Refactor: Isomorphic Runs

[AdityaVG13]

Summary

Living PR on refactor/de-monolithize-isomorphic for isomorphic module splits and follow-on product fixes. Same branch, same PR -- append work here instead of opening a new PR.

Standing contract (every commit on this branch):

• Behavior: full suite pass/fail/skip counts must not regress vs the last recorded baseline
• Public API: cargo +nightly public-api --simplified for ast-sgrep-core and ast-sgrep-mcp is empty or additions-only (existing import paths keep working via façades)
• No extract+rename+reformat in one commit; rustfmt is its own commit when needed
• No invented bench/RSS numbers

Last measured suite: 488 passed / 0 failed / 4 ignored. Clippy -D warnings is green after WS-01.

Landed so far

Isomorphic splits of post-#27 over-1k files. Suite 488/0/4, public-api 0/0.

Extract	New module
IndexStore query/read	store/sqlite/queries.rs
IndexStore writes	store/sqlite/writes.rs
Corrupt-index recovery	index_recovery.rs
Prepare/hash	index_prepare.rs
Watch-path helpers	index_watch.rs
finish_response ranking/gates	search/finish.rs
MCP sandbox reads	mcp/sandbox.rs
Metamorphic mr_pred_*	tests/core/metamorphic_preds.rs

index.rs (~1034) left as the Indexer hub plus FORCE_SIDECAR injects. Compile RSS / Criterion not re-baselined.

Product follow-ons on this branch

• Clippy -D warnings (const TLS cells)
• CONTRIBUTING / surface-parity / mcp.md / Homebrew / VS Code langs aligned with the tree
• Pi check:pi-dist (porcelain) and check:agent-plugin in CI
• Product unwraps → invariant-safe control flow
• Writer-gen fail-open documented; advertise after partial watch-batch error

Test plan

• CI cargo fmt --check, cargo check --workspace, cargo test (forbid #[test] in crates/*/src)
• cargo +nightly public-api --simplified -p ast-sgrep-core -p ast-sgrep-mcp has no removals vs main
• Spot-check façades: ast_sgrep_core::search::finish_response, store::IndexStore, canonicalize_affected_path
• Clippy cargo clippy --workspace --all-targets -- -D warnings
• npm run check:pi-dist and check:agent-plugin in the Pi CI job

Adversarial review remediation

• Moved in-process native hybrid search off the Node event loop so Pi requests do not block unrelated JS work.
• Removed the unsupported warm-under-1ms product assertion and its test instead of turning a local observation into a contract.
• Review fix: 88928ead. CI was not awaited.