fix pipeline

Author: GiggleLiu

.claude/CLAUDE.md

@@ -6,23 +6,25 @@ Rust library for NP-hard problem reductions. Implements computational problems w
 ## Skills
 These repo-local skills live under `.claude/skills/*/SKILL.md`.
 
+- [run-pipeline](skills/run-pipeline/SKILL.md) -- Pick a Ready issue from the GitHub Project board, move it through In Progress -> issue-to-pr -> Review pool. One issue at a time; forever-loop handles iteration.
 - [issue-to-pr](skills/issue-to-pr/SKILL.md) -- Convert a GitHub issue into a PR with an implementation plan. One item per PR: `[Rule]` issues require both models to exist on `main`; never bundle model + rule in the same PR.
 - [add-model](skills/add-model/SKILL.md) -- Add a new problem model. Can be used standalone (brainstorms with user) or called from `issue-to-pr`.
 - [add-rule](skills/add-rule/SKILL.md) -- Add a new reduction rule. Can be used standalone (brainstorms with user) or called from `issue-to-pr`.
-- [review-implementation](skills/review-implementation/SKILL.md) -- Review implementation completeness by dispatching parallel subagents (structural + quality) with fresh context. Auto-detects new models/rules from git diff. Called automatically at the end of `add-model`/`add-rule`, after each `executing-plans` batch, or standalone via `/review-implementation`.
-- [fix-pr](skills/fix-pr/SKILL.md) -- Resolve PR review comments (user + Copilot), fix CI failures, and address codecov coverage gaps. Uses `gh api` for codecov (not local `cargo-llvm-cov`).
+- [review-structural](skills/review-structural/SKILL.md) -- Project-specific structural completeness check: model/rule checklists, build, semantic correctness, issue compliance. Read-only, no code changes. Called by `review-pipeline`.
+- [review-quality](skills/review-quality/SKILL.md) -- Generic code quality review: DRY, KISS, cohesion/coupling, test quality, HCI. Read-only, no code changes. Called by `review-pipeline`.
+- [fix-pr](skills/fix-pr/SKILL.md) -- Resolve PR review comments, fix CI failures, and address codecov coverage gaps. Uses `gh api` for codecov (not local `cargo-llvm-cov`).
 - [write-model-in-paper](skills/write-model-in-paper/SKILL.md) -- Write or improve a problem-def entry in the Typst paper (standalone, for improving existing entries). Core instructions are inlined in `add-model` Step 6.
 - [write-rule-in-paper](skills/write-rule-in-paper/SKILL.md) -- Write or improve a reduction-rule entry in the Typst paper (standalone, for improving existing entries). Core instructions are inlined in `add-rule` Step 5.
 - [release](skills/release/SKILL.md) -- Create a new crate release. Determines version bump from diff, verifies tests/clippy, then runs `make release`.
 - [check-issue](skills/check-issue/SKILL.md) -- Quality gate for `[Rule]` and `[Model]` issues. Checks usefulness, non-triviality, correctness of literature, and writing quality. Posts structured report and adds failure labels.
+- [fix-issue](skills/fix-issue/SKILL.md) -- Fix quality issues found by check-issue — auto-fixes mechanical problems, brainstorms substantive issues with human, then re-checks and moves to Ready.
 - [topology-sanity-check](skills/topology-sanity-check/SKILL.md) -- Run sanity checks on the reduction graph: detect orphan (isolated) problems and redundant reduction rules.
   - `topology-sanity-check orphans` -- Detect isolated problem types (runs `examples/detect_isolated_problems.rs`)
   - `topology-sanity-check np-hardness` -- Verify NP-hardness proof chains from 3-SAT (runs `examples/detect_unreachable_from_3sat.rs`)
   - `topology-sanity-check redundancy [source target]` -- Check for dominated reduction rules
-- [project-pipeline](skills/project-pipeline/SKILL.md) -- Pick a Ready issue from the GitHub Project board, move it through In Progress -> issue-to-pr --execute -> Review pool.
-- [review-pipeline](skills/review-pipeline/SKILL.md) -- Pick a PR from Review pool column, fix Copilot review comments, run structural completeness check, fix CI, run agentic feature tests, move to Final review.
+- [review-pipeline](skills/review-pipeline/SKILL.md) -- Agentic review for PRs in Review pool: runs structural check, quality check, and agentic feature tests (no code changes), posts combined verdict, always moves to Final review.
 - [propose](skills/propose/SKILL.md) -- Interactive brainstorming to help domain experts propose a new model or rule. Asks one question at a time, uses mathematical language (no programming jargon), and files a GitHub issue.
-- [final-review](skills/final-review/SKILL.md) -- Interactive maintainer review for PRs in "Final review" column. Assesses usefulness, safety, completeness, quality ranking, then merge or hold.
+- [final-review](skills/final-review/SKILL.md) -- Interactive maintainer review for PRs in "Final review" column. Merges main, walks through agentic review bullets with human, then merge or hold.
 - [dev-setup](skills/dev-setup/SKILL.md) -- Interactive wizard to install and configure all development tools for new maintainers.
 - [tutorial](skills/tutorial/SKILL.md) -- Interactive tutorial — walk through the pred CLI to explore, reduce, and solve NP-hard problems. No Rust internals.
 
@@ -62,10 +64,10 @@ make run-issue N=42 # Run issue-to-pr --execute for a GitHub issue
 make run-pipeline  # Pick next Ready issue from project board, implement, move to Review pool
 make run-pipeline N=97 # Process a specific issue from the project board
 make run-pipeline-forever # Poll Ready column, run-pipeline when new issues appear
-make run-review    # Pick next PR from Review pool column, fix Copilot comments, fix CI, run agentic tests
+make run-review    # Pick next PR from Review pool column, run agentic review, move to Final review
 make run-review N=570 # Process a specific PR from the Review pool column
-make run-review-forever # Poll Review pool, auto-request Copilot reviews, dispatch run-review when reviewed
-make copilot-review # Request Copilot code review on current PR (requires: gh extension install ChrisCarini/gh-copilot-review)
+make run-review-forever # Poll Review pool for eligible PRs, dispatch run-review
+make copilot-review # (Optional) Request Copilot code review on current PR
 make release V=x.y.z  # Tag and push a new release (CI publishes to crates.io)
 # Set RUNNER=claude to use Claude instead of Codex (default: codex)
 # Default Codex model: CODEX_MODEL=gpt-5.4

.claude/skills/add-model/SKILL.md

@@ -259,7 +259,7 @@ Checklist: display name registered, notation self-contained, background present,
 make test clippy  # Must pass
 ```
 
-If running standalone (not inside `make run-plan`), invoke [review-implementation](../review-implementation/SKILL.md) to verify all structural and semantic checks pass. When running inside a plan, the outer orchestrator handles the review.
+Structural and quality review is handled by the `review-pipeline` stage, not here. The run stage just needs to produce working code.
 
 ## Naming Conventions
 

.claude/skills/add-rule/SKILL.md

@@ -175,7 +175,7 @@ cargo run --example export_schemas  # Generate problem schemas for docs/paper bu
 make test clippy                    # Must pass
 ```
 
-If running standalone (not inside `make run-plan`), invoke [review-implementation](../review-implementation/SKILL.md) to verify all structural and semantic checks pass. When running inside a plan, the outer orchestrator handles the review.
+Structural and quality review is handled by the `review-pipeline` stage, not here. The run stage just needs to produce working code.
 
 ## Solver Rules
 

.claude/skills/dev-setup/SKILL.md

@@ -31,7 +31,7 @@ When scanning, read these files for tool references:
 
 Organize tools into three tiers in `dependencies.md`:
 - **Core** — needed to build, test, and generate docs
-- **Skill** — needed for the AI-assisted pipeline (gh, claude, pred, copilot-review)
+- **Skill** — needed for the AI-assisted pipeline (gh, claude, pred)
 - **Optional** — nice to have but not required (julia)
 
 Each tool needs: name, check command, install command (macOS), install command (Linux), purpose.
@@ -54,7 +54,7 @@ For each tool in the **Core Tools** table of `dependencies.md`:
 3. **If missing** → print the install command for the detected platform, then execute it
 
 After all core tools are done, ask:
-> "Core tools are installed. Do you also want to set up the AI pipeline tools (gh, claude, pred, copilot-review)?"
+> "Core tools are installed. Do you also want to set up the AI pipeline tools (gh, claude, pred)?"
 
 - **Yes** → proceed to Step 4
 - **No** → skip to Step 6
@@ -148,14 +148,7 @@ If this fails, the user likely needs org-level project scopes:
 gh auth refresh -s read:project,project
 ```
 
-**6c: Test `make run-review` prerequisites**
-
-```bash
-# Verify gh-copilot-review works
-gh copilot-review --help
-```
-
-**6d: Test claude CLI**
+**6c: Test claude CLI**
 
 ```bash
 claude --version
@@ -179,7 +172,7 @@ If all pipeline checks pass, explain the project-based contribution pipeline:
 > Picks the next **Ready** issue, moves it to **In Progress**, implements it (using `/issue-to-pr` → `/add-model` or `/add-rule`), creates a PR, then moves it to **Review pool**.
 >
 > ### `make run-review` (PR → review)
-> Picks the next **Review pool** PR, waits for Copilot review, fixes comments and CI failures, runs agentic feature tests, then moves it to **Final review** for human approval.
+> Picks the next **Review pool** PR, runs agentic review (structural + quality + feature tests), then moves it to **Final review** for human approval.
 >
 > ### Targeting specific items
 > - `make run-pipeline N=42` — process issue #42

.claude/skills/dev-setup/dependencies.md

@@ -25,7 +25,6 @@ Rescan by running `/dev-setup` and choosing "rescan".
 | Tool | Check Command | Install (macOS) | Install (Linux) | Purpose |
 |------|--------------|-----------------|-----------------|---------|
 | gh | `gh --version` | `brew install gh` | `sudo apt install gh` | GitHub CLI |
-| gh-copilot-review | `gh copilot-review --help` | `gh extension install ChrisCarini/gh-copilot-review` | same | Copilot PR reviews |
 | claude | `claude --version` | `npm install -g @anthropic-ai/claude-code` | same | AI-assisted pipeline |
 | pred | `pred --version` | `make cli` or `cargo install --path problemreductions-cli` | same | Project CLI (check-issue, topology-sanity-check, propose) |