chore: fix doc paths and drift, drop unused mypy overrides, ignore tool caches

[dsmcewan]

What changed

• FRAGMENTS.md: six references to layers/<module>.py now read convergence/layers/<module>.py. The bare paths do not exist from the repo root; README received the same fix in a1719e6.
• pyproject.toml: removed pexpect.* and wexpect.* from the mypy ignore_missing_imports override list. Nothing imports either module, and mypy itself reported the entries as unused.
• .gitignore: added .mypy_cache/ and .ruff_cache/, both created by the CI-mandated tools.
• README.md: "Fourteen data files" now says fourteen corpus files and mentions the adversarial, holdout and regression sets the tests use (34 tracked JSON files in total); the layout block lists them. The Run section gains the --db-table, --db-limit, --summary, --sender and --seq flags from demo.py (each example was run).
• .env.example: added CONVERGENCE_MAX_BODY_BYTES and CONVERGENCE_LLM_TIMEOUT_S, both read by web/server.py, with their defaults.
• ENGINEERING.md: "the SDK is touched in exactly one file (adapters/)" now says vendor SDKs are imported only inside convergence/adapters/, one module per backend (verified by grep).

Verification

Same commands as .github/workflows/ci.yml, run on the final head:

ruff check .                                   All checks passed
mypy convergence web                           Success: no issues (unused-section note gone)
pytest -q                                      272 passed
pytest --cov=convergence --cov=web --cov-fail-under=80   84.92%, gate met
python -m web.build && git diff --exit-code web/site/data/   no drift

The claude-review check fails for a reason outside this diff; see the PR comment (repository OAuth token).

Left for a maintainer

• web/VERIFICATION.md test counts are stale versus the current suite (it cites 173 deterministic tests; there are 272). It reads as a point-in-time evidence record, so it was not rewritten.
• The llm extra in pyproject lists anthropic and openai only; requirements.txt also lists google-generativeai and pywinpty. Whether the extra should match is a packaging decision.
• docs/plans/* and docs/specs/* are not linked from anywhere outside docs/.

🤖 Generated with Claude Code

https://claude.ai/code/session_01U142aAXSzf4pUt89HSvXTH

[dsmcewan]

CI status on 586b8c3: the test (3.10/3.11/3.12) matrix is green. The only red check is claude-review (Claude Code Review workflow).

That failure is not this PR's. The job reaches the Claude Code SDK and gets back is_error: true after one turn in about two seconds, with total_cost_usd: 0 and an empty modelUsage, so no model call was ever made. That is the signature of the CLAUDE_CODE_OAUTH_TOKEN repository secret being expired or unset, and the same workflow failed the same way on both runs of PR #39 on 2026-08-25 (runs 8 and 9), before this branch existed. The last successful run was on 2026-08-13.

Nothing in this diff (FRAGMENTS.md, pyproject.toml, .gitignore) can affect it, and no fix exists in-repo since the token is a repository secret. Re-minting it with claude setup-token and updating the secret should restore the check. I do not have permission to re-run the job from this session.

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