Add reproducible pred CLI commands to paper examples

[GiggleLiu]

Summary

• Add pred-commands() Typst helper that renders styled CLI command blocks in the paper
• Retrofit all ~79 model entries and ~29 rule entries with pred create/solve/evaluate and pred create/reduce/solve/evaluate pipelines
• Update authoring skills (write-model-in-paper, write-rule-in-paper, add-model, add-rule) with instructions for the new pattern
• Update final-review skill to remove redundant CLI section from issue comments (now in PDF)
• Remove unused CLI functions to fix compiler warnings

Test plan

• make paper compiles successfully
• Spot-checked pred commands from the paper (MIS, MVC, SAT, TSP, MVC→MIS round-trip)
• Verified only additions — no existing content removed (728 insertions, 0 deletions in paper)
• No compiler warnings

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.62%. Comparing base (a4e05bd) to head (46f59c6).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #724   +/-   ##
=======================================
  Coverage   97.62%   97.62%           
=======================================
  Files         403      403           
  Lines       50112    50112           
=======================================
  Hits        48923    48923           
  Misses       1189     1189           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.