Remove browser dependencies from E2E test cases

[isaacroldan]

WHY are these changes introduced?

Browser-based app cleanup causes E2E failures unrelated to CLI behavior.

WHAT is this pull request doing?

Use authenticated HTTP for app lookup and deletion, with app identity checks, CSRF protection, and deletion confirmation. After a successful uninstall, retry stale installation-count rejections for up to 15 seconds. Also move malformed-TOML checks to the local suite and remove a terminal-wrapping assertion.

Browsers remain necessary for shared login and legacy bulk cleanup. Remote E2E jobs remain non-blocking in CI.

How to manually test your changes?

With E2E credentials configured, select an uninstalled disposable E2E app. Run pnpm --filter e2e exec tsx scripts/cleanup-apps.ts --delete --pattern <exact-owned-app-name> and confirm the app is gone from the dashboard.

Checklist

• I've considered possible cross-platform impacts (Mac, Linux, Windows)
• I've considered possible documentation changes
• I've considered analytics changes to measure impact

[github-actions]

Differences in type declarations

We detected differences in the type declarations generated by Typescript for this branch compared to the baseline ('main' branch). Please, review them to ensure they are backward-compatible. Here are some important things to keep in mind:

• Some seemingly private modules might be re-exported through public modules.
• If the branch is behind main you might see odd diffs, rebase main into this branch.

New type declarations

We found no new type declarations in this PR

Existing type declarations

packages/cli-kit/dist/public/node/base-command.d.ts

@@ -21,7 +21,6 @@ declare abstract class BaseCommand extends Command {
     static descriptionWithoutMarkdown(): string | undefined;
     static analyticsNameOverride(): string | undefined;
     static analyticsStopCommand(): string | undefined;
-    private jsonOutputFromFlags;
     catch(error: Error & {
         skipOclifErrorHandling: boolean;
     }): Promise<void>;
@@ -37,7 +36,6 @@ declare abstract class BaseCommand extends Command {
     }, TGlobalFlags extends FlagOutput, TArgs extends ArgOutput>(options?: Input<TFlags, TGlobalFlags, TArgs>, argv?: string[]): Promise<ParserOutput<TFlags, TGlobalFlags, TArgs> & {
         argv: string[];
     }>;
-    protected runWithParsedOutput<T>(flags: FlagOutput, execute: () => T): T;
     protected environmentsFilename(): string | undefined;
     protected parseEnvironmentFlags<TFlags extends FlagOutput, TGlobalFlags extends FlagOutput, TArgs extends ArgOutput>(environment: JsonMap, options: Input<TFlags, TGlobalFlags, TArgs>, explicitFlags: FlagOutput): Promise<FlagOutput>;
     protected validateNonTTYFlags(flags: FlagOutput): void;

packages/cli-kit/dist/public/node/themes/theme-manager.d.ts

@@ -11,12 +11,5 @@ export declare abstract class ThemeManager {
     findOrCreate(name?: string, role?: Role): Promise<Theme>;
     fetch(name?: string, role?: Role): Promise<Theme | undefined>;
     generateThemeName(context: string): string;
-    create(themeRole?: Role, themeName?: string): Promise<{
-        createdAtRuntime: boolean;
-        id: number;
-        name: string;
-        processing: boolean;
-        role: string;
-        src?: string;
-    }>;
+    create(themeRole?: Role, themeName?: string): Promise<Theme>;
 }
\ No newline at end of file

packages/cli-kit/dist/cli/api/graphql/admin/generated/metafield_definitions_by_owner_type.d.ts

@@ -2,14 +2,9 @@ import * as Types from './types.js';
 import { TypedDocumentNode as DocumentNode } from '@graphql-typed-document-node/core';
 export type MetafieldDefinitionsByOwnerTypeQueryVariables = Types.Exact<{
     ownerType: Types.MetafieldOwnerType;
-    after?: Types.InputMaybe<Types.Scalars['String']['input']>;
 }>;
 export type MetafieldDefinitionsByOwnerTypeQuery = {
     metafieldDefinitions: {
-        pageInfo: {
-            hasNextPage: boolean;
-            endCursor?: string | null;
-        };
         nodes: {
             key: string;
             name: string;