Remove obsolete app startup hook

[isaacroldan]

Why

Every CLI command runs the app init hook, including commands that do not use app code. The hook clears a disk-backed command cache and sets COMMAND_RUN_ID.

The cache was intended to pass the selected TOML file from the app prompt to config linking. It does not do that in the normal flow: selectOrCreateApp() reads the cache before selectAppPrompt() populates it, so no selected TOML is stored. Config linking already scans the real TOML files and matches the selected app by client_id.

This means the hook adds global startup work without changing config selection. Signed-upload URL isolation is still required, so this change keeps it with a process-local UUID in the app client.

What

• Remove the global app init hook and obsolete command cache.
• Scope signed-upload cache keys by app and CLI process.

Testing

• 114 focused app tests
• App and CLI lint and type-check
• Knip and CLI bundle
• Version and organization help smoke tests