docs: render remaining exported docstrings

[ChrisRackauckas-Claude]

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

What changed

This gives every exported docstring reported by strict Documenter a canonical rendered location:

• the dynamic-optimization API page now owns the collocation and dynamic-problem docs through their declaring ModelingToolkitBase bindings;
• isinitial, homotopy diagnostics, and the StateSelection matrix helpers are rendered in their relevant manual sections;
• the two package-module docstrings are rendered on a small package-modules API page.

The four dynamic-problem entries formerly canonicalized on the general problems page moved to the dedicated dynamic-optimization page. Their public documentation remains rendered exactly once.

Failing before

The clean-master strict docs build reported:

12 docstrings not included in the manual:
    ModelingToolkitBase.isinitial :: Tuple{...SymReal}
    ModelingToolkitBase.PyomoCollocation
    ModelingToolkit.ModelingToolkit
    ModelingToolkitBase.NonPolynomialReason
    ModelingToolkitBase.ModelingToolkitBase
    ModelingToolkitBase.InfiniteOptCollocation
    ModelingToolkitBase.CasADiCollocation
    StateSelection.bareiss.bareiss! :: ...
    StateSelection.CLIL.SparseMatrixCLIL
    ModelingToolkitBase.JuMPCollocation
    ModelingToolkitBase.AbstractCollocation
    ModelingToolkitBase.PyomoDynamicOptProblem

A formal bisect of the strict missing-docs gate identified 92c27bb as the first commit that enabled fatal checkdocs = :exports without warning-only handling.

Passing after

On exact upstream f3248317cb51e08e78fb3d1729286905ad61d6d4, I ran:

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

Documenter emitted no docstrings not included in the manual diagnostic, and :missing_docs disappeared from the terminal error set:

makedocs encountered errors [:docs_block, :cross_references, :linkcheck]

The remaining failures are independent clean-master clusters. The duplicate clusters are isolated in #4977 and #4978. Four invalid StateSelection entries and unresolved links remain under separate investigation. Link checking encountered transient remote failures.

Other local verification

git diff --check
julia +lts --startup-file=no -e 'using Runic; exit(Runic.main(ARGS))' -- --check docs/pages.jl
git diff --no-ext-diff | typos -

These pass. The Julia invocation is used because an unrelated executable named runic shadows Runic.jl on this host.

GROUP=QA julia +lts --startup-file=no --project -e 'using Pkg; Pkg.test()' completed with 38 pass, 4 error. The four errors are the independently reproduced clean-master ExplicitImports checks: no_implicit_imports, no_stale_explicit_imports, all_explicit_imports_via_owners, and all_qualified_accesses_via_owners.

I did not run GPU, downstream, or GROUP=Everything jobs.

Links

• Strict-docs gate commit: 92c27bb
• Linear duplicate fix: docs: remove duplicate linear analysis entries #4977
• Dependency duplicate fix: docs: remove duplicate dependency graph entries #4978
• Clean-master docs job: https://github.com/SciML/ModelingToolkit.jl/actions/runs/31869817836/job/94981845495

[ChrisRackauckas-Claude]

Pushed facd7a3e0c973c2d954be6dfc89dbeee833e7544 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.

The standalone docs build was started but stopped after Documenter reported no docs found for ModelingToolkit.StructuralTransformations in docs/src/API/modules.md; this is separate from the Runic fix and remains to investigate.