fix(core): revert broken merge and stabilize privateattr typed contract - #413

Reverts broken merge 52a3b14 and applies typed privateattr contract stabilization:

• Revert merge: 52a3b14
• Modify: .mise.toml

Summary by cubic

Reverts broken merge 52a3b14, which pulled in unrelated agent skills and tooling configs, then re-applies the privateattr typed contract stabilization on a clean base. The .mise.toml beads entry now pins gastownhall/beads 1.2.2 instead of tracking latest.

Revert scope

• Removes the git hook installer, .markdownlint*, .shellcheckrc, and the waza backup file.
• Restores the .agents/skills symlink tree and re-enables the ruff qlty plugin.
• Adds the generated api-reference module docs.

^{Written for commit 82cd906. Summary will update on new commits.}