fix(skills/understand): bundle build-fingerprints.mjs and reorder Phase 7

The Phase 7 step 2.5 code example in SKILL.md called
buildFingerprintStore() with 2 arguments, but the real signature
requires 4 (projectDir, filePaths, registry: PluginRegistry,
gitCommitHash: string). It also omitted the required
`await TreeSitterPlugin.init()`. Any LLM following the example
threw TypeError on `registry.analyzeFile()` and never produced a
baseline — which is why fingerprints.json never existed in a usable
form after a fresh /understand, and is the root cause behind
issue #152's "every auto-update escalates to FULL_UPDATE" cascade.

Replace the LLM-written script with a bundled `build-fingerprints.mjs`
that mirrors `extract-structure.mjs`: resolves @understand-anything/core
via createRequire, initializes TreeSitterPlugin + PluginRegistry
correctly, calls buildFingerprintStore with all four arguments, and
persists via saveFingerprints. Smoke-tested on this repo (3 files,
correct functions/classes/imports extracted).

Reorder Phase 7 so fingerprints are written BEFORE meta.json. If
fingerprint generation fails, the new step explicitly says to abort
Phase 7 — meta.json must not advance without a valid baseline, or
the next auto-update sees a fresh commit hash with no fingerprints
and classifies every file as STRUCTURAL.

Affects every install since 2.7.0 (when the broken example was
introduced). Users running /understand --full on 2.7.3+ will get
a usable fingerprints.json on the first try.

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

@@ -682,7 +682,30 @@ Pass these parameters in the dispatch prompt:
 
 1. Write the final knowledge graph to `$PROJECT_ROOT/.understand-anything/knowledge-graph.json`.
 
-2. Write metadata to `$PROJECT_ROOT/.understand-anything/meta.json`:
+2. **Generate structural fingerprints baseline.** This creates the basis for future automatic incremental updates and **must succeed before `meta.json` is written** — otherwise auto-update sees a fresh commit hash with no fingerprints to compare against, classifies every file as STRUCTURAL, and escalates to `FULL_UPDATE` on every subsequent commit (issue #152).
+
+   Write the input file:
+   ```bash
+   cat > $PROJECT_ROOT/.understand-anything/intermediate/fingerprint-input.json <<EOF
+   {
+     "projectRoot": "$PROJECT_ROOT",
+     "sourceFilePaths": [<all source file paths from Phase 1, as JSON array>],
+     "gitCommitHash": "<current commit hash>"
+   }
+   EOF
+   ```
+
+   Then invoke the bundled script (located next to this SKILL.md):
+   ```bash
+   node <SKILL_DIR>/build-fingerprints.mjs \
+     $PROJECT_ROOT/.understand-anything/intermediate/fingerprint-input.json
+   ```
+
+   The script uses `TreeSitterPlugin + PluginRegistry` exactly like `extract-structure.mjs`, so the baseline matches the comparison logic used during auto-updates.
+
+   **If the script exits non-zero or stdout does not include `Fingerprints baseline:`, abort Phase 7 and report the error. Do NOT proceed to step 3 (writing `meta.json`).**
+
+3. Write metadata to `$PROJECT_ROOT/.understand-anything/meta.json` (only after step 2 succeeded):
    ```json
    {
      "lastAnalyzedAt": "<ISO 8601 timestamp>",
@@ -692,25 +715,13 @@ 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 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:
+4. Clean up intermediate files:
    ```bash
    rm -rf $PROJECT_ROOT/.understand-anything/intermediate
    rm -rf $PROJECT_ROOT/.understand-anything/tmp
    ```
 
-4. Report a summary to the user containing:
+5. Report a summary to the user containing:
    - Project name and description
    - Files analyzed / total files (with breakdown by fileCategory: code, config, docs, infra, data, script, markup)
    - Nodes created (broken down by type: file, function, class, config, document, service, table, endpoint, pipeline, schema, resource)
@@ -720,7 +731,7 @@ Pass these parameters in the dispatch prompt:
    - Any warnings from the reviewer
    - Path to the output file: `$PROJECT_ROOT/.understand-anything/knowledge-graph.json`
 
-5. Only automatically launch the dashboard by invoking the `/understand-dashboard` skill if final graph validation passed after normalization/review fixes.
+6. Only automatically launch the dashboard by invoking the `/understand-dashboard` skill if final graph validation passed after normalization/review fixes.
    If final validation did not pass, report that the graph was saved with warnings and dashboard launch was skipped.
 
 ---

understand-anything-plugin/skills/understand/build-fingerprints.mjs

@@ -0,0 +1,90 @@
+#!/usr/bin/env node
+/**
+ * build-fingerprints.mjs
+ *
+ * Builds the structural-fingerprint baseline used by auto-update's
+ * incremental change detection. Runs once per /understand full rebuild
+ * (Phase 7 step 2.5), generating .understand-anything/fingerprints.json.
+ *
+ * Replaces the LLM-written fingerprint script that previously sat in
+ * SKILL.md as a code example — that example had the wrong signature
+ * for buildFingerprintStore() and never successfully produced a baseline,
+ * which silently broke auto-update for every install (see issue #152).
+ *
+ * Usage:
+ *   node build-fingerprints.mjs <input.json>
+ *
+ * Input JSON:
+ *   { projectRoot: string, sourceFilePaths: string[], gitCommitHash: string }
+ *
+ * Writes: <projectRoot>/.understand-anything/fingerprints.json
+ * Exit code: 0 on success (including 0 files analyzed); non-zero on error.
+ */
+
+import { createRequire } from 'node:module';
+import { dirname, resolve } from 'node:path';
+import { fileURLToPath, pathToFileURL } from 'node:url';
+import { readFileSync } from 'node:fs';
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+// skills/understand/ -> plugin root is two dirs up
+const pluginRoot = resolve(__dirname, '../..');
+const require = createRequire(resolve(pluginRoot, 'package.json'));
+
+// ---------------------------------------------------------------------------
+// Resolve @understand-anything/core (matches extract-structure.mjs).
+// pathToFileURL() is required for Windows: dynamic import() of a raw
+// "C:\..." path throws ERR_UNSUPPORTED_ESM_URL_SCHEME.
+// ---------------------------------------------------------------------------
+let core;
+try {
+  core = await import(pathToFileURL(require.resolve('@understand-anything/core')).href);
+} catch {
+  core = await import(pathToFileURL(resolve(pluginRoot, 'packages/core/dist/index.js')).href);
+}
+
+const {
+  TreeSitterPlugin,
+  PluginRegistry,
+  builtinLanguageConfigs,
+  registerAllParsers,
+  buildFingerprintStore,
+  saveFingerprints,
+} = core;
+
+async function main() {
+  const [, , inputPath] = process.argv;
+  if (!inputPath) {
+    process.stderr.write('Usage: node build-fingerprints.mjs <input.json>\n');
+    process.exit(1);
+  }
+
+  const { projectRoot, sourceFilePaths, gitCommitHash } = JSON.parse(
+    readFileSync(inputPath, 'utf-8'),
+  );
+
+  if (!projectRoot || !Array.isArray(sourceFilePaths) || typeof gitCommitHash !== 'string') {
+    throw new Error(
+      'Invalid input: requires { projectRoot: string, sourceFilePaths: string[], gitCommitHash: string }',
+    );
+  }
+
+  // Create tree-sitter plugin with all configs that have WASM grammars,
+  // mirroring extract-structure.mjs so the baseline matches the comparison
+  // logic used during auto-updates.
+  const tsConfigs = builtinLanguageConfigs.filter((c) => c.treeSitter);
+  const tsPlugin = new TreeSitterPlugin(tsConfigs);
+  await tsPlugin.init();
+
+  const registry = new PluginRegistry();
+  registry.register(tsPlugin);
+  registerAllParsers(registry);
+
+  const store = buildFingerprintStore(projectRoot, sourceFilePaths, registry, gitCommitHash);
+  saveFingerprints(projectRoot, store);
+
+  const fileCount = Object.keys(store.files).length;
+  process.stdout.write(`Fingerprints baseline: ${fileCount} files\n`);
+}
+
+await main();