Hooks config in settings.json silently stripped by active sessions

Bug Description

When adding a "hooks" key to ~/.claude/settings.json while a Claude Code session is running, the hooks configuration is silently removed within seconds. This happens because active sessions keep an in-memory copy of settings and overwrite the file on any save event, dropping the externally-added hooks key.

Steps to Reproduce

1. Open a Claude Code session (or multiple sessions/tabs)
2. Add a valid hooks configuration to ~/.claude/settings.json (via any method: manual edit, script, or Claude's Edit tool)
3. Verify it's present: cat ~/.claude/settings.json | python3 -c "import json,sys; print('hooks' in json.load(sys.stdin))" → True
4. Wait a few seconds or trigger any settings write (permission grant, etc.)
5. Check again → False — the hooks key has been removed

Expected Behavior

• The hooks key should persist in settings.json
• Active sessions should either watch for external file changes and reload, or preserve unknown/unmanaged keys when writing back

Actual Behavior

• The hooks key is silently stripped every time an active session writes its in-memory settings state back to disk
• /hooks dialog shows "0 hooks configured" even immediately after adding them
• All other keys (model, permissions, statusLine, etc.) are preserved because they exist in the session's in-memory state

Workaround

Adding hooks to ~/.claude/settings.local.json instead of settings.json works — this file is not overwritten by active sessions.

Environment

• OS: macOS (Darwin 25.3.0)
• Claude Code: Latest version (as of April 2026)
• Shell: zsh

Additional Context

• Confirmed with only a single session open — the current session itself overwrites the file
• The hooks JSON is valid (verified with python3 -m json.tool)
• Multiple methods tried (Edit tool, python script, manual edit) — all get stripped
• The issue is particularly problematic because /hooks dialog itself says "edit settings.json directly" to configure hooks, but settings.json is the file being overwritten