fix: small misc fixes (substrate comment, pred_stats heap accounting, docs nav, virtuoso isql port)

[jeswr]

Requested by Jesse · project thread

Summary

Four small, independent fixes:

• sparq-substrate/Cargo.toml comment is stale: claims nothing depends on it, but it IS in the feature-OFF wasm graph #3806: the crates/sparq-substrate/Cargo.toml scaffold comment said nothing in the workspace depends on the crate, so the wasm build never compiles it. That stopped being true: sparq-engine depends on it unconditionally (numeric + join + compare) and so does sparq-reason (numeric), so the crate is part of the feature-OFF wasm graph. The comment now says so and points at bench/feature-off-declarations/. No other Cargo.toml has the same "nothing depends on it" wording.
• sq-7d3dj.32.6: chore(memory-accounting): TripleStore::heap_bytes omits pred_stats (planner statistics map) #3115: TripleStore::heap_bytes now counts the pred_stats planner map, as capacity × (entry + 1 control byte), the same model Dict uses for its tables. The new unit test heap_bytes_counts_pred_stats failed before the fix and passes after it. Any memstat or B/triple metric built on heap_bytes will rise a little, by a fixed amount: about 1 KiB for ~90 predicates.
• chore: have the docs tab of the website link to actual documentation #2549: the site's Docs nav item pointed at skills/SKILL.md on GitHub, which is the agent-skills router. It now points at the human-facing mdBook guide, which pages.yml overlays at /guide/ (Decide + implement the Pages mount for the mdBook guide (the actual blocker on publishing docs) #5022). It is an external hard-navigation slot like /app, with the basePath prefix and a trailing slash. The e2e witness in site/e2e/site-nav.spec.ts now asserts the /guide/ href.
• sq-24pqs: virtuoso-same-box.sh: when VIRTUOSO_ISQL_PORT is overridden to non-1111, 'docker exec isql $PORT' targets a non-existent container-internal port (container always binds 1111 internally) — one-line fix; default (1111) path is correct, only bites non-default port configs (found on #1362) #3361: scripts/virtuoso-same-box.sh ran docker exec … isql $VIRTUOSO_ISQL_PORT, but inside the container isql always listens on 1111. VIRTUOSO_ISQL_PORT is only the host-side -p mapping. Both docker exec calls (the readiness poll and the bulk load) now use 1111.

Not changed: #3090 (glib >= 0.20 in gui/src-tauri/Cargo.lock). Running cargo update -p glib --precise 0.20.0 fails with failed to select a version for the requirement glib = "^0.18", required by gtk v0.18.2 ← tauri v2.11.3. On Linux, Tauri 2 is tied to the gtk-rs 0.18 / GTK3 stack (see #2818), so the bump needs a Tauri major migration and is not possible as a lockfile change.

Closes #3806
Closes #3115
Closes #2549
Closes #3361

Base gate (always required)

• cargo build --workspace succeeds. (Left to CI. I ran checks scoped to the crate only.)
• cargo clippy --workspace --exclude sparq-py --all-targets -- -D warnings is clean. (Left to CI. cargo clippy -p sparq-core --all-targets --all-features -- -D warnings is clean.)
• The code this PR touches is formatted (rustfmt reports no diff in the touched hunks).
• cargo test passes for every crate this PR touches (cargo test -p sparq-core). I did not run the site e2e locally because there is no node_modules; it is left to CI.

Targeted re-evaluation (check the rows that apply to your change)

• Storage / encoding: only the heap_bytes accounting changed; storage and encoding are untouched. Expect a small, fixed rise in heap_bytes-derived metrics.
• Wasm: heap_bytes is a benchmarking accessor in always-compiled sparq-core. Its effect on the bundle size is left to the wasm_bundle_bytes gate.

Ratchets and conventions

• I did not lower any conformance / perf / coverage ratchet.
• No hard-coded performance numbers added to markdown.
• No TODO/FIXME markers added.
• If this change makes a doc statement false, I updated that doc in the same change (the substrate comment and the Docs-link comment are both corrected).

Security

• This change does not introduce a security regression.

🤖 Generated with Claude Code

https://claude.ai/code/session_01ScyGGohDhirnbLbrUSnA5n

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[jeswr]

🔎 Codex reviewer — gpt-6.1-sol

Automated review by the Codex reviewer (OpenAI gpt-6.1-sol via Codex CLI) of head 334b0135c04e. Scope: correctness, security, soundness and design; style nits omitted. A new head gets a fresh review.

Findings

1. [high] New Docs link blocks Pages deployment — site/src/components/layout/app-shell.tsx:61
   The production export now contains /guide/ links, but pages.yml runs scripts/check-site-links.sh site/out before building and overlaying the guide. That script checks root-relative links against site/out, where guide/index.html does not yet exist, so the link check fails and prevents deployment.
   Build and overlay the guide before checking the site’s links. If the guide’s own HTML requires separate validation, exclude it from the scanned inputs while still validating site links into it.

Verdict: The PR needs the deployment-order fix before merging.

[jeswr]

🔎 Codex reviewer — gpt-6.1-sol

Automated review by the Codex reviewer (OpenAI gpt-6.1-sol via Codex CLI) of head df20b34abd38. Scope: correctness, security, soundness and design; style nits omitted. A new head gets a fresh review.

Findings

No correctness, security, soundness or design problems found.

Verdict: The PR is safe to merge as is.

[jeswr]

🔎 Codex reviewer — gpt-6.1-sol

Automated review by the Codex reviewer (OpenAI gpt-6.1-sol via Codex CLI) of head df20b34abd38. Scope: correctness, security, soundness and design; style nits omitted. A new head gets a fresh review.

Findings

No correctness, security, soundness or design problems found.

Verdict: The PR is safe to merge as is.

[jeswr]

Local ci-fast gate (GitHub Actions outage; Jesse approved local-gate merges). PR head df20b34a merged with main 4faff096:

• clippy -D warnings (core crates, all targets): pass
• nextest (core crates, ci profile): pass
• doctests (core crates): pass
• W3C SPARQL conformance 1229/1229 (ratchet 1229): pass

Main moved to 85d5ede5 after the run. 4faff096..85d5ede5 touches no Rust source, manifest, lockfile, toolchain, ci-fast workflow, test data, include_str! target or file this PR changes, so the result stands.

Squash-merging under the local-gate rule.

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