manual: SpaDES.docs 0.2.0 stages chapters under the book root

[achubaty]

Draft — the manual has not been tackled on this branch yet. Groundwork.

SpaDES.docs 0.2.0 writes the generated <module>2.Rmd to a staging directory under the book root (_manual_rmds) instead of into each module's own directory, so _bookdown.yml has to list them from there.

Why the change was made upstream

The module directories are git submodules. Before this, a build wrote into 10 separate repositories, a failed build left a <module>2.Rmd in each one, and every module repo carries a .gitignore line to hide it. Each generated file also embedded an absolute host path.

There were 11 such files sitting in this repo's modules/ when the work started; they have been cleared.

This PR

file	change
manual/_bookdown.yml	10 chapters ../modules/<M>/<M>2.Rmd → _manual_rmds/<M>2.Rmd
manual/.gitignore	_manual_rmds/
manual/build.R	cleanup is now unlink("_manual_rmds", recursive = TRUE)
DESCRIPTION	SpaDES.docs (== 0.0.1.9002) → (== 0.2.0); Remotes → @v0.2.0

Verified upstream that this does not change the rendered book: the same chapters rendered from both locations produce byte-identical HTML, including relative images, cross-references and citations.

This branch makes it simpler than it would have been on development

development pins r-version: 4.2.3, and SpaDES.docs 0.2.0 needs R ≥ 4.3 — so migrating there would have required an R bump that invalidates the renv library. This branch is already on R 4.6.1, so that problem does not arise.

Still needs you

renv.lock pins SpaDES.docs 0.0.1.9002 at 757c320. Updating it means

renv::install("PredictiveEcology/SpaDES.docs@v0.2.0", lock = TRUE, prompt = FALSE)

which writes to the shared project library, so it is not done here. This PR and that install must land together — 0.0.1.9002 writes chapters where the new _bookdown.yml no longer looks, and 0.2.0 writes where the old one no longer looks.

Also in 0.2.0

Fixes this book benefits from: _bookdown.yml is parsed as YAML rather than by indentation; a module with no setup chunk no longer aborts the whole book; and a (ref:key) used mid-paragraph is no longer mistaken for a duplicate definition and deleted — Biomass_core.Rmd:612 has exactly one of those.

🤖 Generated with Claude Code

[achubaty]

Superseded by #172, which landed the same _bookdown.yml staging change (byte-identical hunk), the same manual/.gitignore entry, and a more general build.R cleanup. The DESCRIPTION bump this PR carried was not lost: #172 pins SpaDES.docs 0.4.0 in both DESCRIPTION and renv.lock.