fix(cli): revert broken merge and stabilize pyrefly gate - #111

Reverts broken merge d58c2f2 and applies pyrefly gate stabilization:

• Revert merge: d58c2f2
• Modify: model base parts, docx/pptx pipeline, xlsx snapshot/style, prompts, tests

Summary by cubic

Reverts the broken merge d58c2f2 that pulled unrelated agent-tooling and docs changes into the branch, then applies pyrefly type-checking stabilization to the CLI codebase.

Changes

• Removes the merge's .codex/ hook config, install-git-hooks.sh, .markdownlintignore, and .terminus-e2e-new-cli.txt.
• Restores .claude/settings.json, .markdownlint.json, .qlty/qlty.toml (ruff lint re-enabled), AGENTS.md, CLAUDE.md, and README.md to their pre-merge contents.
• Adds the .agents/ skill symlinks, provider config, and generated api-reference/ module docs.
• Applies pyrefly gate fixes to model base parts, the docx/pptx pipeline, xlsx snapshot/style parity, prompts, and tests.

^{Written for commit ec5b61b. Summary will update on new commits.}