fix: preserve snapshot paths and reject malformed skill tracking rows

manifests/context-packs/skill-triggers@1.json

@@ -10,7 +10,7 @@
     "id": "hand-seeded",
     "source": "manual-curation-pending-regeneration"
   },
-  "registryDigest": "7144a76d4b920efacf5a8d678ec6757ea34410834c82f4e226b6a32af6f8c540",
+  "registryDigest": "cb89b3434da17c00988095077f61208ab81c2f0611f0edbd5c90d3672bce7ac1",
   "schemaVersion": 1,
   "triggers": {
     "skill:agent-runtime-gateway-smoke-test": [

scripts/lib/skill-evolution/tracker.js

@@ -103,7 +103,10 @@ function readJsonl(filePath) {
     .reduce((rows, line) => {
       try {
         const record = JSON.parse(line);
-        if (record && typeof record === 'object' && !Array.isArray(record)) {
+        if (record && typeof record === 'object' && !Array.isArray(record)
+          && typeof record.skill_id === 'string' && record.skill_id.trim().length > 0
+          && VALID_OUTCOMES.has(record.outcome)
+          && typeof record.recorded_at === 'string' && !Number.isNaN(Date.parse(record.recorded_at))) {
           rows.push(record);
         }
       } catch {

scripts/lib/skill-evolution/versioning.js

@@ -100,7 +100,14 @@ function listVersions(skillPath) {
       }
 
       const filePath = path.join(versionsDir, fileName);
-      const stats = fs.statSync(filePath);
+      let stats;
+      try {
+        stats = fs.statSync(filePath);
+      } catch (error) {
+        // A dangling link still occupies a path, but is not a readable snapshot.
+        if (error.code === 'ENOENT') return null;
+        throw error;
+      }
       if (!stats.isFile()) {
         return null;
       }
@@ -146,7 +153,10 @@ function readJsonl(filePath) {
     .filter(Boolean)
     .reduce((rows, line) => {
       try {
-        rows.push(JSON.parse(line));
+        const record = JSON.parse(line);
+        if (record && typeof record === 'object' && !Array.isArray(record)) {
+          rows.push(record);
+        }
       } catch {
         // Ignore malformed rows so the log remains append-only and resilient.
       }
@@ -163,12 +173,18 @@ function createVersion(skillPath, options = {}) {
   ensureSkillVersioning(skillPath);
 
   const versions = listVersions(skillPath);
-  const nextVersion = versions.length === 0 ? 1 : versions[versions.length - 1].version + 1;
-  const snapshotPath = path.join(getVersionsDir(skillPath), `v${nextVersion}.md`);
+  const versionsDir = getVersionsDir(skillPath);
+  const occupiedPaths = new Set(fs.readdirSync(versionsDir));
+  let nextVersion = versions.length === 0 ? 1 : versions[versions.length - 1].version + 1;
+  // Listing excludes non-files, but their paths remain user-owned and occupied.
+  while (occupiedPaths.has(`v${nextVersion}.md`)) {
+    nextVersion += 1;
+  }
+  const snapshotPath = path.join(versionsDir, `v${nextVersion}.md`);
   const skillContent = fs.readFileSync(skillFilePath, 'utf8');
   const createdAt = options.timestamp || new Date().toISOString();
 
-  fs.writeFileSync(snapshotPath, skillContent, 'utf8');
+  fs.writeFileSync(snapshotPath, skillContent, { encoding: 'utf8', flag: 'wx' });
   appendEvolutionRecord(skillPath, 'amendments', {
     event: 'snapshot',
     version: nextVersion,

tests/lib/skill-evolution-storage.test.js

@@ -0,0 +1,70 @@
+'use strict';
+
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const os = require('node:os');
+const path = require('node:path');
+const versioning = require('../../scripts/lib/skill-evolution/versioning');
+const health = require('../../scripts/lib/skill-evolution/health');
+
+let passed = 0;
+let failed = 0;
+
+function createFixture() {
+  const root = fs.mkdtempSync(path.join(os.tmpdir(), 'skill-evolution-storage-'));
+  const skillDir = path.join(root, 'skills', 'demo');
+  fs.mkdirSync(skillDir, { recursive: true });
+  fs.writeFileSync(path.join(skillDir, 'SKILL.md'), '# Original\n');
+  return { root, skillDir, versionsDir: versioning.getVersionsDir(skillDir) };
+}
+
+function test(name, fn) {
+  const fixture = createFixture();
+  try {
+    fn(fixture);
+    passed += 1;
+    console.log(`  ✓ ${name}`);
+  } catch (error) {
+    failed += 1;
+    console.error(`  ✗ ${name}: ${error.message}`);
+  } finally {
+    fs.rmSync(fixture.root, { recursive: true, force: true });
+  }
+}
+
+test('snapshot creation preserves occupied directories and links plus earlier snapshots', fixture => {
+  const { root, skillDir, versionsDir } = fixture;
+  versioning.createVersion(skillDir);
+  fs.mkdirSync(path.join(versionsDir, 'v2.md'));
+  fs.writeFileSync(path.join(versionsDir, 'v2.md', 'keep.txt'), 'preserve');
+  if (process.platform !== 'win32') {
+    fs.symlinkSync(path.join(root, 'missing'), path.join(versionsDir, 'v3.md'));
+  }
+  fs.writeFileSync(path.join(skillDir, 'SKILL.md'), '# Updated\n');
+  const snapshot = versioning.createVersion(skillDir);
+  assert.equal(snapshot.version, process.platform === 'win32' ? 3 : 4);
+  assert.equal(fs.readFileSync(snapshot.path, 'utf8'), '# Updated\n');
+  assert.equal(fs.readFileSync(path.join(versionsDir, 'v1.md'), 'utf8'), '# Original\n');
+  assert.equal(fs.readFileSync(path.join(versionsDir, 'v2.md', 'keep.txt'), 'utf8'), 'preserve');
+  assert.equal(versioning.getEvolutionLog(skillDir, 'amendments').at(-1).version, snapshot.version);
+  if (process.platform !== 'win32') {
+    assert.ok(fs.lstatSync(path.join(versionsDir, 'v3.md')).isSymbolicLink());
+    fs.symlinkSync(path.join(versionsDir, 'v1.md'), path.join(versionsDir, 'v5.md'));
+    assert.deepEqual(versioning.listVersions(skillDir).map(entry => entry.version), [1, 4, 5]);
+    assert.equal(versioning.getCurrentVersion(skillDir), 5);
+  }
+});
+
+test('health skips malformed amendment rows while retaining a valid pending proposal', fixture => {
+  const { root, skillDir } = fixture;
+  versioning.ensureSkillVersioning(skillDir);
+  fs.writeFileSync(versioning.getEvolutionLogPath(skillDir, 'amendments'),
+    'null\n[]\n42\n{bad}\n{"event":"proposal","status":"pending"}\n');
+  const report = health.collectSkillHealth({
+    skillsRoot: path.join(root, 'skills'), homeDir: root, now: '2026-03-15T12:00:00.000Z',
+  });
+  assert.equal(report.skills.find(skill => skill.skill_id === 'demo').pending_amendments, 1);
+});
+
+console.log(`Results: Passed: ${passed}, Failed: ${failed}`);
+process.exitCode = failed > 0 ? 1 : 0;

tests/lib/skill-evolution.test.js

@@ -320,7 +320,7 @@ function runTests() {
           duration_ms: 1,
           user_feedback: 'accepted',
           recorded_at: '2026-03-15T11:45:00.000Z',
-        })}\n{bad-json}\nnull\n42\nfalse\n"not a record"\n[]\n`,
+        })}\n{bad-json}\nnull\n42\nfalse\n"not a record"\n[]\n{}\n{"skill_id":42}\n{"skill_id":""}\n{"skill_id":"alpha","outcome":"invalid","recorded_at":"2026-03-15T11:45:00.000Z"}\n{"skill_id":"alpha","outcome":"success","recorded_at":"bad-date"}\n`,
         'utf8'
       );