update

Author: GiggleLiu

.claude/skills/final-review/SKILL.md

@@ -141,6 +141,7 @@ Check that the PR only touches files expected for its type. Any file outside the
 - `docs/src/reductions/problem_schemas.json` — schema export
 - `docs/src/reductions/reduction_graph.json` — graph export
 - `tests/suites/trait_consistency.rs` — trait consistency entry
+- `problemreductions-cli/tests/cli_tests.rs` — CLI integration tests for `pred create`
 
 **Whitelist for [Rule] PRs:**
 - `src/rules/<source>_<target>.rs` — reduction implementation
@@ -151,6 +152,7 @@ Check that the PR only touches files expected for its type. Any file outside the
 - `docs/paper/reductions.typ` — paper entry
 - `docs/src/reductions/reduction_graph.json` — graph export
 - `docs/src/reductions/problem_schemas.json` — only if updating field descriptions
+- `problemreductions-cli/tests/cli_tests.rs` — CLI integration tests if adding CLI support
 
 If any file falls outside these whitelists, flag it:
 
@@ -185,6 +187,13 @@ Verify the PR includes all required components. Check:
 - [ ] Canonical rule example in `src/example_db/rule_builders.rs`
 - [ ] Paper section in `docs/paper/reductions.typ` (`reduction-rule` entry)
 
+**Paper-example consistency check (both Model and Rule PRs):**
+
+The paper example must use data from the generated JSON (`docs/paper/examples/generated/`), not hand-written data. To verify:
+1. Run `make examples` on the PR branch to regenerate `docs/paper/examples/generated/models.json` and `rules.json`.
+2. For **[Rule] PRs**: the paper's `reduction-rule` entry must call `load-example(source, target)` (defined in `reductions.typ`) to load the canonical example from `rules.json`, and derive all concrete values from the loaded data using Typst array operations — no hand-written instance data.
+3. For **[Model] PRs**: read the problem's entry in `models.json` and compare its `instance` field against the paper's `problem-def` example. The paper example must use the same instance (allowing 0-indexed JSON vs 1-indexed math notation). If they differ, flag: "Paper example does not match `example_db` canonical instance in `models.json`."
+
 Report missing items:
 
 > **Completeness Check**

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

@@ -126,17 +126,28 @@ achieves $O^*(2^n)$ @bjorklund2009.
 
 ### 3c. Example with Visualization
 
-A concrete small instance that illustrates the problem. Requirements:
+A concrete small instance that illustrates the problem. **The example must use data from the generated `models.json`**, not an independently invented instance.
+
+#### Sourcing example data
+
+1. Run `make examples` to ensure `docs/paper/examples/generated/models.json` is up to date.
+2. Find the problem's entry in `models.json` — it contains the canonical `instance`, `samples`, and `optimal` fields.
+3. Use the values from `instance` in the paper example (translating 0-indexed code values to 1-indexed math notation where conventional, e.g., vertices {0,...,n-1} → {1,...,n}).
+4. Use `optimal` configurations to show the solution.
+
+**Do not invent a different instance.** If the canonical example is too large or not pedagogically ideal, fix it in `canonical_model_example_specs()` first, re-run `make examples`, then write the paper entry from the updated JSON.
+
+#### Requirements
 
 1. **Small enough to verify by hand** — readers should be able to check the solution
 2. **Include a diagram/graph** using the paper's visualization helpers
 3. **Show a valid/optimal solution** and explain why it is valid/optimal
 4. **Walk through evaluation** — show how the objective/verifier computes the solution value
 
-Structure:
+#### Structure
 
 ```typst
-*Example.* Consider [instance description with concrete numbers].
+*Example.* Consider [instance description with concrete numbers from models.json].
 [Describe the solution and why it's valid/optimal].
 
 #figure({
@@ -174,7 +185,7 @@ make paper
 - [ ] **Notation self-contained**: every symbol in `def` is defined before first use
 - [ ] **Background present**: historical context, applications, or structural properties
 - [ ] **Algorithms cited**: every complexity claim has `@citation` or footnote warning
-- [ ] **Example present**: concrete small instance with visualization
+- [ ] **Example from JSON**: instance data matches `models.json` canonical example (not independently invented)
 - [ ] **Evaluation shown**: objective/verifier computed on the example solution
 - [ ] **Diagram included**: figure with caption and label for graph/matrix/set visualization
 - [ ] **Paper compiles**: `make paper` succeeds without errors