fix: address remaining Copilot review findings

- SKILL.md Phase 7: use core buildFingerprintStore instead of ad-hoc regex script
- change-classifier: accurate FULL_UPDATE reason message (count vs percentage)
- persistence: add saveConfig/loadConfig tests (round-trip, missing, corrupted)

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

understand-anything-plugin/packages/core/src/change-classifier.ts

@@ -43,13 +43,21 @@ export function classifyUpdate(
   }
 
   // Too many structural changes — suggest full rebuild
-  if (structuralCount > 30 || (totalFilesInGraph > 0 && structuralCount / totalFilesInGraph > 0.5)) {
+  const triggeredByCount = structuralCount > 30;
+  const triggeredByPercentage = totalFilesInGraph > 0 && structuralCount / totalFilesInGraph > 0.5;
+  if (triggeredByCount || triggeredByPercentage) {
+    const thresholdReason =
+      triggeredByCount && triggeredByPercentage
+        ? ">30 files and >50% of project"
+        : triggeredByCount
+          ? ">30 files"
+          : ">50% of project";
     return {
       action: "FULL_UPDATE",
       filesToReanalyze: [...structurallyChangedFiles, ...newFiles],
       rerunArchitecture: true,
       rerunTour: true,
-      reason: `${structuralCount} files have structural changes (>${totalFilesInGraph > 0 ? "50% of project" : "30 files"}) — full rebuild recommended`,
+      reason: `${structuralCount} files have structural changes (${thresholdReason}) — full rebuild recommended`,
     };
   }
 

understand-anything-plugin/packages/core/src/persistence/persistence.test.ts

@@ -3,7 +3,7 @@ import { mkdtempSync, rmSync, existsSync } from "node:fs";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 import { writeFileSync } from "node:fs";
-import { saveGraph, loadGraph, saveMeta, loadMeta, saveFingerprints, loadFingerprints } from "./index.js";
+import { saveGraph, loadGraph, saveMeta, loadMeta, saveFingerprints, loadFingerprints, saveConfig, loadConfig } from "./index.js";
 import type { KnowledgeGraph, AnalysisMeta } from "../types.js";
 import type { FingerprintStore } from "../fingerprint.js";
 
@@ -159,4 +159,28 @@ describe("persistence", () => {
       expect(loaded).toBeNull();
     });
   });
+
+  describe("saveConfig / loadConfig", () => {
+    it("should round-trip config correctly", () => {
+      saveConfig(tempDir, { autoUpdate: true });
+      const loaded = loadConfig(tempDir);
+
+      expect(loaded).toEqual({ autoUpdate: true });
+    });
+
+    it("should return default config when no file exists", () => {
+      const loaded = loadConfig(tempDir);
+
+      expect(loaded).toEqual({ autoUpdate: false });
+    });
+
+    it("should return default config when config.json is corrupted", () => {
+      saveConfig(tempDir, { autoUpdate: true });
+      const dir = join(tempDir, ".understand-anything");
+      writeFileSync(join(dir, "config.json"), "not json!!", "utf-8");
+
+      const loaded = loadConfig(tempDir);
+      expect(loaded).toEqual({ autoUpdate: false });
+    });
+  });
 });

understand-anything-plugin/skills/understand/SKILL.md

@@ -482,34 +482,15 @@ Pass these parameters in the dispatch prompt:
 
 2.5. **Generate structural fingerprints** for all analyzed files and save to `$PROJECT_ROOT/.understand-anything/fingerprints.json`. This creates the baseline for future automatic incremental updates.
 
-   Write and execute a Node.js script that:
-   1. Reads each source file path from the scan results (Phase 1)
-   2. For each file: computes a SHA-256 content hash, then extracts function/class/import/export declarations via regex matching:
-      - Functions: `function NAME(`, `const NAME = (`, `export function NAME(`, arrow functions assigned to const/let
-      - Classes: `class NAME`, `export class NAME`
-      - Imports: `import ... from '...'`, `import '...'`
-      - Exports: `export { ... }`, `export default`, `export function`, `export class`, `export const`
-   3. For each function: record name, parameter names, whether exported, and line count
-   4. For each class: record name, method names, property names, whether exported
-   5. Writes the fingerprint store JSON to `$PROJECT_ROOT/.understand-anything/fingerprints.json`:
-      ```json
-      {
-        "version": "1.0.0",
-        "gitCommitHash": "<commit hash>",
-        "generatedAt": "<ISO timestamp>",
-        "files": {
-          "<filePath>": {
-            "filePath": "<filePath>",
-            "contentHash": "<sha256>",
-            "functions": [{ "name": "...", "params": ["..."], "exported": true, "lineCount": 35 }],
-            "classes": [{ "name": "...", "methods": ["..."], "properties": ["..."], "exported": true, "lineCount": 50 }],
-            "imports": [{ "source": "...", "specifiers": ["..."] }],
-            "exports": ["name1", "name2"],
-            "totalLines": 120
-          }
-        }
-      }
-      ```
+   Write and execute a Node.js script that uses the core fingerprint module (tree-sitter-based, not regex):
+   ```javascript
+   import { buildFingerprintStore } from '@understand-anything/core';
+   import { saveFingerprints } from '@understand-anything/core';
+
+   const store = await buildFingerprintStore('<PROJECT_ROOT>', sourceFilePaths);
+   saveFingerprints('<PROJECT_ROOT>', store);
+   ```
+   Where `sourceFilePaths` is the list of all analyzed source file paths from Phase 1. This uses the same tree-sitter analysis pipeline as the main fingerprint engine, ensuring the baseline matches the comparison logic used during auto-updates.
 
 3. Clean up intermediate files:
    ```bash