fix(config): make env vars win over persisted JSON across all aliases

[sean-kim05]

Closes #688

What

_read_json_overrides in strix/config/loader.py is documented to let environment variables outrank the persisted cli-config.json (load_settings: "env vars win, then the JSON file"). Since its result is passed to Settings(**init_kwargs) and pydantic-settings ranks the init source above env, it must not emit a field whose env var is already set.

The old per-field loop decided per-alias and breakd on the first alias found in either env or the file, so it missed two cases:

1. Multi-alias fields. api_key = AliasChoices("LLM_API_KEY", "OPENAI_API_KEY"). With env OPENAI_API_KEY=sk-env and file {"env": {"LLM_API_KEY": "sk-file"}}, the loop hit the file alias first and emitted {"llm": {"api_key": "sk-file"}} → load_settings().llm.api_key == "sk-file" instead of the live sk-env. OPENAI_API_KEY/OPENAI_BASE_URL are commonly exported, and persist_current can save the other alias, so a stale key silently wins.

2. Case sensitivity. Settings use case_sensitive=False, but key in os.environ is exact-case, so a lowercase env var (strix_llm) was not seen as set and the file value won.

Change

Decide whether a field is already set in the environment by checking all of its aliases case-insensitively (env_present = {k.upper() for k in os.environ}) before consulting the file:

aliases = [alias.upper() for alias in _aliases_for(finfo)]
if any(alias in env_present for alias in aliases):
    continue  # env wins under some alias; skip the JSON file for this field
for alias in aliases:
    if alias in env_block_upper:
        sub_data[fname] = env_block_upper[alias]
        break

Tests

Added to tests/test_config_loader.py:

• env_wins_across_field_aliases — env OPENAI_API_KEY, file LLM_API_KEY → {} (env wins)
• env_wins_case_insensitively — lowercase strix_llm set → {}
• uses_json_when_no_alias_in_environ — no env alias set → file value still used (guard)

The first two fail on the old code and pass with the fix; existing precedence/mapping tests still pass. Full suite: 86 passed; ruff/mypy clean.

Note

Same root cause, left out to keep this focused: persist_current uses os.environ.get(alias.upper()), so a lowercase-set env var is silently not persisted. Happy to address separately if desired.

[greptile-apps]

Greptile Summary

This PR updates config loading so live environment values take precedence over persisted JSON. The main changes are:

• Case-insensitive detection of environment variables in _read_json_overrides.
• Cross-alias skipping of persisted JSON when any alias is set in the environment.
• Regression tests for alias precedence, lowercase environment names, and JSON fallback.

Confidence Score: 5/5

This looks safe to merge.

• No blocking issues found in the changed code.
• The updated alias and case handling matches the documented environment-over-JSON behavior.

Important Files Changed

Filename	Overview
strix/config/loader.py	Updates JSON override loading to check all aliases against the current environment before emitting init kwargs.
tests/test_config_loader.py	Adds focused tests for environment-over-JSON precedence across aliases and case-insensitive environment names.

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