Replace include= source dumps with MFIIDD.source_for

[sbfnk-bot]

Addresses seabbs's review on #39 (sessions/pmcmc.qmd:99 thread): "use codetracking rather than include".

Summary

• Add CodeTracking as a direct dep (it was already transitive).
• Add MFIIDD.source_for(file) — reads pkgdir(MFIIDD)/src/<file> so the displayed code tracks the live package rather than a path relative to the qmd.
• Add MFIIDD.source_for(f::Function) — returns the source of every method of f via CodeTracking.definition. Useful for students who want to inspect one function after using MFIIDD.
• Swap every {.julia include="../src/X.jl"} block in pmcmc.qmd, particle_filters.qmd, mcmc.qmd, mcmc_diagnostics.qmd for a {julia} chunk that prints a markdown code fence around source_for("X.jl").

The Documenter half of seabbs's suggestion is split into a follow-up PR.

Summary by CodeRabbit

• New Features

  • Documentation examples now display source code more reliably in rendered notebooks and session pages.
  • Added a new way to reuse and present package source snippets consistently across the docs.

• Bug Fixes

  • Updated package dependencies and compatibility to support the new source-display workflow.
  • Refreshed an existing component version to keep documentation rendering stable.

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Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@src/MFIIDD.jl`:
- Around line 51-57: In source_for(f::Function), the result from
CodeTracking.definition(String, m) is already a String, so pushing first(d)
incorrectly stores only the first character and breaks the chunks vector. Update
the loop over methods(f) to push d directly into chunks after the nothing check,
keeping the return type consistent with Vector{String}.

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Fix all unresolved CodeRabbit comments on this PR:

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• Create a new PR with the fixes

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Configuration used: Organization UI

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📥 Commits

Reviewing files that changed from the base of the PR and between 315518c and 89e8952.

📒 Files selected for processing (7)

• Manifest.toml
• Project.toml
• sessions/mcmc.qmd
• sessions/mcmc_diagnostics.qmd
• sessions/particle_filters.qmd
• sessions/pmcmc.qmd
• src/MFIIDD.jl