Fix documentation examples for current dependency APIs

[ChrisRackauckas-Claude]

This PR should be ignored until reviewed by @ChrisRackauckas.

Dependency

This PR is stacked on #4745, which fixes the pre-existing spell-check typo on master. Review and merge #4745 first; the documentation fix remains a separate commit on top.

Summary

• Add direct documentation dependencies for Graphs, OrdinaryDiffEqFunctionMap, and OrdinaryDiffEqRosenbrock.
• Replace the removed accidental BipartiteGraphs incidence_matrix re-export and internal tearing-state access with documented public APIs from Graphs.LinAlg and ModelingToolkitBase.
• Update BifurcationKit and OrdinaryDiffEq examples to their current public owner APIs.

Regression attribution

• BipartiteGraphs commit 6f9fbf5701e4 stopped accidentally exposing Graphs.incidence_matrix after switching to explicit imports.
• BifurcationKit 0.8 removed the old PeriodicOrbitOCollProblem compatibility name in favor of Collocation.
• OrdinaryDiffEq 7 reduced its umbrella exports, so FunctionMap and Rodas4 must be imported from their owning sublibraries.

Verification

• Exact discrete-system tutorial example: exit 0; retcode=Success, points=101, final_t=100.0.
• Public-API smoke covering incidence_matrix/asgraph, a Rodas4 solve, and Collocation construction: exit 0; incidence=Bool[1;;], retcode=Success, collocation=(0, 5, 20).
• Full Julia LTS CI-style documentation build from a fresh normal HTTPS clone detached at the documentation commit before stacking (90a21a1d7c86dbc042eec75e3b5af89b08ac0911): exit 0. All examples, link checks, and HTML rendering completed successfully.
• Typos CLI 1.48.0 on the stacked tree: exit 0.
• Runic 1.7.0 over every tracked Julia file on the stacked tree: exit 0.
• git diff --check upstream/master...HEAD: exit 0.

[ChrisRackauckas-Claude]

Post-stack verification is complete.

• Stack: Correct alias elimination docstring typo #4745 commit 94efb41cdb1423c7d35f42140a88e503bd554183, then documentation commit 742e993783728637cd15875ccd6acda069d13fde.
• Before rewriting the documentation commit for the stack, I fetched PR Fix documentation examples for current dependency APIs #4746 into a fresh normal HTTPS clone (a normal .git directory), detached exactly at 90a21a1d7c86dbc042eec75e3b5af89b08ac0911, and used workspace-local depot and temporary directories.
• The full documentation command was:

CI=true GITHUB_ACTIONS=true GITHUB_EVENT_NAME=push \
GITHUB_REF=refs/heads/agent/fix-docs-example-regressions \
GITHUB_REF_NAME=agent/fix-docs-example-regressions GITHUB_REF_TYPE=branch \
GITHUB_REPOSITORY=SciML/ModelingToolkit.jl GITHUB_REPOSITORY_OWNER=SciML \
GITHUB_SHA=90a21a1d7c86dbc042eec75e3b5af89b08ac0911 \
GITHUB_WORKSPACE=/home/crackauc/sandbox/tmp_20260713_111059_49183/_verification/modelingtoolkit-pr4746 \
GITHUB_SERVER_URL=https://github.com JULIA_DEBUG=Documenter \
JULIA_DEPOT_PATH=/home/crackauc/sandbox/tmp_20260713_111059_49183/_verification/depot-pr4746 \
TMPDIR=/home/crackauc/sandbox/tmp_20260713_111059_49183/_verification/tmp-pr4746 \
DISPLAY=:0 xvfb-run -a -s '-screen 0 1024x768x24' \
/home/crackauc/.juliaup/bin/julia +lts --startup-file=no --project=docs/ --code-coverage=user docs/make.jl

It exited 0 after completing all examples, link checks, and HTML rendering. In particular, the repaired tearing/Graphs, BifurcationKit Collocation, discrete FunctionMap, and Rodas4 examples all evaluated successfully.

On the final stacked tree:

• /home/crackauc/sandbox/tmp_20260713_111059_49183/_tools/typos-1.48.0/typos --version reported typos-cli 1.48.0; running that binary at the repository root exited 0.
• Runic 1.7.0 with --check over every path from git ls-files -z '*.jl' exited 0.
• git diff --check upstream/master...HEAD exited 0.

[ChrisRackauckas-Claude]

Current red-check classification after independent clean-base reproduction:

• Both benchmark failures are the pre-existing MTK/MTKBase runner load-order bug fixed in draft Resolve benchmark MTKBase before runner startup #4747. The exact patched AirspeedVelocity run exits 0 and executes the mtkcompile benchmark.
• Both Catalyst Modeling failures are the pre-existing Catalyst test dependency on non-public AffectSystem internals fixed in draft Test symbolic jump affects through public API Catalyst.jl#1509. The focused test and full symbolic_stoichiometry.jl pass locally on Julia 1.12.6.

These are independent of the documentation-example repairs here. The fresh-clone CI-style docs build for this exact patch already exited 0, including examples, rendering, and link checks.