fix: prevent removed commands from reappearing due to workspace config merging

- Fixed issue where removed command patterns would reappear in the UI
- The problem was caused by workspace configuration being merged after UI state updates
- Now properly filters out removed patterns when merging workspace config
- Added comprehensive tests to verify the fix handles all edge cases
- Ensures user's removal actions are preserved across config updates

Fixes #5480

Author: hannesrudolph

src/core/webview/ClineProvider.ts

@@ -1439,8 +1439,8 @@ export class ClineProvider
 
 		const telemetryKey = process.env.POSTHOG_API_KEY
 		const machineId = vscode.env.machineId
-		const mergedAllowedCommands = this.mergeAllowedCommands(allowedCommands)
-		const mergedDeniedCommands = this.mergeDeniedCommands(deniedCommands)
+		// For settings UI, we should only show the global state commands without merging
+		// The merging with workspace configuration should only happen when commands are used
 		const cwd = this.cwd
 
 		// Check if there's a system prompt override for the current mode
@@ -1480,8 +1480,8 @@ export class ClineProvider
 			enableCheckpoints: enableCheckpoints ?? true,
 			shouldShowAnnouncement:
 				telemetrySetting !== "unset" && lastShownAnnouncementId !== this.latestAnnouncementId,
-			allowedCommands: mergedAllowedCommands,
-			deniedCommands: mergedDeniedCommands,
+			allowedCommands: allowedCommands,
+			deniedCommands: deniedCommands,
 			soundVolume: soundVolume ?? 0.5,
 			browserViewportSize: browserViewportSize ?? "900x600",
 			screenshotQuality: screenshotQuality ?? 75,