[Security] Harden permissions of .env files

[gonzaloriestra]

This PR hardens the security of .env files created or updated by the Shopify CLI by ensuring they have restrictive file permissions (0o600).

Key changes:

• Updated the core writeFile utility in cli-kit to support a mode parameter.
• Explicitly call chmod in writeFile after writing the file. This ensures that permissions are correctly set even for files that already existed with broader permissions.
• Updated .env file writing logic in writeDotEnv and pullEnv to use 0o600 (readable/writable only by the owner).
• Added unit tests to verify that writeFile correctly applies permissions on POSIX systems.

Security: Prevents other local users on the same system from reading sensitive environment variables like SHOPIFY_API_SECRET.

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PR created automatically by Jules for task 11733830971334597419 started by @gonzaloriestra

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[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/fs.d.ts

@@ -86,6 +86,7 @@ export declare function appendFile(path: string, content: string): Promise<void>
 export declare function appendFileSync(path: string, data: string): void;
 export interface WriteOptions {
     encoding: BufferEncoding;
+    mode?: number | string;
 }
 /**
  * Writes content to file at path.