patch: Define agent-specific file categories and exclusions

[rdwj]

Problem

FILE_CATEGORIES and NEVER_PATCH in tools/patching.py are hardcoded for MCP server directory layout. Agent projects have a completely different structure — no src/core/, no .fips-agents-cli/generators/, but they do have chart/, src/base_agent/, and deployment scripts.

Proposed change

Make FILE_CATEGORIES and NEVER_PATCH type-aware. When patching, select the right set based on template.type from .template-info.

Agent file categories

AGENT_FILE_CATEGORIES = {
    "framework": {
        "description": "Agent framework code (base_agent package)",
        "patterns": [
            "src/base_agent/**/*.py",
        ],
        "ask_before_patch": True,
    },
    "chart": {
        "description": "Helm chart templates and values",
        "patterns": [
            "chart/templates/**/*",
            "chart/Chart.yaml",
        ],
        "ask_before_patch": True,
    },
    "docs": {
        "description": "Documentation files",
        "patterns": [
            "CLAUDE.md",
            "AGENTS.md",
            "docs/**/*",
        ],
        "ask_before_patch": False,
    },
    "build": {
        "description": "Build and deployment files",
        "patterns": [
            "Makefile",
            "Containerfile",
            "deploy.sh",
            "redeploy.sh",
        ],
        "ask_before_patch": True,
    },
}

Agent never-patch list

AGENT_NEVER_PATCH = [
    "src/agent.py",         # User's agent implementation
    "agent.yaml",           # User's agent config
    "chart/values.yaml",    # User's deploy values
    "tests/**/*.py",
    ".env*",
    "README.md",
    "pyproject.toml",
]

Implementation

A function like get_categories_for_type(project_type: str) that returns the right (FILE_CATEGORIES, NEVER_PATCH) tuple. The existing MCP constants become MCP_FILE_CATEGORIES / MCP_NEVER_PATCH, and check_for_updates() / patch_category() call the function instead of referencing module-level constants.

The patch CLI subcommands (generators, core, etc.) are MCP-specific category names. Agent projects would expose different subcommands (framework, chart, etc.). The patch check and patch all commands should work for any project type. Type-specific subcommands can either be added directly or patch <category> can become a dynamic argument validated against the project's available categories.

Part of

Tracking issue: #12
Depends on: #13 (needs template.type to select the right category set)