Add scientific research tool detectors

[andrew]

Add knowledge-base detectors for 17 tools found in scientific and research repositories. The set covers Jupyter and Quarto, workflow tools such as Snakemake and Nextflow, R package development, Julia documentation and formatting, Python testing and benchmarks, and Fortitude for Fortran.

Add a mixed-language detector test that exercises file, dependency, and configuration signals through the normal scan path.

[Copilot]

Pull request overview

Adds knowledge-base tool detectors aimed at scientific/research repositories, plus an integration-style detector test that exercises file-, dependency-, and config-based signals via the normal scan path.

Changes:

• Added new tool definitions for common research workflows and tooling across R, Python, Julia, Fortran, and shared ecosystems (e.g., Jupyter/Quarto, Snakemake/Nextflow, R package tooling).
• Added a mixed-language detector test that builds a synthetic project and asserts the expected detections.

Reviewed changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
knowledge/r/testthat.toml	Adds detector metadata for the R testthat testing framework.
knowledge/r/roxygen2.toml	Adds detector metadata for roxygen2 R documentation generation.
knowledge/r/rmarkdown.toml	Adds detector metadata for rmarkdown / .Rmd usage.
knowledge/r/renv.toml	Adds detector metadata for the renv R package manager / lockfile.
knowledge/r/pkgdown.toml	Adds detector metadata for pkgdown site generation.
knowledge/r/knitr.toml	Adds detector metadata for knitr vignette/document tooling.
knowledge/r/covr.toml	Adds detector metadata for covr coverage reporting.
knowledge/python/tox.toml	Adds detector metadata for tox via tox.ini and pyproject.toml keys.
knowledge/python/asv.toml	Adds detector metadata for asv benchmarking via asv.conf.json.
knowledge/julia/runic.toml	Adds detector metadata for the Runic Julia formatter.
knowledge/julia/juliaformatter.toml	Adds detector metadata for JuliaFormatter and its config file.
knowledge/julia/documenter.toml	Adds detector metadata for Documenter.jl docs generation.
knowledge/fortran/fortitude.toml	Adds detector metadata for Fortitude Fortran linting.
knowledge/_shared/snakemake.toml	Adds detector metadata for Snakemake workflow detection.
knowledge/_shared/quarto.toml	Adds detector metadata for Quarto publishing detection.
knowledge/_shared/nextflow.toml	Adds detector metadata for Nextflow pipeline detection.
knowledge/_shared/jupyter.toml	Adds detector metadata for Jupyter notebook detection.
detect/research_test.go	Adds a mixed-language detector test covering the new research tool detectors.

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