 +0200
Subject: [PATCH 15/18] Add comment about default `console.log` handling

---
 apps/lsp/src/logging.ts | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 81812f55..1bf2bc10 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -149,6 +149,13 @@ export class Logger extends Disposable implements ILogger {
           break;
       }
     } else {
+      // Note that by default, languageserver redirects `console.log` to the
+      // client. However this is only the case with StdIo connections:
+      // https://github.com/microsoft/vscode-languageserver-node/blob/df56e720/server/src/node/main.ts#L262-L264
+      // While we currently only use StdIo to connect the LSP, and so the branch
+      // above to explicitly log via our connection object is not strictly
+      // necessary, it's still better to use our own logger abstraction that we
+      // are in control of.
       this._logFn(value);
     }
   }

From d9dc9d3b8c0c095556df89e9f68d6bb1dd4637dd Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Mon, 7 Jul 2025 11:00:02 +0200
Subject: [PATCH 16/18] Actually pass init option to logger

---
 apps/lsp/src/config.ts  | 8 ++------
 apps/lsp/src/index.ts   | 6 +++++-
 apps/lsp/src/logging.ts | 6 +++++-
 3 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index cc0e78f7..e34cf99b 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -140,16 +140,12 @@ export class ConfigurationManager extends Disposable {
     this._settings = defaultSettings();
   }
 
-  public init(logLevel?: string) {
-    const initLogLevel = Logger.parseLogLevel(
-      logLevel ?? "warn"
-    );
-
+  public init(logLevel: LogLevel) {
     this._settings = {
       ...this._settings,
       quarto: {
         ...this._settings.quarto,
-        logLevel: initLogLevel,
+        logLevel,
       }
     };
   }
diff --git a/apps/lsp/src/index.ts b/apps/lsp/src/index.ts
index 8b9599e7..bac4465d 100644
--- a/apps/lsp/src/index.ts
+++ b/apps/lsp/src/index.ts
@@ -75,7 +75,11 @@ let mdLs: IMdLanguageService | undefined;
 connection.onInitialize((params: InitializeParams) => {
   // Set log level from initialization options if provided so that we use the
   // expected level as soon as possible
-  configManager.init(params.initializationOptions?.logLevel);
+  const initLogLevel = Logger.parseLogLevel(
+    params.initializationOptions?.logLevel ?? "warn"
+  );
+  logger.init(initLogLevel);
+  configManager.init(initLogLevel);
 
   // We're connected, log messages via LSP
   logger.setConnection(connection);
diff --git a/apps/lsp/src/logging.ts b/apps/lsp/src/logging.ts
index 1bf2bc10..c48fa109 100644
--- a/apps/lsp/src/logging.ts
+++ b/apps/lsp/src/logging.ts
@@ -46,7 +46,7 @@ export class Logger extends Disposable implements ILogger {
     return JSON.stringify(data, undefined, 2);
   }
 
-  private _logLevel: LogLevel;
+  private _logLevel = LogLevel.Warn;
   private _connection?: Connection;
   private _config?: ConfigurationManager;
 
@@ -56,6 +56,10 @@ export class Logger extends Disposable implements ILogger {
     super();
   }
 
+  init(logLevel: LogLevel): void {
+    this._logLevel = logLevel;
+  }
+
   setConnection(connection: Connection) {
     this._connection = connection;
     this.logInfo('LSP is now connected');

From b260250243a6ca60fcea890d3b13c181b5882adf Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Mon, 7 Jul 2025 11:05:03 +0200
Subject: [PATCH 17/18] Remove justfile

---
 apps/vscode/justfile | 8 --------
 1 file changed, 8 deletions(-)
 delete mode 100644 apps/vscode/justfile

diff --git a/apps/vscode/justfile b/apps/vscode/justfile
deleted file mode 100644
index a5f5e7e4..00000000
--- a/apps/vscode/justfile
+++ /dev/null
@@ -1,8 +0,0 @@
-install:
-  rm -rf *.vsix && vsce package && code --install-extension *.vsix && positron --install-extension *.vsix
-
-install-vscode:
-  rm -rf *.vsix && vsce package && code --install-extension *.vsix
-
-install-positron:
-  rm -rf *.vsix && vsce package && positron --install-extension *.vsix

From 11d3479baca651614ad8b520b919710c844f3cda Mon Sep 17 00:00:00 2001
From: Lionel Henry <lionel.hry@proton.me>
Date: Mon, 7 Jul 2025 12:15:22 +0200
Subject: [PATCH 18/18] Remove redundant config watching

---
 apps/lsp/src/config.ts        |  5 +++--
 apps/vscode/src/lsp/client.ts | 11 -----------
 2 files changed, 3 insertions(+), 13 deletions(-)

diff --git a/apps/lsp/src/config.ts b/apps/lsp/src/config.ts
index e34cf99b..7af97ba1 100644
--- a/apps/lsp/src/config.ts
+++ b/apps/lsp/src/config.ts
@@ -172,8 +172,9 @@ export class ConfigurationManager extends Disposable {
   }
 
   public async subscribe() {
-    // Ignore the settings in parameters, the modern usage is to fetch the settings
-    // when we get this notification
+    // Ignore the settings in parameters, the modern usage is to fetch the
+    // settings when we get this notification. This causes the client to send
+    // any updates for settings under the `quarto` section.
     this.connection_.onDidChangeConfiguration((_params) => {
       this._logger.logNotification('didChangeConfiguration');
       this.update();
diff --git a/apps/vscode/src/lsp/client.ts b/apps/vscode/src/lsp/client.ts
index f70cccd7..5cf9fca3 100644
--- a/apps/vscode/src/lsp/client.ts
+++ b/apps/vscode/src/lsp/client.ts
@@ -147,17 +147,6 @@ export async function activateLsp(
     clientOptions
   );
 
-  // Notify LSP of quarto setting changes
-  context.subscriptions.push(workspace.onDidChangeConfiguration(e => {
-    if (client.state !== State.Running) {
-      return;
-    }
-
-    if (e.affectsConfiguration("quarto")) {
-      client.sendNotification("workspace/didChangeConfiguration", {});
-    }
-  }));
-
   // return once the server is running
   return new Promise<LanguageClient>((resolve, reject) => {