graph scope takes 9-18 s per call on Hono, 3x slower than on the larger mex repo

[theyashasvipandey]

mex graph scope takes 9–18 s per call on Hono (p50 13.4 s), against 2–5 s on mex, which
is the larger repository. impact on the same Hono store takes about 3 s.

repository	indexed files	nodes	Scope p50
honojs/hono @ 52febbcc + setup scaffold	387	14.1k	13.4 s (range 9–18 s)
mex @ 2f074dc	851	37.7k	~4 s (range 2–5 s)

Measured with sequential calls on an otherwise idle machine; a rerun reproduced the numbers, so
this isn't contention. Both stores were fresh, on main after #196 (the #190 read-path fix).

Retrieval quality on Hono is fine (every expected file was found), so this is only latency. The
likely suspects are per-call work that scales with something Hono has more of than mex:
per-file source reads for the source-first response, text-fallback scans, or the freshness audit
on a different corpus shape. Profiling one call would settle it.

Also worth looking at while profiling: three Scope misses

• Hono request-dispatch: the fetch span is not returned (it was in August, before 43
  upstream commits).
• mex BudgetLedger and beginResponse spans are not returned for queries that describe budget
  enforcement.