Fix remaining skill gaps: variant docs, branch guards, prerequisites

- add-model: Document variant_params! macro usage for variant() implementation
- issue-to-pr: Add pre-flight checks (clean tree, existing branch) before
  branch creation; add retry/dirty-tree to Common Mistakes
- write-model-in-paper: Fix wrong make rust-export → use make paper (which
  auto-runs export_graph + export_schemas)
- write-rule-in-paper: Fix wrong make rust-export → correct export commands

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

Author: GiggleLiu

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

@@ -84,6 +84,7 @@ Key decisions:
 - **Weight management:** use inherent methods (`weights()`, `set_weights()`, `is_weighted()`), NOT traits
 - **`dims()`:** returns the configuration space dimensions (e.g., `vec![2; n]` for binary variables)
 - **`evaluate()`:** must check feasibility first, then compute objective
+- **`variant()`:** use the `variant_params!` macro — e.g., `crate::variant_params![G, W]` for `Problem<G, W>`, or `crate::variant_params![]` for problems with no type parameters. Each type parameter must implement `VariantParam` (already done for standard types like `SimpleGraph`, `i32`, `One`). See `src/variant.rs`.
 
 ## Step 2.5: Register variant complexity
 

.claude/skills/issue-to-pr/SKILL.md

@@ -81,8 +81,13 @@ Include the concrete details from the issue (problem definition, reduction algor
 
 Create a pull request with only the plan file.
 
+**Pre-flight checks** (before creating the branch):
+1. Verify clean working tree: `git status --porcelain` must be empty. If not, STOP and ask user to stash or commit.
+2. Check if branch already exists: `git rev-parse --verify issue-<number>-<slug> 2>/dev/null`. If it exists, switch to it with `git checkout` (no `-b`) instead of creating a new one.
+
 ```bash
-# Create branch
+# Create branch (from main)
+git checkout main
 git checkout -b issue-<number>-<slug>
 
 # Stage the plan file
@@ -131,3 +136,5 @@ Created PR #45: Fix #42: Add IndependentSet -> QUBO reduction
 | Generic plan | Use specifics from the issue, mapped to add-model/add-rule steps |
 | Skipping CLI registration in plan | add-model requires CLI dispatch updates -- include in plan |
 | Not verifying facts from issue | Use WebSearch/WebFetch to cross-check claims |
+| Branch already exists on retry | Check with `git rev-parse --verify` before `git checkout -b` |
+| Dirty working tree | Verify `git status --porcelain` is empty before branching |

.claude/skills/write-model-in-paper/SKILL.md

@@ -12,7 +12,7 @@ Full authoring guide for writing a `problem-def` entry in `docs/paper/reductions
 Before using this skill, ensure:
 - The problem model is implemented (`src/models/<category>/<name>.rs`)
 - The problem is registered with schema and variant metadata
-- JSON exports are up to date (`make rust-export && make export-schemas`)
+- JSON exports are up to date (`cargo run --example export_graph && cargo run --example export_schemas`)
 
 ## Reference Example
 
@@ -161,10 +161,7 @@ This can be woven into the example text (as MIS does: "$w(S) = sum_(v in S) w(v)
 ## Step 4: Build and Verify
 
 ```bash
-# Regenerate exports (if not already done)
-make rust-export && make export-schemas
-
-# Build the paper
+# Build the paper (auto-runs export_graph + export_schemas)
 make paper
 ```
 

.claude/skills/write-rule-in-paper/SKILL.md

@@ -17,7 +17,7 @@ Before using this skill, ensure:
 - The reduction is implemented and tested (`src/rules/<source>_<target>.rs`)
 - An example program exists (`examples/reduction_<source>_to_<target>.rs`)
 - Example JSON is generated (`make examples`)
-- The reduction graph is up to date (`make rust-export`)
+- The reduction graph and schemas are up to date (`cargo run --example export_graph && cargo run --example export_schemas`)
 
 ## Step 1: Load Example Data