graphify/graphify/__main__.py

"""graphify CLI - `graphify install` sets up the Claude Code skill."""
from __future__ import annotations
import json
import os
import platform
import re
import shutil
import sys
from pathlib import Path

try:
    from importlib.metadata import version as _pkg_version
    __version__ = _pkg_version("graphifyy")
except Exception:
    __version__ = "unknown"

# Output directory — override with GRAPHIFY_OUT env var for worktrees or shared-output setups.
# Accepts a relative name ("graphify-out-feature") or an absolute path ("/shared/graphify-out").
_GRAPHIFY_OUT = os.environ.get("GRAPHIFY_OUT", "graphify-out")


def _default_graph_path() -> str:
    return str(Path(_GRAPHIFY_OUT) / "graph.json")


def _enforce_graph_size_cap_or_exit(gp: Path) -> None:
    """Reject oversized graph files before parsing (CLI exit-on-fail flavor).

    Delegates to ``graphify.security.check_graph_file_size_cap`` and turns the
    raised ``ValueError`` into a CLI-style ``error: ...`` message + exit 1.
    Use this from ``__main__.py`` subcommands that already use the ``print +
    sys.exit(1)`` idiom. Library/MCP/loader callers (``serve._load_graph``,
    ``build``, ``benchmark``, ``tree_html``, ``callflow_html``, ``prs``,
    ``global_graph``, ``watch``, ``export``) call the security helper directly
    and let the ``ValueError`` propagate.
    """
    from graphify.security import check_graph_file_size_cap
    try:
        check_graph_file_size_cap(gp)
    except ValueError as exc:
        print(f"error: {exc}", file=sys.stderr)
        sys.exit(1)


def _check_skill_version(skill_dst: Path) -> None:
    """Warn if the installed skill is from an older graphify version."""
    version_file = skill_dst.parent / ".graphify_version"
    if not version_file.exists():
        return
    if not skill_dst.exists():
        print("  warning: skill dir exists but SKILL.md is missing. Run 'graphify install' to repair.")
        return
    installed = version_file.read_text(encoding="utf-8").strip()
    if installed != __version__:
        print(f"  warning: skill is from graphify {installed}, package is {__version__}. Run 'graphify install' to update.", file=sys.stderr)


def _refresh_all_version_stamps() -> None:
    """After a successful install, update .graphify_version in all other known skill dirs.

    Prevents stale-version warnings from platforms that were installed previously
    but not explicitly re-installed during this upgrade.
    """
    for cfg in _PLATFORM_CONFIG.values():
        skill_dst = Path.home() / cfg["skill_dst"]
        vf = skill_dst.parent / ".graphify_version"
        if skill_dst.exists():
            vf.write_text(__version__, encoding="utf-8")

_SETTINGS_HOOK = {
    # Claude Code v2.1.117+ removed dedicated Grep/Glob tools; searches now go through Bash.
    # We match on Bash and inspect the command string to avoid firing on every shell call.
    "matcher": "Bash",
    "hooks": [
        {
            "type": "command",
            "command": (
                "CMD=$(python3 -c \""
                "import json,sys; d=json.load(sys.stdin); "
                "print(d.get('tool_input',d).get('command',''))\" 2>/dev/null || true); "
                "case \"$CMD\" in "
                r"*grep*|*rg\ *|*ripgrep*|*find\ *|*fd\ *|*ack\ *|*ag\ *) "
                "  [ -f graphify-out/graph.json ] && "
                r"""  echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","additionalContext":"graphify: knowledge graph at graphify-out/. For focused questions, run `graphify query \"<question>\"` (scoped subgraph, usually much smaller than GRAPH_REPORT.md) instead of grepping raw files. Read GRAPH_REPORT.md only for broad architecture context."}}' """
                "  || true ;; "
                "esac"
            ),
        }
    ],
}

_SKILL_REGISTRATION = (
    "\n# graphify\n"
    "- **graphify** (`~/.claude/skills/graphify/SKILL.md`) "
    "- any input to knowledge graph. Trigger: `/graphify`\n"
    "When the user types `/graphify`, invoke the Skill tool "
    "with `skill: \"graphify\"` before doing anything else.\n"
)


_PLATFORM_CONFIG: dict[str, dict] = {
    "claude": {
        "skill_file": "skill.md",
        "skill_dst": Path(".claude") / "skills" / "graphify" / "SKILL.md",
        "claude_md": True,
    },
    "codex": {
        "skill_file": "skill-codex.md",
        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "opencode": {
        "skill_file": "skill-opencode.md",
        "skill_dst": Path(".config") / "opencode" / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "aider": {
        "skill_file": "skill-aider.md",
        "skill_dst": Path(".aider") / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "copilot": {
        "skill_file": "skill-copilot.md",
        "skill_dst": Path(".copilot") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "claw": {
        "skill_file": "skill-claw.md",
        "skill_dst": Path(".openclaw") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "droid": {
        "skill_file": "skill-droid.md",
        "skill_dst": Path(".factory") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "trae": {
        "skill_file": "skill-trae.md",
        "skill_dst": Path(".trae") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "trae-cn": {
        "skill_file": "skill-trae.md",
        "skill_dst": Path(".trae-cn") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "hermes": {
        "skill_file": "skill-claw.md",
        "skill_dst": Path(".hermes") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "kiro": {
        "skill_file": "skill-kiro.md",
        "skill_dst": Path(".kiro") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "pi": {
        "skill_file": "skill-pi.md",
        "skill_dst": Path(".pi") / "agent" / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "antigravity": {
        "skill_file": "skill.md",
        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "antigravity-windows": {
        "skill_file": "skill-windows.md",
        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
    "windows": {
        "skill_file": "skill-windows.md",
        "skill_dst": Path(".claude") / "skills" / "graphify" / "SKILL.md",
        "claude_md": True,
    },
    "kimi": {
        "skill_file": "skill.md",
        "skill_dst": Path(".kimi") / "skills" / "graphify" / "SKILL.md",
        "claude_md": False,
    },
}


def _replace_or_append_section(content: str, marker: str, new_section: str) -> str:
    """Idempotently update or append a graphify-owned section in shared files.

    If ``marker`` is not in ``content``, append ``new_section`` to the end
    (with a blank-line separator if there's existing content).

    If ``marker`` IS in ``content``, replace the existing section in place.
    The section runs from the first line containing ``marker`` to the line
    before the next H2 heading (``## `` at line start), or to EOF if no later
    H2 exists. This lets older installs receive the updated copy without
    users having to uninstall and reinstall — important for the issue #580
    fix where existing report-first text would otherwise silently linger.
    """
    if marker not in content:
        if content.strip():
            return content.rstrip() + "\n\n" + new_section.lstrip()
        return new_section.lstrip()

    lines = content.split("\n")
    start = next((i for i, line in enumerate(lines) if marker in line), None)
    if start is None:
        return content.rstrip() + "\n\n" + new_section.lstrip()

    end = len(lines)
    for j in range(start + 1, len(lines)):
        if lines[j].startswith("## "):
            end = j
            break

    head = "\n".join(lines[:start]).rstrip()
    tail = "\n".join(lines[end:]).lstrip()
    section = new_section.strip()

    parts: list[str] = []
    if head:
        parts.append(head)
    parts.append(section)
    if tail:
        parts.append(tail)
    out = "\n\n".join(parts)
    if not out.endswith("\n"):
        out += "\n"
    return out


def install(platform: str = "claude") -> None:
    if platform == "gemini":
        gemini_install()
        return
    if platform == "cursor":
        _cursor_install(Path("."))
        return
    # On Windows, antigravity needs the PowerShell skill, not the bash one
    if platform == "antigravity" and sys.platform == "win32":
        platform = "antigravity-windows"
    if platform not in _PLATFORM_CONFIG:
        print(
            f"error: unknown platform '{platform}'. Choose from: {', '.join(_PLATFORM_CONFIG)}, gemini, cursor",
            file=sys.stderr,
        )
        sys.exit(1)

    cfg = _PLATFORM_CONFIG[platform]
    skill_src = Path(__file__).parent / cfg["skill_file"]
    if not skill_src.exists():
        print(f"error: {cfg['skill_file']} not found in package - reinstall graphify", file=sys.stderr)
        sys.exit(1)

    import os as _os
    if platform in ("claude", "windows") and _os.environ.get("CLAUDE_CONFIG_DIR"):
        _claude_base = Path(_os.environ["CLAUDE_CONFIG_DIR"])
        skill_dst = _claude_base / "skills" / "graphify" / "SKILL.md"
    else:
        skill_dst = Path.home() / cfg["skill_dst"]
    skill_dst.parent.mkdir(parents=True, exist_ok=True)
    tmp_dst = skill_dst.with_suffix(skill_dst.suffix + ".tmp")
    try:
        shutil.copy(skill_src, tmp_dst)
        os.replace(tmp_dst, skill_dst)
    except Exception:
        try:
            tmp_dst.unlink(missing_ok=True)
        except OSError:
            pass
        raise
    (skill_dst.parent / ".graphify_version").write_text(__version__, encoding="utf-8")
    print(f"  skill installed  ->  {skill_dst}")

    if cfg["claude_md"]:
        # Register in ~/.claude/CLAUDE.md (Claude Code only)
        claude_md = Path.home() / ".claude" / "CLAUDE.md"
        if claude_md.exists():
            content = claude_md.read_text(encoding="utf-8")
            if "graphify" in content:
                print(f"  CLAUDE.md        ->  already registered (no change)")
            else:
                claude_md.write_text(content.rstrip() + _SKILL_REGISTRATION, encoding="utf-8")
                print(f"  CLAUDE.md        ->  skill registered in {claude_md}")
        else:
            claude_md.parent.mkdir(parents=True, exist_ok=True)
            claude_md.write_text(_SKILL_REGISTRATION.lstrip(), encoding="utf-8")
            print(f"  CLAUDE.md        ->  created at {claude_md}")

    if platform == "opencode":
        _install_opencode_plugin(Path("."))

    # Refresh version stamps in all other previously-installed skill dirs so
    # stale-version warnings don't fire for platforms not explicitly re-installed.
    _refresh_all_version_stamps()

    print()
    print("Done. Open your AI coding assistant and type:")
    print()
    print("  /graphify .")
    print()


def _print_install_usage() -> None:
    platforms = ", ".join([*_PLATFORM_CONFIG, "gemini", "cursor"])
    print("Usage: graphify install [--platform P|P]")
    print(f"Platforms: {platforms}")


_CLAUDE_MD_SECTION = """\
## graphify

This project has a knowledge graph at graphify-out/ with god nodes, community structure, and cross-file relationships.

Rules:
- For codebase questions, first run `graphify query "<question>"` when graphify-out/graph.json exists. Use `graphify path "<A>" "<B>"` for relationships and `graphify explain "<concept>"` for focused concepts. These return a scoped subgraph, usually much smaller than GRAPH_REPORT.md or raw grep output.
- If graphify-out/wiki/index.md exists, use it for broad navigation instead of raw source browsing.
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context.
- After modifying code, run `graphify update .` to keep the graph current (AST-only, no API cost).
"""

_CLAUDE_MD_MARKER = "## graphify"

# AGENTS.md section for Codex, OpenCode, and OpenClaw.
# All three platforms read AGENTS.md in the project root for persistent instructions.
_AGENTS_MD_SECTION = """\
## graphify

This project has a knowledge graph at graphify-out/ with god nodes, community structure, and cross-file relationships.

When the user types `/graphify`, invoke the `skill` tool with `skill: "graphify"` before doing anything else.

Rules:
- For codebase questions, first run `graphify query "<question>"` when graphify-out/graph.json exists. Use `graphify path "<A>" "<B>"` for relationships and `graphify explain "<concept>"` for focused concepts. These return a scoped subgraph, usually much smaller than GRAPH_REPORT.md or raw grep output.
- Dirty graphify-out/ files are expected after hooks or incremental updates; dirty graph files are not a reason to skip graphify. Only skip graphify if the task is about stale or incorrect graph output, or the user explicitly says not to use it.
- If graphify-out/wiki/index.md exists, use it for broad navigation instead of raw source browsing.
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context.
- After modifying code, run `graphify update .` to keep the graph current (AST-only, no API cost).
"""

_AGENTS_MD_MARKER = "## graphify"

_GEMINI_MD_SECTION = """\
## graphify

This project has a knowledge graph at graphify-out/ with god nodes, community structure, and cross-file relationships.

Rules:
- For codebase questions, first run `graphify query "<question>"` when graphify-out/graph.json exists. Use `graphify path "<A>" "<B>"` for relationships and `graphify explain "<concept>"` for focused concepts. These return a scoped subgraph, usually much smaller than GRAPH_REPORT.md or raw grep output.
- If graphify-out/wiki/index.md exists, use it for broad navigation instead of raw source browsing.
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context.
- After modifying code, run `graphify update .` to keep the graph current (AST-only, no API cost).
"""

_GEMINI_MD_MARKER = "## graphify"

_GEMINI_HOOK = {
    "matcher": "read_file|list_directory",
    "hooks": [
        {
            "type": "command",
            "command": (
                'python -c "'
                "import sys,pathlib,json;"
                "e=pathlib.Path('graphify-out/graph.json').exists();"
                "d={'decision':'allow'};"
                "e and d.update({'additionalContext':'graphify: knowledge graph at graphify-out/. For focused questions, run `graphify query \"<question>\"` (scoped subgraph, usually much smaller than GRAPH_REPORT.md) instead of grepping raw files. Read GRAPH_REPORT.md only for broad architecture context.'});"
                "sys.stdout.write(json.dumps(d))"
                '"'
            ),
        }
    ],
}


def gemini_install(project_dir: Path | None = None) -> None:
    """Copy skill file to ~/.gemini/skills/graphify/, write GEMINI.md section, and install BeforeTool hook."""
    # Copy skill file to ~/.gemini/skills/graphify/SKILL.md
    # On Windows, Gemini CLI prioritises ~/.agents/skills/ over ~/.gemini/skills/
    skill_src = Path(__file__).parent / "skill.md"
    if platform.system() == "Windows":
        skill_dst = Path.home() / ".agents" / "skills" / "graphify" / "SKILL.md"
    else:
        skill_dst = Path.home() / ".gemini" / "skills" / "graphify" / "SKILL.md"
    skill_dst.parent.mkdir(parents=True, exist_ok=True)
    shutil.copy(skill_src, skill_dst)
    (skill_dst.parent / ".graphify_version").write_text(__version__, encoding="utf-8")
    print(f"  skill installed  ->  {skill_dst}")

    target = (project_dir or Path(".")) / "GEMINI.md"

    if target.exists():
        content = target.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _GEMINI_MD_MARKER, _GEMINI_MD_SECTION
        )
    else:
        new_content = _GEMINI_MD_SECTION

    if target.exists() and new_content == target.read_text(encoding="utf-8"):
        print(f"graphify already configured in {target.resolve()} (no change)")
    else:
        target.write_text(new_content, encoding="utf-8")
        print(f"graphify section written to {target.resolve()}")

    # Always re-install the Gemini hook so an older payload (e.g. pre-issue-#580
    # wording) is replaced on upgrade.
    _install_gemini_hook(project_dir or Path("."))
    print()
    print("Gemini CLI will now check the knowledge graph before answering")
    print("codebase questions and rebuild it after code changes.")


def _install_gemini_hook(project_dir: Path) -> None:
    settings_path = project_dir / ".gemini" / "settings.json"
    settings_path.parent.mkdir(parents=True, exist_ok=True)
    try:
        settings = json.loads(settings_path.read_text(encoding="utf-8")) if settings_path.exists() else {}
    except json.JSONDecodeError:
        settings = {}
    before_tool = settings.setdefault("hooks", {}).setdefault("BeforeTool", [])
    settings["hooks"]["BeforeTool"] = [h for h in before_tool if "graphify" not in str(h)]
    settings["hooks"]["BeforeTool"].append(_GEMINI_HOOK)
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print("  .gemini/settings.json  ->  BeforeTool hook registered")


def _uninstall_gemini_hook(project_dir: Path) -> None:
    settings_path = project_dir / ".gemini" / "settings.json"
    if not settings_path.exists():
        return
    try:
        settings = json.loads(settings_path.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    before_tool = settings.get("hooks", {}).get("BeforeTool", [])
    filtered = [h for h in before_tool if "graphify" not in str(h)]
    if len(filtered) == len(before_tool):
        return
    settings["hooks"]["BeforeTool"] = filtered
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print("  .gemini/settings.json  ->  BeforeTool hook removed")


def gemini_uninstall(project_dir: Path | None = None) -> None:
    """Remove the graphify section from GEMINI.md, uninstall hook, and remove skill file."""
    # Remove skill file (mirror the install path detection)
    if platform.system() == "Windows":
        skill_dst = Path.home() / ".agents" / "skills" / "graphify" / "SKILL.md"
    else:
        skill_dst = Path.home() / ".gemini" / "skills" / "graphify" / "SKILL.md"
    if skill_dst.exists():
        skill_dst.unlink()
        print(f"  skill removed    ->  {skill_dst}")
    version_file = skill_dst.parent / ".graphify_version"
    if version_file.exists():
        version_file.unlink()
    for d in (skill_dst.parent, skill_dst.parent.parent):
        try:
            d.rmdir()
        except OSError:
            break

    target = (project_dir or Path(".")) / "GEMINI.md"
    if not target.exists():
        print("No GEMINI.md found in current directory - nothing to do")
        return
    content = target.read_text(encoding="utf-8")
    if _GEMINI_MD_MARKER not in content:
        print("graphify section not found in GEMINI.md - nothing to do")
        return
    cleaned = re.sub(r"\n*## graphify\n.*?(?=\n## |\Z)", "", content, flags=re.DOTALL).rstrip()
    if cleaned:
        target.write_text(cleaned + "\n", encoding="utf-8")
        print(f"graphify section removed from {target.resolve()}")
    else:
        target.unlink()
        print(f"GEMINI.md was empty after removal - deleted {target.resolve()}")
    _uninstall_gemini_hook(project_dir or Path("."))


_VSCODE_INSTRUCTIONS_MARKER = "## graphify"
_VSCODE_INSTRUCTIONS_SECTION = """\
## graphify

For any question about this repo's architecture, structure, components, or how to add/modify/find
code, your first action should be `graphify query "<question>"` when `graphify-out/graph.json`
exists. Use `graphify path "<A>" "<B>"` for relationship questions and `graphify explain "<concept>"`
for focused-concept questions. These return a scoped subgraph, usually much smaller than the full
report or raw grep output.

Triggers: "how do I…", "where is…", "what does … do", "add/modify a <component>",
"explain the architecture", or anything that depends on how files or classes relate.

If `graphify-out/wiki/index.md` exists, use it for broad navigation. Read `graphify-out/GRAPH_REPORT.md`
only for broad architecture review or when query/path/explain do not surface enough context. Only read
source files when (a) modifying/debugging specific code, (b) the graph lacks the needed detail, or
(c) the graph is missing or stale.

Type `/graphify` in Copilot Chat to build or update the graph.
"""


def vscode_install(project_dir: Path | None = None) -> None:
    """Install graphify skill for VS Code Copilot Chat + write .github/copilot-instructions.md."""
    skill_src = Path(__file__).parent / "skill-vscode.md"
    if not skill_src.exists():
        skill_src = Path(__file__).parent / "skill-copilot.md"
    skill_dst = Path.home() / ".copilot" / "skills" / "graphify" / "SKILL.md"
    skill_dst.parent.mkdir(parents=True, exist_ok=True)
    shutil.copy(skill_src, skill_dst)
    (skill_dst.parent / ".graphify_version").write_text(__version__, encoding="utf-8")
    print(f"  skill installed  ->  {skill_dst}")

    instructions = (project_dir or Path(".")) / ".github" / "copilot-instructions.md"
    instructions.parent.mkdir(parents=True, exist_ok=True)
    if instructions.exists():
        content = instructions.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _VSCODE_INSTRUCTIONS_MARKER, _VSCODE_INSTRUCTIONS_SECTION
        )
        if new_content == content:
            print(f"  {instructions}  ->  already configured (no change)")
        else:
            instructions.write_text(new_content, encoding="utf-8")
            print(f"  {instructions}  ->  graphify section {'updated' if _VSCODE_INSTRUCTIONS_MARKER in content else 'added'}")
    else:
        instructions.write_text(_VSCODE_INSTRUCTIONS_SECTION, encoding="utf-8")
        print(f"  {instructions}  ->  created")

    print()
    print("VS Code Copilot Chat configured. Type /graphify in the chat panel to build the graph.")
    print("Note: for GitHub Copilot CLI (terminal), use: graphify copilot install")


def vscode_uninstall(project_dir: Path | None = None) -> None:
    """Remove graphify VS Code Copilot Chat skill and .github/copilot-instructions.md section."""
    skill_dst = Path.home() / ".copilot" / "skills" / "graphify" / "SKILL.md"
    if skill_dst.exists():
        skill_dst.unlink()
        print(f"  skill removed    ->  {skill_dst}")
    version_file = skill_dst.parent / ".graphify_version"
    if version_file.exists():
        version_file.unlink()
    for d in (skill_dst.parent, skill_dst.parent.parent, skill_dst.parent.parent.parent):
        try:
            d.rmdir()
        except OSError:
            break

    instructions = (project_dir or Path(".")) / ".github" / "copilot-instructions.md"
    if not instructions.exists():
        return
    content = instructions.read_text(encoding="utf-8")
    if _VSCODE_INSTRUCTIONS_MARKER not in content:
        return
    cleaned = re.sub(r"\n*## graphify\n.*?(?=\n## |\Z)", "", content, flags=re.DOTALL).rstrip()
    if cleaned:
        instructions.write_text(cleaned + "\n", encoding="utf-8")
        print(f"  graphify section removed from {instructions}")
    else:
        instructions.unlink()
        print(f"  {instructions}  ->  deleted (was empty after removal)")


_ANTIGRAVITY_RULES_PATH = Path(".agents") / "rules" / "graphify.md"
_ANTIGRAVITY_WORKFLOW_PATH = Path(".agents") / "workflows" / "graphify.md"

_ANTIGRAVITY_RULES = """\
---
trigger: always_on
description: Consult the graphify knowledge graph at graphify-out/ for codebase and architecture questions.
---

## graphify

This project has a graphify knowledge graph at graphify-out/.

Rules:
- For codebase or architecture questions, when `graphify-out/graph.json` exists, first run `graphify query "<question>"` (CLI) or `query_graph` (MCP). Use `graphify path "<A>" "<B>"` / `shortest_path` for relationships and `graphify explain "<concept>"` / `get_node` for focused concepts. These return a scoped subgraph, usually much smaller than `GRAPH_REPORT.md` or raw grep output.
- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context
- After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)
"""

_ANTIGRAVITY_WORKFLOW = """\
---
name: graphify
description: Turn any folder of files into a navigable knowledge graph
---

# Workflow: graphify

Follow the graphify skill installed at ~/.agents/skills/graphify/SKILL.md to run the full pipeline.

If no path argument is given, use `.` (current directory).
"""


_KIRO_STEERING = """\
---
inclusion: always
---

graphify: A knowledge graph of this project lives in `graphify-out/`. \
For codebase, architecture, or dependency questions, when `graphify-out/graph.json` exists, \
first run `graphify query "<question>"` (or `graphify path "<A>" "<B>"` / `graphify explain "<concept>"`). \
These return a scoped subgraph, usually much smaller than `GRAPH_REPORT.md` or raw grep output. \
Read `GRAPH_REPORT.md` only for broad architecture review or when those commands do not surface enough context.
"""

_KIRO_STEERING_MARKER = "graphify: A knowledge graph of this project"


def _kiro_install(project_dir: Path) -> None:
    """Write graphify skill + steering file for Kiro IDE/CLI."""
    project_dir = project_dir or Path(".")

    # Skill file → .kiro/skills/graphify/SKILL.md
    skill_src = Path(__file__).parent / "skill-kiro.md"
    skill_dst = project_dir / ".kiro" / "skills" / "graphify" / "SKILL.md"
    skill_dst.parent.mkdir(parents=True, exist_ok=True)
    skill_dst.write_text(skill_src.read_text(encoding="utf-8"), encoding="utf-8")
    print(f"  {skill_dst.relative_to(project_dir)}  ->  /graphify skill")

    # Steering file → .kiro/steering/graphify.md (always-on)
    steering_dir = project_dir / ".kiro" / "steering"
    steering_dir.mkdir(parents=True, exist_ok=True)
    steering_dst = steering_dir / "graphify.md"
    if steering_dst.exists() and steering_dst.read_text(encoding="utf-8") == _KIRO_STEERING:
        print(f"  .kiro/steering/graphify.md  ->  already configured (no change)")
    else:
        # File is wholly graphify-owned. Overwrite on upgrade so older
        # report-first wording does not silently linger (issue #580).
        action = "updated" if steering_dst.exists() else "written"
        steering_dst.write_text(_KIRO_STEERING, encoding="utf-8")
        print(f"  .kiro/steering/graphify.md  ->  always-on steering {action}")

    print()
    print("Kiro will now read the knowledge graph before every conversation.")
    print("Use /graphify to build or update the graph.")


def _kiro_uninstall(project_dir: Path) -> None:
    """Remove graphify skill + steering file for Kiro."""
    project_dir = project_dir or Path(".")
    removed = []

    skill_dst = project_dir / ".kiro" / "skills" / "graphify" / "SKILL.md"
    if skill_dst.exists():
        skill_dst.unlink()
        removed.append(str(skill_dst.relative_to(project_dir)))
        # Remove parent dir if empty
        try:
            skill_dst.parent.rmdir()
        except OSError:
            pass

    steering_dst = project_dir / ".kiro" / "steering" / "graphify.md"
    if steering_dst.exists():
        steering_dst.unlink()
        removed.append(str(steering_dst.relative_to(project_dir)))

    print("Removed: " + (", ".join(removed) if removed else "nothing to remove"))


def _antigravity_install(project_dir: Path) -> None:
    """Install graphify for Google Antigravity: skill + .agents/rules + .agents/workflows."""
    # 1. Copy skill file to ~/.agents/skills/graphify/SKILL.md
    install(platform="antigravity")

    # 1.5. Inject YAML frontmatter for native Antigravity tool discovery
    skill_dst = _PLATFORM_CONFIG["antigravity"]["skill_dst"]
    if skill_dst.exists():
        content = skill_dst.read_text(encoding="utf-8")
        if not content.startswith("---\n"):
            frontmatter = "---\nname: graphify-manager\ndescription: Rebuild the code graph or perform manual CLI queries when MCP server is offline.\n---\n\n"
            skill_dst.write_text(frontmatter + content, encoding="utf-8")

    # 2. Write .agents/rules/graphify.md
    rules_path = project_dir / _ANTIGRAVITY_RULES_PATH
    rules_path.parent.mkdir(parents=True, exist_ok=True)
    if rules_path.exists():
        existing = rules_path.read_text(encoding="utf-8")
        if _ANTIGRAVITY_RULES.strip() != existing.strip():
            rules_path.write_text(_ANTIGRAVITY_RULES, encoding="utf-8")
            print(f"graphify rule updated at {rules_path.resolve()}")
        else:
            print(f"graphify rule already configured at {rules_path.resolve()} (no change)")
    else:
        rules_path.write_text(_ANTIGRAVITY_RULES, encoding="utf-8")
        print(f"graphify rule written to {rules_path.resolve()}")

    # 3. Write .agents/workflows/graphify.md
    wf_path = project_dir / _ANTIGRAVITY_WORKFLOW_PATH
    wf_path.parent.mkdir(parents=True, exist_ok=True)
    if wf_path.exists():
        existing = wf_path.read_text(encoding="utf-8")
        if _ANTIGRAVITY_WORKFLOW.strip() != existing.strip():
            wf_path.write_text(_ANTIGRAVITY_WORKFLOW, encoding="utf-8")
            print(f"graphify workflow updated at {wf_path.resolve()}")
        else:
            print(f"graphify workflow already configured at {wf_path.resolve()} (no change)")
    else:
        wf_path.write_text(_ANTIGRAVITY_WORKFLOW, encoding="utf-8")
        print(f"graphify workflow written to {wf_path.resolve()}")

    print()
    print("Antigravity will now check the knowledge graph before answering")
    print("codebase questions. Run /graphify first to build the graph.")
    print()
    print("To enable full MCP architecture navigation, add this to ~/.gemini/antigravity/mcp_config.json:")
    print('  "graphify": {')
    print('    "command": "uv",')
    print('    "args": ["run", "--with", "graphifyy", "--with", "mcp", "-m", "graphify.serve", "${workspace.path}/graphify-out/graph.json"]')
    print('  }')


def _antigravity_uninstall(project_dir: Path) -> None:
    """Remove graphify Antigravity rules, workflow, and skill files."""
    # Remove rules file
    rules_path = project_dir / _ANTIGRAVITY_RULES_PATH
    if rules_path.exists():
        rules_path.unlink()
        print(f"graphify rule removed from {rules_path.resolve()}")
    else:
        print("No graphify Antigravity rule found - nothing to do")

    # Remove workflow file
    wf_path = project_dir / _ANTIGRAVITY_WORKFLOW_PATH
    if wf_path.exists():
        wf_path.unlink()
        print(f"graphify workflow removed from {wf_path.resolve()}")

    # Remove skill file
    skill_dst = _PLATFORM_CONFIG["antigravity"]["skill_dst"]
    if skill_dst.exists():
        skill_dst.unlink()
        print(f"graphify skill removed from {skill_dst}")
    version_file = skill_dst.parent / ".graphify_version"
    if version_file.exists():
        version_file.unlink()
    for d in (skill_dst.parent, skill_dst.parent.parent, skill_dst.parent.parent.parent):
        try:
            d.rmdir()
        except OSError:
            break


_CURSOR_RULE_PATH = Path(".cursor") / "rules" / "graphify.mdc"
_CURSOR_RULE = """\
---
description: graphify knowledge graph context
alwaysApply: true
---

This project has a graphify knowledge graph at graphify-out/.

- For codebase or architecture questions, when `graphify-out/graph.json` exists, first run `graphify query "<question>"` (or `graphify path "<A>" "<B>"` / `graphify explain "<concept>"`). These return a scoped subgraph, usually much smaller than `GRAPH_REPORT.md` or raw grep output.
- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context
- After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)
"""


def _cursor_install(project_dir: Path) -> None:
    """Write .cursor/rules/graphify.mdc with alwaysApply: true."""
    rule_path = (project_dir or Path(".")) / _CURSOR_RULE_PATH
    rule_path.parent.mkdir(parents=True, exist_ok=True)
    if rule_path.exists() and rule_path.read_text(encoding="utf-8") == _CURSOR_RULE:
        print(f"graphify rule at {rule_path} already configured (no change)")
        return
    # File is wholly graphify-owned. Overwrite on upgrade so older
    # report-first wording does not silently linger (issue #580).
    action = "updated" if rule_path.exists() else "written"
    rule_path.write_text(_CURSOR_RULE, encoding="utf-8")
    print(f"graphify rule {action} at {rule_path.resolve()}")
    print()
    print("Cursor will now always include the knowledge graph context.")
    print("Run /graphify . first to build the graph if you haven't already.")


def _cursor_uninstall(project_dir: Path) -> None:
    """Remove .cursor/rules/graphify.mdc."""
    rule_path = (project_dir or Path(".")) / _CURSOR_RULE_PATH
    if not rule_path.exists():
        print("No graphify Cursor rule found - nothing to do")
        return
    rule_path.unlink()
    print(f"graphify Cursor rule removed from {rule_path.resolve()}")


# OpenCode tool.execute.before plugin — fires before every tool call.
# Injects a graph reminder into bash command output when graph.json exists.
_OPENCODE_PLUGIN_JS = """\
// graphify OpenCode plugin
// Injects a knowledge graph reminder before bash tool calls when the graph exists.
import { existsSync } from "fs";
import { join } from "path";

export const GraphifyPlugin = async ({ directory }) => {
  let reminded = false;

  return {
    "tool.execute.before": async (input, output) => {
      if (reminded) return;
      if (!existsSync(join(directory, "graphify-out", "graph.json"))) return;

      if (input.tool === "bash") {
        output.args.command =
          'echo "[graphify] knowledge graph at graphify-out/. For focused questions, run \\`graphify query \\"<question>\\"\\` (scoped subgraph, usually much smaller than GRAPH_REPORT.md) instead of grepping raw files. Read GRAPH_REPORT.md only for broad architecture context." && ' +
          output.args.command;
        reminded = true;
      }
    },
  };
};
"""

_OPENCODE_PLUGIN_PATH = Path(".opencode") / "plugins" / "graphify.js"
_OPENCODE_CONFIG_PATH = Path(".opencode") / "opencode.json"


def _install_opencode_plugin(project_dir: Path) -> None:
    """Write graphify.js plugin and register it in opencode.json."""
    plugin_file = project_dir / _OPENCODE_PLUGIN_PATH
    plugin_file.parent.mkdir(parents=True, exist_ok=True)
    plugin_file.write_text(_OPENCODE_PLUGIN_JS, encoding="utf-8")
    print(f"  {_OPENCODE_PLUGIN_PATH}  ->  tool.execute.before hook written")

    config_file = project_dir / _OPENCODE_CONFIG_PATH
    if config_file.exists():
        try:
            config = json.loads(config_file.read_text(encoding="utf-8"))
        except json.JSONDecodeError:
            config = {}
    else:
        config = {}

    plugins = config.setdefault("plugin", [])
    entry = _OPENCODE_PLUGIN_PATH.as_posix()
    if entry not in plugins:
        plugins.append(entry)
        config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
        print(f"  {_OPENCODE_CONFIG_PATH}  ->  plugin registered")
    else:
        print(f"  {_OPENCODE_CONFIG_PATH}  ->  plugin already registered (no change)")


def _uninstall_opencode_plugin(project_dir: Path) -> None:
    """Remove graphify.js plugin and deregister from opencode.json."""
    plugin_file = project_dir / _OPENCODE_PLUGIN_PATH
    if plugin_file.exists():
        plugin_file.unlink()
        print(f"  {_OPENCODE_PLUGIN_PATH}  ->  removed")

    config_file = project_dir / _OPENCODE_CONFIG_PATH
    if not config_file.exists():
        return
    try:
        config = json.loads(config_file.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    plugins = config.get("plugin", [])
    entry = _OPENCODE_PLUGIN_PATH.as_posix()
    if entry in plugins:
        plugins.remove(entry)
        if not plugins:
            config.pop("plugin")
        config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
        print(f"  {_OPENCODE_CONFIG_PATH}  ->  plugin deregistered")


_CODEX_HOOK = {
    "hooks": {
        "PreToolUse": [
            {
                "matcher": "Bash",
                "hooks": [
                    {
                        "type": "command",
                        # Use the graphify CLI itself so the hook is shell-agnostic:
                        # no [ -f ] bash syntax, no python3 vs python Conda issue,
                        # no JSON escaping inside PowerShell strings. Works on
                        # Windows (PowerShell/cmd.exe), macOS, and Linux.
                        "command": "graphify hook-check",
                    }
                ],
            }
        ]
    }
}


def _resolve_graphify_exe() -> str:
    """Return the absolute path to the graphify executable.

    Falls back to bare 'graphify' if resolution fails. Using an absolute path
    ensures the hook works in environments where the venv Scripts/ directory is
    not on PATH (e.g. VS Code Codex extension on Windows).
    """
    import shutil
    found = shutil.which("graphify")
    if found:
        return found
    # Derive from sys.executable: same Scripts/ (Windows) or bin/ (Unix) dir
    scripts_dir = Path(sys.executable).parent
    for name in ("graphify.exe", "graphify"):
        candidate = scripts_dir / name
        if candidate.exists():
            return str(candidate)
    return "graphify"


def _install_codex_hook(project_dir: Path) -> None:
    """Add graphify PreToolUse hook to .codex/hooks.json."""
    hooks_path = project_dir / ".codex" / "hooks.json"
    hooks_path.parent.mkdir(parents=True, exist_ok=True)

    if hooks_path.exists():
        try:
            existing = json.loads(hooks_path.read_text(encoding="utf-8"))
        except json.JSONDecodeError:
            existing = {}
    else:
        existing = {}

    graphify_exe = _resolve_graphify_exe()
    hook_entry = {
        "hooks": {
            "PreToolUse": [
                {
                    "matcher": "Bash",
                    "hooks": [{"type": "command", "command": f"{graphify_exe} hook-check"}],
                }
            ]
        }
    }

    pre_tool = existing.setdefault("hooks", {}).setdefault("PreToolUse", [])
    existing["hooks"]["PreToolUse"] = [h for h in pre_tool if "graphify" not in str(h)]
    existing["hooks"]["PreToolUse"].extend(hook_entry["hooks"]["PreToolUse"])
    hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
    print(f"  .codex/hooks.json  ->  PreToolUse hook registered ({graphify_exe} hook-check)")


def _uninstall_codex_hook(project_dir: Path) -> None:
    """Remove graphify PreToolUse hook from .codex/hooks.json."""
    hooks_path = project_dir / ".codex" / "hooks.json"
    if not hooks_path.exists():
        return
    try:
        existing = json.loads(hooks_path.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    pre_tool = existing.get("hooks", {}).get("PreToolUse", [])
    filtered = [h for h in pre_tool if "graphify" not in str(h)]
    existing["hooks"]["PreToolUse"] = filtered
    hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
    print(f"  .codex/hooks.json  ->  PreToolUse hook removed")


def _agents_install(project_dir: Path, platform: str) -> None:
    """Write the graphify section to the local AGENTS.md (Codex/OpenCode/OpenClaw)."""
    target = (project_dir or Path(".")) / "AGENTS.md"

    if target.exists():
        content = target.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _AGENTS_MD_MARKER, _AGENTS_MD_SECTION
        )
    else:
        new_content = _AGENTS_MD_SECTION

    if target.exists() and new_content == target.read_text(encoding="utf-8"):
        print(f"graphify already configured in {target.resolve()} (no change)")
    else:
        target.write_text(new_content, encoding="utf-8")
        print(f"graphify section written to {target.resolve()}")

    if platform == "codex":
        _install_codex_hook(project_dir or Path("."))
    elif platform == "opencode":
        _install_opencode_plugin(project_dir or Path("."))

    print()
    print(f"{platform.capitalize()} will now check the knowledge graph before answering")
    print("codebase questions and rebuild it after code changes.")
    if platform not in ("codex", "opencode"):
        print()
        print("Note: unlike Claude Code, there is no PreToolUse hook equivalent for")
        print(f"{platform.capitalize()} — the AGENTS.md rules are the always-on mechanism.")


def _agents_uninstall(project_dir: Path, platform: str = "") -> None:
    """Remove the graphify section from the local AGENTS.md."""
    target = (project_dir or Path(".")) / "AGENTS.md"

    if not target.exists():
        print("No AGENTS.md found in current directory - nothing to do")
        return

    content = target.read_text(encoding="utf-8")
    if _AGENTS_MD_MARKER not in content:
        print("graphify section not found in AGENTS.md - nothing to do")
        return

    cleaned = re.sub(
        r"\n*## graphify\n.*?(?=\n## |\Z)",
        "",
        content,
        flags=re.DOTALL,
    ).rstrip()
    if cleaned:
        target.write_text(cleaned + "\n", encoding="utf-8")
        print(f"graphify section removed from {target.resolve()}")
    else:
        target.unlink()
        print(f"AGENTS.md was empty after removal - deleted {target.resolve()}")

    if platform == "opencode":
        _uninstall_opencode_plugin(project_dir or Path("."))


def claude_install(project_dir: Path | None = None) -> None:
    """Write the graphify section to the local CLAUDE.md."""
    target = (project_dir or Path(".")) / "CLAUDE.md"

    if target.exists():
        content = target.read_text(encoding="utf-8")
        new_content = _replace_or_append_section(
            content, _CLAUDE_MD_MARKER, _CLAUDE_MD_SECTION
        )
    else:
        new_content = _CLAUDE_MD_SECTION

    if target.exists() and new_content == target.read_text(encoding="utf-8"):
        print(f"graphify already configured in {target.resolve()} (no change)")
    else:
        target.write_text(new_content, encoding="utf-8")
        print(f"graphify section written to {target.resolve()}")

    # Always re-install the Claude Code PreToolUse hook so an old hook
    # payload (e.g. pre-issue-#580 wording) is replaced on upgrade.
    _install_claude_hook(project_dir or Path("."))

    print()
    print("Claude Code will now check the knowledge graph before answering")
    print("codebase questions and rebuild it after code changes.")


def _install_claude_hook(project_dir: Path) -> None:
    """Add graphify PreToolUse hook to .claude/settings.json."""
    settings_path = project_dir / ".claude" / "settings.json"
    settings_path.parent.mkdir(parents=True, exist_ok=True)

    if settings_path.exists():
        try:
            settings = json.loads(settings_path.read_text(encoding="utf-8"))
        except json.JSONDecodeError:
            settings = {}
    else:
        settings = {}

    hooks = settings.setdefault("hooks", {})
    pre_tool = hooks.setdefault("PreToolUse", [])

    hooks["PreToolUse"] = [h for h in pre_tool if not (h.get("matcher") in ("Glob|Grep", "Bash") and "graphify" in str(h))]
    hooks["PreToolUse"].append(_SETTINGS_HOOK)
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print(f"  .claude/settings.json  ->  PreToolUse hook registered")


def _uninstall_claude_hook(project_dir: Path) -> None:
    """Remove graphify PreToolUse hook from .claude/settings.json."""
    settings_path = project_dir / ".claude" / "settings.json"
    if not settings_path.exists():
        return
    try:
        settings = json.loads(settings_path.read_text(encoding="utf-8"))
    except json.JSONDecodeError:
        return
    pre_tool = settings.get("hooks", {}).get("PreToolUse", [])
    filtered = [h for h in pre_tool if not (h.get("matcher") in ("Glob|Grep", "Bash") and "graphify" in str(h))]
    if len(filtered) == len(pre_tool):
        return
    settings["hooks"]["PreToolUse"] = filtered
    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
    print(f"  .claude/settings.json  ->  PreToolUse hook removed")


def uninstall_all(project_dir: Path | None = None, purge: bool = False) -> None:
    """Remove graphify from every platform detected in the current project."""
    pd = project_dir or Path(".")
    print("Uninstalling graphify from all detected platforms...\n")

    # Skill-file / config-section uninstallers
    claude_uninstall(pd)
    gemini_uninstall(pd)
    vscode_uninstall(pd)
    _cursor_uninstall(pd)
    _kiro_uninstall(pd)
    _antigravity_uninstall(pd)
    # AGENTS.md covers: codex, aider, opencode, claw, droid, trae, trae-cn, hermes, copilot
    _agents_uninstall(pd)
    _uninstall_opencode_plugin(pd)
    _uninstall_codex_hook(pd)

    # Git hook
    try:
        from graphify.hooks import uninstall as hook_uninstall
        result = hook_uninstall(pd)
        if result:
            print(result)
    except Exception:
        pass

    if purge:
        import shutil as _shutil
        out = pd / "graphify-out"
        if out.exists():
            _shutil.rmtree(out)
            print(f"\n  graphify-out/  ->  deleted (--purge)")
        else:
            print("\n  graphify-out/  ->  not found (nothing to purge)")

    print("\nDone. Run 'pip uninstall graphifyy' to remove the package itself.")


def claude_uninstall(project_dir: Path | None = None) -> None:
    """Remove the graphify section from the local CLAUDE.md."""
    target = (project_dir or Path(".")) / "CLAUDE.md"

    if not target.exists():
        print("No CLAUDE.md found in current directory - nothing to do")
        return

    content = target.read_text(encoding="utf-8")
    if _CLAUDE_MD_MARKER not in content:
        print("graphify section not found in CLAUDE.md - nothing to do")
        return

    # Remove the ## graphify section: from the marker to the next ## heading or EOF
    cleaned = re.sub(
        r"\n*## graphify\n.*?(?=\n## |\Z)",
        "",
        content,
        flags=re.DOTALL,
    ).rstrip()
    if cleaned:
        target.write_text(cleaned + "\n", encoding="utf-8")
        print(f"graphify section removed from {target.resolve()}")
    else:
        target.unlink()
        print(f"CLAUDE.md was empty after removal - deleted {target.resolve()}")

    _uninstall_claude_hook(project_dir or Path("."))


def _clone_repo(url: str, branch: str | None = None, out_dir: Path | None = None) -> Path:
    """Clone a GitHub repo to a local cache dir and return the path.

    Clones into ~/.graphify/repos/<owner>/<repo> by default so repeated
    runs on the same URL reuse the existing clone (git pull instead of clone).
    """
    import subprocess as _sp
    import re as _re

    # Normalise URL — strip trailing .git if present
    url = url.rstrip("/")
    if not url.endswith(".git"):
        git_url = url + ".git"
    else:
        git_url = url
        url = url[:-4]

    # Extract owner/repo from URL
    m = _re.search(r"github\.com[:/]([^/]+)/([^/]+?)(?:\.git)?$", url)
    if not m:
        print(f"error: not a recognised GitHub URL: {url}", file=sys.stderr)
        sys.exit(1)
    owner, repo = m.group(1), m.group(2)

    if out_dir:
        dest = out_dir
    else:
        dest = Path.home() / ".graphify" / "repos" / owner / repo

    if branch and branch.startswith("-"):
        print(f"error: invalid branch name: {branch!r}", file=sys.stderr)
        sys.exit(1)

    if dest.exists():
        print(f"Repo already cloned at {dest} — pulling latest...", flush=True)
        cmd = ["git", "-C", str(dest), "pull"]
        if branch:
            cmd += ["origin", "--", branch]
        result = _sp.run(cmd, capture_output=True, text=True)
        if result.returncode != 0:
            print(f"warning: git pull failed:\n{result.stderr}", file=sys.stderr)
    else:
        dest.parent.mkdir(parents=True, exist_ok=True)
        print(f"Cloning {url} → {dest} ...", flush=True)
        cmd = ["git", "clone", "--depth", "1"]
        if branch:
            cmd += ["--branch", branch]
        cmd += ["--", git_url, str(dest)]
        result = _sp.run(cmd, capture_output=True, text=True)
        if result.returncode != 0:
            print(f"error: git clone failed:\n{result.stderr}", file=sys.stderr)
            sys.exit(1)

    print(f"Ready at: {dest}", flush=True)
    return dest


def main() -> None:
    # Check all known skill install locations for a stale version stamp.
    # Skip during install/uninstall (hook writes trigger a fresh check anyway).
    # Skip during hook-check — it runs on every editor tool use and must be silent.
    # Deduplicate paths so platforms sharing the same install dir don't warn twice.
    _silent_cmds = {"install", "uninstall", "hook-check"}
    if not any(arg in _silent_cmds for arg in sys.argv):
        for skill_dst in {Path.home() / cfg["skill_dst"] for cfg in _PLATFORM_CONFIG.values()}:
            _check_skill_version(skill_dst)

    if len(sys.argv) >= 2 and sys.argv[1] in ("-v", "--version", "version"):
        print(f"graphify {__version__}")
        return

    if len(sys.argv) < 2 or sys.argv[1] in ("-h", "--help", "-?"):
        print("Usage: graphify <command>")
        print()
        print("Commands:")
        print("  install [--platform P]  copy skill to platform config dir (claude|windows|codex|opencode|aider|claw|droid|trae|trae-cn|gemini|cursor|antigravity|hermes|kiro|pi)")
        print("  uninstall               remove graphify from all detected platforms in one shot")
        print("    --purge                 also delete graphify-out/ directory")
        print("  path \"A\" \"B\"            shortest path between two nodes in graph.json")
        print("    --graph <path>          path to graph.json (default graphify-out/graph.json)")
        print("  explain \"X\"             plain-language explanation of a node and its neighbors")
        print("    --graph <path>          path to graph.json (default graphify-out/graph.json)")
        print("  diagnose multigraph    report same-endpoint edge collapse risk in graph.json")
        print("    --graph <path>          path to graph/extraction JSON")
        print("                            (default graphify-out/graph.json)")
        print("    --json                  emit machine-readable JSON")
        print("    --max-examples N        max same-endpoint examples to print (default 5)")
        print("    --directed              force directed post-build simulation")
        print("    --undirected            force undirected post-build simulation")
        print("                            (default follows JSON directed flag;")
        print("                             raw extraction with no flag defaults directed)")
        print("    --extract-path PATH     extractor source for suppression scan")
        print("  clone <github-url>      clone a GitHub repo locally and print its path for /graphify")
        print("  merge-driver <base> <current> <other>  git merge driver: union-merge two graph.json files (set up via hook install)")
        print("  merge-graphs <g1> <g2>  merge two or more graph.json files into one cross-repo graph")
        print("    --out <path>            output path (default: graphify-out/merged-graph.json)")
        print("    --branch <branch>       checkout a specific branch (default: repo default)")
        print("    --out <dir>             clone to a custom directory (default: ~/.graphify/repos/<owner>/<repo>)")
        print("  add <url>               fetch a URL and save it to ./raw, then update the graph")
        print("    --author \"Name\"         tag the author of the content")
        print("    --contributor \"Name\"    tag who added it to the corpus")
        print("    --dir <path>            target directory (default: ./raw)")
        print("  watch <path>            watch a folder and rebuild the graph on code changes")
        print("  update <path>           re-extract code files and update the graph (no LLM needed)")
        print("    --force                 overwrite graph.json even if the rebuild has fewer nodes")
        print("                            (also: GRAPHIFY_FORCE=1 env var; use after refactors that delete code)")
        print("    --no-cluster            skip clustering, write raw extraction only")
        print("  cluster-only <path>     rerun clustering on an existing graph.json and regenerate report")
        print("    --no-viz                skip graph.html generation (useful for >5000 node graphs / CI)")
        print("    --graph <path>          path to graph.json (default <path>/graphify-out/graph.json)")
        print("  query \"<question>\"       BFS traversal of graph.json for a question")
        print("    --dfs                   use depth-first instead of breadth-first")
        print("    --context C             explicit edge-context filter (repeatable)")
        print("    --budget N              cap output at N tokens (default 2000)")
        print("    --graph <path>          path to graph.json (default graphify-out/graph.json)")
        print("  save-result             save a Q&A result to graphify-out/memory/ for graph feedback loop")
        print("    --question Q            the question asked")
        print("    --answer A              the answer to save")
        print("    --type T                query type: query|path_query|explain (default: query)")
        print("    --nodes N1 N2 ...       source node labels cited in the answer")
        print("    --memory-dir DIR        memory directory (default: graphify-out/memory)")
        print("  check-update <path>     check needs_update flag and notify if semantic re-extraction is pending (cron-safe)")
        print("  tree                    emit a D3 v7 collapsible-tree HTML for graph.json")
        print("    --graph PATH            path to graph.json (default graphify-out/graph.json)")
        print("    --output HTML           output path (default graphify-out/GRAPH_TREE.html)")
        print("    --root PATH             filesystem root for the hierarchy")
        print("    --max-children N        cap children per node (default 200)")
        print("    --top-k-edges N         per-symbol outbound edges in inspector (default 12)")
        print("    --label NAME            project label in header")
        print("  extract <path>          headless full extraction (AST + semantic LLM) for CI/scripts")
        print("    --backend B             gemini|kimi|claude|openai|deepseek|ollama (default: whichever API key is set)")
        print("    --model M               override backend default model")
        print("    --max-workers N         AST extraction subprocess count (default: cpu_count)")
        print("    --token-budget N        per-chunk token cap for semantic extraction (default: 60000)")
        print("    --max-concurrency N     parallel semantic chunks in flight (default: 4; set 1 for local LLMs)")
        print("    --api-timeout S         per-request timeout in seconds for the LLM client (default: 600)")
        print("    --out DIR               output dir (default: <path>); writes <DIR>/graphify-out/")
        print("    --google-workspace      export .gdoc/.gsheet/.gslides shortcuts via gws before extraction")
        print("    --no-cluster            skip clustering, write raw extraction only")
        print("    --global                also merge the resulting graph into the global graph")
        print("    --as <tag>              repo tag for --global (default: target directory name)")
        print("  global add <graph.json>  add/update a project graph in the global graph (~/.graphify/global-graph.json)")
        print("    --as <tag>               repo tag (default: parent directory name)")
        print("  global remove <tag>      remove a repo's nodes from the global graph")
        print("  global list              list repos in the global graph")
        print("  global path              print path to the global graph file")
        print("  benchmark [graph.json]  measure token reduction vs naive full-corpus approach")
        print("  export callflow-html    emit Mermaid-based architecture/call-flow HTML")
        print("  hook install            install post-commit/post-checkout git hooks (all platforms)")
        print("  hook uninstall          remove git hooks")
        print("  hook status             check if git hooks are installed")
        print("  gemini install          write GEMINI.md section + BeforeTool hook (Gemini CLI)")
        print("  gemini uninstall        remove GEMINI.md section + BeforeTool hook")
        print("  cursor install          write .cursor/rules/graphify.mdc (Cursor)")
        print("  cursor uninstall        remove .cursor/rules/graphify.mdc")
        print("  claude install          write graphify section to CLAUDE.md + PreToolUse hook (Claude Code)")
        print("  claude uninstall        remove graphify section from CLAUDE.md + PreToolUse hook")
        print("  codex install           write graphify section to AGENTS.md (Codex)")
        print("  codex uninstall         remove graphify section from AGENTS.md")
        print("  opencode install        write graphify section to AGENTS.md + tool.execute.before plugin (OpenCode)")
        print("  opencode uninstall      remove graphify section from AGENTS.md + plugin")
        print("  aider install           write graphify section to AGENTS.md (Aider)")
        print("  aider uninstall         remove graphify section from AGENTS.md")
        print("  copilot install         copy graphify skill to ~/.copilot/skills (GitHub Copilot CLI)")
        print("  copilot uninstall       remove graphify skill from ~/.copilot/skills")
        print("  vscode install          configure VS Code Copilot Chat (skill + .github/copilot-instructions.md)")
        print("  vscode uninstall        remove VS Code Copilot Chat configuration")
        print("  claw install            write graphify section to AGENTS.md (OpenClaw)")
        print("  claw uninstall          remove graphify section from AGENTS.md")
        print("  droid install           write graphify section to AGENTS.md (Factory Droid)")
        print("  droid uninstall        remove graphify section from AGENTS.md")
        print("  trae install            write graphify section to AGENTS.md (Trae)")
        print("  trae uninstall         remove graphify section from AGENTS.md")
        print("  trae-cn install         write graphify section to AGENTS.md (Trae CN)")
        print("  trae-cn uninstall      remove graphify section from AGENTS.md")
        print("  antigravity install     write .agents/rules + .agents/workflows + skill (Google Antigravity)")
        print("  antigravity uninstall   remove .agents/rules, .agents/workflows, and skill")
        print("  hermes install          write skill to ~/.hermes/skills/graphify/ (Hermes)")
        print("  hermes uninstall        remove skill from ~/.hermes/skills/graphify/")
        print("  kiro install            write skill to .kiro/skills/graphify/ + steering file (Kiro IDE/CLI)")
        print("  kiro uninstall          remove skill + steering file")
        print("  pi install              write skill to ~/.pi/agent/skills/graphify/ (Pi coding agent)")
        print("  pi uninstall            remove skill from ~/.pi/agent/skills/graphify/")
        print()
        return

    cmd = sys.argv[1]

    # Universal help guard: -h/--help/-? anywhere after the command shows help
    # and stops — prevents flags from silently triggering destructive subcommands
    # (e.g. "cursor install --help" was silently installing into Cursor, #821).
    # Exempt: free-text commands (user string may contain these tokens), and
    # "install"/"uninstall" which have their own per-subcommand help handlers.
    _FREE_TEXT_CMDS = {"query", "explain", "path", "save-result", "install", "uninstall"}
    if cmd not in _FREE_TEXT_CMDS and any(a in {"-h", "--help", "-?"} for a in sys.argv[2:]):
        print(f"Run 'graphify --help' for full usage.")
        return

    if cmd == "install":
        # Default to windows platform on Windows, claude elsewhere
        default_platform = "windows" if platform.system() == "Windows" else "claude"
        selected_platform: str | None = None
        args = sys.argv[2:]
        i = 0
        while i < len(args):
            arg = args[i]
            if arg in ("-h", "--help"):
                _print_install_usage()
                return
            if arg.startswith("--platform="):
                candidate = arg.split("=", 1)[1]
                if selected_platform and selected_platform != candidate:
                    print("error: specify install platform only once", file=sys.stderr)
                    sys.exit(1)
                selected_platform = candidate
                i += 1
            elif arg == "--platform":
                if i + 1 >= len(args):
                    print("error: --platform requires a value", file=sys.stderr)
                    sys.exit(1)
                candidate = args[i + 1]
                if selected_platform and selected_platform != candidate:
                    print("error: specify install platform only once", file=sys.stderr)
                    sys.exit(1)
                selected_platform = candidate
                i += 2
            elif arg.startswith("-"):
                print(f"error: unknown install option '{arg}'", file=sys.stderr)
                sys.exit(1)
            else:
                if selected_platform and selected_platform != arg:
                    print("error: specify install platform only once", file=sys.stderr)
                    sys.exit(1)
                selected_platform = arg
                i += 1
        chosen_platform = selected_platform or default_platform
        install(platform=chosen_platform)
    elif cmd == "uninstall":
        purge = "--purge" in sys.argv[2:]
        uninstall_all(purge=purge)
    elif cmd == "claude":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            claude_install()
        elif subcmd == "uninstall":
            claude_uninstall()
        else:
            print("Usage: graphify claude [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "gemini":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            gemini_install()
        elif subcmd == "uninstall":
            gemini_uninstall()
        else:
            print("Usage: graphify gemini [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "cursor":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            _cursor_install(Path("."))
        elif subcmd == "uninstall":
            _cursor_uninstall(Path("."))
        else:
            print("Usage: graphify cursor [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "vscode":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            vscode_install()
        elif subcmd == "uninstall":
            vscode_uninstall()
        else:
            print("Usage: graphify vscode [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "copilot":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            install(platform="copilot")
        elif subcmd == "uninstall":
            skill_dst = Path.home() / _PLATFORM_CONFIG["copilot"]["skill_dst"]
            removed = []
            if skill_dst.exists():
                skill_dst.unlink()
                removed.append(f"skill removed: {skill_dst}")
            version_file = skill_dst.parent / ".graphify_version"
            if version_file.exists():
                version_file.unlink()
            for d in (skill_dst.parent, skill_dst.parent.parent, skill_dst.parent.parent.parent):
                try:
                    d.rmdir()
                except OSError:
                    break
            print("; ".join(removed) if removed else "nothing to remove")
        else:
            print("Usage: graphify copilot [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "kiro":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            _kiro_install(Path("."))
        elif subcmd == "uninstall":
            _kiro_uninstall(Path("."))
        else:
            print("Usage: graphify kiro [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "pi":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            install("pi")
        elif subcmd == "uninstall":
            skill_dst = Path.home() / ".pi" / "agent" / "skills" / "graphify" / "SKILL.md"
            if skill_dst.exists():
                skill_dst.unlink()
                print(f"  skill removed    ->  {skill_dst}")
            version_file = skill_dst.parent / ".graphify_version"
            if version_file.exists():
                version_file.unlink()
            for d in (skill_dst.parent, skill_dst.parent.parent, skill_dst.parent.parent.parent):
                try:
                    d.rmdir()
                except OSError:
                    break
        else:
            print("Usage: graphify pi [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd in ("aider", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            _agents_install(Path("."), cmd)
        elif subcmd == "uninstall":
            _agents_uninstall(Path("."), platform=cmd)
            if cmd == "codex":
                _uninstall_codex_hook(Path("."))
        else:
            print(f"Usage: graphify {cmd} [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "antigravity":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            _antigravity_install(Path("."))
        elif subcmd == "uninstall":
            _antigravity_uninstall(Path("."))
        else:
            print("Usage: graphify antigravity [install|uninstall]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "prs":
        from graphify.prs import cmd_prs
        cmd_prs(sys.argv[2:])
    elif cmd == "hook":
        from graphify.hooks import install as hook_install, uninstall as hook_uninstall, status as hook_status
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd == "install":
            print(hook_install(Path(".")))
        elif subcmd == "uninstall":
            print(hook_uninstall(Path(".")))
        elif subcmd == "status":
            print(hook_status(Path(".")))
        else:
            print("Usage: graphify hook [install|uninstall|status]", file=sys.stderr)
            sys.exit(1)
    elif cmd == "query":
        if len(sys.argv) < 3:
            print("Usage: graphify query \"<question>\" [--dfs] [--context C] [--budget N] [--graph path]", file=sys.stderr)
            sys.exit(1)
        from graphify.serve import _query_graph_text
        from graphify.security import sanitize_label
        from networkx.readwrite import json_graph
        question = sys.argv[2]
        use_dfs = "--dfs" in sys.argv
        budget = 2000
        graph_path = _default_graph_path()
        context_filters: list[str] = []
        args = sys.argv[3:]
        i = 0
        while i < len(args):
            if args[i] == "--budget" and i + 1 < len(args):
                try:
                    budget = int(args[i + 1])
                except ValueError:
                    print(f"error: --budget must be an integer", file=sys.stderr)
                    sys.exit(1)
                i += 2
            elif args[i].startswith("--budget="):
                try:
                    budget = int(args[i].split("=", 1)[1])
                except ValueError:
                    print(f"error: --budget must be an integer", file=sys.stderr)
                    sys.exit(1)
                i += 1
            elif args[i] == "--context" and i + 1 < len(args):
                context_filters.append(args[i + 1])
                i += 2
            elif args[i].startswith("--context="):
                context_filters.append(args[i].split("=", 1)[1])
                i += 1
            elif args[i] == "--graph" and i + 1 < len(args):
                graph_path = args[i + 1]; i += 2
            else:
                i += 1
        gp = Path(graph_path).resolve()
        if not gp.exists():
            print(f"error: graph file not found: {gp}", file=sys.stderr)
            sys.exit(1)
        if not gp.suffix == ".json":
            print(f"error: graph file must be a .json file", file=sys.stderr)
            sys.exit(1)
        _enforce_graph_size_cap_or_exit(gp)
        try:
            import json as _json
            import networkx as _nx
            _raw = _json.loads(gp.read_text(encoding="utf-8"))
            if "links" not in _raw and "edges" in _raw:
                _raw = dict(_raw, links=_raw["edges"])
            try:
                G = json_graph.node_link_graph(_raw, edges="links")
            except TypeError:
                G = json_graph.node_link_graph(_raw)
        except Exception as exc:
            print(f"error: could not load graph: {exc}", file=sys.stderr)
            sys.exit(1)
        print(
            _query_graph_text(
                G,
                question,
                mode="dfs" if use_dfs else "bfs",
                depth=2,
                token_budget=budget,
                context_filters=context_filters,
            )
        )
    elif cmd == "save-result":
        # graphify save-result --question Q --answer A --type T [--nodes N1 N2 ...]
        import argparse as _ap
        p = _ap.ArgumentParser(prog="graphify save-result")
        p.add_argument("--question", required=True)
        p.add_argument("--answer", required=True)
        p.add_argument("--type", dest="query_type", default="query")
        p.add_argument("--nodes", nargs="*", default=[])
        p.add_argument("--memory-dir", default="graphify-out/memory")
        opts = p.parse_args(sys.argv[2:])
        from graphify.ingest import save_query_result as _sqr
        out = _sqr(
            question=opts.question,
            answer=opts.answer,
            memory_dir=Path(opts.memory_dir),
            query_type=opts.query_type,
            source_nodes=opts.nodes or None,
        )
        print(f"Saved to {out}")
    elif cmd == "path":
        if len(sys.argv) < 4:
            print("Usage: graphify path \"<source>\" \"<target>\" [--graph path]", file=sys.stderr)
            sys.exit(1)
        from graphify.serve import _score_nodes
        from networkx.readwrite import json_graph
        import networkx as _nx
        source_label = sys.argv[2]
        target_label = sys.argv[3]
        graph_path = _default_graph_path()
        args = sys.argv[4:]
        for i, a in enumerate(args):
            if a == "--graph" and i + 1 < len(args):
                graph_path = args[i + 1]
        gp = Path(graph_path).resolve()
        if not gp.exists():
            print(f"error: graph file not found: {gp}", file=sys.stderr)
            sys.exit(1)
        _enforce_graph_size_cap_or_exit(gp)
        _raw = json.loads(gp.read_text(encoding="utf-8"))
        if "links" not in _raw and "edges" in _raw:
            _raw = dict(_raw, links=_raw["edges"])
        # Force directed so the renderer can recover stored caller→callee direction.
        _raw = {**_raw, "directed": True}
        try:
            G = json_graph.node_link_graph(_raw, edges="links")
        except TypeError:
            G = json_graph.node_link_graph(_raw)
        src_scored = _score_nodes(G, [t.lower() for t in source_label.split()])
        tgt_scored = _score_nodes(G, [t.lower() for t in target_label.split()])
        if not src_scored:
            print(f"No node matching '{source_label}' found.", file=sys.stderr)
            sys.exit(1)
        if not tgt_scored:
            print(f"No node matching '{target_label}' found.", file=sys.stderr)
            sys.exit(1)
        src_nid, tgt_nid = src_scored[0][1], tgt_scored[0][1]
        # Ambiguity guard: when both queries resolve to the same node, the
        # shortest path is trivially zero hops, which is almost never what the
        # caller wanted (see bug #828).
        if src_nid == tgt_nid:
            print(
                f"'{source_label}' and '{target_label}' both resolved to the same "
                f"node '{src_nid}'. Use a more specific label or the exact node ID.",
                file=sys.stderr,
            )
            sys.exit(1)
        for _name, _scored in (("source", src_scored), ("target", tgt_scored)):
            if len(_scored) >= 2:
                _top, _runner = _scored[0][0], _scored[1][0]
                if _top > 0 and (_top - _runner) / _top < 0.10:
                    print(
                        f"warning: {_name} match was ambiguous "
                        f"(top score {_top:g}, runner-up {_runner:g})",
                        file=sys.stderr,
                    )
        try:
            path_nodes = _nx.shortest_path(G.to_undirected(as_view=True), src_nid, tgt_nid)
        except (_nx.NetworkXNoPath, _nx.NodeNotFound):
            print(f"No path found between '{source_label}' and '{target_label}'.")
            sys.exit(0)
        hops = len(path_nodes) - 1
        segments = []
        from graphify.build import edge_data
        for i in range(len(path_nodes) - 1):
            u, v = path_nodes[i], path_nodes[i + 1]
            # Check which direction the stored edge points.
            if G.has_edge(u, v):
                edata = edge_data(G, u, v)
                forward = True
            else:
                edata = edge_data(G, v, u)
                forward = False
            rel = edata.get("relation", "")
            conf = edata.get("confidence", "")
            conf_str = f" [{conf}]" if conf else ""
            if i == 0:
                segments.append(G.nodes[u].get("label", u))
            if forward:
                segments.append(f"--{rel}{conf_str}--> {G.nodes[v].get('label', v)}")
            else:
                segments.append(f"<--{rel}{conf_str}-- {G.nodes[v].get('label', v)}")
        print(f"Shortest path ({hops} hops):\n  " + " ".join(segments))

    elif cmd == "explain":
        if len(sys.argv) < 3:
            print("Usage: graphify explain \"<node>\" [--graph path]", file=sys.stderr)
            sys.exit(1)
        from graphify.serve import _find_node
        from networkx.readwrite import json_graph
        label = sys.argv[2]
        graph_path = _default_graph_path()
        args = sys.argv[3:]
        for i, a in enumerate(args):
            if a == "--graph" and i + 1 < len(args):
                graph_path = args[i + 1]
        gp = Path(graph_path).resolve()
        if not gp.exists():
            print(f"error: graph file not found: {gp}", file=sys.stderr)
            sys.exit(1)
        _enforce_graph_size_cap_or_exit(gp)
        _raw = json.loads(gp.read_text(encoding="utf-8"))
        if "links" not in _raw and "edges" in _raw:
            _raw = dict(_raw, links=_raw["edges"])
        # Force directed so the renderer can recover stored caller→callee direction.
        _raw = {**_raw, "directed": True}
        try:
            G = json_graph.node_link_graph(_raw, edges="links")
        except TypeError:
            G = json_graph.node_link_graph(_raw)
        matches = _find_node(G, label)
        if not matches:
            print(f"No node matching '{label}' found.")
            sys.exit(0)
        nid = matches[0]
        d = G.nodes[nid]
        print(f"Node: {d.get('label', nid)}")
        print(f"  ID:        {nid}")
        print(f"  Source:    {d.get('source_file', '')} {d.get('source_location', '')}".rstrip())
        print(f"  Type:      {d.get('file_type', '')}")
        print(f"  Community: {d.get('community', '')}")
        print(f"  Degree:    {G.degree(nid)}")
        from graphify.build import edge_data
        connections: list[tuple[str, str, dict]] = []  # (direction, neighbor_id, edge_data)
        for nb in G.successors(nid):
            connections.append(("out", nb, edge_data(G, nid, nb)))
        for nb in G.predecessors(nid):
            connections.append(("in", nb, edge_data(G, nb, nid)))
        if connections:
            print(f"\nConnections ({len(connections)}):")
            connections.sort(key=lambda c: G.degree(c[1]), reverse=True)
            for direction, nb, edata in connections[:20]:
                rel = edata.get("relation", "")
                conf = edata.get("confidence", "")
                arrow = "-->" if direction == "out" else "<--"
                print(f"  {arrow} {G.nodes[nb].get('label', nb)} [{rel}] [{conf}]")
            if len(connections) > 20:
                print(f"  ... and {len(connections) - 20} more")

    elif cmd == "diagnose":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd != "multigraph":
            print(
                "Usage: graphify diagnose multigraph "
                "[--graph path] [--json] [--max-examples N] "
                "[--directed] [--undirected] [--extract-path path]",
                file=sys.stderr,
            )
            sys.exit(1)

        graph_path = Path(_default_graph_path())
        max_examples = 5
        directed: bool | None = None
        direction_flag: str | None = None
        json_output = False
        extract_path: Path | None = None

        i = 3
        while i < len(sys.argv):
            arg = sys.argv[i]
            if arg == "--graph":
                i += 1
                if i >= len(sys.argv):
                    print("error: --graph requires a path", file=sys.stderr)
                    sys.exit(1)
                graph_path = Path(sys.argv[i])
            elif arg == "--json":
                json_output = True
            elif arg == "--max-examples":
                i += 1
                if i >= len(sys.argv):
                    print("error: --max-examples requires an integer", file=sys.stderr)
                    sys.exit(1)
                try:
                    max_examples = int(sys.argv[i])
                except ValueError:
                    print("error: --max-examples requires an integer", file=sys.stderr)
                    sys.exit(1)
                if max_examples < 0:
                    print("error: --max-examples must be >= 0", file=sys.stderr)
                    sys.exit(1)
            elif arg == "--directed":
                if direction_flag == "undirected":
                    print(
                        "error: --directed and --undirected are mutually exclusive",
                        file=sys.stderr,
                    )
                    sys.exit(1)
                direction_flag = "directed"
                directed = True
            elif arg == "--undirected":
                if direction_flag == "directed":
                    print(
                        "error: --directed and --undirected are mutually exclusive",
                        file=sys.stderr,
                    )
                    sys.exit(1)
                direction_flag = "undirected"
                directed = False
            elif arg == "--extract-path":
                i += 1
                if i >= len(sys.argv):
                    print("error: --extract-path requires a path", file=sys.stderr)
                    sys.exit(1)
                extract_path = Path(sys.argv[i])
            else:
                print(f"error: unknown diagnose option {arg}", file=sys.stderr)
                sys.exit(1)
            i += 1

        from graphify.diagnostics import (
            diagnose_file,
            format_diagnostic_json,
            format_diagnostic_report,
        )

        try:
            summary = diagnose_file(
                graph_path,
                directed=directed,
                root=Path(".").resolve(),
                max_examples=max_examples,
                extract_path=extract_path,
            )
        except Exception as exc:
            print(f"error: {exc}", file=sys.stderr)
            sys.exit(1)

        if json_output:
            print(json.dumps(format_diagnostic_json(summary), indent=2))
        else:
            print(format_diagnostic_report(summary))

    elif cmd == "add":
        if len(sys.argv) < 3:
            print("Usage: graphify add <url> [--author Name] [--contributor Name] [--dir ./raw]", file=sys.stderr)
            sys.exit(1)
        from graphify.ingest import ingest as _ingest
        url = sys.argv[2]
        author: str | None = None
        contributor: str | None = None
        target_dir = Path("raw")
        args = sys.argv[3:]
        i = 0
        while i < len(args):
            if args[i] == "--author" and i + 1 < len(args):
                author = args[i + 1]; i += 2
            elif args[i] == "--contributor" and i + 1 < len(args):
                contributor = args[i + 1]; i += 2
            elif args[i] == "--dir" and i + 1 < len(args):
                target_dir = Path(args[i + 1]); i += 2
            else:
                i += 1
        try:
            saved = _ingest(url, target_dir, author=author, contributor=contributor)
            print(f"Saved to {saved}")
            print("Run /graphify --update in your AI assistant to update the graph.")
        except Exception as exc:
            print(f"error: {exc}", file=sys.stderr)
            sys.exit(1)

    elif cmd == "watch":
        watch_path = Path(sys.argv[2]) if len(sys.argv) > 2 else Path(".")
        if not watch_path.exists():
            print(f"error: path not found: {watch_path}", file=sys.stderr)
            sys.exit(1)
        from graphify.watch import watch as _watch
        try:
            _watch(watch_path)
        except ImportError as exc:
            print(f"error: {exc}", file=sys.stderr)
            sys.exit(1)

    elif cmd == "cluster-only":
        # Mirror the tree/export arg-parsing pattern: walk argv so flags and
        # the optional positional path can appear in any order (#724).
        no_viz = "--no-viz" in sys.argv
        _min_cs_arg = next((a for a in sys.argv if a.startswith("--min-community-size=")), None)
        min_community_size = int(_min_cs_arg.split("=")[1]) if _min_cs_arg else 3
        args = sys.argv[2:]
        watch_path: Path | None = None
        graph_override: Path | None = None
        co_resolution: float = 1.0
        co_exclude_hubs: float | None = None
        i_arg = 0
        while i_arg < len(args):
            a = args[i_arg]
            if a == "--graph" and i_arg + 1 < len(args):
                graph_override = Path(args[i_arg + 1]); i_arg += 2
            elif a == "--resolution" and i_arg + 1 < len(args):
                co_resolution = float(args[i_arg + 1]); i_arg += 2
            elif a.startswith("--resolution="):
                co_resolution = float(a.split("=", 1)[1]); i_arg += 1
            elif a == "--exclude-hubs" and i_arg + 1 < len(args):
                co_exclude_hubs = float(args[i_arg + 1]); i_arg += 2
            elif a.startswith("--exclude-hubs="):
                co_exclude_hubs = float(a.split("=", 1)[1]); i_arg += 1
            elif a == "--no-viz" or a.startswith("--min-community-size="):
                i_arg += 1
            elif a.startswith("--"):
                i_arg += 1
            elif watch_path is None:
                watch_path = Path(a); i_arg += 1
            else:
                i_arg += 1
        if watch_path is None:
            watch_path = Path(".")
        graph_json = graph_override if graph_override is not None else watch_path / "graphify-out" / "graph.json"
        if not graph_json.exists():
            print(f"error: no graph found at {graph_json} — run /graphify first", file=sys.stderr)
            sys.exit(1)
        from networkx.readwrite import json_graph as _jg
        from graphify.build import build_from_json
        from graphify.cluster import cluster, score_all
        from graphify.analyze import god_nodes, surprising_connections, suggest_questions
        from graphify.report import generate
        from graphify.export import to_json, to_html
        print("Loading existing graph...")
        _enforce_graph_size_cap_or_exit(graph_json)
        _raw = json.loads(graph_json.read_text(encoding="utf-8"))
        _directed = bool(_raw.get("directed", False))
        G = build_from_json(_raw, directed=_directed)
        print(f"Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges")
        print("Re-clustering...")
        communities = cluster(G, resolution=co_resolution, exclude_hubs_percentile=co_exclude_hubs)
        cohesion = score_all(G, communities)
        gods = god_nodes(G)
        surprises = surprising_connections(G, communities)
        out = watch_path / "graphify-out"
        out.mkdir(parents=True, exist_ok=True)
        labels_path = out / ".graphify_labels.json"
        if labels_path.exists():
            try:
                labels = {int(k): v for k, v in json.loads(labels_path.read_text(encoding="utf-8")).items()}
            except Exception:
                labels = {cid: f"Community {cid}" for cid in communities}
        else:
            labels = {cid: f"Community {cid}" for cid in communities}
        questions = suggest_questions(G, communities, labels)
        tokens = {"input": 0, "output": 0}
        from graphify.export import _git_head as _gh
        _commit = _gh()
        report = generate(G, communities, cohesion, labels, gods, surprises,
                          {"warning": "cluster-only mode — file stats not available"},
                          tokens, str(watch_path), suggested_questions=questions,
                          min_community_size=min_community_size, built_at_commit=_commit)
        (out / "GRAPH_REPORT.md").write_text(report, encoding="utf-8")
        from graphify.export import backup_if_protected as _backup
        _backup(out)
        to_json(G, communities, str(out / "graph.json"))
        labels_path.write_text(json.dumps({str(k): v for k, v in labels.items()}, ensure_ascii=False), encoding="utf-8")

        # Mirror watch.py pattern: gate to_html so core outputs (graph.json +
        # GRAPH_REPORT.md) always land. Honor --no-viz explicitly; otherwise
        # fall back to ValueError handling so an oversized graph doesn't crash
        # the CLI mid-write and leave a stale graph.html on disk.
        html_target = out / "graph.html"
        if no_viz:
            if html_target.exists():
                html_target.unlink()
            print(f"Done — {len(communities)} communities. GRAPH_REPORT.md and graph.json updated (--no-viz; graph.html removed).")
        else:
            try:
                to_html(G, communities, str(html_target), community_labels=labels or None)
                print(f"Done — {len(communities)} communities. GRAPH_REPORT.md, graph.json and graph.html updated.")
            except ValueError as viz_err:
                if html_target.exists():
                    html_target.unlink()
                print(f"Skipped graph.html: {viz_err}")
                print(f"Done — {len(communities)} communities. GRAPH_REPORT.md and graph.json updated.")

    elif cmd == "update":
        force = os.environ.get("GRAPHIFY_FORCE", "").lower() in ("1", "true", "yes")
        no_cluster = False
        args = sys.argv[2:]
        watch_arg: str | None = None
        for a in args:
            if a == "--force":
                force = True
                continue
            if a == "--no-cluster":
                no_cluster = True
                continue
            if a.startswith("-"):
                print(f"error: unknown update option: {a}", file=sys.stderr)
                sys.exit(2)
            if watch_arg is not None:
                print("error: update accepts at most one path argument", file=sys.stderr)
                sys.exit(2)
            watch_arg = a

        if watch_arg is not None:
            watch_path = Path(watch_arg)
        else:
            # Try to recover the scan root saved by the last full build
            saved = Path(_GRAPHIFY_OUT) / ".graphify_root"
            if saved.exists():
                watch_path = Path(saved.read_text(encoding="utf-8").strip())
            else:
                watch_path = Path(".")
        if not watch_path.exists():
            print(f"error: path not found: {watch_path}", file=sys.stderr)
            sys.exit(1)
        from graphify.watch import _rebuild_code
        print(f"Re-extracting code files in {watch_path} (no LLM needed)...")
        # Interactive CLI: block on the per-repo lock rather than skip, so the
        # user sees their explicit `graphify update` complete instead of
        # exiting silently when a hook-driven rebuild happens to be running.
        ok = _rebuild_code(watch_path, force=force, no_cluster=no_cluster, block_on_lock=True)
        if ok:
            print("Code graph updated. For doc/paper/image changes run /graphify --update in your AI assistant.")
            if not (
                os.environ.get("GEMINI_API_KEY")
                or os.environ.get("GOOGLE_API_KEY")
                or os.environ.get("MOONSHOT_API_KEY")
                or os.environ.get("DEEPSEEK_API_KEY")
                or os.environ.get("GRAPHIFY_NO_TIPS")
            ):
                print("Tip: set GEMINI_API_KEY or GOOGLE_API_KEY to use Gemini for semantic extraction.")
        else:
            print("Nothing to update or rebuild failed — check output above.", file=sys.stderr)
            sys.exit(1)

    elif cmd == "hook-check":
        # Codex Desktop rejects hookSpecificOutput.additionalContext on PreToolUse.
        # Keep this as a cross-platform no-op so installed hooks never break Bash
        # tool calls. Graph guidance reaches the agent via AGENTS.md / skill instead.
        sys.exit(0)
    elif cmd == "check-update":
        if len(sys.argv) < 3:
            print("Usage: graphify check-update <path>", file=sys.stderr)
            sys.exit(1)
        from graphify.watch import check_update
        check_update(Path(sys.argv[2]).resolve())
        sys.exit(0)
    elif cmd == "tree":
        # Emit a D3 v7 collapsible-tree HTML view of graph.json:
        # expand-all / collapse-all / reset-view buttons, multi-line
        # wrapText labels with separately-coloured name + count,
        # depth-based palette, click-to-toggle subtree, hover inspector
        # showing top-K outbound edges per symbol.
        from typing import Optional as _Opt
        from graphify.tree_html import write_tree_html, DEFAULT_MAX_CHILDREN
        graph_path = Path(_GRAPHIFY_OUT) / "graph.json"
        output_path: "_Opt[Path]" = None
        root: "_Opt[str]" = None
        max_children = DEFAULT_MAX_CHILDREN
        top_k_edges = 0
        project_label: "_Opt[str]" = None
        args = sys.argv[2:]
        i_arg = 0
        while i_arg < len(args):
            a = args[i_arg]
            if a == "--graph" and i_arg + 1 < len(args):
                graph_path = Path(args[i_arg + 1]); i_arg += 2
            elif a == "--output" and i_arg + 1 < len(args):
                output_path = Path(args[i_arg + 1]); i_arg += 2
            elif a == "--root" and i_arg + 1 < len(args):
                root = args[i_arg + 1]; i_arg += 2
            elif a == "--max-children" and i_arg + 1 < len(args):
                max_children = int(args[i_arg + 1]); i_arg += 2
            elif a == "--top-k-edges" and i_arg + 1 < len(args):
                top_k_edges = int(args[i_arg + 1]); i_arg += 2
            elif a == "--label" and i_arg + 1 < len(args):
                project_label = args[i_arg + 1]; i_arg += 2
            elif a in ("-h", "--help"):
                print("Usage: graphify tree [--graph PATH] [--output HTML]")
                print("  --graph PATH         path to graph.json (default graphify-out/graph.json)")
                print("  --output HTML        output path (default graphify-out/GRAPH_TREE.html)")
                print("  --root PATH          filesystem root (default: longest common dir of all source_files)")
                print("  --max-children N     cap visible children per node (default 200)")
                print("  --top-k-edges N      pre-compute top-K outbound edges per symbol (default 12)")
                print("  --label NAME         project label shown in the page header")
                return
            else:
                i_arg += 1
        if not graph_path.is_file():
            print(f"error: graph.json not found at {graph_path}", file=sys.stderr)
            sys.exit(1)
        _enforce_graph_size_cap_or_exit(graph_path)
        if output_path is None:
            output_path = graph_path.parent / "GRAPH_TREE.html"
        out = write_tree_html(
            graph_path=graph_path, output_path=output_path,
            root=root, max_children=max_children,
            top_k_edges=top_k_edges, project_label=project_label,
        )
        size_kb = out.stat().st_size / 1024
        print(f"wrote {out} ({size_kb:.1f} KB)")
        print(f"open with: xdg-open {out}  (or file://{out.resolve()})")
        sys.exit(0)

    elif cmd == "merge-driver":
        # git merge driver for graph.json — takes (base, current, other) and writes
        # the union of current+other nodes/edges back to current. Exits 1 on
        # corrupt input so git surfaces the conflict instead of silently
        # accepting a poisoned merge (see F-005).
        # Usage: graphify merge-driver %O %A %B  (set in .git/config merge driver)
        if len(sys.argv) < 5:
            print("Usage: graphify merge-driver <base> <current> <other>", file=sys.stderr)
            sys.exit(1)
        _base_path, _current_path, _other_path = sys.argv[2], sys.argv[3], sys.argv[4]
        # Hard caps so a malicious or corrupted graph.json cannot exhaust memory
        # at parse time. 50 MB / 100k nodes are well above any realistic graph
        # (typical graphs are <5 MB / <50k nodes); anything larger should fail
        # the merge so a human can investigate.
        _MERGE_MAX_BYTES = 50 * 1024 * 1024
        _MERGE_MAX_NODES = 100_000
        import networkx as _nx
        from networkx.readwrite import json_graph as _jg
        def _load_graph(p: str):
            path_obj = Path(p)
            try:
                size = path_obj.stat().st_size
            except OSError as exc:
                raise RuntimeError(f"cannot stat {p}: {exc}") from exc
            if size > _MERGE_MAX_BYTES:
                raise RuntimeError(
                    f"graph.json {p} is {size} bytes, exceeds {_MERGE_MAX_BYTES}-byte cap"
                )
            data = json.loads(path_obj.read_text(encoding="utf-8"))
            try:
                return _jg.node_link_graph(data, edges="links"), data
            except TypeError:
                return _jg.node_link_graph(data), data
        try:
            G_cur, _ = _load_graph(_current_path)
            G_oth, _ = _load_graph(_other_path)
        except Exception as exc:
            print(f"[graphify merge-driver] error loading graphs: {exc}", file=sys.stderr)
            sys.exit(1)  # surface the conflict so git doesn't accept a corrupt merge
        merged = _nx.compose(G_cur, G_oth)
        if merged.number_of_nodes() > _MERGE_MAX_NODES:
            print(
                f"[graphify merge-driver] merged graph has {merged.number_of_nodes()} nodes, "
                f"exceeds {_MERGE_MAX_NODES}-node cap; aborting merge.",
                file=sys.stderr,
            )
            sys.exit(1)
        try:
            out_data = _jg.node_link_data(merged, edges="links")
        except TypeError:
            out_data = _jg.node_link_data(merged)
        Path(_current_path).write_text(json.dumps(out_data, indent=2), encoding="utf-8")
        sys.exit(0)

    elif cmd == "merge-graphs":
        # graphify merge-graphs graph1.json graph2.json ... --out merged.json
        args = sys.argv[2:]
        graph_paths: list[Path] = []
        out_path = Path(_GRAPHIFY_OUT) / "merged-graph.json"
        i = 0
        while i < len(args):
            if args[i] == "--out" and i + 1 < len(args):
                out_path = Path(args[i + 1]); i += 2
            else:
                graph_paths.append(Path(args[i])); i += 1
        if len(graph_paths) < 2:
            print("Usage: graphify merge-graphs <graph1.json> <graph2.json> [...] [--out merged.json]", file=sys.stderr)
            sys.exit(1)
        import networkx as _nx
        from networkx.readwrite import json_graph as _jg
        from graphify.build import prefix_graph_for_global as _prefix
        graphs = []
        for gp in graph_paths:
            if not gp.exists():
                print(f"error: not found: {gp}", file=sys.stderr)
                sys.exit(1)
            _enforce_graph_size_cap_or_exit(gp)
            data = json.loads(gp.read_text(encoding="utf-8"))
            # Normalize edges/links key before loading — graphify writes "links"
            # via node_link_data but older runs may have used "edges" (#738).
            if "links" not in data and "edges" in data:
                data = dict(data, links=data["edges"])
            try:
                G = _jg.node_link_graph(data, edges="links")
            except TypeError:
                G = _jg.node_link_graph(data)
            graphs.append(G)
        merged = _nx.Graph()
        for G, gp in zip(graphs, graph_paths):
            repo_tag = gp.parent.parent.name  # graphify-out/../ → repo dir name
            prefixed = _prefix(G, repo_tag)
            merged = _nx.compose(merged, prefixed)
        try:
            out_data = _jg.node_link_data(merged, edges="links")
        except TypeError:
            out_data = _jg.node_link_data(merged)
        out_path.parent.mkdir(parents=True, exist_ok=True)
        out_path.write_text(json.dumps(out_data, indent=2), encoding="utf-8")
        print(f"Merged {len(graphs)} graphs → {merged.number_of_nodes()} nodes, {merged.number_of_edges()} edges")
        print(f"Written to: {out_path}")

    elif cmd == "clone":
        if len(sys.argv) < 3:
            print("Usage: graphify clone <github-url> [--branch <branch>] [--out <dir>]", file=sys.stderr)
            sys.exit(1)
        url = sys.argv[2]
        branch: str | None = None
        out_dir: Path | None = None
        args = sys.argv[3:]
        i = 0
        while i < len(args):
            if args[i] == "--branch" and i + 1 < len(args):
                branch = args[i + 1]; i += 2
            elif args[i] == "--out" and i + 1 < len(args):
                out_dir = Path(args[i + 1]); i += 2
            else:
                i += 1
        local_path = _clone_repo(url, branch=branch, out_dir=out_dir)
        print(local_path)

    elif cmd == "export":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        if subcmd not in ("html", "callflow-html", "obsidian", "wiki", "svg", "graphml", "neo4j"):
            print("Usage: graphify export <format>", file=sys.stderr)
            print("  html      [--graph PATH] [--labels PATH] [--node-limit N] [--no-viz]", file=sys.stderr)
            print("  callflow-html [GRAPH|DIR] [--graph PATH] [--labels PATH] [--report PATH] [--sections PATH] [--output HTML]", file=sys.stderr)
            print("            [--lang auto|zh-CN|en] [--max-sections N] [--diagram-scale N]", file=sys.stderr)
            print("  obsidian  [--graph PATH] [--labels PATH] [--dir PATH]", file=sys.stderr)
            print("  wiki      [--graph PATH] [--labels PATH]", file=sys.stderr)
            print("  svg       [--graph PATH] [--labels PATH]", file=sys.stderr)
            print("  graphml   [--graph PATH]", file=sys.stderr)
            print("  neo4j     [--graph PATH] [--push URI] [--user U] [--password P]", file=sys.stderr)
            print("            (or set NEO4J_PASSWORD instead of --password to keep it off argv)", file=sys.stderr)
            sys.exit(1)

        # Parse shared args
        args = sys.argv[3:]
        graph_path = Path(_GRAPHIFY_OUT) / "graph.json"
        graph_path_explicit = False
        labels_path = Path(_GRAPHIFY_OUT) / ".graphify_labels.json"
        labels_path_explicit = False
        report_path = Path(_GRAPHIFY_OUT) / "GRAPH_REPORT.md"
        report_path_explicit = False
        sections_path: Path | None = None
        callflow_output: Path | None = None
        callflow_lang = "auto"
        callflow_max_sections = 15
        callflow_diagram_scale = 1.0
        callflow_max_diagram_nodes = 18
        callflow_max_diagram_edges = 24
        analysis_path = Path(_GRAPHIFY_OUT) / ".graphify_analysis.json"
        node_limit = 5000
        no_viz = False
        obsidian_dir = Path(_GRAPHIFY_OUT) / "obsidian"
        neo4j_uri: str | None = None
        neo4j_user = "neo4j"
        # F-031: prefer the NEO4J_PASSWORD env var so the password never
        # appears on argv (visible in `ps` output / shell history). The
        # explicit --password flag still overrides it for compatibility.
        neo4j_password: str | None = os.environ.get("NEO4J_PASSWORD") or None
        i = 0
        while i < len(args):
            a = args[i]
            if a == "--graph" and i + 1 < len(args):
                graph_path = Path(args[i + 1])
                graph_path_explicit = True
                i += 2
            elif a == "--labels" and i + 1 < len(args):
                labels_path = Path(args[i + 1])
                labels_path_explicit = True
                i += 2
            elif a == "--report" and i + 1 < len(args):
                report_path = Path(args[i + 1])
                report_path_explicit = True
                i += 2
            elif a == "--sections" and i + 1 < len(args):
                sections_path = Path(args[i + 1]); i += 2
            elif a == "--output" and i + 1 < len(args):
                callflow_output = Path(args[i + 1]).expanduser()
                if not callflow_output.is_absolute():
                    callflow_output = Path.cwd() / callflow_output
                i += 2
            elif a == "--lang" and i + 1 < len(args):
                callflow_lang = args[i + 1]; i += 2
            elif a == "--max-sections" and i + 1 < len(args):
                callflow_max_sections = int(args[i + 1]); i += 2
            elif a == "--diagram-scale" and i + 1 < len(args):
                callflow_diagram_scale = float(args[i + 1]); i += 2
            elif a == "--max-diagram-nodes" and i + 1 < len(args):
                callflow_max_diagram_nodes = int(args[i + 1]); i += 2
            elif a == "--max-diagram-edges" and i + 1 < len(args):
                callflow_max_diagram_edges = int(args[i + 1]); i += 2
            elif a in ("-h", "--help") and subcmd == "callflow-html":
                print("Usage: graphify export callflow-html [GRAPH|DIR] [--graph PATH] [--labels PATH]")
                print("  --report PATH          path to GRAPH_REPORT.md")
                print("  --sections PATH        JSON section definitions")
                print("  --output HTML          output path (default graphify-out/<project>-callflow.html)")
                print("  --lang LANG            auto, zh-CN, en, etc. (default auto)")
                print("  --max-sections N       maximum auto-derived sections (default 15)")
                print("  --diagram-scale N      Mermaid diagram scale (default 1.0)")
                print("  --max-diagram-nodes N  representative nodes per section (default 18)")
                print("  --max-diagram-edges N  representative edges per section (default 24)")
                sys.exit(0)
            elif a == "--node-limit" and i + 1 < len(args):
                node_limit = int(args[i + 1]); i += 2
            elif a == "--no-viz":
                no_viz = True; i += 1
            elif a == "--dir" and i + 1 < len(args):
                obsidian_dir = Path(args[i + 1]); i += 2
            elif a == "--push" and i + 1 < len(args):
                neo4j_uri = args[i + 1]; i += 2
            elif a == "--user" and i + 1 < len(args):
                neo4j_user = args[i + 1]; i += 2
            elif a == "--password" and i + 1 < len(args):
                neo4j_password = args[i + 1]; i += 2
            elif subcmd == "callflow-html" and not a.startswith("-") and not graph_path_explicit:
                candidate = Path(a)
                if candidate.name == "graph.json" or candidate.suffix.lower() == ".json":
                    graph_path = candidate
                elif (candidate / "graph.json").exists():
                    graph_path = candidate / "graph.json"
                else:
                    graph_path = candidate / _GRAPHIFY_OUT / "graph.json"
                graph_path_explicit = True
                i += 1
            else:
                i += 1

        graph_path = graph_path.expanduser()
        if graph_path_explicit:
            graph_out_dir = graph_path.parent
            if not labels_path_explicit:
                labels_path = graph_out_dir / ".graphify_labels.json"
            if not report_path_explicit:
                report_path = graph_out_dir / "GRAPH_REPORT.md"
        labels_path = labels_path.expanduser()
        report_path = report_path.expanduser()

        if not graph_path.exists():
            print(f"error: graph not found: {graph_path}. Run /graphify <path> first.", file=sys.stderr)
            sys.exit(1)

        if subcmd == "callflow-html":
            from graphify.callflow_html import write_callflow_html as _write_callflow_html
            out = _write_callflow_html(
                graph=graph_path,
                report=report_path,
                labels=labels_path,
                sections=sections_path,
                output=callflow_output,
                lang=callflow_lang,
                max_sections=callflow_max_sections,
                diagram_scale=callflow_diagram_scale,
                max_diagram_nodes=callflow_max_diagram_nodes,
                max_diagram_edges=callflow_max_diagram_edges,
                verbose=True,
            )
            print(f"callflow HTML written - open in any browser: {out}")
            sys.exit(0)

        from networkx.readwrite import json_graph as _jg
        from graphify.build import build_from_json as _bfj

        _enforce_graph_size_cap_or_exit(graph_path)
        _raw = json.loads(graph_path.read_text(encoding="utf-8"))
        if "links" not in _raw and "edges" in _raw:
            _raw = dict(_raw, links=_raw["edges"])
        try:
            G = _jg.node_link_graph(_raw, edges="links")
        except TypeError:
            G = _jg.node_link_graph(_raw)

        # Load optional analysis/labels
        communities: dict[int, list[str]] = {}
        if analysis_path.exists():
            _an = json.loads(analysis_path.read_text(encoding="utf-8"))
            communities = {int(k): v for k, v in _an.get("communities", {}).items()}
            cohesion: dict[int, float] = {int(k): v for k, v in _an.get("cohesion", {}).items()}
            gods_data = _an.get("gods", [])
        else:
            cohesion = {}
            gods_data = []

        labels: dict[int, str] = {}
        if labels_path.exists():
            labels = {int(k): v for k, v in json.loads(labels_path.read_text(encoding="utf-8")).items()}

        out_dir = graph_path.parent

        if subcmd == "html":
            from graphify.export import to_html as _to_html
            if no_viz:
                html_target = out_dir / "graph.html"
                if html_target.exists():
                    html_target.unlink()
                print("--no-viz: skipped graph.html")
            else:
                _to_html(G, communities, str(out_dir / "graph.html"),
                         community_labels=labels or None, node_limit=node_limit)
                if G.number_of_nodes() <= node_limit:
                    print(f"graph.html written - open in any browser, no server needed")

        elif subcmd == "obsidian":
            from graphify.export import to_obsidian as _to_obsidian, to_canvas as _to_canvas
            n = _to_obsidian(G, communities, str(obsidian_dir),
                             community_labels=labels or None, cohesion=cohesion or None)
            print(f"Obsidian vault: {n} notes in {obsidian_dir}/")
            _to_canvas(G, communities, str(obsidian_dir / "graph.canvas"),
                       community_labels=labels or None)
            print(f"Canvas: {obsidian_dir}/graph.canvas")
            print(f"Open {obsidian_dir}/ as a vault in Obsidian.")

        elif subcmd == "wiki":
            from graphify.wiki import to_wiki as _to_wiki
            from graphify.analyze import god_nodes as _god_nodes
            if not communities:
                print(
                    "error: .graphify_analysis.json is missing or empty — refusing to export wiki to prevent data loss.\n"
                    "Run `graphify extract .` (or `graphify cluster-only .`) to regenerate community data first.",
                    file=sys.stderr,
                )
                sys.exit(1)
            if not gods_data:
                gods_data = _god_nodes(G)
            n = _to_wiki(G, communities, str(out_dir / "wiki"),
                         community_labels=labels or None, cohesion=cohesion or None,
                         god_nodes_data=gods_data)
            print(f"Wiki: {n} articles written to {out_dir}/wiki/")
            print(f"  {out_dir}/wiki/index.md  ->  agent entry point")

        elif subcmd == "svg":
            from graphify.export import to_svg as _to_svg
            _to_svg(G, communities, str(out_dir / "graph.svg"),
                    community_labels=labels or None)
            print(f"graph.svg written - embeds in Obsidian, Notion, GitHub READMEs")

        elif subcmd == "graphml":
            from graphify.export import to_graphml as _to_graphml
            _to_graphml(G, communities, str(out_dir / "graph.graphml"))
            print(f"graph.graphml written - open in Gephi, yEd, or any GraphML tool")

        elif subcmd == "neo4j":
            if neo4j_uri:
                from graphify.export import push_to_neo4j as _push
                if neo4j_password is None:
                    print("error: --password required for --push", file=sys.stderr)
                    sys.exit(1)
                result = _push(G, uri=neo4j_uri, user=neo4j_user,
                               password=neo4j_password, communities=communities)
                print(f"Pushed to Neo4j: {result['nodes']} nodes, {result['edges']} edges")
            else:
                from graphify.export import to_cypher as _to_cypher
                _to_cypher(G, str(out_dir / "cypher.txt"))
                print(f"cypher.txt written - import with: cypher-shell < {out_dir}/cypher.txt")

    elif cmd == "benchmark":
        from graphify.benchmark import run_benchmark, print_benchmark
        graph_path = sys.argv[2] if len(sys.argv) > 2 else "graphify-out/graph.json"
        _enforce_graph_size_cap_or_exit(Path(graph_path))
        # Try to load corpus_words from detect output
        corpus_words = None
        detect_path = Path(".graphify_detect.json")
        if detect_path.exists():
            try:
                detect_data = json.loads(detect_path.read_text(encoding="utf-8"))
                corpus_words = detect_data.get("total_words")
            except Exception:
                pass
        result = run_benchmark(graph_path, corpus_words=corpus_words)
        print_benchmark(result)

    elif cmd == "global":
        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
        from graphify.global_graph import (
            global_add as _global_add,
            global_remove as _global_remove,
            global_list as _global_list,
            global_path as _global_path,
        )
        if subcmd == "add":
            # graphify global add <graph.json> [--as <tag>]
            args = sys.argv[3:]
            source = None
            tag = None
            i = 0
            while i < len(args):
                if args[i] == "--as" and i + 1 < len(args):
                    tag = args[i + 1]; i += 2
                elif not source:
                    source = Path(args[i]); i += 1
                else:
                    i += 1
            if not source:
                print("Usage: graphify global add <graph.json> [--as <repo-tag>]", file=sys.stderr)
                sys.exit(1)
            tag = tag or source.parent.parent.name
            try:
                result = _global_add(source, tag)
                if result["skipped"]:
                    print(f"'{tag}' unchanged since last add — global graph not modified.")
                else:
                    print(f"Added '{tag}' to global graph: +{result['nodes_added']} nodes, "
                          f"-{result['nodes_removed']} pruned. Global: {_global_path()}")
            except Exception as exc:
                print(f"error: {exc}", file=sys.stderr); sys.exit(1)
        elif subcmd == "remove":
            tag = sys.argv[3] if len(sys.argv) > 3 else ""
            if not tag:
                print("Usage: graphify global remove <repo-tag>", file=sys.stderr); sys.exit(1)
            try:
                removed = _global_remove(tag)
                print(f"Removed '{tag}' from global graph ({removed} nodes pruned).")
            except KeyError as exc:
                print(f"error: {exc}", file=sys.stderr); sys.exit(1)
        elif subcmd == "list":
            repos = _global_list()
            if not repos:
                print("Global graph is empty. Use 'graphify global add' to add a project.")
            else:
                print(f"Global graph: {_global_path()}")
                for tag, info in repos.items():
                    print(f"  {tag}: {info.get('node_count', '?')} nodes, added {info.get('added_at', '?')[:10]}")
        elif subcmd == "path":
            print(_global_path())
        else:
            print("Usage: graphify global [add|remove|list|path]", file=sys.stderr); sys.exit(1)

    elif cmd == "extract":
        # Headless full-pipeline extraction for CI / scripts (#698).
        # Runs detect -> AST extraction on code -> semantic LLM extraction on
        # docs/papers/images -> merge -> build -> cluster -> write outputs.
        # Unlike the skill.md path (which runs through Claude Code subagents),
        # this calls extract_corpus_parallel directly using whichever backend
        # has an API key set.
        if len(sys.argv) < 3:
            print(
                "Usage: graphify extract <path> [--backend gemini|kimi|claude|openai|deepseek|ollama] "
                "[--model M] [--out DIR] [--google-workspace] [--no-cluster] "
                "[--max-workers N] [--token-budget N] [--max-concurrency N] "
                "[--api-timeout S]",
                file=sys.stderr,
            )
            sys.exit(1)

        target = Path(sys.argv[2]).resolve()
        if not target.exists():
            print(f"error: path not found: {target}", file=sys.stderr)
            sys.exit(1)

        backend: str | None = None
        model: str | None = None
        out_dir: Path | None = None
        no_cluster = False
        dedup_llm = False
        google_workspace = False
        global_merge = False
        global_repo_tag: str | None = None
        # Performance/tuning knobs (issue #792). None means "use library default".
        cli_max_workers: int | None = None
        cli_token_budget: int | None = None
        cli_max_concurrency: int | None = None
        cli_api_timeout: float | None = None
        # Clustering tuning knobs
        cli_resolution: float = 1.0
        cli_exclude_hubs: float | None = None
        cli_excludes: list[str] = []

        def _parse_int(name: str, raw: str) -> int:
            try:
                v = int(raw)
            except ValueError:
                print(f"error: {name} must be a positive integer (got {raw!r})", file=sys.stderr)
                sys.exit(2)
            if v <= 0:
                print(f"error: {name} must be > 0 (got {v})", file=sys.stderr)
                sys.exit(2)
            return v

        def _parse_float(name: str, raw: str) -> float:
            try:
                v = float(raw)
            except ValueError:
                print(f"error: {name} must be a positive number (got {raw!r})", file=sys.stderr)
                sys.exit(2)
            if v <= 0:
                print(f"error: {name} must be > 0 (got {v})", file=sys.stderr)
                sys.exit(2)
            return v

        args = sys.argv[3:]
        i = 0
        while i < len(args):
            a = args[i]
            if a == "--backend" and i + 1 < len(args):
                backend = args[i + 1]; i += 2
            elif a.startswith("--backend="):
                backend = a.split("=", 1)[1]; i += 1
            elif a == "--model" and i + 1 < len(args):
                model = args[i + 1]; i += 2
            elif a.startswith("--model="):
                model = a.split("=", 1)[1]; i += 1
            elif a == "--out" and i + 1 < len(args):
                out_dir = Path(args[i + 1]); i += 2
            elif a.startswith("--out="):
                out_dir = Path(a.split("=", 1)[1]); i += 1
            elif a == "--no-cluster":
                no_cluster = True; i += 1
            elif a == "--dedup-llm":
                dedup_llm = True; i += 1
            elif a == "--google-workspace":
                google_workspace = True; i += 1
            elif a == "--global":
                global_merge = True; i += 1
            elif a == "--as" and i + 1 < len(args):
                global_repo_tag = args[i + 1]; i += 2
            elif a == "--max-workers" and i + 1 < len(args):
                cli_max_workers = _parse_int("--max-workers", args[i + 1]); i += 2
            elif a.startswith("--max-workers="):
                cli_max_workers = _parse_int("--max-workers", a.split("=", 1)[1]); i += 1
            elif a == "--token-budget" and i + 1 < len(args):
                cli_token_budget = _parse_int("--token-budget", args[i + 1]); i += 2
            elif a.startswith("--token-budget="):
                cli_token_budget = _parse_int("--token-budget", a.split("=", 1)[1]); i += 1
            elif a == "--max-concurrency" and i + 1 < len(args):
                cli_max_concurrency = _parse_int("--max-concurrency", args[i + 1]); i += 2
            elif a.startswith("--max-concurrency="):
                cli_max_concurrency = _parse_int("--max-concurrency", a.split("=", 1)[1]); i += 1
            elif a == "--api-timeout" and i + 1 < len(args):
                cli_api_timeout = _parse_float("--api-timeout", args[i + 1]); i += 2
            elif a.startswith("--api-timeout="):
                cli_api_timeout = _parse_float("--api-timeout", a.split("=", 1)[1]); i += 1
            elif a == "--resolution" and i + 1 < len(args):
                cli_resolution = _parse_float("--resolution", args[i + 1]); i += 2
            elif a.startswith("--resolution="):
                cli_resolution = _parse_float("--resolution", a.split("=", 1)[1]); i += 1
            elif a == "--exclude-hubs" and i + 1 < len(args):
                cli_exclude_hubs = float(args[i + 1]); i += 2
            elif a.startswith("--exclude-hubs="):
                cli_exclude_hubs = float(a.split("=", 1)[1]); i += 1
            elif a == "--exclude" and i + 1 < len(args):
                cli_excludes.append(args[i + 1]); i += 2
            elif a.startswith("--exclude="):
                cli_excludes.append(a.split("=", 1)[1]); i += 1
            else:
                i += 1

        # CLI flag wins over env var. Setting GRAPHIFY_API_TIMEOUT here so
        # _call_openai_compat picks it up without needing a new kwarg path.
        if cli_api_timeout is not None:
            os.environ["GRAPHIFY_API_TIMEOUT"] = str(cli_api_timeout)
        if cli_max_workers is not None:
            os.environ["GRAPHIFY_MAX_WORKERS"] = str(cli_max_workers)

        # Backend resolution. If user did not pass --backend, sniff env.
        # If backend was explicitly requested, validate its key is present
        # and surface a clear error early — don't let extract_corpus_parallel
        # raise mid-run after we've spent time on AST extraction.
        from graphify.llm import (
            BACKENDS as _BACKENDS,
            detect_backend as _detect_backend,
            estimate_cost as _estimate_cost,
            extract_corpus_parallel as _extract_corpus_parallel,
            _format_backend_env_keys,
            _get_backend_api_key,
        )
        if backend is None:
            backend = _detect_backend()
            if backend is None:
                print(
                    "error: no LLM API key found. Set GEMINI_API_KEY or GOOGLE_API_KEY "
                    "(gemini), MOONSHOT_API_KEY (kimi), ANTHROPIC_API_KEY (claude), "
                    "OPENAI_API_KEY (openai), DEEPSEEK_API_KEY (deepseek), "
                    "or pass --backend.",
                    file=sys.stderr,
                )
                sys.exit(1)
        if backend not in _BACKENDS:
            print(
                f"error: unknown backend '{backend}'. "
                f"Available: {', '.join(sorted(_BACKENDS))}",
                file=sys.stderr,
            )
            sys.exit(1)
        if not _get_backend_api_key(backend):
            # Ollama on a loopback URL ignores auth entirely; don't block
            # the run just because OLLAMA_API_KEY is unset (issue #792).
            # extract_files_direct already prints a warning and substitutes
            # a placeholder key in that case.
            allow_no_key = False
            if backend == "ollama":
                from urllib.parse import urlparse
                ollama_url = os.environ.get(
                    "OLLAMA_BASE_URL",
                    _BACKENDS["ollama"].get("base_url", ""),
                )
                try:
                    host = (urlparse(ollama_url).hostname or "").lower()
                except Exception:
                    host = ""
                allow_no_key = (
                    host in ("localhost", "127.0.0.1", "::1")
                    or host.startswith("127.")
                )
            elif backend == "bedrock":
                allow_no_key = bool(
                    os.environ.get("AWS_PROFILE")
                    or os.environ.get("AWS_REGION")
                    or os.environ.get("AWS_DEFAULT_REGION")
                    or os.environ.get("AWS_ACCESS_KEY_ID")
                )
            elif backend == "claude-cli":
                import shutil as _shutil
                allow_no_key = _shutil.which("claude") is not None
                if not allow_no_key:
                    print(
                        "error: backend 'claude-cli' requires the `claude` CLI on $PATH "
                        "(install Claude Code and run `claude` once to authenticate).",
                        file=sys.stderr,
                    )
                    sys.exit(1)
            if not allow_no_key:
                print(
                    f"error: backend '{backend}' requires {_format_backend_env_keys(backend)} to be set.",
                    file=sys.stderr,
                )
                sys.exit(1)

        # Resolve output dir. The user-facing contract is "<out>/graphify-out/"
        # so a fresh checkout writes graphify-out/ at the project root, matching
        # the skill.md pipeline.
        out_root = (out_dir.resolve() if out_dir else target)
        graphify_out = out_root / "graphify-out"
        graphify_out.mkdir(parents=True, exist_ok=True)

        from graphify.detect import (
            detect as _detect,
            detect_incremental as _detect_incremental,
            save_manifest as _save_manifest,
        )
        manifest_path = graphify_out / "manifest.json"
        existing_graph_path = graphify_out / "graph.json"
        incremental_mode = manifest_path.exists() and existing_graph_path.exists()

        if incremental_mode:
            print(f"[graphify extract] incremental scan of {target}")
            detection = _detect_incremental(
                target,
                manifest_path=str(manifest_path),
                google_workspace=google_workspace or None,
                extra_excludes=cli_excludes or None,
            )
        else:
            print(f"[graphify extract] scanning {target}")
            detection = _detect(target, google_workspace=google_workspace or None, extra_excludes=cli_excludes or None)

        files_by_type = detection.get("files", {})
        if incremental_mode:
            new_by_type = detection.get("new_files", {})
            code_files = [Path(p) for p in new_by_type.get("code", [])]
            doc_files = [Path(p) for p in new_by_type.get("document", [])]
            paper_files = [Path(p) for p in new_by_type.get("paper", [])]
            image_files = [Path(p) for p in new_by_type.get("image", [])]
            deleted_files = list(detection.get("deleted_files", []))
            unchanged_total = sum(len(v) for v in detection.get("unchanged_files", {}).values())
        else:
            code_files = [Path(p) for p in files_by_type.get("code", [])]
            doc_files = [Path(p) for p in files_by_type.get("document", [])]
            paper_files = [Path(p) for p in files_by_type.get("paper", [])]
            image_files = [Path(p) for p in files_by_type.get("image", [])]
            deleted_files = []
            unchanged_total = 0

        semantic_files = doc_files + paper_files + image_files
        if incremental_mode:
            print(
                f"[graphify extract] {len(code_files)} code, {len(doc_files)} docs, "
                f"{len(paper_files)} papers, {len(image_files)} images changed; "
                f"{unchanged_total} unchanged; {len(deleted_files)} deleted"
            )
        else:
            print(
                f"[graphify extract] found {len(code_files)} code, "
                f"{len(doc_files)} docs, {len(paper_files)} papers, "
                f"{len(image_files)} images"
            )

        # AST extraction on code files. Empty code list (docs-only corpus) is
        # the issue #698 case — skip cleanly instead of crashing inside extract().
        ast_result: dict = {"nodes": [], "edges": [], "input_tokens": 0, "output_tokens": 0}
        if code_files:
            from graphify.extract import extract as _ast_extract
            ast_kwargs: dict = {"cache_root": target}
            if cli_max_workers is not None:
                ast_kwargs["max_workers"] = cli_max_workers
            print(f"[graphify extract] AST extraction on {len(code_files)} code files...")
            try:
                ast_result = _ast_extract(code_files, **ast_kwargs)
            except Exception as exc:
                print(f"[graphify extract] AST extraction failed: {exc}", file=sys.stderr)
                ast_result = {"nodes": [], "edges": [], "input_tokens": 0, "output_tokens": 0}

        # Semantic extraction on docs/papers/images. Check cache first.
        from graphify.cache import (
            check_semantic_cache as _check_semantic_cache,
            save_semantic_cache as _save_semantic_cache,
        )
        sem_result: dict = {
            "nodes": [], "edges": [], "hyperedges": [],
            "input_tokens": 0, "output_tokens": 0,
        }
        sem_cache_hits = 0
        sem_cache_misses = 0
        if semantic_files:
            sem_paths_str = [str(p) for p in semantic_files]
            cached_nodes, cached_edges, cached_hyperedges, uncached_paths = (
                _check_semantic_cache(sem_paths_str, root=target)
            )
            sem_cache_hits = len(semantic_files) - len(uncached_paths)
            sem_cache_misses = len(uncached_paths)
            sem_result["nodes"].extend(cached_nodes)
            sem_result["edges"].extend(cached_edges)
            sem_result["hyperedges"].extend(cached_hyperedges)
            if sem_cache_hits:
                print(f"[graphify extract] semantic cache: {sem_cache_hits} hit / {sem_cache_misses} miss")

            if uncached_paths:
                print(f"[graphify extract] semantic extraction on {len(uncached_paths)} files via {backend}...")
                corpus_kwargs: dict = {
                    "backend": backend,
                    "model": model,
                    "root": target,
                }
                if cli_token_budget is not None:
                    corpus_kwargs["token_budget"] = cli_token_budget
                if cli_max_concurrency is not None:
                    corpus_kwargs["max_concurrency"] = cli_max_concurrency

                # Minimal progress callback so the CLI is no longer silent
                # during long local-inference runs (issue #792 addendum).
                _total_chunks = {"n": 0}
                def _progress(idx: int, total: int, _result: dict) -> None:
                    _total_chunks["n"] = total
                    print(
                        f"[graphify extract] chunk {idx + 1}/{total} done",
                        flush=True,
                    )
                corpus_kwargs["on_chunk_done"] = _progress

                try:
                    fresh = _extract_corpus_parallel(
                        [Path(p) for p in uncached_paths],
                        **corpus_kwargs,
                    )
                except ImportError as exc:
                    print(f"error: {exc}", file=sys.stderr)
                    sys.exit(1)
                except Exception as exc:
                    print(
                        f"[graphify extract] semantic extraction failed: {exc}",
                        file=sys.stderr,
                    )
                    fresh = {"nodes": [], "edges": [], "hyperedges": [], "input_tokens": 0, "output_tokens": 0}
                try:
                    _save_semantic_cache(
                        fresh.get("nodes", []),
                        fresh.get("edges", []),
                        fresh.get("hyperedges", []),
                        root=target,
                    )
                except Exception as exc:
                    print(f"[graphify extract] warning: could not write semantic cache: {exc}", file=sys.stderr)
                sem_result["nodes"].extend(fresh.get("nodes", []))
                sem_result["edges"].extend(fresh.get("edges", []))
                sem_result["hyperedges"].extend(fresh.get("hyperedges", []))
                sem_result["input_tokens"] += fresh.get("input_tokens", 0)
                sem_result["output_tokens"] += fresh.get("output_tokens", 0)

        # Merge AST + semantic. Order matters for deduplication: passing AST
        # first means semantic node attributes win on collision (richer labels
        # for symbols also referenced in docs). Hyperedges only come from the
        # semantic side.
        merged: dict = {
            "nodes": list(ast_result.get("nodes", [])) + list(sem_result.get("nodes", [])),
            "edges": list(ast_result.get("edges", [])) + list(sem_result.get("edges", [])),
            "hyperedges": list(sem_result.get("hyperedges", [])),
            "input_tokens": ast_result.get("input_tokens", 0) + sem_result.get("input_tokens", 0),
            "output_tokens": ast_result.get("output_tokens", 0) + sem_result.get("output_tokens", 0),
        }

        graph_json_path = graphify_out / "graph.json"
        analysis_path = graphify_out / ".graphify_analysis.json"

        # Build a manifest-safe files dict: only stamp semantic_hash for files
        # that actually produced output (cache hit or fresh extraction). Files
        # whose chunk failed have no source_file entry in sem_result — leaving
        # their semantic_hash empty so detect_incremental re-queues them (#933).
        _sem_extracted: set[str] = {
            n.get("source_file", "") for n in sem_result.get("nodes", [])
        } | {
            e.get("source_file", "") for e in sem_result.get("edges", [])
        }
        _sem_extracted.discard("")
        _sem_types = {"document", "paper", "image"}
        _manifest_files = {
            ftype: [f for f in flist if ftype not in _sem_types or f in _sem_extracted]
            for ftype, flist in files_by_type.items()
        }

        if no_cluster:
            # --no-cluster: dump the raw merged extraction as graph.json.
            # No NetworkX, no community detection, no analysis sidecar.
            from graphify.export import backup_if_protected as _backup
            _backup(graphify_out)
            graph_json_path.write_text(
                json.dumps(merged, indent=2), encoding="utf-8"
            )
            cost = _estimate_cost(
                backend, merged["input_tokens"], merged["output_tokens"]
            )
            print(
                f"[graphify extract] wrote {graph_json_path} — "
                f"{len(merged['nodes'])} nodes, {len(merged['edges'])} edges "
                f"(no clustering)"
            )
            if merged["input_tokens"] or merged["output_tokens"]:
                print(
                    f"[graphify extract] tokens: "
                    f"{merged['input_tokens']:,} in / "
                    f"{merged['output_tokens']:,} out, "
                    f"est. cost: ${cost:.4f}"
                )
            try:
                _save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both")
            except Exception as exc:
                print(f"[graphify extract] warning: could not write manifest: {exc}", file=sys.stderr)
            if global_merge:
                from graphify.global_graph import global_add as _global_add
                _tag = global_repo_tag or target.name
                try:
                    result = _global_add(graphify_out / "graph.json", _tag)
                    if result["skipped"]:
                        print(f"[graphify global] '{_tag}' unchanged since last add — skipped.")
                    else:
                        print(f"[graphify global] '{_tag}' merged into global graph "
                              f"(+{result['nodes_added']} nodes, -{result['nodes_removed']} pruned).")
                except Exception as exc:
                    print(f"[graphify global] warning: failed to merge into global graph: {exc}", file=sys.stderr)
            sys.exit(0)

        # Build graph + cluster + score + write.
        from graphify.build import (
            build as _build,
            build_from_json as _build_from_json,
            build_merge as _build_merge,
        )
        from graphify.cluster import cluster as _cluster, score_all as _score_all
        from graphify.export import to_json as _to_json
        from graphify.analyze import god_nodes as _god_nodes, surprising_connections as _surprising
        dedup_backend = backend if dedup_llm else None
        if incremental_mode:
            G = _build_merge(
                [merged],
                graph_path=existing_graph_path,
                prune_sources=deleted_files or None,
                dedup=True,
                dedup_llm_backend=dedup_backend,
                root=target,
            )
        else:
            G = _build([merged], dedup=True, dedup_llm_backend=dedup_backend, root=target)
        if G.number_of_nodes() == 0:
            print(
                "[graphify extract] graph is empty — extraction produced no nodes. "
                "Possible causes: all files skipped, binary-only corpus, or LLM "
                "returned no edges.",
                file=sys.stderr,
            )
            sys.exit(1)

        communities = _cluster(G, resolution=cli_resolution, exclude_hubs_percentile=cli_exclude_hubs)
        cohesion = _score_all(G, communities)
        try:
            gods = _god_nodes(G)
        except Exception:
            gods = []
        try:
            surprises = _surprising(G, communities)
        except Exception:
            surprises = []

        from graphify.export import backup_if_protected as _backup
        _backup(graphify_out)
        _to_json(G, communities, str(graph_json_path), force=True)
        if merged.get("output_tokens", 0) > 0:
            (graphify_out / ".graphify_semantic_marker").write_text(
                json.dumps({"output_tokens": merged["output_tokens"]}), encoding="utf-8"
            )
        if global_merge:
            from graphify.global_graph import global_add as _global_add
            _tag = global_repo_tag or target.name
            try:
                result = _global_add(graphify_out / "graph.json", _tag)
                if result["skipped"]:
                    print(f"[graphify global] '{_tag}' unchanged since last add — skipped.")
                else:
                    print(f"[graphify global] '{_tag}' merged into global graph "
                          f"(+{result['nodes_added']} nodes, -{result['nodes_removed']} pruned).")
            except Exception as exc:
                print(f"[graphify global] warning: failed to merge into global graph: {exc}", file=sys.stderr)
        analysis = {
            "communities": {str(k): v for k, v in communities.items()},
            "cohesion": {str(k): v for k, v in cohesion.items()},
            "gods": gods,
            "surprises": surprises,
            "tokens": {
                "input": merged["input_tokens"],
                "output": merged["output_tokens"],
            },
        }
        analysis_path.write_text(json.dumps(analysis, indent=2), encoding="utf-8")
        try:
            _save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both")
        except Exception as exc:
            print(f"[graphify extract] warning: could not write manifest: {exc}", file=sys.stderr)

        cost = _estimate_cost(backend, merged["input_tokens"], merged["output_tokens"])
        print(
            f"[graphify extract] wrote {graph_json_path}: "
            f"{G.number_of_nodes()} nodes, {G.number_of_edges()} edges, "
            f"{len(communities)} communities"
        )
        print(f"[graphify extract] wrote {analysis_path}")
        if incremental_mode:
            print(
                f"[graphify extract] incremental summary: "
                f"{sem_cache_hits + unchanged_total} files cached/unchanged, "
                f"{len(code_files) + sem_cache_misses} re-extracted, "
                f"{len(deleted_files)} deleted"
            )
        elif sem_cache_hits:
            print(f"[graphify extract] semantic cache: {sem_cache_hits} cached, {sem_cache_misses} re-extracted")
        if merged["input_tokens"] or merged["output_tokens"]:
            print(
                f"[graphify extract] tokens: "
                f"{merged['input_tokens']:,} in / "
                f"{merged['output_tokens']:,} out, "
                f"est. cost (~{backend}): ${cost:.4f}"
            )

    elif cmd == "cache-check":
        # graphify cache-check <files_from> [--root <dir>]
        # Reads file paths (one per line) from <files_from>, checks semantic cache.
        # Writes:
        #   graphify-out/.graphify_cached.json   — already-cached nodes/edges/hyperedges
        #   graphify-out/.graphify_uncached.txt  — paths that need extraction
        # Stdout: "Cache: N hit, M miss"
        from graphify.cache import check_semantic_cache
        if len(sys.argv) < 3:
            print("Usage: graphify cache-check <files_from> [--root <dir>]", file=sys.stderr)
            sys.exit(1)
        files_from = Path(sys.argv[2])
        root = Path(".")
        i = 3
        while i < len(sys.argv):
            if sys.argv[i] == "--root" and i + 1 < len(sys.argv):
                root = Path(sys.argv[i + 1])
                i += 2
            else:
                i += 1
        files = [f for f in files_from.read_text(encoding="utf-8").splitlines() if f.strip()]
        cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(files, root)
        out = root / "graphify-out"
        out.mkdir(parents=True, exist_ok=True)
        if cached_nodes or cached_edges or cached_hyperedges:
            (out / ".graphify_cached.json").write_text(
                json.dumps({"nodes": cached_nodes, "edges": cached_edges, "hyperedges": cached_hyperedges},
                           ensure_ascii=False),
                encoding="utf-8",
            )
        (out / ".graphify_uncached.txt").write_text("\n".join(uncached), encoding="utf-8")
        print(f"Cache: {len(files) - len(uncached)} hit, {len(uncached)} miss")

    elif cmd == "merge-chunks":
        # graphify merge-chunks <chunk_glob_or_files...> --out <path>
        # Concatenates .graphify_chunk_*.json files written by semantic subagents.
        # Deduplicates nodes by id (first writer wins). Sums token counts.
        import glob as _glob
        if len(sys.argv) < 3:
            print("Usage: graphify merge-chunks <chunk_files...> --out <path>", file=sys.stderr)
            sys.exit(1)
        out_path: Path | None = None
        chunk_args: list[str] = []
        i = 2
        while i < len(sys.argv):
            if sys.argv[i] == "--out" and i + 1 < len(sys.argv):
                out_path = Path(sys.argv[i + 1])
                i += 2
            else:
                chunk_args.append(sys.argv[i])
                i += 1
        if not out_path:
            print("error: --out <path> required", file=sys.stderr)
            sys.exit(1)
        chunk_files: list[str] = []
        for arg in chunk_args:
            expanded = _glob.glob(arg)
            chunk_files.extend(sorted(expanded) if expanded else [arg])
        merged: dict = {"nodes": [], "edges": [], "hyperedges": [], "input_tokens": 0, "output_tokens": 0}
        seen_ids: set[str] = set()
        for cf in chunk_files:
            try:
                chunk = json.loads(Path(cf).read_text(encoding="utf-8"))
            except (json.JSONDecodeError, OSError) as exc:
                print(f"[graphify merge-chunks] warning: skipping {cf}: {exc}", file=sys.stderr)
                continue
            for n in chunk.get("nodes", []):
                if n.get("id") not in seen_ids:
                    seen_ids.add(n["id"])
                    merged["nodes"].append(n)
            merged["edges"].extend(chunk.get("edges", []))
            merged["hyperedges"].extend(chunk.get("hyperedges", []))
            merged["input_tokens"] += chunk.get("input_tokens", 0)
            merged["output_tokens"] += chunk.get("output_tokens", 0)
        out_path.parent.mkdir(parents=True, exist_ok=True)
        out_path.write_text(json.dumps(merged, ensure_ascii=False), encoding="utf-8")
        print(
            f"Merged {len(chunk_files)} chunks: {merged['nodes']} nodes, {len(merged['edges'])} edges, "
            f"{merged['input_tokens']:,} in / {merged['output_tokens']:,} out tokens"
        )

    elif cmd == "merge-semantic":
        # graphify merge-semantic --cached <path> --new <path> --out <path>
        # Merges cached semantic results with freshly-extracted chunk results.
        # Deduplicates nodes by id (cached entries take priority over new ones).
        if len(sys.argv) < 3:
            print("Usage: graphify merge-semantic --cached <path> --new <path> --out <path>", file=sys.stderr)
            sys.exit(1)
        cached_path: Path | None = None
        new_path: Path | None = None
        out_path2: Path | None = None
        i = 2
        while i < len(sys.argv):
            if sys.argv[i] == "--cached" and i + 1 < len(sys.argv):
                cached_path = Path(sys.argv[i + 1]); i += 2
            elif sys.argv[i] == "--new" and i + 1 < len(sys.argv):
                new_path = Path(sys.argv[i + 1]); i += 2
            elif sys.argv[i] == "--out" and i + 1 < len(sys.argv):
                out_path2 = Path(sys.argv[i + 1]); i += 2
            else:
                i += 1
        if not out_path2:
            print("error: --out <path> required", file=sys.stderr)
            sys.exit(1)
        empty: dict = {"nodes": [], "edges": [], "hyperedges": []}
        cached_data = json.loads(cached_path.read_text(encoding="utf-8")) if cached_path and cached_path.exists() else empty
        new_data = json.loads(new_path.read_text(encoding="utf-8")) if new_path and new_path.exists() else empty
        seen_ids2: set[str] = set()
        all_nodes: list[dict] = []
        for n in cached_data.get("nodes", []) + new_data.get("nodes", []):
            if n.get("id") not in seen_ids2:
                seen_ids2.add(n["id"])
                all_nodes.append(n)
        merged2 = {
            "nodes": all_nodes,
            "edges": cached_data.get("edges", []) + new_data.get("edges", []),
            "hyperedges": cached_data.get("hyperedges", []) + new_data.get("hyperedges", []),
        }
        out_path2.parent.mkdir(parents=True, exist_ok=True)
        out_path2.write_text(json.dumps(merged2, ensure_ascii=False), encoding="utf-8")
        print(f"Merged: {len(merged2['nodes'])} nodes, {len(merged2['edges'])} edges")

    elif Path(cmd).exists() or cmd in (".", "..") or cmd.startswith(("./", "../", "/", "~")):
        # User ran `graphify <path>` directly — treat as `graphify extract <path>`.
        # Common when following the PowerShell note in README (`graphify .`) or
        # copy-pasting skill invocations without the leading slash.
        sys.argv.insert(2, sys.argv[1])
        sys.argv[1] = "extract"
        main()
    else:
        print(f"error: unknown command '{cmd}'", file=sys.stderr)
        print("Run 'graphify --help' for usage.", file=sys.stderr)
        sys.exit(1)


if __name__ == "__main__":
    main()