Bug: trust_profile: balanced in pack.yaml silently overrides render.allow_query_shell: true in config.yaml

[tcconnally]

When pack.yaml sets trust_profile: balanced, the @query directive is disabled even if trust.allow_query_shell: true is set in config.yaml and even if perseus trust profile reports allow_query_shell: True. The render silently outputs > ⚠ @query is disabled by config (render.allow_query_shell=false) with no indication that a pack.yaml trust_profile is the cause.

Steps to reproduce:

1. Set trust.allow_query_shell: true in ~/.perseus/config.yaml
2. Set trust_profile: balanced in a workspace pack.yaml
3. Run perseus trust profile → shows allow_query_shell: True
4. Run perseus render → @query is still disabled

Expected

Either trust profile output reflects the pack.yaml override, or the render error message identifies which config file is disabling the feature.

Actual

trust profile shows True but render disables @query silently.

Fix

The effective permission for render.allow_query_shell must be explicitly set in the render: block of config.yaml (not just trust: block). This is a documentation gap AND a confusing dual-namespace issue.

[tcconnally]

Code review verification (v1.0.3)

Confirmed root cause. _apply_permission_profile in src/perseus/config.py:267–285 uses a destructive merge:

for section, vals in profile.items():
    if section not in cfg or not isinstance(cfg[section], dict):
        cfg[section] = {}
    cfg[section].update(vals)   # destructive — overwrites user values

Whether explicit user config survives depends entirely on call ordering inside load_config, which is not documented and not protected by regression tests. The PERMISSION_PROFILES['balanced'] block at config.py:242–252 hard-sets allow_query_shell: False.

Suggested fix

Make the merge non-destructive — fill only keys the user hasn't explicitly set. Track user-set keys with a sentinel set populated by the config loader as it walks the user's YAML:

def _apply_permission_profile(cfg: dict, profile_name: object, user_set: set[tuple]) -> str | None:
    ...
    for section, vals in profile.items():
        cfg.setdefault(section, {})
        for k, v in vals.items():
            if (section, k) not in user_set:
                cfg[section][k] = v
    return name

Or invert load order: defaults → profile → user config (last wins).

Acceptance criteria

• New test test_permission_profiles.py::test_explicit_user_override_beats_balanced_profile.
• Document precedence in README: defaults → profile → explicit user keys (explicit always wins).

[tcconnally]

Fixed in PR #179 (integration branch targeting main).