docs: correct the stale headline figures and document the new knobs

The user-facing numbers had drifted a long way from reality.

README claimed ~353,000 documents and a 1.89 GB archive. Current measured
values from snapshot-20260805-beta.2: 393,266 documents, 1.16 GB archive —
the archive got SMALLER while the corpus grew, because the embedding matrix
now ships int8-quantized.

The per-profile disk table (4.6 / 7.1 / 10.5 GB) is from the last full
`verify-profiles` run against snapshot-20260611 and has not been re-measured
since. Rather than invent updated numbers or leave them presented as
current, both README and configuration.md now state the provenance and give
the one figure that IS measured on the new snapshot (a balanced install is
~11 GB), pointing at scripts/verify-profiles.mjs to re-measure.

Also:
- README's "sync merges Xcode docs when available locally" predated the
  CLI defaults flip. sync now runs fonts + model fetch + Xcode enrich by
  default and finishes on the semantic index; documented with the
  --no-download-fonts / --no-fetch-models / --no-enrich-fetch opt-outs.
- configuration.md gained APPLE_DOCS_LOG_STDOUT (with the stdio-MCP
  warning) and APPLE_DOCS_SKIP_DISK_CHECK, neither of which was documented.
- installing.md now says outright that semantic search works in the
  standalone binary — true since the embedder became pure JS with no native
  addon, and the thing a reader would reasonably doubt.