refactor(pgpm): rename upgrade-modules to upgrade with pnpm-like behavior

[pyramation]

Summary

Renames pgpm upgrade-modules to pgpm upgrade (with up alias) and changes the default behavior to match pnpm's upgrade command:

• Default behavior: Now upgrades all modules without prompting (previously was interactive)
• Interactive mode: Use -i or --interactive flag to select modules interactively
• Specific modules: Use positional args instead of --modules flag (e.g., pgpm upgrade @pgpm/base32)
• Removed flags: --all (now default) and --modules (use positional args)

pgpm upgrade                    # Upgrade all modules (new default)
pgpm upgrade -i                 # Interactive selection
pgpm upgrade @pgpm/base32       # Upgrade specific module
pgpm up                         # Alias for upgrade

Updates since last revision

• New interactive UI: Replaced checkbox prompt with pnpm-style upgradePrompt component from inquirerer 4.2.0
  • Arrow key navigation, version selection, filtering support
  • Shows package list with current → target version
• Added spinner: Shows animated spinner while checking for updates
• Dependency updates:
  • inquirerer 4.1.2 → 4.2.0 (across pgpm/cli, pgpm/core, packages/cli, packages/csv-to-pg)
  • genomic 5.0.3 → 5.2.0 (pgpm/cli, pgpm/core)

Review & Testing Checklist for Human

• Test interactive UI: Run pgpm upgrade -i in a module with outdated dependencies and verify the new pnpm-style UI works correctly (arrow keys, space to select, enter to confirm)
• Breaking change: The upgrade-modules command is completely removed. Update any documentation/scripts that reference the old command.
• Spinner behavior: Verify the spinner displays correctly during update checks and doesn't interfere with CI output
• Dependency compatibility: Verify inquirerer 4.2.0 and genomic 5.2.0 don't break other CLI commands that use these packages

Recommended test plan:

1. In a pgpm module with outdated dependencies, run pgpm upgrade and verify it upgrades all without prompting
2. Run pgpm upgrade -i and verify the new interactive UI appears with package list, version selection, and filtering
3. Run pgpm upgrade @pgpm/base32 with a specific module and verify only that module is upgraded
4. Run pgpm up and verify the alias works

Notes

• Requested by: Dan Lynch (@pyramation)
• Session: https://app.devin.ai/sessions/95ea22c05e164e99ac7770c57aed8b2d

[devin-ai-integration]

🤖 Devin AI Engineer

I'll be helping with this pull request! Here's what you should know:

✅ I will automatically:

• Address comments on this PR. Add '(aside)' to your comment to have me ignore it.
• Look at CI failures and help fix them

Note: I can only respond to comments from users who have write access to this repository.

⚙️ Control Options:

• Disable automatic comment and CI monitoring