fix(codex-runtime): de-dup [plugins.X] tables and stop leaking HERMES_HOME into config.toml

Builds on @steezkelly's Bug A fix (#25857, top-level default_permissions
via _insert_managed_block_at_top_level) by addressing the other two
config-corruption bugs described in #26250:

Bug B (duplicate [plugins.X] tables)
  - Codex itself writes [plugins."<name>@<marketplace>"] tables to
    config.toml when the user runs `codex plugins enable` directly,
    before hermes-agent's managed block exists. On the next migrate run,
    _query_codex_plugins() re-discovers the same plugins via plugin/list
    and render_codex_toml_section() re-emits them inside the managed
    block. Codex's strict TOML parser then rejects the duplicate table
    header on startup.
  - Add _strip_unmanaged_plugin_tables() that drops [plugins.*] tables
    from the user-content portion of the file. Only run it when
    plugin/list succeeded — if the RPC failed we can't re-emit and
    must preserve the user's tables. plugin/list is the source of
    truth when it answers.

Bug C (HERMES_HOME pytest-tempdir leak into ~/.codex/config.toml)
  - _build_hermes_tools_mcp_entry() read HERMES_HOME directly from
    os.environ, so a sibling pytest's monkeypatch.setenv("HERMES_HOME",
    tmp_path) silently burned a transient pytest tempdir into the
    user's real ~/.codex/config.toml. After pytest reaped the tempdir,
    every codex-routed hermes-tools tool call failed silently.
  - Derive HERMES_HOME from get_hermes_home() (the canonical resolver
    that goes through the profile-aware path) and refuse to emit
    obvious test-tempdir paths via _looks_like_test_tempdir() as
    belt-and-suspenders for any other callsite that forgets to patch
    migrate().
  - test_enable_succeeds_when_codex_present in test_codex_runtime_switch.py
    invoked the real migrate() (no mock), writing to Path.home() / .codex
    using whatever HERMES_HOME the running pytest session had set. Add
    the same migrate patch the other apply() tests already use, so the
    suite stops touching the user's real ~/.codex/config.toml.

E2E verification (replicating the issue's repro):
  - Pre-state config.toml with user [mcp_servers.omx_team_run] +
    codex-installed [plugins."tasks@openai-curated"],
    HERMES_HOME="/private/var/folders/.../pytest-of-.../..."
  - On origin/main: tomllib refuses to load the result with
    "Cannot declare ('plugins', 'tasks@openai-curated') twice" AND
    the pytest-tempdir HERMES_HOME is burned in.
  - On this branch: file parses cleanly, default_permissions is
    top-level, exactly one [plugins."tasks@openai-curated"] table
    inside the managed block, no HERMES_HOME in the MCP env.

7 new regression tests covering all three bugs + the test-leak guard.
`bash scripts/run_tests.sh tests/hermes_cli/test_codex_runtime_*.py` —
95 passed, 0 failed.

Closes #26250

tests/hermes_cli/test_codex_runtime_switch.py

@@ -114,8 +114,15 @@ class TestApply:
         def persist(c):
             persisted.update(c)
 
+        # Patch migrate so this test doesn't reach into the user's real
+        # ~/.codex/config.toml. See issue #26250 Bug C — without this patch,
+        # crs.apply() invokes the real migrate() which writes to
+        # Path.home() / ".codex" using whatever HERMES_HOME the running pytest
+        # session has set, leaking pytest tempdir paths into the user's
+        # codex config.
         with patch.object(crs, "check_codex_binary_ok",
-                          return_value=(True, "0.130.0")):
+                          return_value=(True, "0.130.0")), \
+             patch("hermes_cli.codex_runtime_plugin_migration.migrate"):
             r = crs.apply(cfg, "codex_app_server", persist_callback=persist)
         assert r.success
         assert r.new_value == "codex_app_server"