* R - update renv version and all R packages deps

* python - update Python 3.14.3, uv  version and lockfile

* Julia - update to 1.12.5 and update all packages

Add type declarations for functions exported in init.lua that were
missing from the lua-types annotations. This feeds into the autogen
docs effort (quarto-dev/quarto-web#1649).

quarto.doc: add_resource, add_supporting, is_filter_active
quarto.utils: type, table.isarray, table.contains, table.sortedPairs,
  resolve_path_relative_to_document, as_inlines, as_blocks,
  is_empty_node, render, match, add_to_blocks

- EndBug/add-and-commit: v9.1.4 (node20) → v10.0.0 (node24)
- softprops/action-gh-release: v1-era (node20) → v2.6.1, remove deprecated env GITHUB_TOKEN
- julia-actions/setup-julia: @v2 (node20) → master SHA with node24 (no release yet)

Follow-up to #14199 which updated official actions/* and other third-party actions.

Add typst-gather to the dependency system, following the same pattern
as Pandoc, Typst, esbuild, and other binary dependencies. Pre-built
binaries are downloaded from GitHub releases (quarto-dev/typst-gather).

- Add TYPST_GATHER=0.2.2 to configuration
- Add typst-gather dependency definition with platform-specific URLs
- Register typst-gather in the dependency list

Remove the Rust source tree at package/typst-gather/ and switch to the
downloaded binary registered in the previous commit.

- Remove archiveOnly flag to enable download during configure
- Remove cargo build from configure.sh and configure.cmd
- Remove typst-gather staging from prepare-dist.ts
- Remove Cargo cache step from CI workflow
- Add QUARTO_TYPST_GATHER env var override support

…mand for gathering

Replace the TypeScript regex-based import scanning with a call to
`typst-gather analyze`, which uses Typst's own parser for robust import
discovery including nested imports and transitive @Local dependencies.

- Remove parseSimpleToml(), discoverImportsFromFiles(), and related types
- Add runAnalyze() that pipes TOML config to `typst-gather analyze -` on stdin
- Rewrite generateConfigFromAnalysis() to consume structured JSON output
- Pipe config on stdin for auto-detected gather (no temp files)
- Use `gather` subcommand for all gather invocations
- Add QUARTO_TYPST_GATHER env var override to call version
- Extract typstGatherBinaryPath() shared helper
- Add 12 unit tests for generateConfigFromAnalysis()

Instead of copying ALL packages from built-in resources and extensions
into the scratch directory, use typst-gather analyze to determine the
exact set of packages needed (including transitive deps), then stage
only those.

- Create src/core/typst-gather.ts shared module (moved from cmd.ts)
- Decompose stageTypstPackages into collectPackageSources,
  analyzeNeededPackages, stageSelectedPackages, stageAllPackages
- Change from first-write-wins to last-write-wins so extensions can
  override built-in packages
- Falls back to staging everything if typst-gather binary is missing
  or analyze fails
- 14 unit tests for staging functions and TOML building
- 1 smoke test verifying no packages staged for import-free documents

Fixes #14157

- Use quarto.cmd on Windows in runQuarto helper
- Switch fallback tests from orange-book (requires R/knitr) to
  marginalia-only-project (pure typst)
- Use cross-platform approach for non-zero exit test
- Clean up .quarto dir after fallback tests to avoid polluting
  the subsequent selective-staging test

Fix preview browse URL for single-file documents

After #13804 made the project variable always non-null via
singleFileProjectContext(), two code paths in preview() broke for
single-file documents: the browse URL included the output filename
(e.g. /hello.html instead of /), and GET / returned 404 because
the project handler expected index.html as the default file.

Guard both the URL path computation and the handler selection with
!project.isSingleFile so single-file previews use the correct
handler and root URL. Extract URL path logic into a testable
previewInitialPath() function.

- Fix initialPath using relative path instead of empty string
- Fix handler selection using projectHtmlFileRequestHandler with
  wrong default file instead of htmlFileRequestHandler
- Add unit tests for previewInitialPath() (single-file, project,
  project-subdir, undefined-project cases)
- Add manual preview test entries T17-T19

Fixes #14298

* Fix inverted logic in quarto.utils.is_empty_node for text nodes

The text branch (`node.text`) used `~=` (not-equal) where it should
use `==` (equal), causing is_empty_node to return true for non-empty
text nodes and false for empty ones.

Text nodes like Str and Code should follow the same emptiness
semantics as container nodes like Para and Div: a Str('') is empty
just as Para({}) is empty -- a node of the right type but with
nothing in it.

Internal callers all pass container nodes (caption, preamble) so
nothing was visibly broken, but extension authors calling the public
API on text nodes get wrong results.

* Add changelog entry for is_empty_node fix (#14297)

Verifies that suppress-bibliography: true works with Typst's native
citation system (not just citeproc). The test checks that the generated
.typ file contains the #show bibliography: none rule, and that the
PDF output includes citations but no bibliography section.

Refs #14327

Also sort #13878 into numerical order.

Since v1.9.35, `quarto inspect` on a standalone .qmd file emits a
`project` field because `singleFileProjectContext` now always sets
`config`. RStudio's publishing wizard reads `project.dir`, assumes
`_quarto.yml` exists there, and crashes on the missing file.

Gate `project` emission on `!(isSingleFile && isRStudio())` so
RStudio gets the pre-1.9.35 output while other consumers still see
the project metadata. Add `_setIsRStudioForTest()` to avoid
`Deno.env.set()` race conditions in parallel tests.

The RStudio-side fix (rstudio/rstudio#17336) is merged but won't be
backported — this protects users on older RStudio who upgrade Quarto.

Ref: rstudio/rstudio#17333

When a user explicitly specifies `format: orange-book-typst` in a book
project, prefer a locally installed copy of the extension over the
built-in one, so customizations take effect. The default behavior for
`format: typst` (which auto-assigns orange-book) is unchanged.

Adds a `preferLocal` flag threaded through the extension lookup chain
that, when set, checks local `_extensions/` before built-in extensions.
Only the explicit typst book extension case sets this flag.

Fixes #14326

* Add CI workflow for tool install on arm64 Linux and macOS

Integration test for quarto install tinytex and chrome-headless-shell on
platforms not covered by smoke tests (arm64 Linux, macOS). Path-filtered
to src/tools/** with weekly schedule for upstream breakage detection.

Also add test-install.yml to paths-ignore in test-smokes-parallel.yml
and test-ff-matrix.yml so changes to the new workflow don't trigger
unrelated test suites.

* Skip chrome-headless-shell install on arm64 until #14334 lands

…less-shell (#14334)

Deprecate `quarto install chromium` in favor of `chrome-headless-shell`.
The chromium command now prints a deprecation warning and transparently
redirects to chrome-headless-shell, preserving `--no-prompt` for CI
pipelines. The `afterInstall` hook automatically removes any legacy
chromium installation when chrome-headless-shell is installed.

Add arm64 Linux support for `quarto install chrome-headless-shell`
using Microsoft's Playwright CDN as the download source, since Chrome
for Testing has no arm64 Linux builds. The arm64 binary name difference
(`headless_shell` vs `chrome-headless-shell`) is abstracted by a
platform-aware helper.

- Chromium marked "(deprecated)" in tool registry, removed from help
  text examples; full removal planned for v1.11
- `quarto check install` warns when legacy chromium is detected
- Binder post-build scripts use chrome-headless-shell instead of
  chromium
- Path/version utilities extracted to chrome-headless-shell-paths.ts
  to break a circular dependency
- New `test-install.yml` CI workflow for arm64 install and chromium
  deprecation across all platforms

Closes #11877
Fixes #9710