Code Directory Cleanup

Audit and tidy the ~/code/ directory. Run from the home directory (~/).

Phase 1: Inventory

For every subdirectory in ~/code/ (including inside org folders), collect:

1. Git remote (git remote get-url origin, or "no-git")
2. GitHub org (parsed from remote URL)
3. Repo type (R package = has DESCRIPTION, Julia package = has Project.toml, paper/grant = has .qmd/.tex/submission/, website = has _quarto.yml without package files, org-config = .github repos, other)
4. Last commit date (git log -1 --format="%ci")
5. Folder name vs remote name mismatch
6. Worktrees (git worktree list in each repo, flag any worktrees whose branch no longer exists on the remote)

Phase 2: Flag Problems

Report a table for each category: