Add Publisher v2 + 5 extracted skills

Publisher fixes:
- Checkout new branch before push (was pushing main ref)
- Verify files staged before commit
- Handle duplicate files gracefully
- Clean error reporting per stage

Skills merged to main:
- mcp-server-setup (from pipeshub-ai)
- research-pipeline (from Blacknode)
- multi-agent-sequential-workflow (from Fast-LLM-Agent-MCP)
- unifai-workflow-execution (from UnifAI)
- code-review-agent-workflow (from AgentKit)

pipeline/publisher.py

@@ -1,10 +1,10 @@
 """Stage 8: Publisher — Create branch, commit, open PR on Gitea."""
-import json
 import subprocess
 import os
 import tempfile
-import shutil
 import datetime
+import requests
+
 
 def publish_skill(review_result, config):
     """
@@ -33,23 +33,20 @@ def publish_skill(review_result, config):
     branch_name = f"skill/{skill_name}-{ts}"
 
     with tempfile.TemporaryDirectory() as tmpdir:
-        # Clone repo
         repo_dir = os.path.join(tmpdir, "agent-skills")
+
+        # Clone repo
         result = subprocess.run(
-            ["git", "clone", "--branch", "main", "--single-branch", clone_url, repo_dir],
+            ["git", "clone", "--branch", "main", "--depth", "1", clone_url, repo_dir],
             capture_output=True, text=True, timeout=30
         )
         if result.returncode != 0:
-            # Try without --branch (might not exist yet)
             result = subprocess.run(
-                ["git", "clone", clone_url, repo_dir],
+                ["git", "clone", "--depth", "1", clone_url, repo_dir],
                 capture_output=True, text=True, timeout=30
             )
             if result.returncode != 0:
-                return {
-                    "status": "CLONE_ERROR",
-                    "error": result.stderr[:500],
-                }
+                return {"status": "CLONE_ERROR", "error": result.stderr[:500]}
 
         # Configure git
         subprocess.run(["git", "config", "user.email", "hermes@agent.local"], cwd=repo_dir)
@@ -59,34 +56,80 @@ def publish_skill(review_result, config):
         skill_dir = os.path.join(repo_dir, "skills", skill_name)
         os.makedirs(skill_dir, exist_ok=True)
 
-        # Write files
+        # Write skill files
         for filename, content in files.items():
             filepath = os.path.join(skill_dir, filename)
-            with open(filepath, 'w') as f:
+            with open(filepath, "w") as f:
                 f.write(content)
 
-        # Add and commit
-        subprocess.run(["git", "add", "."], cwd=repo_dir, capture_output=True)
-        subprocess.run(
-            ["git", "commit", "-m", f"Add Skill: {skill_name}\n\nExtracted from: {gen.get('metadata', {}).get('source_repo', 'unknown')}\nScore: {gen.get('metadata', {}).get('score', 0)}"],
-            cwd=repo_dir, capture_output=True
+        # Verify files were written
+        written_files = []
+        for root, dirs, fnames in os.walk(skill_dir):
+            for fn in fnames:
+                written_files.append(os.path.join(root, fn))
+
+        if not written_files:
+            return {"status": "EMPTY_SKILL", "reason": "No files written to skill directory"}
+
+        # Stage and commit
+        add_result = subprocess.run(
+            ["git", "add", "skills/"], cwd=repo_dir, capture_output=True, text=True
         )
 
+        # Check if there are actually staged changes
+        status_result = subprocess.run(
+            ["git", "diff", "--cached", "--name-only"],
+            cwd=repo_dir, capture_output=True, text=True
+        )
+        staged_files = status_result.stdout.strip().split("\n") if status_result.stdout.strip() else []
+
+        if not staged_files:
+            # Nothing to commit — files might already exist. Force add.
+            subprocess.run(["git", "add", "-f", "skills/"], cwd=repo_dir, capture_output=True, text=True)
+            status_result = subprocess.run(
+                ["git", "diff", "--cached", "--name-only"],
+                cwd=repo_dir, capture_output=True, text=True
+            )
+            staged_files = status_result.stdout.strip().split("\n") if status_result.stdout.strip() else []
+
+        if not staged_files:
+            return {
+                "status": "NO_CHANGES",
+                "reason": f"No new files to commit for {skill_name}. Files already exist in repo.",
+            }
+
+        commit_result = subprocess.run(
+            [
+                "git", "commit", "-m",
+                f"Add Skill: {skill_name}\n\nExtracted from: {gen.get('metadata', {}).get('source_repo', 'unknown')}\nScore: {gen.get('metadata', {}).get('score', 0)}"
+            ],
+            cwd=repo_dir, capture_output=True, text=True
+        )
+
+        if commit_result.returncode != 0:
+            return {
+                "status": "COMMIT_ERROR",
+                "error": commit_result.stderr[:500],
+            }
+
+        # Checkout new branch
+        checkout_result = subprocess.run(
+            ["git", "checkout", "-b", branch_name],
+            cwd=repo_dir, capture_output=True, text=True
+        )
+        if checkout_result.returncode != 0:
+            return {
+                "status": "CHECKOUT_ERROR",
+                "error": checkout_result.stderr[:500],
+            }
+
         # Push branch
         auth_url = clone_url.replace("http://", f"http://tonyjbala:{token}@")
         push_result = subprocess.run(
-            ["git", "push", "-u", auth_url, f"main:{branch_name}"],
-            capture_output=True, text=True, timeout=30
+            ["git", "push", "-u", auth_url, branch_name],
+            cwd=repo_dir, capture_output=True, text=True, timeout=30
         )
 
-        if push_result.returncode != 0:
-            # Try creating from current branch
-            subprocess.run(["git", "checkout", "-b", branch_name], cwd=repo_dir, capture_output=True)
-            push_result = subprocess.run(
-                ["git", "push", "-u", auth_url, branch_name],
-                capture_output=True, text=True, timeout=30
-            )
-
         if push_result.returncode != 0:
             return {
                 "status": "PUSH_ERROR",
@@ -97,19 +140,19 @@ def publish_skill(review_result, config):
         pr_url = f"{base_url}/api/v1/repos/{owner}/{repo_name}/pulls"
         pr_payload = {
             "title": f"Add Skill: {skill_name}",
-            "body": f"## Skill: {skill_name}\n\n"
-                    f"**Goal:** {gen.get('metadata', {}).get('goal', '')}\n"
-                    f"**Source:** {gen.get('metadata', {}).get('source_repo', '')}\n"
-                    f"**Score:** {gen.get('metadata', {}).get('score', 0)}\n"
-                    f"**Confidence:** {gen.get('metadata', {}).get('confidence', 0)}\n"
-                    f"**Review:** {review_result.get('reason', '')}\n\n"
-                    f"### Files\n"
-                    + "".join(f"- `{f}`\n" for f in files.keys()),
+            "body": (
+                f"## Skill: {skill_name}\n\n"
+                f"**Goal:** {gen.get('metadata', {}).get('goal', '')}\n"
+                f"**Source:** {gen.get('metadata', {}).get('source_repo', '')}\n"
+                f"**Score:** {gen.get('metadata', {}).get('score', 0)}\n"
+                f"**Confidence:** {gen.get('metadata', {}).get('confidence', 0)}\n\n"
+                f"### Files\n"
+                + "".join(f"- `{f}`\n" for f in files.keys())
+            ),
             "head": branch_name,
             "base": "main",
         }
 
-        import requests
         headers = {
             "Authorization": f"token {token}",
             "Content-Type": "application/json",
@@ -127,7 +170,6 @@ def publish_skill(review_result, config):
                 "message": f"PR opened: {pr_data.get('html_url', '')}",
             }
         elif resp.status_code == 409:
-            # PR already exists for this branch
             return {
                 "status": "PUBLISHED",
                 "skill_name": skill_name,