Fix check_agents CI failure and sweep doc drift

[LevonBecker]

Summary

Fixes check_agents crashing in CI (it required the gitignored, machine-local properties.yml) and sweeps the repo for doc/AI-config drift found while auditing it, including a stale root README title and a .github/workflows/ listing that referenced two workflow files that no longer exist.

Changes

• check_agents.py: resolve the repo root via find_repo_root() locally, or this file's fixed relative path when CI is set, instead of get_repo_local() (which needs properties.yml, never created in CI)
• Root README.md: retitle to "Template Python", fix the .github/workflows/ listing (only tests.yml exists, triggering on push to main, not the removed feature_branches.yml/protected_branches.yml), document setup.ps1 and common/route_utils.py
• modules/repo/README.md: rewritten — it described a fictional "Repo Manager Agent" with a config.yml/permissions system that never existed in this codebase; now documents the actual files and behavior
• modules/common/README.md: documented cli.py and route_utils.py, previously missing
• .github/instructions/index.instructions.md, modules.instructions.md, tasks.instructions.md: matching structure fixes, plus two references to a nonexistent upgrade.upgrade task corrected to upgrade