arch: add src/runtime scaffold + migration runbook (#2044)

[yastman]

This pull request was created by @kiro-agent on behalf of @yastman 👻

Comment with /kiro fix to address specific feedback or /kiro all to address everything.
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Summary

Parent: #1948 (reverse layering). Related: #1265.

The ratchet contract test for #1948 is already on dev:

• tests/contract/test_layering_no_telegram_bot_imports_contract.py
• tests/data/known_layering_violations.json (5 entries, all in src/api/main.py)

What is missing is the destination package the migration slices (#2045 phase 1, #2047 phase 3, #2049 cleanup) need to land into. This PR adds the scaffold so each follow-up slice can do a single git mv without also creating the package on its first PR.

Changes

• src/runtime/__init__.py — module docstring explaining the package role: this is the destination kernel. Imports as a working empty namespace; future slices fill it via git mv.
• src/runtime/README.md — migration runbook with the per-phase plan (arch: extract pure shared runtime modules to src/runtime (#1948 phase 1) #2045 / arch: migrate coupled runtime modules cache, qdrant, and graph (#1948 phase 3) #2047 / arch: remove reverse-layering allowlist and verify mini_app separability (#1948 cleanup) #2049), the per-slice procedure (git mv → update callers → add compat shim → drop allowlist row → run contract), and an explicit list of what this scaffold PR does not do.

What this PR does NOT do

• No module relocation — that's arch: extract pure shared runtime modules to src/runtime (#1948 phase 1) #2045 / arch: migrate coupled runtime modules cache, qdrant, and graph (#1948 phase 3) #2047.
• No behaviour change — src.runtime imports as an empty namespace.
• No contract / allowlist change — tests/data/known_layering_violations.json and the ratchet test are untouched.

Verification

uv run pytest tests/contract/test_layering_no_telegram_bot_imports_contract.py -q   # 4 passed
uv run pytest tests/contract/ -q                                                     # 1095 passed
uv run python -c 'import src.runtime'                                                # OK
uv run python scripts/check_markdown_links.py                                        # OK
uvx ruff check src/runtime/                                                          # OK

Closes #2044