@@ -112,7 +112,8 @@ export class McpHub {
112112 this . watchMcpSettingsFile ( )
113113 this . watchProjectMcpFile ( )
114114 this . setupWorkspaceFoldersWatcher ( )
115- this . initializeMcpServers ( )
115+ this . initializeGlobalMcpServers ( )
116+ this . initializeProjectMcpServers ( )
116117 }
117118
118119 public setupWorkspaceFoldersWatcher ( ) : void {
@@ -149,17 +150,20 @@ export class McpHub {
149150 }
150151
151152 private async updateProjectMcpServers ( ) : Promise < void > {
153+ // Only clean up and initialize project servers, not affecting global servers
152154 await this . cleanupProjectMcpServers ( )
153155 await this . initializeProjectMcpServers ( )
154156 }
155157
156158 private async cleanupProjectMcpServers ( ) : Promise < void > {
159+ // Only filter and delete project servers
157160 const projectServers = this . connections . filter ( ( conn ) => conn . server . source === "project" )
158161
159162 for ( const conn of projectServers ) {
160163 await this . deleteConnection ( conn . server . name )
161164 }
162165
166+ // Notify webview of changes after cleanup
163167 await this . notifyWebviewOfServerChanges ( )
164168 }
165169
@@ -299,7 +303,8 @@ export class McpHub {
299303 return
300304 }
301305 try {
302- await this . updateServerConnections ( result . data . mcpServers || { } )
306+ // Only update global servers when global settings change
307+ await this . updateServerConnections ( result . data . mcpServers || { } , "global" )
303308 } catch ( error ) {
304309 this . showErrorMessage ( "Failed to process MCP settings change" , error )
305310 }
@@ -308,9 +313,9 @@ export class McpHub {
308313 )
309314 }
310315
311- private async initializeMcpServers ( ) : Promise < void > {
316+ private async initializeGlobalMcpServers ( ) : Promise < void > {
312317 try {
313- // 1. Initialize global MCP servers
318+ // Initialize global MCP servers
314319 const settingsPath = await this . getMcpSettingsFilePath ( )
315320 const content = await fs . readFile ( settingsPath , "utf-8" )
316321 let config : any
@@ -340,15 +345,12 @@ export class McpHub {
340345 // Still try to connect with the raw config, but show warnings
341346 try {
342347 await this . updateServerConnections ( config . mcpServers || { } , "global" )
343-
344- // 2. Initialize project-level MCP servers
345- await this . initializeProjectMcpServers ( )
346348 } catch ( error ) {
347- this . showErrorMessage ( "Failed to initialize MCP servers with raw config" , error )
349+ this . showErrorMessage ( "Failed to initialize global MCP servers with raw config" , error )
348350 }
349351 }
350352 } catch ( error ) {
351- this . showErrorMessage ( "Failed to initialize MCP servers" , error )
353+ this . showErrorMessage ( "Failed to initialize global MCP servers" , error )
352354 }
353355 }
354356
@@ -454,15 +456,22 @@ export class McpHub {
454456 const stderrStream = transport . stderr
455457 if ( stderrStream ) {
456458 stderrStream . on ( "data" , async ( data : Buffer ) => {
457- const errorOutput = data . toString ( )
458- console . error ( `Server "${ name } " stderr:` , errorOutput )
459- const connection = this . connections . find ( ( conn ) => conn . server . name === name )
460- if ( connection ) {
461- // NOTE: we do not set server status to "disconnected" because stderr logs do not necessarily mean the server crashed or disconnected, it could just be informational. In fact when the server first starts up, it immediately logs "<name> server running on stdio" to stderr.
462- this . appendErrorMessage ( connection , errorOutput )
463- // Only need to update webview right away if it's already disconnected
464- if ( connection . server . status === "disconnected" ) {
465- await this . notifyWebviewOfServerChanges ( )
459+ const output = data . toString ( )
460+
461+ // Check if this is a startup info message or a real error
462+ const isStartupInfo = output . includes ( "server running" ) || output . includes ( "MCP server running" )
463+
464+ if ( ! isStartupInfo ) {
465+ // Only log and process real errors, ignore startup info messages
466+ console . error ( `Server "${ name } " stderr:` , output )
467+ const connection = this . connections . find ( ( conn ) => conn . server . name === name )
468+ if ( connection ) {
469+ // NOTE: we do not set server status to "disconnected" because stderr logs do not necessarily mean the server crashed or disconnected
470+ this . appendErrorMessage ( connection , output )
471+ // Only need to update webview right away if it's already disconnected
472+ if ( connection . server . status === "disconnected" ) {
473+ await this . notifyWebviewOfServerChanges ( )
474+ }
466475 }
467476 }
468477 } )
@@ -630,7 +639,12 @@ export class McpHub {
630639
631640 // Update or add servers
632641 for ( const [ name , config ] of Object . entries ( newServers ) ) {
633- const currentConnection = this . connections . find ( ( conn ) => conn . server . name === name )
642+ // Only consider connections that match the current source
643+ const currentConnection = this . connections . find (
644+ ( conn ) =>
645+ conn . server . name === name &&
646+ ( conn . server . source === source || ( ! conn . server . source && source === "global" ) ) ,
647+ )
634648
635649 // Validate and transform the config
636650 let validatedConfig : z . infer < typeof ServerConfigSchema >
@@ -735,20 +749,49 @@ export class McpHub {
735749 }
736750
737751 private async notifyWebviewOfServerChanges ( ) : Promise < void > {
738- // servers should always be sorted in the order they are defined in the settings file
752+ // Get global server order from settings file
739753 const settingsPath = await this . getMcpSettingsFilePath ( )
740754 const content = await fs . readFile ( settingsPath , "utf-8" )
741755 const config = JSON . parse ( content )
742- const serverOrder = Object . keys ( config . mcpServers || { } )
756+ const globalServerOrder = Object . keys ( config . mcpServers || { } )
757+
758+ // Get project server order if available
759+ const projectMcpPath = await this . getProjectMcpPath ( )
760+ let projectServerOrder : string [ ] = [ ]
761+ if ( projectMcpPath ) {
762+ try {
763+ const projectContent = await fs . readFile ( projectMcpPath , "utf-8" )
764+ const projectConfig = JSON . parse ( projectContent )
765+ projectServerOrder = Object . keys ( projectConfig . mcpServers || { } )
766+ } catch ( error ) {
767+ console . error ( "Failed to read project MCP config:" , error )
768+ }
769+ }
770+
771+ // Sort connections: first global servers in their defined order, then project servers in their defined order
772+ const sortedConnections = [ ...this . connections ] . sort ( ( a , b ) => {
773+ const aIsGlobal = a . server . source === "global" || ! a . server . source
774+ const bIsGlobal = b . server . source === "global" || ! b . server . source
775+
776+ // If both are global or both are project, sort by their respective order
777+ if ( aIsGlobal && bIsGlobal ) {
778+ const indexA = globalServerOrder . indexOf ( a . server . name )
779+ const indexB = globalServerOrder . indexOf ( b . server . name )
780+ return indexA - indexB
781+ } else if ( ! aIsGlobal && ! bIsGlobal ) {
782+ const indexA = projectServerOrder . indexOf ( a . server . name )
783+ const indexB = projectServerOrder . indexOf ( b . server . name )
784+ return indexA - indexB
785+ }
786+
787+ // Global servers come before project servers
788+ return aIsGlobal ? - 1 : 1
789+ } )
790+
791+ // Send sorted servers to webview
743792 await this . providerRef . deref ( ) ?. postMessageToWebview ( {
744793 type : "mcpServers" ,
745- mcpServers : [ ...this . connections ]
746- . sort ( ( a , b ) => {
747- const indexA = serverOrder . indexOf ( a . server . name )
748- const indexB = serverOrder . indexOf ( b . server . name )
749- return indexA - indexB
750- } )
751- . map ( ( connection ) => connection . server ) ,
794+ mcpServers : sortedConnections . map ( ( connection ) => connection . server ) ,
752795 } )
753796 }
754797
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