Summary

save_config_overrides blindly wrote every mutable field each call. A Web UI "save section" with default-False MMR thus pinned mmr.enabled=false into ~/.memtomem/config.json, permanently shadowing any config.d/ fragment that set it True. Memory-dirs add/remove and mm config set leaked the same way because all persist paths funnel through this one function.

Closes two follow-ups from #255: the memory-dirs dump leak (follow-up #1) and the Web UI section-save symmetric case (follow-up #2). The stated fix in both follow-ups was "Drop-equal-to-default-on-write" — same code change.

What this does

• Compare each mutable field to its class-level default via model_fields[key].get_default(call_default_factory=True).
• If equal, drop from the write dict and prune any matching existing entry (auto-cleans historical leftovers on next save).
• Empty sections are removed — no orphan {} survives.
• Covers every persist path: mm config set, PATCH /api/config?persist=true, POST /api/config/save, /memory-dirs/add|remove, mem_config MCP.

What this does NOT do

• No UX affordance. Users still have no explicit "reset this field to default" button in the Web UI. Server auto-prunes defaults on save, but users need to know the current default to type it in. Tracked as a separate follow-up (new endpoint GET /api/config/defaults + ↺ buttons in settings-config.js, including custom widgets rrf_weights/exclude_patterns).
• No schema-driven rewrite. Two hardcoded sets still exist: _FRESH_PRESERVE_KEYS (12 keys) and _EXTRA_PERSIST_FIELDS (1 key). Unifying them via Pydantic field metadata is a follow-up, deferred until either list grows or a drift incident.

Critical exemption: _EXTRA_PERSIST_FIELDS

indexing.memory_dirs is excluded from drop-default. Its factory _default_memory_dirs() auto-discovers AI tool dirs via is_dir() fs checks — environment-dependent. "Equal to default" on machine A does not hold on machine B. Dropping env-dependent defaults would silently lose user-curated dir lists across environments.

Criterion documented in the comment so future additions have an objective test: if a field's default_factory reads filesystem, network, hostname, or other runtime state, add it to _EXTRA_PERSIST_FIELDS.

Before / after

Before (leak)

User unchecks MMR in Web UI → section save:

{
  "mmr": {"enabled": false},
  "indexing": {"memory_dirs": [...]}
}

mmr.enabled=false is the default, but it's now pinned and permanently overrides any config.d/ fragment setting it True.

After (clean)

{
  "indexing": {"memory_dirs": [...]}
}

mmr section omitted — fragment precedence restored. Existing leaks from prior installs get pruned on the next save.

Testing

• 1680 CI tests pass, ruff + format + mypy clean.
• 5 new tests in TestSaveConfigOverrides:
  • test_default_valued_field_not_persisted — fresh save omits default-only mmr section
  • test_existing_default_entry_pruned_on_save — pinned mmr.enabled=false leftover is pruned
  • test_non_default_value_still_persists — explicit non-defaults survive
  • test_memory_dirs_equal_to_default_still_persisted — locks in the exemption (test name reflects intentional asymmetry)
  • test_section_with_only_defaults_dropped_entirely — empty section removed, no orphan {}
• Manual smoke (check → uncheck → verify drop, memory_dirs stays) passed.

Internal consumers

grep confirmed only internal readers touch config.json (init_cmd wizard read-merge-write, policy.py parses a separate config string, tests). No external parsers, no breaking change for library users.

Follow-ups (after this PR)

Updated list in project_wizard_leftovers_cleanup.md:

1. Web UI per-field reset button + GET /api/config/defaults endpoint.
2. Web UI hot-reload of config.json (mtime watcher invalidates cache).
3. Schema-driven rewrite of _FRESH_PRESERVE_KEYS and _EXTRA_PERSIST_FIELDS.
4. --fresh write-after-backup atomicity (tempfile + atomic rename).

Test plan

• uv run pytest -m "not ollama" green (1680 passed)
• uv run ruff check + ruff format --check clean
• uv run mypy packages/memtomem/src clean
• Manual smoke: check MMR → save → confirm mmr.enabled=true persisted; uncheck → save → confirm mmr section dropped
• Manual smoke: memory_dirs = _default_memory_dirs() → save → confirm still persisted (exemption)