fix: resolve CI failures on main — lint, hooks validator, and test alignment

- Fix MD012 trailing blank lines in commands/projects.md and commands/promote.md
- Fix MD050 strong-style in continuous-learning-v2 (escape __tests__ as inline code)
- Extract doc-file-warning hook to standalone script to fix hooks validator regex parsing
- Update session-end test to match #317 behavior (always update summary content)
- Allow shell script hooks in integration test format validation

All 992 tests passing.

commands/projects.md

@@ -37,4 +37,3 @@ python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py projects
    - Observation event count
    - Last seen timestamp
 3. Also display global instinct totals
-

commands/promote.md

@@ -39,4 +39,3 @@ python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py promote
    - Appear in at least 2 projects
    - Meet confidence threshold
 4. Write promoted instincts to `~/.claude/homunculus/instincts/personal/` with `scope: global`
-

hooks/hooks.json

@@ -37,7 +37,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "node -e \"let d='';process.stdin.on('data',c=>d+=c);process.stdin.on('end',()=>{try{const i=JSON.parse(d);const p=i.tool_input?.file_path||'';if(/\\.(md|txt)$/.test(p)&&!/(README|CLAUDE|AGENTS|CONTRIBUTING|CHANGELOG|LICENSE|SKILL)\\.md$/i.test(p)&&!/\\.claude[\\/\\\\]plans[\\/\\\\]/.test(p)&&!/(^|[\\/\\\\])(docs|skills)[\\/\\\\]/.test(p)){console.error('[Hook] WARNING: Non-standard documentation file detected');console.error('[Hook] File: '+p);console.error('[Hook] Consider consolidating into README.md or docs/ directory')}}catch{}console.log(d)})\""
+            "command": "node \"${CLAUDE_PLUGIN_ROOT}/scripts/hooks/doc-file-warning.js\""
           }
         ],
         "description": "Doc file warning: warn about non-standard documentation files (exit code 0; warns only)"

scripts/hooks/doc-file-warning.js

@@ -0,0 +1,24 @@
+/**
+ * Doc file warning hook (PreToolUse - Write)
+ * Warns about non-standard documentation files.
+ * Exit code 0 always (warns only, never blocks).
+ */
+
+let data = '';
+process.stdin.on('data', c => data += c);
+process.stdin.on('end', () => {
+  try {
+    const input = JSON.parse(data);
+    const filePath = input.tool_input?.file_path || '';
+
+    if (/\.(md|txt)$/.test(filePath) &&
+        !/(README|CLAUDE|AGENTS|CONTRIBUTING|CHANGELOG|LICENSE|SKILL)\.md$/i.test(filePath) &&
+        !/\.claude[\/\\]plans[\/\\]/.test(filePath) &&
+        !/(^|[\/\\])(docs|skills)[\/\\]/.test(filePath)) {
+      console.error('[Hook] WARNING: Non-standard documentation file detected');
+      console.error('[Hook] File: ' + filePath);
+      console.error('[Hook] Consider consolidating into README.md or docs/ directory');
+    }
+  } catch { /* ignore parse errors */ }
+  console.log(data);
+});

skills/continuous-learning-v2/SKILL.md

@@ -276,7 +276,7 @@ Other behavior (observation capture, instinct thresholds, project scoping, promo
 | Pattern Type | Scope | Examples |
 |-------------|-------|---------|
 | Language/framework conventions | **project** | "Use React hooks", "Follow Django REST patterns" |
-| File structure preferences | **project** | "Tests in __tests__/", "Components in src/components/" |
+| File structure preferences | **project** | "Tests in `__tests__`/", "Components in src/components/" |
 | Code style | **project** | "Use functional style", "Prefer dataclasses" |
 | Error handling strategies | **project** | "Use Result type for errors" |
 | Security practices | **global** | "Validate user input", "Sanitize SQL" |

skills/continuous-learning-v2/agents/observer.md

@@ -124,7 +124,7 @@ When creating instincts, determine scope based on these heuristics:
 | Pattern Type | Scope | Examples |
 |-------------|-------|---------|
 | Language/framework conventions | **project** | "Use React hooks", "Follow Django REST patterns" |
-| File structure preferences | **project** | "Tests in __tests__/", "Components in src/components/" |
+| File structure preferences | **project** | "Tests in `__tests__`/", "Components in src/components/" |
 | Code style | **project** | "Use functional style", "Prefer dataclasses" |
 | Error handling strategies | **project** (usually) | "Use Result type for errors" |
 | Security practices | **global** | "Validate user input", "Sanitize SQL" |

tests/hooks/hooks.test.js

@@ -1724,7 +1724,7 @@ async function runTests() {
     assert.ok(updated.includes('/src/auth.ts'), 'Should include modified file');
   })) passed++; else failed++;
 
-  if (await asyncTest('preserves existing session content when no blank template marker', async () => {
+  if (await asyncTest('always updates session summary content on session end', async () => {
     const testDir = createTestDir();
     const sessionsDir = path.join(testDir, '.claude', 'sessions');
     fs.mkdirSync(sessionsDir, { recursive: true });
@@ -1734,7 +1734,7 @@ async function runTests() {
 
     const shortId = 'update03';
     const sessionFile = path.join(sessionsDir, `${today}-${shortId}-session.tmp`);
-    // Pre-existing file with ALREADY-FILLED summary (no blank template marker)
+    // Pre-existing file with already-filled summary
     const existingContent = `# Session: ${today}\n**Date:** ${today}\n**Started:** 08:00\n**Last Updated:** 08:30\n\n---\n\n## Session Summary\n\n### Tasks\n- Previous task from earlier\n`;
     fs.writeFileSync(sessionFile, existingContent);
 
@@ -1749,9 +1749,9 @@ async function runTests() {
     assert.strictEqual(result.code, 0);
 
     const updated = fs.readFileSync(sessionFile, 'utf8');
-    // Should NOT overwrite existing summary (no blank template marker found)
-    assert.ok(updated.includes('Previous task from earlier'), 'Should preserve existing content');
-    assert.ok(!updated.includes('New task'), 'Should not replace non-template content');
+    // Session summary should always be refreshed with current content (#317)
+    assert.ok(updated.includes('## Session Summary'), 'Should have Session Summary section');
+    assert.ok(updated.includes('# Session:'), 'Should preserve session header');
   })) passed++; else failed++;
 
   console.log('\nRound 23: pre-compact.js (glob specificity):');

tests/integration/hooks.test.js

@@ -692,10 +692,11 @@ async function runTests() {
 
           const isInline = hook.command.startsWith('node -e');
           const isFilePath = hook.command.startsWith('node "');
+          const isShellScript = hook.command.endsWith('.sh');
 
           assert.ok(
-            isInline || isFilePath,
-            `Hook command in ${hookType} should be inline (node -e) or file path (node "), got: ${hook.command.substring(0, 50)}`
+            isInline || isFilePath || isShellScript,
+            `Hook command in ${hookType} should be inline (node -e), file path (node "), or shell script (.sh), got: ${hook.command.substring(0, 80)}`
           );
         }
       }