Modernize jaspTools with rappdirs, gh package, and new options

[Copilot]

Addresses modernization requests: persistent clone storage, gh package for GitHub API, configurable module loading strategy, and streamlined setup flow.

New Dependencies

• rappdirs - Platform-agnostic cache directory for jasp-desktop clone (replaces tempdir)
• gh - GitHub API interactions with proper auth handling (httr fallback retained)

New Package Options

• module.load.strategy: "pkgload" | "install" | "nothing" - Controls how modules are loaded during runAnalysis()
• update.clone: "always" | "ask" | "never" - Controls jasp-desktop clone update behavior
• restore.lockfile: "ask" | "never" - Prompt about renv lockfile mismatch (directs user to run renv::restore() manually)

New Exported Function

• updateDesktopClone(branch = "development", quiet = FALSE) - Manually update the cached jasp-desktop clone

Setup Changes

• Removed installJaspModules prompt from interactive setup (function still available for manual use)
• Clone persists in rappdirs::user_cache_dir("jaspTools", "jasp-stats")
• Prompts to update clone if >7 days old (when update.clone = "ask")

Module Loading

# Use pkgload for faster iterative development
setPkgOption("module.load.strategy", "pkgload")

# Skip reloading entirely (use installed version)
setPkgOption("module.load.strategy", "nothing")

Notes

• reinstall.modules option still works but deprecated in favor of module.load.strategy
• Man pages need regeneration via devtools::document() after merge

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• cran.r-project.org
  • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

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• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

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This section details on the original issue you should resolve

<issue_title>modernize jaspTools a bit</issue_title>
<issue_description>We should:

• use rappdirs for the location of the clone of jasp-stats/jasp-desktop.
• use gh to do the github interactions.
  • use some setting to update this clone (update: [always | ask | never]
  • have an exported function to update the clone as well
• do not install all jasp-packages for a user, also do not ask if a user wants to do this.
• do ask if a user wants to restore the renv lockfile if the library does not match.
  • use some setting for asking this (restore lockfile: [ask | never]
  • do not have an exported function to do the restore, but make it clear this just call renv::restore.
• offer to use pkgload::load_all when calling runAnalysis rather than reinstalling the module everytime.
  • use some setting for asking this (restore lockfile: [pkgload::load_all | install | nothing]</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes modernize jaspTools a bit #61

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