feat(query): per-project config.json defaults for budget/depth (#1654)

[TPAteeq]

Fixes #1654

What

Adds an optional per-project config sidecar so graphify query defaults for
budget and depth can be set once per repo instead of being retyped on
every invocation. CLI flags still win.

Previously both values were hardcoded in the query handler (budget = 2000,
and depth=2 passed as a literal into both _query_graph_text(...) and
querylog.log_query(...)), and the query command had no --depth flag at
all — depth was not overridable from the CLI.

Config file shape

Location: graphify-out/config.json (honours the GRAPHIFY_OUT override, same
as every other sidecar). Documented shape — a nested query object:

{ "query": { "default_budget": 4000, "default_depth": 3 } }

Flat top-level keys are also accepted for convenience, and either spelling
works (default_budget/default_depth or bare budget/depth):

{ "budget": 4000, "depth": 3 }

When both a nested and a flat value are present, the nested query object
wins. Only positive integers are honoured.

Precedence

built-in default  <  graphify-out/config.json  <  CLI flag

• No config, no flag → unchanged behavior (budget 2000, depth 2).
• Config present → its values seed budget/depth before flag parsing.
• A CLI flag (--budget N, --depth N, or the --budget=N/--depth=N form)
  always overrides the config.

Changes

• graphify/paths.py — new query_config_defaults() reader. A missing
  file, unreadable file, malformed JSON, wrong top-level type, or
  non-positive/non-integer values all degrade to built-in defaults, so a bad
  config can never crash a query.
• graphify/__main__.py — seed budget/depth from the config before the
  arg loop; add --depth N / --depth=N parsing to the query command; use
  the resolved depth in both the _query_graph_text(...) and
  querylog.log_query(...) calls (replacing the literal 2s); update the
  usage line and --help block to document --depth and the config file.

This also resolves a latent inconsistency: the CLI forced depth=2 while
serve._query_graph_text's own default is depth=3. Rather than silently
change behavior, depth is now explicit and configurable — the effective CLI
default stays 2, but users can raise it via config or --depth. No changes
to serve.py.

Tests

• tests/test_paths.py — unit tests for the reader: nested object, flat keys,
  partial config, nested-wins-over-flat, missing file, malformed JSON, bad
  value types (string/bool/zero/negative rejected), and non-dict top level.
• tests/test_query_cli.py — end-to-end via main(): config sets budget/depth
  and they reach both _query_graph_text and log_query; a CLI flag overrides
  the config; absence of config → current defaults (2000/2); malformed config →
  falls back without error.

Run:

uv run python -m pytest tests/test_query_cli.py tests/test_paths.py tests/test_querylog.py -q

Result: 65 passed. (Broader related run — test_serve.py included — 141 passed.)

Notes