diff --git a/src/Analysis/Engine/Impl/Definitions/Diagnostic.cs b/src/Analysis/Engine/Impl/Definitions/Diagnostic.cs
index fc3657320..bff9e11de 100644
--- a/src/Analysis/Engine/Impl/Definitions/Diagnostic.cs
+++ b/src/Analysis/Engine/Impl/Definitions/Diagnostic.cs
@@ -48,7 +48,7 @@ public class Diagnostic {
     }
 
     public enum DiagnosticSeverity : int {
-        Unspecified = 0,
+        Suppressed = 0,
         Error = 1,
         Warning = 2,
         Information = 3,
diff --git a/src/Analysis/Engine/Impl/DependencyResolution/PathResolverSnapshot.cs b/src/Analysis/Engine/Impl/DependencyResolution/PathResolverSnapshot.cs
index c1f69c132..66d4c7fee 100644
--- a/src/Analysis/Engine/Impl/DependencyResolution/PathResolverSnapshot.cs
+++ b/src/Analysis/Engine/Impl/DependencyResolution/PathResolverSnapshot.cs
@@ -69,6 +69,7 @@ private PathResolverSnapshot(PythonLanguageVersion pythonLanguageVersion, string
 
         public IEnumerable<string> GetAllModuleNames() => GetModuleNames(_roots.Prepend(_nonRooted).Append(_builtins));
         public IEnumerable<string> GetInterpreterModuleNames() => GetModuleNames(_roots.Skip(_userRootsCount).Append(_builtins));
+        public IEnumerable<string> GetRootPaths() => _roots.Select(r => r.Name);
 
         private static IEnumerable<string> GetModuleNames(IEnumerable<Node> roots) => roots
             .SelectMany(r => r.TraverseBreadthFirst(n => n.IsModule ? Enumerable.Empty<Node>() : n.Children))
diff --git a/src/Analysis/Engine/Impl/PythonAnalyzer.cs b/src/Analysis/Engine/Impl/PythonAnalyzer.cs
index 982fde416..5694a89ee 100644
--- a/src/Analysis/Engine/Impl/PythonAnalyzer.cs
+++ b/src/Analysis/Engine/Impl/PythonAnalyzer.cs
@@ -68,7 +68,7 @@ public partial class PythonAnalyzer : IPythonAnalyzer, IDisposable {
         public static async Task<PythonAnalyzer> CreateAsync(IPythonInterpreterFactory factory, CancellationToken token = default) {
             var analyzer = new PythonAnalyzer(factory);
             try {
-                await analyzer.ReloadModulesAsync(token).ConfigureAwait(false);
+                await analyzer.ReloadModulesAsync(false, token).ConfigureAwait(false);
             } catch(Exception) {
                 analyzer.Dispose();
                 throw;
@@ -140,7 +140,9 @@ private void ReloadModulePaths(in IEnumerable<string> rootPaths) {
         /// This method should be called on the analysis thread and is usually invoked
         /// when the interpreter signals that it's modules have changed.
         /// </summary>
-        public async Task ReloadModulesAsync(CancellationToken token = default) {
+        public Task ReloadModulesAsync(CancellationToken token = default) => ReloadModulesAsync(true, token);
+
+        private async Task ReloadModulesAsync(bool reScanRoots, CancellationToken token) {
             if (!_reloadLock.Wait(0)) {
                 // If we don't lock immediately, wait for the current reload to
                 // complete and then return.
@@ -156,6 +158,11 @@ public async Task ReloadModulesAsync(CancellationToken token = default) {
                 InterpreterFactory.NotifyImportNamesChanged();
                 // Now initialize the interpreter
                 Interpreter.Initialize(this);
+                // Rescan roots for modules if requested
+                if (reScanRoots) {
+                    ReloadModulePaths(CurrentPathResolver.GetRootPaths());
+                }
+
                 // Reload importable modules
                 Modules.Reload();
                 // Load known types from the selected interpreter
@@ -760,7 +767,7 @@ public void AnalyzeQueuedEntries(CancellationToken cancel) {
 
             if (_builtinModule == null) {
                 Debug.Fail("Used analyzer without reloading modules");
-                ReloadModulesAsync(cancel).WaitAndUnwrapExceptions();
+                ReloadModulesAsync(true, cancel).WaitAndUnwrapExceptions();
             }
 
             var ddg = new DDG();
diff --git a/src/Analysis/Engine/Test/LanguageServerTests.cs b/src/Analysis/Engine/Test/LanguageServerTests.cs
index 974499161..f8e7ee28e 100644
--- a/src/Analysis/Engine/Test/LanguageServerTests.cs
+++ b/src/Analysis/Engine/Test/LanguageServerTests.cs
@@ -298,7 +298,7 @@ public async Task ParseIndentationDiagnostics() {
                 DiagnosticSeverity.Error,
                 DiagnosticSeverity.Warning,
                 DiagnosticSeverity.Information,
-                DiagnosticSeverity.Unspecified
+                DiagnosticSeverity.Suppressed
             }) {
                 // For now, these options have to be configured directly
                 s.ParseQueue.InconsistentIndentation = tc;
@@ -317,7 +317,7 @@ await s.DidChangeTextDocument(new DidChangeTextDocumentParams {
                 await s.WaitForCompleteAnalysisAsync(CancellationToken.None);
 
                 var messages = GetDiagnostics(diags, mod).ToArray();
-                if (tc == DiagnosticSeverity.Unspecified) {
+                if (tc == DiagnosticSeverity.Suppressed) {
                     messages.Should().BeEmpty();
                 } else {
                     messages.Should().OnlyContain($"{tc};inconsistent whitespace;Python;2;0;1");
@@ -359,7 +359,7 @@ public async Task DiagnosticsSettingChange() {
                 await s.SendDidChangeConfiguration(newSettings);
 
                 await s.WaitForCompleteAnalysisAsync(CancellationToken.None);
-                GetDiagnostics(diags, u).Where(st => !st.StartsWith($"{DiagnosticSeverity.Unspecified}")).Should().BeEmpty();
+                GetDiagnostics(diags, u).Where(st => !st.StartsWith($"{DiagnosticSeverity.Suppressed}")).Should().BeEmpty();
             }
         }
 
diff --git a/src/LanguageServer/Core/Impl/Definitions/ServerSettings.cs b/src/LanguageServer/Core/Impl/Definitions/ServerSettings.cs
index 982446351..b73ce2a8a 100644
--- a/src/LanguageServer/Core/Impl/Definitions/ServerSettings.cs
+++ b/src/LanguageServer/Core/Impl/Definitions/ServerSettings.cs
@@ -48,7 +48,7 @@ public void SetErrorSeverityOptions(string[] errors, string[] warnings, string[]
                     _map[x] = DiagnosticSeverity.Error;
                 }
                 foreach (var x in disabled) {
-                    _map[x] = DiagnosticSeverity.Unspecified;
+                    _map[x] = DiagnosticSeverity.Suppressed;
                 }
 
                 this.errors = errors;
diff --git a/src/LanguageServer/Core/Impl/Implementation/DiagnosticsErrorSink.cs b/src/LanguageServer/Core/Impl/Implementation/DiagnosticsErrorSink.cs
index ec40f3c22..f06a585ea 100644
--- a/src/LanguageServer/Core/Impl/Implementation/DiagnosticsErrorSink.cs
+++ b/src/LanguageServer/Core/Impl/Implementation/DiagnosticsErrorSink.cs
@@ -72,18 +72,18 @@ public void ProcessTaskComment(object sender, CommentEventArgs e) {
 
         internal static DiagnosticSeverity GetSeverity(Severity severity) {
             switch (severity) {
-                case Severity.Ignore: return DiagnosticSeverity.Unspecified;
+                case Severity.Ignore: return DiagnosticSeverity.Suppressed;
                 case Severity.Information: return DiagnosticSeverity.Information;
                 case Severity.Warning: return DiagnosticSeverity.Warning;
                 case Severity.Error: return DiagnosticSeverity.Error;
                 case Severity.FatalError: return DiagnosticSeverity.Error;
-                default: return DiagnosticSeverity.Unspecified;
+                default: return DiagnosticSeverity.Suppressed;
             }
         }
 
         internal static Severity GetSeverity(DiagnosticSeverity severity) {
             switch (severity) {
-                case DiagnosticSeverity.Unspecified: return Severity.Ignore;
+                case DiagnosticSeverity.Suppressed: return Severity.Ignore;
                 case DiagnosticSeverity.Information: return Severity.Information;
                 case DiagnosticSeverity.Warning: return Severity.Warning;
                 case DiagnosticSeverity.Error: return Severity.Error;
diff --git a/src/LanguageServer/Impl/LanguageServer.cs b/src/LanguageServer/Impl/LanguageServer.cs
index 7c09d1cd2..bbba9bb4f 100644
--- a/src/LanguageServer/Impl/LanguageServer.cs
+++ b/src/LanguageServer/Impl/LanguageServer.cs
@@ -423,7 +423,7 @@ private void PublishPendingDiagnostics() {
             foreach (var kvp in list) {
                 var parameters = new PublishDiagnosticsParams {
                     uri = kvp.Key,
-                    diagnostics = kvp.Value.Where(d => d.severity != DiagnosticSeverity.Unspecified).ToArray()
+                    diagnostics = kvp.Value.Where(d => d.severity != DiagnosticSeverity.Suppressed).ToArray()
                 };
                 _rpc.NotifyWithParameterObjectAsync("textDocument/publishDiagnostics", parameters).DoNotWait();
             }
diff --git a/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/Intellisense/AnalysisProtocol.cs b/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/Intellisense/AnalysisProtocol.cs
index 46873b01a..5d642465b 100644
--- a/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/Intellisense/AnalysisProtocol.cs
+++ b/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/Intellisense/AnalysisProtocol.cs
@@ -59,8 +59,6 @@ public sealed class InitializeRequest : Request<InitializeResponse> {
             public bool analyzeAllFiles;
             [JsonProperty(DefaultValueHandling = DefaultValueHandling.Ignore)]
             public bool traceLogging;
-            [JsonProperty(DefaultValueHandling = DefaultValueHandling.Ignore)]
-            public bool liveLinting;
         }
 
         public sealed class InterpreterInfo {
@@ -824,6 +822,8 @@ public sealed class SetAnalysisOptionsRequest : Request<Response> {
 
         public sealed class AnalysisOptions {
             public Severity indentationInconsistencySeverity;
+            public bool enableUnresolvedImportWarning;
+            public bool enableUseBeforeDefWarning;
             public Dictionary<string, DiagnosticSeverity> commentTokens;
             public Dictionary<string, int> analysisLimits;
             public LS.MessageType? traceLevel;
diff --git a/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/Intellisense/OutOfProcProjectAnalyzer.cs b/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/Intellisense/OutOfProcProjectAnalyzer.cs
index f1346fbf9..1fb3a6b15 100644
--- a/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/Intellisense/OutOfProcProjectAnalyzer.cs
+++ b/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/Intellisense/OutOfProcProjectAnalyzer.cs
@@ -269,8 +269,7 @@ await _server.Initialize(new LS.InitializeParams {
                     },
                     capabilities = new LS.ClientCapabilities {
                         python = new LS.PythonClientCapabilities {
-                            manualFileLoad = !request.analyzeAllFiles,
-                            liveLinting = request.liveLinting
+                            manualFileLoad = !request.analyzeAllFiles
                         },
                         textDocument = new LS.TextDocumentClientCapabilities {
                             completion = new LS.TextDocumentClientCapabilities.CompletionCapabilities {
@@ -1559,9 +1558,35 @@ private Response SetAnalysisOptions(AP.SetAnalysisOptionsRequest request) {
             _server.ParseQueue.TaskCommentMap = Options.commentTokens;
             _server.Analyzer.SetTypeStubPaths(Options.typeStubPaths ?? Enumerable.Empty<string>());
 
+            SetErrorMessagesSeverity();
+
             return new Response();
         }
 
+        private void SetErrorMessagesSeverity() {
+            var serverSettings = new LS.ServerSettings();
+            var warnings = new List<string>();
+            var disabled = new List<string>();
+
+            if (Options.enableUnresolvedImportWarning) {
+                warnings.Add(ErrorMessages.UnresolvedImportCode);
+            } else {
+                disabled.Add(ErrorMessages.UnresolvedImportCode);
+            }
+
+            if (Options.enableUseBeforeDefWarning) {
+                warnings.Add(ErrorMessages.UseBeforeDefCode);
+            } else {
+                disabled.Add(ErrorMessages.UseBeforeDefCode);
+            }
+
+            serverSettings.analysis.SetErrorSeverityOptions(Array.Empty<string>(), warnings.ToArray(), Array.Empty<string>(), disabled.ToArray());
+
+            _server.DidChangeConfiguration(new LS.DidChangeConfigurationParams {
+                settings = serverSettings
+            }, CancellationToken.None).DoNotWait();
+        }
+
 
         public AP.AnalysisOptions Options { get; set; }
 
@@ -1570,7 +1595,7 @@ private void AnalysisQueue_Complete(object sender, EventArgs e) {
         }
 
         private void OnModulesChanged(object sender, EventArgs args) {
-            _server.DidChangeConfiguration(new LS.DidChangeConfigurationParams(), CancellationToken.None).DoNotWait();
+            _server.ReloadModulesAsync(CancellationToken.None).DoNotWait();
         }
 
         private void OnFileChanged(AP.FileChangedEvent e) {
@@ -1653,7 +1678,7 @@ private void OnPublishDiagnostics(object sender, LS.PublishDiagnosticsEventArgs
                 new AP.DiagnosticsEvent {
                     documentUri = e.uri,
                     version = e._version ?? -1,
-                    diagnostics = e.diagnostics?.ToArray()
+                    diagnostics = e.diagnostics?.Where(d => d.severity != DiagnosticSeverity.Suppressed).ToArray()
                 }
             ).DoNotWait();
         }
diff --git a/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/python-language-server-ptvs.nuspec b/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/python-language-server-ptvs.nuspec
index 280da818c..7ed8aeb6c 100644
--- a/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/python-language-server-ptvs.nuspec
+++ b/src/PTVS/Microsoft.PythonTools.Analyzer/Impl/python-language-server-ptvs.nuspec
@@ -23,7 +23,7 @@
     <file src="Microsoft.PythonTools.Analyzer.exe" target="lib/vs16" />
     <file src="Microsoft.PythonTools.Analyzer.exe.config" target="lib/vs16" />
     <file src="Microsoft.PythonTools.Analyzer.pdb" target="lib/vs16" />
-    <file src="Typeshed/**" target="lib/vs16/Typeshed" />
+    <file src="Typeshed/**" target="lib/vs16" />
     <file src="PythonScraper.py" target="lib/vs16" />
     <file src="BuiltinScraper.py" target="lib/vs16" />
     <file src="ExtensionScraper.py" target="lib/vs16" />