chore: untrack two committed store files, add the rules that let them in

[ywatanabe1989]

The finding this PR exists for. Two database files were tracked in this repo — a 68 KB clew runtime store at .scitex/clew/runtime/db.sqlite, and a second under a legacy clew example. Both are binary, so git grep -I skips them and neither appears in any text scan of this tree; only a binary-inclusive git grep -a surfaced them. They are untracked here, and .gitignore gains the patterns that were missing — the existing rules covered only Django's db.sqlite3, which is exactly why these two slipped in.

Three stale sentences corrected. All three described clew's provenance store as a local file database. scitex-clew moved its stores onto the per-host PostgreSQL and has no database file, so the wording sent a reader looking for something never written: docs/sphinx/core_concepts.rst (×2) and docs/sphinx/modules/io.rst.

pyproject.toml claimed the clew extra pulls in nothing and uses only stdlib. It pins scitex-clew==0.17.0, and clew owns its own store.

One dead test entry removed. scitex_io._load_modules._sqlite3 no longer exists on scitex-io's develop, so that parametrised case was doing nothing but skipping, every run, with "auto-gen snapshot drift". Measured with scitex-python's own venv: 60 skips before, 59 after, 254 passed both times, 2 xfailed — exactly one silent skip removed, none created. The block is auto-generated and its generator (ecosystem write-integration-tests) is not in the installed scitex-dev, so it is corrected by hand; a regeneration would drop it too, since nothing in this tree references the module.

Before / after (excluding examples/_legacy/, as measured): 17 lines → 13, of which the ignore-rule count rose 4 → 6 on purpose. Non-ignore-rule: 13 → 7. What stays, and why:

lines	category	why it stays
README.md ×3, docs/05_ADDITIONAL_MODULES.md ×1	live API, another repo	these document stx.db.SQLite3, a public class that exists in the scitex-db package. scitex-db is mid-cutover (it ships docs/sqlite-to-postgres-cutover.md and a _migrate/ surface). Deleting the docs while the class ships would make this repo misdescribe its own umbrella. scitex-python cannot reach zero until scitex-db retires that class.
tests/integration/test_integration.py:301	live API	assert hasattr(stx.db, "SQLite3") is coverage of that same class. Removing it deletes a check, not a dependency.
scripts/maintenance/_pypi_packages.py:153	detector / reference data	a hardcoded list of CPython stdlib module names, used to tell stdlib imports from PyPI deps. Drop the entry and the script misclassifies import sqlite3 as a missing package. A detector must name what it recognises.
docs/guides/CROSSREF_API_CONFIGURATION.md:149	record	- **Format**: … describes the on-disk shape of an existing 1.2 TB / 167 M-row CrossRef mirror. Rewriting it makes the doc lie about what is on the NAS. Revisit when that mirror moves.
.gitignore ×6	ignore-rule	pattern lines only — the guard. Two of the six are added by this PR.

examples/_legacy/ is left alone (31 further lines, legacy notebooks demonstrating the same live scitex-db API).

Positive control (stx.db) returns 4 files on the same invocation, so the reduced counts are real absences.