Update references, docs, and check-issue skill (#188)

* update refs

* update documents

* update module overview

* remove collaborate.md — content moved to issue #187

The collaboration workflow draft has been reviewed and filed as
GitHub issue #187 for further refinement and discussion.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* update

* update review-implementation

* update skills

* run-issue

* fix-pr: check all review comment sources, prioritize user comments

- Step 1a now prints counts for each source and labels them clearly
- Triage table separates user comments (priority 2) from Copilot (priority 3)
- Added "User comments always take priority" instruction
- Deleted stale plan file per reviewer request

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: GiggleLiu

.claude/CLAUDE.md

@@ -12,6 +12,7 @@ Rust library for NP-hard problem reductions. Implements computational problems w
 - [write-model-in-paper](skills/write-model-in-paper/SKILL.md) -- Write or improve a problem-def entry in the Typst paper. Covers formal definition, background, example with visualization, and algorithm list.
 - [write-rule-in-paper](skills/write-rule-in-paper/SKILL.md) -- Write or improve a reduction-rule entry in the Typst paper. Covers complexity citation, self-contained proof, detailed example, and verification.
 - [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.
 - [meta-power](skills/meta-power/SKILL.md) -- Batch-resolve all open `[Model]` and `[Rule]` issues autonomously: plan, implement, review, fix CI, merge — in dependency order (models first).
 
 ## Commands
@@ -39,6 +40,7 @@ make cli           # Build the pred CLI tool (release mode)
 make cli-demo      # Run closed-loop CLI demo (exercises all commands)
 make mcp-test      # Run MCP server tests (unit + integration)
 make run-plan      # Execute a plan with Claude autorun
+make run-issue N=42 # Run issue-to-pr --execute for a GitHub issue
 make copilot-review # Request Copilot code review on current PR
 make release V=x.y.z  # Tag and push a new release (CI publishes to crates.io)
 ```

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

@@ -147,7 +147,7 @@ Invoke the `/write-model-in-paper` skill to write the problem-def entry in `docs
 make test clippy  # Must pass
 ```
 
-Then run the [review-implementation](../review-implementation/SKILL.md) skill to verify all structural and semantic checks 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.
 
 ## Naming Conventions
 

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

@@ -139,7 +139,7 @@ cargo run --example export_schemas  # Update problem schemas
 make test clippy                    # Must pass
 ```
 
-Then run the [review-implementation](../review-implementation/SKILL.md) skill to verify all structural and semantic checks 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.
 
 ## Solver Rules