diff --git a/docs/B1_COMPLETE_SUMMARY.md b/docs/B1_COMPLETE_SUMMARY.md
index 3828ee7..acc3984 100644
--- a/docs/B1_COMPLETE_SUMMARY.md
+++ b/docs/B1_COMPLETE_SUMMARY.md
@@ -143,7 +143,7 @@ The B1 task group adds complete PDF documentation support to Skill Seeker, enabl
 
 ### ✅ B1.7: Add MCP Tool scrape_pdf
 **Commit:** `3fa1046`
-**File:** `mcp/server.py` (updated)
+**File:** `skill_seeker_mcp/server.py` (updated)
 **Documentation:** `docs/PDF_MCP_TOOL.md`
 
 **Deliverables:**
@@ -190,7 +190,7 @@ The B1 task group adds complete PDF documentation support to Skill Seeker, enabl
 |-----------|-------|-------------|
 | `pdf_extractor_poc.py` | 887 | Complete PDF extractor |
 | `pdf_scraper.py` | 486 | Skill builder CLI |
-| `mcp/server.py` | +35 | MCP tool integration |
+| `skill_seeker_mcp/server.py` | +35 | MCP tool integration |
 | **Total** | **1,408** | New code |
 
 ### Documentation Added
@@ -373,7 +373,7 @@ docs/B1_COMPLETE_SUMMARY.md      # This file
 ### Modified Files
 
 ```
-mcp/server.py                    # +35 lines - Added scrape_pdf tool
+skill_seeker_mcp/server.py       # +35 lines - Added scrape_pdf tool
 ```
 
 ### Total Impact
diff --git a/docs/MCP_SETUP.md b/docs/MCP_SETUP.md
index df90894..fd76f13 100644
--- a/docs/MCP_SETUP.md
+++ b/docs/MCP_SETUP.md
@@ -58,7 +58,7 @@ Step-by-step guide to set up the Skill Seeker MCP server with Claude Code.
 cd /path/to/Skill_Seekers
 
 # Install MCP server dependencies
-pip3 install -r mcp/requirements.txt
+pip3 install -r skill_seeker_mcp/requirements.txt
 
 # Install CLI tool dependencies (for scraping)
 pip3 install requests beautifulsoup4
@@ -73,7 +73,7 @@ Successfully installed mcp-0.9.0 requests-2.31.0 beautifulsoup4-4.12.3
 
 ```bash
 # Test MCP server can start
-timeout 3 python3 mcp/server.py || echo "Server OK (timeout expected)"
+timeout 3 python3 skill_seeker_mcp/server.py || echo "Server OK (timeout expected)"
 
 # Should exit cleanly or timeout (both are normal)
 ```
@@ -134,7 +134,7 @@ nano ~/.config/claude-code/mcp.json
     "skill-seeker": {
       "command": "python3",
       "args": [
-        "/Users/username/Projects/Skill_Seekers/mcp/server.py"
+        "/Users/username/Projects/Skill_Seekers/skill_seeker_mcp/server.py"
       ],
       "cwd": "/Users/username/Projects/Skill_Seekers",
       "env": {}
@@ -157,7 +157,7 @@ nano ~/.config/claude-code/mcp.json
     "skill-seeker": {
       "command": "python3",
       "args": [
-        "/Users/username/Projects/Skill_Seekers/mcp/server.py"
+        "/Users/username/Projects/Skill_Seekers/skill_seeker_mcp/server.py"
       ],
       "cwd": "/Users/username/Projects/Skill_Seekers"
     }
@@ -317,7 +317,7 @@ Claude: [Scraping starts...]
 3. **Test server manually:**
    ```bash
    cd /path/to/Skill_Seekers
-   python3 mcp/server.py
+   python3 skill_seeker_mcp/server.py
    # Should start without errors
    ```
 
@@ -333,14 +333,14 @@ Claude: [Scraping starts...]
 
 **Solution:**
 ```bash
-pip3 install -r mcp/requirements.txt
+pip3 install -r skill_seeker_mcp/requirements.txt
 ```
 
 ### Issue: "Permission denied" when running server
 
 **Solution:**
 ```bash
-chmod +x mcp/server.py
+chmod +x skill_seeker_mcp/server.py
 ```
 
 ### Issue: Tools appear but don't work
@@ -399,7 +399,7 @@ chmod +x mcp/server.py
   "mcpServers": {
     "skill-seeker": {
       "command": "python3",
-      "args": ["/path/to/Skill_Seekers/mcp/server.py"],
+      "args": ["/path/to/Skill_Seekers/skill_seeker_mcp/server.py"],
       "cwd": "/path/to/Skill_Seekers",
       "env": {
         "ANTHROPIC_API_KEY": "sk-ant-...",
@@ -419,7 +419,7 @@ If you have multiple Python versions:
   "mcpServers": {
     "skill-seeker": {
       "command": "/usr/local/bin/python3.11",
-      "args": ["/path/to/Skill_Seekers/mcp/server.py"],
+      "args": ["/path/to/Skill_Seekers/skill_seeker_mcp/server.py"],
       "cwd": "/path/to/Skill_Seekers"
     }
   }
@@ -435,7 +435,7 @@ To use a Python virtual environment:
 cd /path/to/Skill_Seekers
 python3 -m venv venv
 source venv/bin/activate
-pip install -r mcp/requirements.txt
+pip install -r skill_seeker_mcp/requirements.txt
 pip install requests beautifulsoup4
 which python3
 # Copy this path for config
@@ -446,7 +446,7 @@ which python3
   "mcpServers": {
     "skill-seeker": {
       "command": "/path/to/Skill_Seekers/venv/bin/python3",
-      "args": ["/path/to/Skill_Seekers/mcp/server.py"],
+      "args": ["/path/to/Skill_Seekers/skill_seeker_mcp/server.py"],
       "cwd": "/path/to/Skill_Seekers"
     }
   }
@@ -464,7 +464,7 @@ Enable verbose logging:
       "command": "python3",
       "args": [
         "-u",
-        "/path/to/Skill_Seekers/mcp/server.py"
+        "/path/to/Skill_Seekers/skill_seeker_mcp/server.py"
       ],
       "cwd": "/path/to/Skill_Seekers",
       "env": {
@@ -487,7 +487,7 @@ Enable verbose logging:
     "skill-seeker": {
       "command": "python3",
       "args": [
-        "/Users/username/Projects/Skill_Seekers/mcp/server.py"
+        "/Users/username/Projects/Skill_Seekers/skill_seeker_mcp/server.py"
       ],
       "cwd": "/Users/username/Projects/Skill_Seekers"
     }
@@ -503,7 +503,7 @@ Enable verbose logging:
     "skill-seeker": {
       "command": "python3",
       "args": [
-        "/Users/username/Projects/Skill_Seekers/mcp/server.py"
+        "/Users/username/Projects/Skill_Seekers/skill_seeker_mcp/server.py"
       ],
       "cwd": "/Users/username/Projects/Skill_Seekers",
       "env": {
@@ -525,7 +525,7 @@ Enable verbose logging:
 cd ~/Projects
 git clone https://github.com/yusufkaraaslan/Skill_Seekers.git
 cd Skill_Seekers
-pip3 install -r mcp/requirements.txt
+pip3 install -r skill_seeker_mcp/requirements.txt
 pip3 install requests beautifulsoup4
 
 # 2. Configure
@@ -536,7 +536,7 @@ cat > ~/.config/claude-code/mcp.json << 'EOF'
     "skill-seeker": {
       "command": "python3",
       "args": [
-        "/Users/username/Projects/Skill_Seekers/mcp/server.py"
+        "/Users/username/Projects/Skill_Seekers/skill_seeker_mcp/server.py"
       ],
       "cwd": "/Users/username/Projects/Skill_Seekers"
     }
@@ -593,7 +593,7 @@ After successful setup:
 
 ```
 SETUP:
-1. Install dependencies: pip3 install -r mcp/requirements.txt
+1. Install dependencies: pip3 install -r skill_seeker_mcp/requirements.txt
 2. Configure: ~/.config/claude-code/mcp.json
 3. Restart Claude Code
 
@@ -609,7 +609,7 @@ GENERATE SKILL:
 
 TROUBLESHOOTING:
 - Check: cat ~/.config/claude-code/mcp.json
-- Test: python3 mcp/server.py
+- Test: python3 skill_seeker_mcp/server.py
 - Logs: ~/Library/Logs/Claude Code/
 ```
 
diff --git a/docs/PDF_MCP_TOOL.md b/docs/PDF_MCP_TOOL.md
index d349aef..cf9d847 100644
--- a/docs/PDF_MCP_TOOL.md
+++ b/docs/PDF_MCP_TOOL.md
@@ -165,7 +165,7 @@ Returns `TextContent` with:
 
 ### MCP Server Changes
 
-**Location:** `mcp/server.py`
+**Location:** `skill_seeker_mcp/server.py`
 
 **Changes:**
 1. Added `scrape_pdf` to `list_tools()` (lines 220-249)
@@ -304,7 +304,7 @@ Error: json.decoder.JSONDecodeError: Expecting value: line 1 column 1
 
 ```bash
 # 1. Start MCP server
-python3 mcp/server.py
+python3 skill_seeker_mcp/server.py
 
 # 2. Test with MCP client or via Claude Code
 
diff --git a/docs/TEST_MCP_IN_CLAUDE_CODE.md b/docs/TEST_MCP_IN_CLAUDE_CODE.md
index 1cf007e..d8415a2 100644
--- a/docs/TEST_MCP_IN_CLAUDE_CODE.md
+++ b/docs/TEST_MCP_IN_CLAUDE_CODE.md
@@ -45,7 +45,7 @@ Add this configuration (replace `/path/to/` with your actual path):
     "skill-seeker": {
       "command": "python3",
       "args": [
-        "/mnt/1ece809a-2821-4f10-aecb-fcdf34760c0b/Git/Skill_Seekers/mcp/server.py"
+        "/mnt/1ece809a-2821-4f10-aecb-fcdf34760c0b/Git/Skill_Seekers/skill_seeker_mcp/server.py"
       ],
       "cwd": "/mnt/1ece809a-2821-4f10-aecb-fcdf34760c0b/Git/Skill_Seekers"
     }
@@ -245,7 +245,7 @@ Expected result: `output/svelte.zip` ready to upload to Claude!
 2. Verify server can start:
    ```bash
    cd /path/to/Skill_Seekers
-   python3 mcp/server.py
+   python3 skill_seeker_mcp/server.py
    # Should start without errors (Ctrl+C to exit)
    ```
 
@@ -264,13 +264,13 @@ Expected result: `output/svelte.zip` ready to upload to Claude!
 ### Issue: "Permission Denied"
 
 ```bash
-chmod +x mcp/server.py
+chmod +x skill_seeker_mcp/server.py
 ```
 
 ### Issue: "Module Not Found"
 
 ```bash
-pip3 install -r mcp/requirements.txt
+pip3 install -r skill_seeker_mcp/requirements.txt
 pip3 install requests beautifulsoup4
 ```
 
diff --git a/tests/test_setup_scripts.py b/tests/test_setup_scripts.py
new file mode 100644
index 0000000..80c9207
--- /dev/null
+++ b/tests/test_setup_scripts.py
@@ -0,0 +1,221 @@
+#!/usr/bin/env python3
+"""
+Test setup scripts for correctness and path validation.
+
+Tests that bash scripts reference correct paths and are syntactically valid.
+"""
+
+import subprocess
+import re
+from pathlib import Path
+import pytest
+
+
+class TestSetupMCPScript:
+    """Test setup_mcp.sh for path correctness and syntax"""
+
+    @pytest.fixture
+    def script_path(self):
+        """Get path to setup_mcp.sh"""
+        return Path("setup_mcp.sh")
+
+    @pytest.fixture
+    def script_content(self, script_path):
+        """Read setup_mcp.sh content"""
+        with open(script_path, 'r') as f:
+            return f.read()
+
+    def test_setup_mcp_exists(self, script_path):
+        """Test that setup_mcp.sh exists"""
+        assert script_path.exists(), "setup_mcp.sh should exist"
+        assert script_path.is_file(), "setup_mcp.sh should be a file"
+
+    def test_bash_syntax_valid(self, script_path):
+        """Test that setup_mcp.sh has valid bash syntax"""
+        result = subprocess.run(
+            ["bash", "-n", str(script_path)],
+            capture_output=True,
+            text=True
+        )
+        assert result.returncode == 0, f"Bash syntax error: {result.stderr}"
+
+    def test_references_correct_mcp_directory(self, script_content):
+        """Test that script references skill_seeker_mcp/ not old mcp/ directory"""
+        # Should NOT reference old mcp/ directory
+        old_refs = re.findall(r'(?:^|[^a-z_])mcp/(?!\.json)', script_content, re.MULTILINE)
+        assert len(old_refs) == 0, f"Found {len(old_refs)} references to old 'mcp/' directory: {old_refs}"
+
+        # SHOULD reference skill_seeker_mcp/
+        new_refs = re.findall(r'skill_seeker_mcp/', script_content)
+        assert len(new_refs) >= 6, f"Expected at least 6 references to 'skill_seeker_mcp/', found {len(new_refs)}"
+
+    def test_requirements_txt_path(self, script_content):
+        """Test that requirements.txt path is correct"""
+        assert "skill_seeker_mcp/requirements.txt" in script_content, \
+            "Should reference skill_seeker_mcp/requirements.txt"
+        # Check for old mcp/ directory (but not skill_seeker_mcp/)
+        import re
+        old_refs = re.findall(r'(?<!skill_seeker_)mcp/requirements\.txt', script_content)
+        assert len(old_refs) == 0, \
+            f"Should NOT reference old 'mcp/requirements.txt' (found {len(old_refs)}): {old_refs}"
+
+    def test_server_py_path(self, script_content):
+        """Test that server.py path is correct"""
+        import re
+        assert "skill_seeker_mcp/server.py" in script_content, \
+            "Should reference skill_seeker_mcp/server.py"
+        # Check for old mcp/ directory (but not skill_seeker_mcp/)
+        old_refs = re.findall(r'(?<!skill_seeker_)mcp/server\.py', script_content)
+        assert len(old_refs) == 0, \
+            f"Should NOT reference old 'mcp/server.py' (found {len(old_refs)}): {old_refs}"
+
+    def test_referenced_files_exist(self):
+        """Test that all files referenced in setup_mcp.sh actually exist"""
+        # Check critical paths
+        assert Path("skill_seeker_mcp/requirements.txt").exists(), \
+            "skill_seeker_mcp/requirements.txt should exist"
+        assert Path("skill_seeker_mcp/server.py").exists(), \
+            "skill_seeker_mcp/server.py should exist"
+
+    def test_config_directory_exists(self):
+        """Test that referenced config directory exists"""
+        assert Path("configs/").exists(), "configs/ directory should exist"
+        assert Path("configs/").is_dir(), "configs/ should be a directory"
+
+    def test_script_is_executable(self, script_path):
+        """Test that setup_mcp.sh is executable"""
+        import os
+        assert os.access(script_path, os.X_OK), "setup_mcp.sh should be executable"
+
+    def test_json_config_path_format(self, script_content):
+        """Test that JSON config examples use correct format"""
+        # Check for the config path format in the script
+        assert '"$REPO_PATH/skill_seeker_mcp/server.py"' in script_content, \
+            "Config should show correct server.py path with $REPO_PATH variable"
+
+    def test_no_hardcoded_paths(self, script_content):
+        """Test that script doesn't contain hardcoded absolute paths"""
+        # Check for suspicious absolute paths (but allow $REPO_PATH and ~/.config)
+        hardcoded_paths = re.findall(r'(?<![$~])/mnt/[^\s"\']+', script_content)
+        assert len(hardcoded_paths) == 0, f"Found hardcoded absolute paths: {hardcoded_paths}"
+
+    def test_pytest_command_references(self, script_content):
+        """Test that pytest commands reference correct test files"""
+        # Check for test file references
+        if "pytest" in script_content:
+            assert "tests/test_mcp_server.py" in script_content, \
+                "Should reference correct test file path"
+
+
+class TestBashScriptGeneral:
+    """General tests for all bash scripts in repository"""
+
+    @pytest.fixture
+    def all_bash_scripts(self):
+        """Find all bash scripts in repository root"""
+        root = Path(".")
+        return list(root.glob("*.sh"))
+
+    def test_all_scripts_have_shebang(self, all_bash_scripts):
+        """Test that all bash scripts have proper shebang"""
+        for script in all_bash_scripts:
+            with open(script, 'r') as f:
+                first_line = f.readline()
+            assert first_line.startswith("#!"), f"{script} should have shebang"
+            assert "bash" in first_line.lower(), f"{script} should use bash"
+
+    def test_all_scripts_syntax_valid(self, all_bash_scripts):
+        """Test that all bash scripts have valid syntax"""
+        for script in all_bash_scripts:
+            result = subprocess.run(
+                ["bash", "-n", str(script)],
+                capture_output=True,
+                text=True
+            )
+            assert result.returncode == 0, \
+                f"{script} has syntax error: {result.stderr}"
+
+    def test_all_scripts_use_set_e(self, all_bash_scripts):
+        """Test that scripts use 'set -e' for error handling"""
+        for script in all_bash_scripts:
+            with open(script, 'r') as f:
+                content = f.read()
+            # Check for set -e or set -o errexit
+            has_error_handling = (
+                re.search(r'set\s+-[a-z]*e', content) or
+                re.search(r'set\s+-o\s+errexit', content)
+            )
+            assert has_error_handling, \
+                f"{script} should use 'set -e' for error handling"
+
+    def test_no_deprecated_backticks(self, all_bash_scripts):
+        """Test that scripts use $() instead of deprecated backticks"""
+        for script in all_bash_scripts:
+            with open(script, 'r') as f:
+                content = f.read()
+            # Allow backticks in comments
+            lines = [line for line in content.split('\n') if not line.strip().startswith('#')]
+            code_content = '\n'.join(lines)
+            backticks = re.findall(r'`[^`]+`', code_content)
+            assert len(backticks) == 0, \
+                f"{script} uses deprecated backticks: {backticks}. Use $() instead"
+
+
+class TestMCPServerPaths:
+    """Test that MCP server references are consistent across codebase"""
+
+    def test_github_workflows_reference_correct_paths(self):
+        """Test that GitHub workflows reference correct MCP paths"""
+        workflow_file = Path(".github/workflows/tests.yml")
+        if workflow_file.exists():
+            with open(workflow_file, 'r') as f:
+                content = f.read()
+            # Should NOT reference old mcp/ directory
+            assert "mcp/requirements.txt" not in content or "skill_seeker_mcp/requirements.txt" in content, \
+                "GitHub workflow should use correct MCP paths"
+
+    def test_readme_references_correct_paths(self):
+        """Test that README references correct MCP paths"""
+        readme = Path("README.md")
+        if readme.exists():
+            with open(readme, 'r') as f:
+                content = f.read()
+            # Check for old mcp/ directory paths (but allow mcp.json and "mcp" package name)
+            # Use negative lookbehind to exclude skill_seeker_mcp/
+            old_mcp_refs = re.findall(r'(?<!skill_seeker_)mcp/(server\.py|requirements\.txt)', content)
+            if len(old_mcp_refs) > 0:
+                pytest.fail(f"README references old mcp/ directory: {old_mcp_refs}")
+
+    def test_documentation_references_correct_paths(self):
+        """Test that documentation files reference correct MCP paths"""
+        doc_files = list(Path("docs/").glob("*.md")) if Path("docs/").exists() else []
+        for doc_file in doc_files:
+            with open(doc_file, 'r') as f:
+                content = f.read()
+            # Check for old mcp/ directory paths (but allow mcp.json and "mcp" package name)
+            old_mcp_refs = re.findall(r'(?<!skill_seeker_)mcp/(server\.py|requirements\.txt)', content)
+            if len(old_mcp_refs) > 0:
+                pytest.fail(f"{doc_file} references old mcp/ directory: {old_mcp_refs}")
+
+
+def test_mcp_directory_structure():
+    """Test that MCP directory structure is correct"""
+    mcp_dir = Path("skill_seeker_mcp")
+    assert mcp_dir.exists(), "skill_seeker_mcp/ directory should exist"
+    assert mcp_dir.is_dir(), "skill_seeker_mcp should be a directory"
+    assert (mcp_dir / "server.py").exists(), "skill_seeker_mcp/server.py should exist"
+    assert (mcp_dir / "requirements.txt").exists(), "skill_seeker_mcp/requirements.txt should exist"
+
+    # Old directory should NOT exist
+    old_mcp = Path("mcp")
+    if old_mcp.exists():
+        # If it exists, it should not contain server.py (might be leftover empty dir)
+        assert not (old_mcp / "server.py").exists(), \
+            "Old mcp/server.py should not exist - directory was renamed to skill_seeker_mcp/"
+
+
+if __name__ == '__main__':
+    print("=" * 60)
+    print("Testing Setup Scripts")
+    print("=" * 60)
+    pytest.main([__file__, "-v"])