feat: enhancement workflow preset system with multi-target CLI

- Add YAML-based enhancement workflow presets shipped inside the package
  (default, minimal, security-focus, architecture-comprehensive, api-documentation)
- Add `skill-seekers workflows` subcommand: list, show, copy, add, remove, validate
- copy/add/remove all accept multiple names/files in one invocation with partial-failure behaviour
- `add --name` override restricted to single-file operations
- Add 5 MCP tools: list_workflows, get_workflow, create_workflow, update_workflow, delete_workflow
- Fix: create command _add_common_args() now correctly forwards each --enhance-workflow
  as a separate flag instead of passing the whole list as a single argument
- Update README: reposition as "data layer for AI systems" with AI Skills front and centre
- Update CHANGELOG, QUICK_REFERENCE, CLAUDE.md with workflow preset details
- 1,880+ tests passing

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

src/skill_seekers/mcp/server_fastmcp.py

@@ -103,6 +103,12 @@ try:
         submit_config_impl,
         upload_skill_impl,
         validate_config_impl,
+        # Workflow tools
+        list_workflows_impl,
+        get_workflow_impl,
+        create_workflow_impl,
+        update_workflow_impl,
+        delete_workflow_impl,
     )
 except ImportError:
     # Fallback for direct script execution
@@ -137,6 +143,11 @@ except ImportError:
         submit_config_impl,
         upload_skill_impl,
         validate_config_impl,
+        list_workflows_impl,
+        get_workflow_impl,
+        create_workflow_impl,
+        update_workflow_impl,
+        delete_workflow_impl,
     )
 
 # Initialize FastMCP server
@@ -1178,6 +1189,100 @@ async def export_to_qdrant(
     return str(result)
 
 
+# ============================================================================
+# WORKFLOW TOOLS (5 tools)
+# ============================================================================
+
+
+@safe_tool_decorator(
+    description="List all available enhancement workflows (bundled defaults + user-created). Returns name, description, and source (bundled/user) for each."
+)
+async def list_workflows() -> str:
+    """List all available enhancement workflow presets."""
+    result = list_workflows_impl({})
+    if isinstance(result, list) and result:
+        return result[0].text if hasattr(result[0], "text") else str(result[0])
+    return str(result)
+
+
+@safe_tool_decorator(
+    description="Get the full YAML content of a named enhancement workflow. Searches user dir first, then bundled defaults."
+)
+async def get_workflow(name: str) -> str:
+    """
+    Get full YAML content of a workflow.
+
+    Args:
+        name: Workflow name (e.g. 'security-focus', 'default')
+
+    Returns:
+        YAML content of the workflow, or error message if not found.
+    """
+    result = get_workflow_impl({"name": name})
+    if isinstance(result, list) and result:
+        return result[0].text if hasattr(result[0], "text") else str(result[0])
+    return str(result)
+
+
+@safe_tool_decorator(
+    description="Create a new user workflow from YAML content. The workflow is saved to ~/.config/skill-seekers/workflows/."
+)
+async def create_workflow(name: str, content: str) -> str:
+    """
+    Create a new user workflow.
+
+    Args:
+        name: Workflow name (becomes the filename stem, e.g. 'my-custom')
+        content: Full YAML content of the workflow
+
+    Returns:
+        Success message with file path, or error message.
+    """
+    result = create_workflow_impl({"name": name, "content": content})
+    if isinstance(result, list) and result:
+        return result[0].text if hasattr(result[0], "text") else str(result[0])
+    return str(result)
+
+
+@safe_tool_decorator(
+    description="Update (overwrite) an existing user workflow. Cannot update bundled workflows."
+)
+async def update_workflow(name: str, content: str) -> str:
+    """
+    Update an existing user workflow.
+
+    Args:
+        name: Workflow name to update
+        content: New YAML content
+
+    Returns:
+        Success message, or error if workflow is bundled or invalid.
+    """
+    result = update_workflow_impl({"name": name, "content": content})
+    if isinstance(result, list) and result:
+        return result[0].text if hasattr(result[0], "text") else str(result[0])
+    return str(result)
+
+
+@safe_tool_decorator(
+    description="Delete a user workflow by name. Bundled workflows cannot be deleted."
+)
+async def delete_workflow(name: str) -> str:
+    """
+    Delete a user workflow.
+
+    Args:
+        name: Workflow name to delete
+
+    Returns:
+        Success message, or error if workflow is bundled or not found.
+    """
+    result = delete_workflow_impl({"name": name})
+    if isinstance(result, list) and result:
+        return result[0].text if hasattr(result[0], "text") else str(result[0])
+    return str(result)
+
+
 # ============================================================================
 # MAIN ENTRY POINT
 # ============================================================================

src/skill_seekers/mcp/tools/__init__.py

@@ -96,6 +96,21 @@ from .vector_db_tools import (
 from .vector_db_tools import (
     export_to_weaviate_impl,
 )
+from .workflow_tools import (
+    create_workflow_tool as create_workflow_impl,
+)
+from .workflow_tools import (
+    delete_workflow_tool as delete_workflow_impl,
+)
+from .workflow_tools import (
+    get_workflow_tool as get_workflow_impl,
+)
+from .workflow_tools import (
+    list_workflows_tool as list_workflows_impl,
+)
+from .workflow_tools import (
+    update_workflow_tool as update_workflow_impl,
+)
 
 __all__ = [
     "__version__",
@@ -132,4 +147,10 @@ __all__ = [
     "export_to_chroma_impl",
     "export_to_faiss_impl",
     "export_to_qdrant_impl",
+    # Workflow tools
+    "list_workflows_impl",
+    "get_workflow_impl",
+    "create_workflow_impl",
+    "update_workflow_impl",
+    "delete_workflow_impl",
 ]

src/skill_seekers/mcp/tools/workflow_tools.py

@@ -0,0 +1,226 @@
+"""
+MCP Tool Implementations for Workflow Management
+
+5 tools:
+  list_workflows   – list all workflows (bundled + user) with source info
+  get_workflow     – return full YAML of a named workflow
+  create_workflow  – write a new YAML to user dir
+  update_workflow  – overwrite an existing user workflow
+  delete_workflow  – remove a user workflow by name
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import yaml
+
+try:
+    from mcp.types import TextContent
+except ImportError:
+    # Graceful degradation for testing without mcp installed
+    class TextContent:  # type: ignore[no-redef]
+        def __init__(self, type: str, text: str):
+            self.type = type
+            self.text = text
+
+USER_WORKFLOWS_DIR = Path.home() / ".config" / "skill-seekers" / "workflows"
+
+
+def _ensure_user_dir() -> Path:
+    USER_WORKFLOWS_DIR.mkdir(parents=True, exist_ok=True)
+    return USER_WORKFLOWS_DIR
+
+
+def _bundled_names() -> list[str]:
+    from importlib.resources import files as importlib_files
+
+    try:
+        pkg = importlib_files("skill_seekers.workflows")
+        names = []
+        for item in pkg.iterdir():
+            name = str(item.name)
+            if name.endswith((".yaml", ".yml")):
+                names.append(name.removesuffix(".yaml").removesuffix(".yml"))
+        return sorted(names)
+    except Exception:
+        return []
+
+
+def _user_names() -> list[str]:
+    if not USER_WORKFLOWS_DIR.exists():
+        return []
+    return sorted(
+        p.stem for p in USER_WORKFLOWS_DIR.iterdir() if p.suffix in (".yaml", ".yml")
+    )
+
+
+def _read_bundled(name: str) -> str | None:
+    from importlib.resources import files as importlib_files
+
+    for suffix in (".yaml", ".yml"):
+        try:
+            pkg_ref = importlib_files("skill_seekers.workflows").joinpath(name + suffix)
+            return pkg_ref.read_text(encoding="utf-8")
+        except (FileNotFoundError, TypeError, ModuleNotFoundError):
+            continue
+    return None
+
+
+def _read_workflow(name: str) -> str | None:
+    """Read YAML text: user dir first, then bundled."""
+    for suffix in (".yaml", ".yml"):
+        p = USER_WORKFLOWS_DIR / (name + suffix)
+        if p.exists():
+            return p.read_text(encoding="utf-8")
+    return _read_bundled(name)
+
+
+def _validate_yaml(text: str) -> dict:
+    """Parse and basic-validate workflow YAML; returns parsed dict."""
+    data = yaml.safe_load(text)
+    if not isinstance(data, dict):
+        raise ValueError("Workflow YAML root must be a mapping")
+    if "stages" not in data:
+        raise ValueError("Workflow must contain a 'stages' key")
+    return data
+
+
+# ──────────────────────────────────────────────────────────────────────────────
+# Tool implementations
+# ──────────────────────────────────────────────────────────────────────────────
+
+
+def list_workflows_tool(args: dict) -> list:
+    """Return all workflows with name, description, and source."""
+    result: list[dict[str, str]] = []
+
+    for name in _bundled_names():
+        desc = ""
+        text = _read_bundled(name)
+        if text:
+            try:
+                data = yaml.safe_load(text)
+                desc = data.get("description", "")
+            except Exception:
+                pass
+        result.append({"name": name, "description": desc, "source": "bundled"})
+
+    for name in _user_names():
+        desc = ""
+        text = _read_workflow(name)
+        if text:
+            try:
+                data = yaml.safe_load(text)
+                desc = data.get("description", "")
+            except Exception:
+                pass
+        result.append({"name": name, "description": desc, "source": "user"})
+
+    output = yaml.dump(result, default_flow_style=False, sort_keys=False)
+    return [TextContent(type="text", text=output)]
+
+
+def get_workflow_tool(args: dict) -> list:
+    """Return full YAML content of a named workflow."""
+    name = args.get("name", "").strip()
+    if not name:
+        return [TextContent(type="text", text="Error: 'name' parameter is required.")]
+
+    text = _read_workflow(name)
+    if text is None:
+        bundled = _bundled_names()
+        user = _user_names()
+        available = bundled + [f"{n} (user)" for n in user]
+        msg = (
+            f"Error: Workflow '{name}' not found.\n"
+            f"Available workflows: {', '.join(available) if available else 'none'}"
+        )
+        return [TextContent(type="text", text=msg)]
+
+    return [TextContent(type="text", text=text)]
+
+
+def create_workflow_tool(args: dict) -> list:
+    """Write a new workflow YAML to the user directory."""
+    name = args.get("name", "").strip()
+    content = args.get("content", "")
+
+    if not name:
+        return [TextContent(type="text", text="Error: 'name' parameter is required.")]
+    if not content:
+        return [TextContent(type="text", text="Error: 'content' parameter is required.")]
+
+    # Validate
+    try:
+        _validate_yaml(content)
+    except Exception as exc:
+        return [TextContent(type="text", text=f"Error: Invalid workflow YAML – {exc}")]
+
+    dest = _ensure_user_dir() / (name + ".yaml")
+    if dest.exists():
+        return [
+            TextContent(
+                type="text",
+                text=f"Error: Workflow '{name}' already exists in user dir. Use update_workflow to overwrite.",
+            )
+        ]
+
+    dest.write_text(content, encoding="utf-8")
+    return [TextContent(type="text", text=f"Created workflow '{name}' at: {dest}")]
+
+
+def update_workflow_tool(args: dict) -> list:
+    """Overwrite an existing user workflow. Cannot update bundled workflows."""
+    name = args.get("name", "").strip()
+    content = args.get("content", "")
+
+    if not name:
+        return [TextContent(type="text", text="Error: 'name' parameter is required.")]
+    if not content:
+        return [TextContent(type="text", text="Error: 'content' parameter is required.")]
+
+    if name in _bundled_names() and name not in _user_names():
+        return [
+            TextContent(
+                type="text",
+                text=(
+                    f"Error: '{name}' is a bundled workflow and cannot be updated. "
+                    "Use create_workflow with a different name, or copy it first with "
+                    "'skill-seekers workflows copy'."
+                ),
+            )
+        ]
+
+    # Validate
+    try:
+        _validate_yaml(content)
+    except Exception as exc:
+        return [TextContent(type="text", text=f"Error: Invalid workflow YAML – {exc}")]
+
+    dest = _ensure_user_dir() / (name + ".yaml")
+    dest.write_text(content, encoding="utf-8")
+    return [TextContent(type="text", text=f"Updated workflow '{name}' at: {dest}")]
+
+
+def delete_workflow_tool(args: dict) -> list:
+    """Remove a user workflow by name. Bundled workflows cannot be deleted."""
+    name = args.get("name", "").strip()
+    if not name:
+        return [TextContent(type="text", text="Error: 'name' parameter is required.")]
+
+    if name in _bundled_names():
+        return [
+            TextContent(
+                type="text",
+                text=f"Error: '{name}' is a bundled workflow and cannot be deleted.",
+            )
+        ]
+
+    for suffix in (".yaml", ".yml"):
+        candidate = USER_WORKFLOWS_DIR / (name + suffix)
+        if candidate.exists():
+            candidate.unlink()
+            return [TextContent(type="text", text=f"Deleted user workflow: {candidate}")]
+
+    return [TextContent(type="text", text=f"Error: User workflow '{name}' not found.")]