fix(claude-code): preserve permissions when removing hooks

[MuskanPaliwal]

Fixes #1924

entire agent remove claude-code is documented as uninstalling Claude Code hooks, but it also removed Read(./.entire/metadata/**) from permissions.deny. When that was the only permission and the file contained only Entire hooks, both top-level objects were deleted and .claude/settings.json became {}.

This PR removes the permissions cleanup from UninstallHooks. Agent removal now filters Entire-managed entries under hooks and leaves the rest of the shared Claude settings file alone. Permissions, user-defined hooks, unknown hook types, and unrelated top-level settings are preserved. A file containing only Entire hooks and no other settings still correctly becomes {}.

Windows amd64 in the issue records the reporter's environment; the issue does not identify this as an OS-specific bug. The affected code path is platform-independent JSON parsing and rewriting.

Testing

• Added regression coverage for permissions containing Entire and user rules, additional permission fields, and unknown nested fields
• Covered settings containing only Entire hooks, mixed Entire and user hooks, and unrelated top-level settings
• Ran mise run lint
• Ran mise run test
• Ran mise run test:ci
• Ran the Claude Code package with the race detector
• Cross-compiled the Claude Code test package for Windows amd64
• Manually built the CLI and verified that agent add claude-code followed by agent remove claude-code removes all seven hooks while preserving the complete permissions object

[MuskanPaliwal]

I took another look, and I think I interpreted the issue too broadly. Entire installs Read(./.entire/metadata/**), so removing it along with the hooks is reasonable cleanup. The existing code already preserves other permissions and settings.

I’m going to pause this PR until we know whether the reporter already had that rule before enabling Entire, or whether they want to remove Claude hooks while keeping Entire active for another agent. Depending on the answer, I’ll either narrow the fix or close the PR.