[Spec 647] Rename af CLI to afx

[waleedkadous]

Summary

Renames the Agent Farm CLI from af to afx to prevent AI assistants from stripping the command name.

• afx is now the primary CLI command
• af remains as a deprecated alias (prints warning to stderr)
• All source code, tests, skill directories, and documentation updated

Changes

• Core CLI: New bin/afx.js shim, bin/af.js converted to deprecated wrapper, package.json updated with both entries
• CLI Parser: .name('afx'), codev afx alias, deprecation warning for codev af
• Source Code: Updated ~30 source files with hardcoded af references
• Skills: Renamed .claude/skills/af/ → .claude/skills/afx/ (repo + skeleton)
• Tests: Updated ~30 test files, added AFX_BIN/runAfx to test helpers
• Documentation: Updated 289 markdown files with ~2,215 replacements

Exclusions (per spec)

• .af-cron/ directory left as-is (filesystem path, not CLI reference)
• af-config.json references left as-is (deprecated config file name)

Testing

• All 2248 unit tests passing (13 pre-existing skips)
• Build passing
• Zero remaining af CLI references in markdown or source

Spec

codev/specs/647-rename-af-cli-to-afx.md

Review

codev/reviews/647-rename-af-cli-to-afx.md

Closes #647