fix(docker): skip symlinked stage2 chown targets

[harjothkhara]

What does this PR do?

Prevents the Docker stage2 ownership repair from following symlinked $HERMES_HOME targets. Recursive repairs now skip symlinked Hermes-owned subdirectories such as home, profiles, and cron; allowlisted top-level state files also skip symlinked paths; and first-boot seed paths refuse to write through symlinks.

This keeps the existing targeted-ownership contract intact: Hermes repairs files and directories it owns, without recursively changing ownership of host-owned paths reached through symlinks.

Related Issue

Fixes #52781

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• Security fix
• Tests (adding or improving test coverage)

Changes Made

• docker/stage2-hook.sh: add a symlink-aware recursive chown helper for Hermes-owned subtrees.
• docker/stage2-hook.sh: skip symlinked allowlisted top-level files before chown/chmod.
• docker/stage2-hook.sh: refuse first-boot seeding through dangling symlink paths.
• tests/tools/test_stage2_hook_symlink_chown.py: cover real-directory repair and symlinked-directory refusal.
• tests/tools/test_stage2_hook_toplevel_chown.py: cover symlinked allowlisted file refusal.
• tests/tools/test_stage2_hook_gateway_bootstrap_state.py: cover gateway bootstrap symlink refusal.
• tests/test_docker_home_override_scripts.py: update the profiles/cron repair contract for the helper.

How to Test

1. scripts/run_tests.sh tests/tools/test_stage2_hook_symlink_chown.py tests/tools/test_stage2_hook_toplevel_chown.py tests/tools/test_stage2_hook_gateway_bootstrap_state.py tests/tools/test_stage2_hook_unraid_uid.py tests/tools/test_stage2_hook_log_dir_seed.py tests/tools/test_dockerfile_immutable_install.py tests/test_docker_home_override_scripts.py
2. sh -n docker/stage2-hook.sh
3. git diff --check

Duplicate-work checks

• Exact issue search: gh pr list --repo NousResearch/hermes-agent --state all --search "52781" -> no PRs.
• Broader keyword search: gh pr list --repo NousResearch/hermes-agent --state all --search "stage2-hook chown symlink destroy home directory docker" -> no PRs.

Checklist

Code

• I've read the Contributing Guide
• My commit messages follow Conventional Commits
• I searched for existing PRs to make sure this isn't a duplicate
• My PR contains only changes related to this fix
• I've run focused tests and all tests pass
• I've added tests for my changes
• I've tested on my platform: macOS local shell harness; Docker runtime behavior is covered by stage2 script contract tests

Documentation & Housekeeping

• Documentation update N/A
• cli-config.yaml.example update N/A
• CONTRIBUTING.md / AGENTS.md update N/A
• Cross-platform impact considered
• Tool descriptions/schemas N/A

Screenshots / Logs

Focused proof passed locally:

39 tests passed, 0 failed