fix(mcp): filter project scope before dedup

Applied the project-scope filter before connection-equivalence deduplication so a project server can no longer shadow a differently-named but equivalent user server and then be dropped, leaving none.

Fixes #6786

packages/coding-agent/src/capability/index.ts

@@ -154,6 +154,10 @@ async function loadImpl<T>(
 				continue;
 			}
 
+			if (options.filter && !options.filter(itemWithSource)) {
+				continue;
+			}
+
 			itemWithSource._source.providerName = provider.displayName;
 			allItems.push(itemWithSource as T & { _source: SourceMeta; _shadowed?: boolean });
 			contributedItemCount += 1;

packages/coding-agent/src/capability/types.ts

@@ -72,6 +72,12 @@ export interface LoadOptions {
 	includeDisabled?: boolean;
 	/** Explicit disabled extension IDs to apply instead of settings. */
 	disabledExtensions?: string[];
+	/**
+	 * Drop items before deduplication. Use when a downstream scope filter must
+	 * precede equivalence collapse, so a to-be-filtered item cannot shadow a
+	 * differently-keyed but equivalent survivor. Receives the item's `_source`.
+	 */
+	filter?(item: { _source: SourceMeta }): boolean;
 }
 
 /**

packages/coding-agent/src/mcp/config.ts

@@ -97,13 +97,14 @@ export async function loadAllMCPConfigs(cwd: string, options?: LoadMCPConfigsOpt
 	const filterExa = options?.filterExa ?? true;
 	const filterBrowser = options?.filterBrowser ?? false;
 
-	// Load MCP servers via capability system
-	const result = await loadCapability<MCPServer>(mcpCapability.id, { cwd });
-
-	// Filter out project-level configs if disabled
-	const servers = enableProjectConfig
-		? result.items
-		: result.items.filter(server => server._source.level !== "project");
+	// Filter project-scoped entries BEFORE the capability layer's equivalence
+	// deduplication so a project server cannot shadow a differently-named but
+	// connection-equivalent user server and then be dropped here, leaving none.
+	const result = await loadCapability<MCPServer>(mcpCapability.id, {
+		cwd,
+		...(enableProjectConfig ? {} : { filter: server => server._source.level !== "project" }),
+	});
+	const servers = result.items;
 
 	// Load user-level disable/force-enable lists. The denylist always wins; the
 	// allowlist overrides a non-writable source config's `enabled: false`.