Replace board-driven pipelines with agent-invoked how-to guides

[GiggleLiu]

Summary

Strategy change: the repo no longer relies on the GitHub project board. Pipelines (run/review/auto/final) are removed; agents auto-invoke short how-to-* guides while working, and a human merges.

Skills: 23 → 12 (~6,700 → ~1,500 lines)

• Guides: how-to-code, how-to-verify, how-to-write-manual, how-to-review, how-to-triage-issue, how-to-ship
• Tools (trimmed): propose, find-solver, find-problem, dev-setup, release, update-papers

Behavior changes (agreed during design)

• how-to-verify posts a ## Verification certificate PR comment (verdict, counts, seeds, scripts)
• how-to-ship requires a fresh-context review subagent (## Agentic Review Report) before merge-ready; the agent pushes (never force) and replies on addressed threads; a human merges
• Triage: mechanical issue fixes are automatic, substantive ones are discussed; "proposed data types" check dropped
• Redundancy check uses pred path --limit all (the removed find_dominated_rules is no longer referenced)
• Plans are uncommitted working notes; make run-plan removed
• dev-setup confirms once before installing; release (skill + Makefile) requires clean, up-to-date main and make check
• find-solver/find-problem use pred reduce --via and pred inspect

Infrastructure

• Deleted: pipeline_board.py, pipeline_worktree.py, project_board_{poll,recover}.py, make_helpers.sh + tests; run-*, board-*, worktree-*, issue-*, pr-* make targets; Codex runner variables
• Trimmed pipeline_pr.py, pipeline_checks.py (issue-context), pipeline_skill_context.py (review-implementation)
• community-call.yml: agenda from open PRs (CI green / needs work) + Good issues without a PR, via GITHUB_TOKEN (tested locally against the live repo). The PROJECT_READ_TOKEN secret can be deleted.

Test plan

• Kept script tests: 47 pass; 1 failure (test_create_pr_uses_gh_pr_create_and_returns_current_context) is pre-existing on main and left unmodified
• Every make target, scripts/*.py subcommand, pred subcommand, and guide cross-reference named in skills/CLAUDE.md resolves
• Repo grep shows no references to deleted skills/targets/scripts (except historical comments in two Rust test files)
• make help and make -n release render correctly
• Rust sources unchanged; CI make check

Paper and docs fixes (second commit)

• Reduction-rule pred create commands now use a new rule-spec(ex) helper (Src/k=v/... --to Tgt/k=v/...), which recreates the rule fixture's source instance so the documented --config applies. Before, 24 rule entries created a different instance, MaximumClique and QUBO/f64 failed outright, and one used invalid syntax. Keyed specs reproduce all 289 rule fixtures (positional specs fail on 84, e.g. ambiguous ILP/i64/bool). Verified with make paper and by running every command.
• The MaximumClique model entry and the MIS/MVC gold-standard entries use problem-spec(x).
• CLAUDE.md: aggregate mappings register via #[aggregate_reduction]; manual ReductionEntry remains only for Turing and metadata-only edges.

Not changed

• Global user skills fix-pr / issue-to-pr (in ~/.claude, outside the repo) may compete with how-to-ship here.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.73%. Comparing base (309ac65) to head (6e254f0).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1173   +/-   ##
=======================================
  Coverage   96.73%   96.73%           
=======================================
  Files        1069     1069           
  Lines      138549   138549           
=======================================
  Hits       134023   134023           
  Misses       4526     4526           

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[GiggleLiu]

@isPANN @zazabap I cleaned up skills in this pr. I removed project board based workflows, and only keep highlevel principles. I will merge it 3 days later, let me know if you have any concern before that.

In this new workflow, principles are mostly followed automatically (skills named: how-to-xxxx are automatically called on need).