diff --git a/CLAUDE.md b/CLAUDE.md
index 8194dc4..6bc44f2 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -9,7 +9,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 **Current Status:** Scaffolding commands implemented: `create mcp-server`, `create agent`, `create gateway`, `create ui`, `create sandbox`, `create model-car`. Post-scaffolding commands: `generate` (tool, resource, prompt, middleware), `patch` (check, all + type-specific category subcommands — see below), `add` (code-executor, files, vision), `vendor`. Note: `create workflow` exists in code but is not yet working.
 
 The `patch` command is type-aware via `template.type` in `.template-info`:
-- **MCP server** projects expose `patch generators | core | docs | build`.
+- **MCP server** projects expose `patch generators | core | docs | build | claude`.
 - **Agent / workflow** projects expose `patch chart | docs | build | claude`.
 Running an MCP-only subcommand inside an agent project (or vice versa) exits with a clear "available categories" error. `patch check` and `patch all` work for any supported type.
 
diff --git a/src/fips_agents_cli/commands/patch.py b/src/fips_agents_cli/commands/patch.py
index d928f14..86bad7c 100644
--- a/src/fips_agents_cli/commands/patch.py
+++ b/src/fips_agents_cli/commands/patch.py
@@ -149,9 +149,10 @@ def chart(dry_run: bool):
 )
 def claude(dry_run: bool):
     """
-    Update Claude Code slash commands (agent / workflow projects only).
+    Update Claude Code slash commands and rules.
 
     Patches files under .claude/commands/ that ship with the template.
+    For agent / workflow projects also patches .claude/rules/.
     """
     _patch_category("claude", dry_run)
 
diff --git a/src/fips_agents_cli/tools/patching.py b/src/fips_agents_cli/tools/patching.py
index 7c6c8c6..f7fd552 100644
--- a/src/fips_agents_cli/tools/patching.py
+++ b/src/fips_agents_cli/tools/patching.py
@@ -27,9 +27,10 @@
     "core": {
         "description": "Core infrastructure (server, auth, etc)",
         "patterns": [
+            "src/main.py",
             "src/core/server.py",
             "src/core/auth.py",
-            "src/*/__ init__.py",  # Package __init__ files
+            "src/*/__init__.py",  # Package __init__ files
             "conftest.py",
         ],
         "ask_before_patch": True,  # May be customized
@@ -39,8 +40,12 @@
         "patterns": [
             "docs/**/*",
             "*/examples/**/*",  # Examples in any directory
+            "AGENTS.md",
             "CLAUDE.md",
             "ARCHITECTURE.md",
+            "CONTRIBUTING.md",
+            "DEVELOPMENT_PROCESS.md",
+            "OPENSHIFT_DEPLOYMENT.md",
             "TESTING.md",
         ],
         "ask_before_patch": False,  # Usually safe to update
@@ -53,9 +58,19 @@
             "openshift.yaml",
             "deploy.sh",
             "remove_examples.sh",
+            ".dockerignore",
+            ".gitignore",
+            ".gitleaks.toml",
         ],
         "ask_before_patch": True,  # May be customized
     },
+    "claude": {
+        "description": "Claude Code slash commands shipped with the template",
+        "patterns": [
+            ".claude/commands/**/*",
+        ],
+        "ask_before_patch": False,  # Safe to overwrite
+    },
 }
 
 # Files to NEVER patch in MCP server projects (user code)
@@ -105,9 +120,10 @@
         "ask_before_patch": True,  # May be customized
     },
     "claude": {
-        "description": "Claude Code slash commands shipped with the template",
+        "description": "Claude Code slash commands and rules shipped with the template",
         "patterns": [
             ".claude/commands/**/*",
+            ".claude/rules/**/*",
         ],
         "ask_before_patch": False,  # Safe to overwrite
     },
@@ -119,8 +135,14 @@
     "agent.yaml",  # User's agent config
     "chart/values.yaml",  # User's deploy values
     "src/fipsagents/**",  # Vendored — managed by `fips-agents vendor --update`
+    "tools/**",  # User-authored tools (target of `fips-agents add code-executor`)
+    "examples/**",  # User-authored examples (target of `fips-agents add vision`)
+    "prompts/**",  # User-customized agent prompts
+    "rules/**",  # User-customized agent rules
+    "skills/**",  # User-customized agent skills
     "tests/**/*.py",
     ".env*",
+    ".memoryhub.yaml",  # User-customized memory hub config
     "README.md",
     "pyproject.toml",  # User may have added dependencies
 ]
diff --git a/tests/test_patch.py b/tests/test_patch.py
index bd7f786..d268fc1 100644
--- a/tests/test_patch.py
+++ b/tests/test_patch.py
@@ -56,6 +56,83 @@ def test_agent_categories_have_no_framework_language(self):
             assert "framework" not in config["description"].lower()
 
 
+class TestMcpCategoryPatterns:
+    """Patterns for MCP categories must match the files the template ships.
+
+    Regression tests for issue #42: the original `core` patterns had a literal
+    space in `src/*/__ init__.py`, and `claude` was missing entirely.
+    """
+
+    def test_core_init_pattern_has_no_space_typo(self):
+        # `src/*/__init__.py` must NOT have a space — that pattern matched nothing
+        patterns = MCP_FILE_CATEGORIES["core"]["patterns"]
+        assert "src/*/__init__.py" in patterns
+        assert not any(" " in p for p in patterns), patterns
+
+    def test_core_init_pattern_matches_real_init_files(self):
+        # Path.match validates the fix — a real package __init__.py matches now
+        assert Path("src/core/__init__.py").match("src/*/__init__.py")
+        assert Path("src/middleware/__init__.py").match("src/*/__init__.py")
+
+    def test_core_includes_main_entry_point(self):
+        # src/main.py is the MCP server entry point and ships with the template
+        assert "src/main.py" in MCP_FILE_CATEGORIES["core"]["patterns"]
+
+    def test_claude_category_exists_for_mcp(self):
+        # MCP template ships .claude/commands/*.md — must be patchable
+        assert "claude" in MCP_FILE_CATEGORIES
+        patterns = MCP_FILE_CATEGORIES["claude"]["patterns"]
+        assert ".claude/commands/**/*" in patterns
+        assert MCP_FILE_CATEGORIES["claude"]["ask_before_patch"] is False
+
+    def test_docs_includes_recently_added_files(self):
+        # AGENTS.md, CONTRIBUTING.md and friends ship in the MCP template root
+        patterns = MCP_FILE_CATEGORIES["docs"]["patterns"]
+        for expected in [
+            "AGENTS.md",
+            "CONTRIBUTING.md",
+            "DEVELOPMENT_PROCESS.md",
+            "OPENSHIFT_DEPLOYMENT.md",
+        ]:
+            assert expected in patterns, f"{expected} missing from MCP docs patterns"
+
+    def test_build_includes_root_dotfiles(self):
+        patterns = MCP_FILE_CATEGORIES["build"]["patterns"]
+        for expected in [".dockerignore", ".gitignore", ".gitleaks.toml"]:
+            assert expected in patterns, f"{expected} missing from MCP build patterns"
+
+
+class TestAgentCategoryPatterns:
+    """Regression tests for issue #42: agent template gaps."""
+
+    def test_claude_category_includes_rules(self):
+        # Agent template ships .claude/rules/agent-development.md
+        patterns = AGENT_FILE_CATEGORIES["claude"]["patterns"]
+        assert ".claude/commands/**/*" in patterns
+        assert ".claude/rules/**/*" in patterns
+
+
+class TestAgentNeverPatchExtensions:
+    """`add` writes user-customized files into well-known directories.
+    Those paths must be in NEVER_PATCH so a future pattern broadening
+    cannot clobber them.
+    """
+
+    @pytest.mark.parametrize(
+        "expected",
+        [
+            "tools/**",
+            "examples/**",
+            "prompts/**",
+            "rules/**",
+            "skills/**",
+            ".memoryhub.yaml",
+        ],
+    )
+    def test_user_directory_is_never_patched(self, expected):
+        assert expected in AGENT_NEVER_PATCH
+
+
 # ---------------------------------------------------------------------------
 # Unit tests — find_fips_project_root walks up to .template-info
 # ---------------------------------------------------------------------------