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:

Folder name mismatches

Local name differs from remote repo name (excluding .git suffix). For .github repos, convention is {org}-.github.

Stale repos (no commits in 6+ months)

Include last commit date and whether it's owned by seabbs orgs or external.

Dead worktrees

Worktrees whose tracking branch no longer exists on the remote, or worktrees with no uncommitted changes that haven't been touched in 30+ days.

Repos not in their org folder

Any repo whose remote belongs to a known org (epinowcast, epiforecasts, EpiAware, nfidd, seabbs) but isn't inside the corresponding ~/code/{org}/ folder.

External repos (not owned by seabbs orgs)

Repos from other orgs/users cloned locally.

No-git directories

Directories with no git remote.

Phase 3: Propose Actions

For each flagged item, propose one of:

• rename: fix folder name to match remote
• move: move into correct org folder
• archive: move to ~/code/archive/
• delete: remove entirely (only for empty dirs or confirmed duplicates)
• clean-worktree: remove dead worktree

Phase 4: Execute (with confirmation)

Present the full action list and ask for confirmation before executing. Group actions by type (renames, moves, archives, deletes, worktree cleanup).

When moving repos into org folders, create the org folder if it doesn't exist. When archiving, move to ~/code/archive/.

After execution, update ~/CLAUDE.md with the current repo inventory.

Phase 5: Summary

Print a final summary showing:

• Total repos by org
• Total archived
• Total cleaned worktrees
• Any items skipped

Known Org Mapping

These GitHub orgs map to ~/code/{org}/:

• epinowcast
• epiforecasts
• EpiAware
• nfidd
• seabbs (personal repos)

External repos go in ~/code/external/. Repos with no git go in ~/code/archive/ unless actively used.