Agent SDK / desktop-app sessions load 0 hooks despite settings declaring them — SessionStart/Stop/UserPromptSubmit/PostToolUse never fire

Summary

Sessions run through the Agent SDK from the Claude desktop app (cc_entrypoint=claude-desktop) load zero hooks: with /debug enabled, the log shows [DEBUG] Hooks: Found 0 total hooks in registry while the same machine's user settings (~/.claude/settings.json) declare four hooks (SessionStart, Stop, UserPromptSubmit, PostToolUse) and the project's settings declare two more. None load, none fire.

CLI-entrypoint sessions on the same machine, same settings files, load and fire all of the same hooks correctly (verified via the hooks' own logging).

Why it matters

Hook-based automation silently doesn't exist for a whole class of sessions — in our case a Stop/SessionStart-armed mail-watcher (async re-wake pattern) that never arms in desktop-app sessions, so those sessions never notice work queued for them. There is no error or warning anywhere — the hooks are simply absent from the registry, and the user only discovers it by enabling /debug and reading the registry line.

Repro

1. Declare any hook (e.g., SessionStart running a logger) in ~/.claude/settings.json.
2. Open a session in the Claude desktop app (Agent SDK entrypoint); run /debug.
3. Observe Hooks: Found 0 total hooks in registry; the hook never fires.
4. Open a CLI session in the same directory: hooks load and fire.

Environment

• Desktop app build 1.32352.1, macOS arm64
• CLI 2.1.234 (native); observed identically under 2.1.220
• Debug log also shows repeated "Fast mode is not available in the Agent SDK" for these sessions, which may help identify the entrypoint/code path

Related: #87641 (unattended message-triggered turns never start in the same session class — filed separately; the two may share a root in how the Agent SDK entrypoint initializes sessions).