docs: repair strict cross-references

[ChrisRackauckas-Claude]

Ignore this PR until it has been reviewed by @ChrisRackauckas.

What changed

Strict Documenter exposed 34 unresolved cross-references on current master.

This PR keeps local ModelingToolkit references as qualified Documenter references, links dependency-owned APIs to their canonical SciML documentation, and renders internal-only helper names as code instead of pretending they are public documentation targets. It does not change behavior or public API.

Failure before

On the unmodified f3248317cb51e08e78fb3d1729286905ad61d6d4 base:

DISPLAY=:0 JULIA_DEBUG=Documenter xvfb-run -a -s '-screen 0 1024x768x24' \
  julia +lts --startup-file=no --project=docs/ --code-coverage=user docs/make.jl

The command exited 1, and:

$ rg -c 'Cannot resolve @ref' docs-before.log
34
ERROR: LoadError: `makedocs` encountered errors [:docs_block, :missing_docs, :cross_references] -- terminating build before rendering.

The same failure is visible in the clean-master docs job:
https://github.com/SciML/ModelingToolkit.jl/actions/runs/31869817836/job/94981845495

A formal bisect of the strict cross-reference gate identified 92c27bb9fdcaa024ff190feb3d665452e33f9bd8 (Adopt SciMLTesting 2.4 strict QA) as the first bad commit.

Verification after

On this branch, based directly on f3248317cb51e08e78fb3d1729286905ad61d6d4:

DISPLAY=:0 JULIA_DEBUG=Documenter xvfb-run -a -s '-screen 0 1024x768x24' \
  julia +lts --startup-file=no --project=docs/ --code-coverage=user docs/make.jl

The command still exits 1 for the independently tracked duplicate-doc and missing-doc failures, but the cross-reference discriminator is clean:

$ rg 'Cannot resolve @ref' docs-after-crossrefs.log | wc -l
0
ERROR: LoadError: `makedocs` encountered errors [:docs_block, :missing_docs] -- terminating build before rendering.

Both new canonical external links returned HTTP 200 during Documenter link checking.

Mechanical checks:

git diff --name-only --diff-filter=ACM | rg '\.jl$' |
  xargs julia +lts --startup-file=no -e 'using Runic; exit(Runic.main(ARGS))' -- --check
git diff --check
git diff --name-only --diff-filter=ACM -z | xargs -0 typos

All three exited 0.

QA:

GROUP=QA julia +lts --startup-file=no --project -e 'using Pkg; Pkg.test()'

The command reproduced the current-master ExplicitImports failure without a branch-specific regression:

Some tests did not pass: 38 passed, 0 failed, 4 errored, 0 broken.
ExplicitImports | 4 errors

GPU, downstream, Julia pre, and non-QA test groups were not run because this is a documentation-only change.

[ChrisRackauckas-Claude]

Pushed 4be377a98a354ce4f7fef9953a413e3100b8d10b to fix the Runic indentation failure at docs/make.jl:50 (], aligned to four spaces).

Verification on the pushed tree:

• /home/crackauc/.juliaup/bin/julia +1.12.4 --project=@runic --startup-file=no -m Runic --check --diff docs/make.jl passed.
• typos docs/make.jl passed.
• git diff --check passed.
• Full docs build passed at the preceding docs commit (0302915bd9); this push changes only whitespace in docs/make.jl.

[ChrisRackauckas-Claude]

Rebased the docs-only strict cross-reference fix onto current master at 17b1a65960a6fe889379ce5fcfd6deb47f50ee48 and pushed it to this draft PR.

Local verification: root ModelingToolkit QA 52/52, Runic passed, git diff --check passed. Typos reports only the pre-existing unrelated inferrable in untouched test/analysis_points.jl. The full docs build is still running locally; I will report its exit result separately. Please ignore until reviewed by @ChrisRackauckas.