Add cross-references to pkgdown package documentation from the book

[divine7022]

Description

The book mentions many PEcAn functions and packages but does not link to the rendered pkgdown documentation where users can find detailed API reference (parameters, return values, examples). The pkgdown documentation exists at https://pecanproject.github.io/package-documentation/develop/ but is underutilized.

The book should focus on explanation (concepts, workflows, how things fit together), while referencing pkgdown for detailed function documentation. Currently function names appear as plain text instead of clickable links.

Current state

Functions mentioned without links to pkgdown:

book_source/03_topical_pages/03_pecan_xml.Rmd:

- `PEcAn.DB::db.open`
- `PEcAn.workflow::start_model_runs`
- `PEcAn.uncertainty::write.ensemble.configs`
- `PEcAn.uncertainty::run.ensemble.analysis`

book_source/03_topical_pages/95_remote_execution.Rmd:

The `PEcAn.remote::remote.execute.cmd`
...see the `PEcAn.remote` package documentation.

(Says "see the package documentation" but doesn't provide a link)

09_rabbitmq.Rmd:
PEcAn.remote::rabbitmq_post_message function

Vignettes linked to raw github Rmd instead of rendered html:
01_introductions_user.Rmd has a table with vignettes
The "html" column is empty, but pkgdown renders these vignettes to html. These could link to the rendered versions at
e.g:

• https://pecanproject.github.io/package-documentation/develop/PEcAn.allometry/articles/AllomVignette.html
• https://pecanproject.github.io/package-documentation/develop/PEcAn.assim.batch/articles/AssimBatchVignette.html

"Under construction" sections that could link to packages:
03_pecan_xml.Rmd -- These mention packages but don't link to their pkgdown documentation.

Proposed approach:

1. Convert plain text function references to hyperlinks pointing to pkgdown reference pages
   • e.g. : PEcAn.DB::db.open --> PEcAn.DB::db.open
2. Link "see the package" statements to actual pkgdown pages
   • e.g. : "see the PEcAn.remote package documentation" -- link to the package index
3. Fill in rendered html links for vignettes table
   • the vignette table has an "html" column that's currently empty
   • these should link to the pkgdown rendered versions
4. Replace "under construction" placeholders with package links
   • if detailed content isn't in the book, at least provide a link to pkgdown
5. Audit the book to identify other places where package names or functions are mentioned and add links to the appropriate pkgdown pages where a reference already exists.

[man080107]

Hey @divine7022 i would like to work on this issue please aasign it to me thanks !

[infotroph]

One issue I see with this plan is that it hardcodes links to point to the develop branch. We intentionally maintain separate documentation for each PEcAn release, so having the (say) 1.10.0 version of the book be linking to the development version of the function documentation feels potentially confusing. Consider especially the case of a function that was available and discussed in the manual of a previous release but we've removed it from develop.

A smaller concern is that we've got to some lengths to make sure the documentation can be available on the user's own machine (e.g. the Docker stack includes a docs container that serves all of the documentation, and make docs creates a fully static on-disk HTML version). But I realize that host-independent cross-links between the book and the package docs are more complex than internal links within one of those.

[shreyannandanwar]

I understand that the core issue is not the absence of documentation, but the lack of effective linkage between the book and the existing pkgdown API references.

I also recognize the risk of hard-coding links to the develop documentation, as this can introduce version mismatches and confusion across releases, as well as weaken support for offline and locally served documentation.

With this in mind, I believe it is possible to design a more robust, version-aware linking approach that improves usability while preserving correctness and portability across PEcAn releases.

@divine7022 I would like to work on this issue.