@oriro/orirocli 0.1.7 → 0.1.9

package/skills/graphify/__main__.py

@@ -0,0 +1,4582 @@
+"""graphify CLI - `graphify install` sets up the Claude Code skill."""
+
+from __future__ import annotations
+import functools
+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")
+
+
+@functools.lru_cache(maxsize=None)
+def _always_on(basename: str) -> str:
+    """Read a packaged always-on instruction block from graphify/always_on/.
+
+    The six always-on blocks (CLAUDE.md / AGENTS.md / GEMINI.md / VS Code
+    Copilot instructions / Antigravity rules / Kiro steering) live as committed
+    markdown next to this module, generated by tools/skillgen from a single
+    human-edited fragment and guarded against drift by ``skillgen --check``. The
+    installer injects them verbatim via ``_replace_or_append_section``, so the
+    bytes here must match the former triple-quoted constant exactly — the
+    always-on-roundtrip validator proves that.
+    """
+    path = Path(__file__).parent / "always_on" / f"{basename}.md"
+    try:
+        return path.read_text(encoding="utf-8")
+    except OSError as exc:
+        # Defer to use-time so a missing/corrupt packaged block can't crash module
+        # import (which would brick every CLI command, not just install). Reached
+        # only by an install/integration path that actually needs this block.
+        raise RuntimeError(
+            f"graphify install is incomplete: missing always-on block '{basename}' "
+            f"at {path}. Reinstall graphifyy (e.g. `uv tool install --reinstall graphifyy`)."
+        ) from exc
+
+
+_ALWAYS_ON_ALIASES = {
+    "_CLAUDE_MD_SECTION": "claude-md",
+    "_AGENTS_MD_SECTION": "agents-md",
+    "_GEMINI_MD_SECTION": "gemini-md",
+    "_VSCODE_INSTRUCTIONS_SECTION": "vscode-instructions",
+    "_ANTIGRAVITY_RULES": "antigravity-rules",
+    "_KIRO_STEERING": "kiro-steering",
+}
+
+
+def __getattr__(name: str) -> str:
+    # PEP 562: lazily resolve the legacy always-on section constants for external
+    # importers (e.g. the install-string tests). In-module code calls _always_on()
+    # directly; nothing is read at import time, so a missing block can no longer
+    # brick the CLI on `import graphify.__main__` (#1121 follow-up).
+    base = _ALWAYS_ON_ALIASES.get(name)
+    if base is not None:
+        return _always_on(base)
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+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
+    # A progressive SKILL.md links to its references/ sidecar. If the body points
+    # at references/ but the dir is gone (manual delete, partial upgrade), the
+    # on-demand fragments won't load — flag it for repair.
+    try:
+        body = skill_dst.read_text(encoding="utf-8")
+    except OSError:
+        body = ""
+    if "references/" in body and not (skill_dst.parent / "references").exists():
+        print("  warning: skill references/ sidecar is missing. Run 'graphify install' to repair.", file=sys.stderr)
+    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 name in _PLATFORM_CONFIG:
+        skill_dst = _platform_skill_destination(name)
+        vf = skill_dst.parent / ".graphify_version"
+        if skill_dst.exists():
+            vf.write_text(__version__, encoding="utf-8")
+
+
+def _platform_skill_destination(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> Path:
+    """Return the skill destination for a platform and scope."""
+    if platform_name == "gemini":
+        if project:
+            return (project_dir or Path(".")) / ".gemini" / "skills" / "graphify" / "SKILL.md"
+        if platform.system() == "Windows":
+            return Path.home() / ".agents" / "skills" / "graphify" / "SKILL.md"
+        return Path.home() / ".gemini" / "skills" / "graphify" / "SKILL.md"
+
+    if platform_name == "opencode":
+        if project:
+            return (project_dir or Path(".")) / ".opencode" / "skills" / "graphify" / "SKILL.md"
+        return Path.home() / ".config" / "opencode" / "skills" / "graphify" / "SKILL.md"
+
+    if platform_name == "devin":
+        if project:
+            return (project_dir or Path(".")) / ".devin" / "skills" / "graphify" / "SKILL.md"
+        return Path.home() / ".config" / "devin" / "skills" / "graphify" / "SKILL.md"
+
+    if platform_name == "amp":
+        if project:
+            return (project_dir or Path(".")) / ".agents" / "skills" / "graphify" / "SKILL.md"
+        return Path.home() / ".config" / "agents" / "skills" / "graphify" / "SKILL.md"
+
+    if platform_name in ("antigravity", "antigravity-windows"):
+        if project:
+            return (project_dir or Path(".")) / ".agents" / "skills" / "graphify" / "SKILL.md"
+        # Global Antigravity skill dir (all workspaces): ~/.gemini/config/skills/
+        return Path.home() / ".gemini" / "config" / "skills" / "graphify" / "SKILL.md"
+
+    cfg = _PLATFORM_CONFIG[platform_name]
+    if project:
+        return (project_dir or Path(".")) / cfg["skill_dst"]
+
+    if platform_name in ("claude", "windows") and os.environ.get("CLAUDE_CONFIG_DIR"):
+        return Path(os.environ["CLAUDE_CONFIG_DIR"]) / "skills" / "graphify" / "SKILL.md"
+    return Path.home() / cfg["skill_dst"]
+
+
+def _packaged_skill_refs_dir(platform_name: str) -> Path | None:
+    """Return the packaged references source dir for a progressive platform, else None.
+
+    A platform opts into progressive disclosure by setting ``skill_refs`` in its
+    ``_PLATFORM_CONFIG`` entry. The value names a bundle under
+    ``graphify/skills/<bundle>/references/``. Reuse keys (e.g. trae-cn) point at
+    their twin's bundle.
+
+    ``gemini`` has no ``_PLATFORM_CONFIG`` entry: it installs claude's
+    ``skill.md`` body verbatim (see ``_copy_skill_file``). Since that body is the
+    lean progressive core that links to ``references/``, gemini needs claude's
+    references/ sidecar too, or its SKILL.md ships with dead pointers. So gemini
+    resolves to the claude bundle rather than opting out.
+
+    Bundles ship one platform-group at a time. A host whose bundle directory
+    ``graphify/skills/<bundle>/`` is not in this build has not gone progressive
+    yet, so this returns None and the host installs today's monolithic SKILL.md
+    with no references/ sidecar. Only when the bundle directory IS present does
+    this return the references path; if that directory then lacks its
+    ``references/`` subdir, ``_copy_skill_file`` hard-fails (a malformed bundle,
+    the empty-sidecar regression the wheel-content test also guards).
+    """
+    if platform_name == "gemini":
+        bundle = "claude"
+    else:
+        bundle = _PLATFORM_CONFIG[platform_name].get("skill_refs")
+    if not bundle:
+        return None
+    bundle_dir = Path(__file__).parent / "skills" / bundle
+    if not bundle_dir.is_dir():
+        return None
+    return bundle_dir / "references"
+
+
+def _install_skill_references(skill_dst: Path, refs_src: Path) -> None:
+    """Atomically install a packaged references/ sidecar next to SKILL.md.
+
+    Stages the packaged dir into ``references.tmp`` (copytree), drops any stale
+    ``references/`` already on disk, then ``os.replace``-renames the staged dir
+    into place. The rename is atomic on the same filesystem, so an interrupted
+    install never leaves a half-written references/ visible to the agent.
+    """
+    refs_dst = skill_dst.parent / "references"
+    refs_staged = skill_dst.parent / "references.tmp"
+    if refs_staged.exists():
+        shutil.rmtree(refs_staged)
+    try:
+        shutil.copytree(refs_src, refs_staged)
+        if refs_dst.exists():
+            shutil.rmtree(refs_dst)
+        os.replace(refs_staged, refs_dst)
+    except Exception:
+        if refs_staged.exists():
+            shutil.rmtree(refs_staged, ignore_errors=True)
+        raise
+
+
+def _copy_skill_file(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> Path:
+    """Copy a packaged skill file and write its version stamp.
+
+    For progressive platforms (those with ``skill_refs`` set), the packaged
+    ``references/`` sidecar is installed alongside SKILL.md and the single
+    ``.graphify_version`` stamp covers both. For monolith platforms (no
+    ``skill_refs``), any orphan ``references/`` left by a prior progressive
+    install is removed so the on-disk layout matches the package.
+    """
+    skill_file = "skill.md" if platform_name == "gemini" else _PLATFORM_CONFIG[platform_name]["skill_file"]
+    skill_src = Path(__file__).parent / skill_file
+    if not skill_src.exists():
+        print(f"error: {skill_file} not found in package - reinstall graphify", file=sys.stderr)
+        sys.exit(1)
+
+    refs_src = _packaged_skill_refs_dir(platform_name)
+    if refs_src is not None and not refs_src.exists():
+        # Progressive platform declared a references bundle that is missing from
+        # the package. Fail loud rather than silently shipping an empty sidecar.
+        print(
+            f"error: references for '{platform_name}' not found in package "
+            f"({refs_src}) - reinstall graphify",
+            file=sys.stderr,
+        )
+        sys.exit(1)
+
+    skill_dst = _platform_skill_destination(platform_name, project=project, project_dir=project_dir)
+    skill_dst.parent.mkdir(parents=True, exist_ok=True)
+
+    # Install the references/ sidecar (or clear an orphan one) BEFORE writing
+    # SKILL.md, so SKILL.md is the last artifact laid down. An install that is
+    # interrupted partway then leaves no SKILL.md rather than a SKILL.md that
+    # points at an absent references/ dir.
+    if refs_src is not None:
+        _install_skill_references(skill_dst, refs_src)
+        print(f"  references       ->  {skill_dst.parent / 'references'}")
+    else:
+        # Monolith (or progressive-with-no-refs): clear any orphan references/.
+        orphan_refs = skill_dst.parent / "references"
+        if orphan_refs.exists():
+            shutil.rmtree(orphan_refs)
+
+    # SKILL.md last (crash-safety), via an atomic temp + rename.
+    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}")
+    return skill_dst
+
+
+def _remove_skill_file(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> bool:
+    """Remove a platform skill file and its version stamp without touching other scopes."""
+    skill_dst = _platform_skill_destination(platform_name, project=project, project_dir=project_dir)
+    removed = False
+    if skill_dst.exists():
+        skill_dst.unlink()
+        print(f"  skill removed    ->  {skill_dst}")
+        removed = True
+    version_file = skill_dst.parent / ".graphify_version"
+    if version_file.exists():
+        version_file.unlink()
+        removed = True
+    refs_dir = skill_dst.parent / "references"
+    if refs_dir.exists():
+        shutil.rmtree(refs_dir)
+        removed = True
+    for d in (skill_dst.parent, skill_dst.parent.parent, skill_dst.parent.parent.parent):
+        try:
+            d.rmdir()
+        except OSError:
+            break
+    return removed
+
+
+def _project_scope_root(path: Path, project_dir: Path) -> Path:
+    """Return the top-level project artifact for a project-scoped skill path."""
+    try:
+        rel = path.relative_to(project_dir)
+    except ValueError:
+        return path
+    return project_dir / rel.parts[0] if rel.parts else path
+
+
+def _remove_claude_skill_registration(project_dir: Path) -> None:
+    """Remove the project-scoped Claude skill registration file/section."""
+    claude_md = project_dir / ".claude" / "CLAUDE.md"
+    if not claude_md.exists():
+        return
+    content = claude_md.read_text(encoding="utf-8")
+    if "# graphify" not in content:
+        return
+    cleaned = re.sub(r"\n*# graphify\n.*?(?=\n# |\Z)", "", content, flags=re.DOTALL).rstrip()
+    if cleaned:
+        claude_md.write_text(cleaned + "\n", encoding="utf-8")
+        print(f"  CLAUDE.md        ->  graphify skill registration removed from {claude_md}")
+    else:
+        claude_md.unlink()
+        print(f"  CLAUDE.md        ->  deleted {claude_md}")
+
+
+def _print_project_git_add_hint(paths: list[Path]) -> None:
+    unique: list[str] = []
+    for path in paths:
+        text = path.as_posix().rstrip("/")
+        if path.exists() and path.is_dir():
+            text += "/"
+        if text not in unique:
+            unique.append(text)
+    if not unique:
+        return
+    print()
+    print("Project-scoped install. Add to version control:")
+    print(f"  git add {' '.join(unique)}")
+
+_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"
+            ),
+        }
+    ],
+}
+
+_READ_SETTINGS_HOOK = {
+    # The Bash hook above never sees a file read through the native Read tool or a
+    # Glob, which is the most common way an agent skips the graph: answering a
+    # codebase question by Read-ing many source files one by one (issue #1114).
+    # Match Read|Glob, inspect the target path, and nudge (never block) only for a
+    # source/doc file outside graphify-out/ when a graph exists. The parser is
+    # python3 (already a graphify dependency), the shell is POSIX, and every branch
+    # fails open, so a legitimate read always goes through. Reading the graph's own
+    # report under graphify-out/ is suppressed so it never starts a feedback loop.
+    "matcher": "Read|Glob",
+    "hooks": [
+        {
+            "type": "command",
+            "command": (
+                "HIT=$(python3 -c \""
+                "import json,sys;"
+                "d=json.load(sys.stdin);"
+                "t=d.get('tool_input',d);"
+                "s=(str(t.get('file_path') or '')+' '+str(t.get('pattern') or '')+' '+str(t.get('path') or '')).lower().replace(chr(92),'/');"
+                "exts=('.py','.js','.ts','.tsx','.jsx','.go','.rs','.java','.rb','.c','.h','.cpp','.hpp','.cc','.cs','.kt','.swift','.php','.scala','.lua','.sh','.md','.rst','.txt','.mdx');"
+                "sys.stdout.write('1' if 'graphify-out/' not in s and any(e in s for e in exts) else '')\" 2>/dev/null || true); "
+                "if [ \"$HIT\" = 1 ] && [ -f graphify-out/graph.json ]; then "
+                r"""echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","additionalContext":"graphify: knowledge graph at graphify-out/. For codebase questions, run `graphify query \"<question>\"` (scoped subgraph, usually much smaller than reading files one by one), `graphify explain \"<concept>\"`, or `graphify path \"<A>\" \"<B>\"`, instead of reading source files to answer. Read raw files to modify or debug specific code, or when the graph lacks the detail."}}'; """
+                "fi || true"
+            ),
+        }
+    ],
+}
+
+def _skill_registration(skill_path: str = "~/.claude/skills/graphify/SKILL.md") -> str:
+    return (
+        "\n# graphify\n"
+        f"- **graphify** (`{skill_path}`) "
+        "- 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,
+        "skill_refs": "claude",
+    },
+    "codex": {
+        "skill_file": "skill-codex.md",
+        "skill_dst": Path(".codex") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "codex",
+    },
+    "opencode": {
+        "skill_file": "skill-opencode.md",
+        "skill_dst": Path(".config") / "opencode" / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "opencode",
+    },
+    "kilo": {
+        "skill_file": "skill-kilo.md",
+        "skill_dst": Path(".config") / "kilo" / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "kilo",
+    },
+    "aider": {
+        # Monolith: aider ships the full SKILL.md inline, no references/ sidecar.
+        "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,
+        "skill_refs": "copilot",
+    },
+    "claw": {
+        "skill_file": "skill-claw.md",
+        "skill_dst": Path(".openclaw") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "claw",
+    },
+    "droid": {
+        "skill_file": "skill-droid.md",
+        "skill_dst": Path(".factory") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "droid",
+    },
+    "trae": {
+        "skill_file": "skill-trae.md",
+        "skill_dst": Path(".trae") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "trae",
+    },
+    "trae-cn": {
+        # Reuses trae's split bundle (same skill body + references).
+        "skill_file": "skill-trae.md",
+        "skill_dst": Path(".trae-cn") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "trae",
+    },
+    "hermes": {
+        # Reuses claw's split bundle.
+        "skill_file": "skill-claw.md",
+        "skill_dst": Path(".hermes") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "claw",
+    },
+    "kiro": {
+        "skill_file": "skill-kiro.md",
+        "skill_dst": Path(".kiro") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "kiro",
+    },
+    "pi": {
+        "skill_file": "skill-pi.md",
+        "skill_dst": Path(".pi") / "agent" / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "pi",
+    },
+    "codebuddy": {
+        # Reuses claude's split bundle (shares skill.md).
+        "skill_file": "skill.md",
+        "skill_dst": Path(".codebuddy") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "claude",
+    },
+    "antigravity": {
+        # Rides claude's split bundle (shares skill.md).
+        "skill_file": "skill.md",
+        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "claude",
+    },
+    "antigravity-windows": {
+        # Rides windows' split bundle.
+        "skill_file": "skill-windows.md",
+        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "windows",
+    },
+    "windows": {
+        "skill_file": "skill-windows.md",
+        "skill_dst": Path(".claude") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": True,
+        "skill_refs": "windows",
+    },
+    "kimi": {
+        # Reuses claude's split bundle (shares skill.md).
+        "skill_file": "skill.md",
+        "skill_dst": Path(".kimi") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "claude",
+    },
+    "amp": {
+        # Amp searches .agents/skills (project) and ~/.config/agents/skills (user),
+        # not .amp/skills. The user-scope path is set in _platform_skill_destination.
+        "skill_file": "skill-amp.md",
+        "skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
+        "claude_md": False,
+        "skill_refs": "amp",
+    },
+    "devin": {
+        # Monolith: devin ships the full SKILL.md inline, no references/ sidecar.
+        "skill_file": "skill-devin.md",
+        # User scope: ~/.config/devin/skills/graphify/SKILL.md
+        # Project scope: .devin/skills/graphify/SKILL.md (overridden in _platform_skill_destination)
+        "skill_dst": Path(".config") / "devin" / "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 _print_banner() -> None:
+    """Amber brain banner on graphify install. TTY-only, never raises."""
+    if not sys.stdout.isatty():
+        return
+    try:
+        if sys.platform == "win32":
+            import ctypes
+            ctypes.windll.kernel32.SetConsoleMode(
+                ctypes.windll.kernel32.GetStdHandle(-11), 7
+            )
+        A = "\033[38;5;214m"
+        D = "\033[38;5;130m"
+        R = "\033[0m"
+        print(f"""{A}
+  ╭──◉──╮     ╭──◉──╮
+ ╱  ◉   ◉ ╲ ╱ ◉   ◉  ╲
+│   ◉─◉─◉  ◉  ◉─◉─◉   │
+│    ◉   ◉ │ ◉   ◉    │
+│   ◉─◉─◉  ◉  ◉─◉─◉   │
+ ╲  ◉   ◉ ╱ ╲ ◉   ◉  ╱
+  ╰──◉──╯     ╰──◉──╯
+           ◉
+
+  █▀▀ █▀█ ▄▀█ █▀█ █ █ █ █▀▀ █▄█
+  █▄█ █▀▄ █▀█ █▀▀ █▀█ █ █▀   █{D}  {__version__}{R}
+""")
+    except Exception:
+        pass
+
+
+def install(platform: str = "claude", *, project: bool = False, project_dir: Path | None = None) -> None:
+    _print_banner()
+    if platform == "gemini":
+        gemini_install(project_dir=project_dir, project=project)
+        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]
+    project_dir = project_dir or Path(".")
+    skill_dst = _copy_skill_file(platform, project=project, project_dir=project_dir)
+
+    if platform == "kilo":
+        # Kilo Code also supports a native /graphify command file.
+        command_src = Path(__file__).parent / "command-kilo.md"
+        if not command_src.exists():
+            print(
+                f"error: command-kilo.md not found in package - reinstall graphify",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+        command_dst = Path.home() / ".config" / "kilo" / "command" / "graphify.md"
+        command_dst.parent.mkdir(parents=True, exist_ok=True)
+        shutil.copy(command_src, command_dst)
+        print(f"  command installed ->  {command_dst}")
+
+    if cfg["claude_md"]:
+        # Register in the matching Claude Code scope.
+        claude_md = (project_dir / ".claude" / "CLAUDE.md") if project else Path.home() / ".claude" / "CLAUDE.md"
+        registration = _skill_registration(".claude/skills/graphify/SKILL.md" if project else "~/.claude/skills/graphify/SKILL.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() + 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(registration.lstrip(), encoding="utf-8")
+            print(f"  CLAUDE.md        ->  created at {claude_md}")
+
+    if platform == "codebuddy":
+        # Register in ~/.codebuddy/CODEBUDDY.md (CodeBuddy only)
+        codebuddy_md = Path.home() / ".codebuddy" / "CODEBUDDY.md"
+        registration = _skill_registration("~/.codebuddy/skills/graphify/SKILL.md")
+        if codebuddy_md.exists():
+            content = codebuddy_md.read_text(encoding="utf-8")
+            if "graphify" in content:
+                print(f"  CODEBUDDY.md     ->  already registered (no change)")
+            else:
+                codebuddy_md.write_text(content.rstrip() + registration, encoding="utf-8")
+                print(f"  CODEBUDDY.md     ->  skill registered in {codebuddy_md}")
+        else:
+            codebuddy_md.parent.mkdir(parents=True, exist_ok=True)
+            codebuddy_md.write_text(registration.lstrip(), encoding="utf-8")
+            print(f"  CODEBUDDY.md     ->  created at {codebuddy_md}")
+
+    if platform == "opencode":
+        _install_opencode_plugin(project_dir if project else Path("."))
+
+    # Refresh version stamps in all other previously-installed skill dirs so
+    # stale-version warnings don't fire for platforms not explicitly re-installed.
+    if project:
+        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir)])
+    else:
+        _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 [--project] [--platform P|P]")
+    print(f"Platforms: {platforms}")
+
+
+# The always-on instruction blocks are packaged markdown under graphify/always_on/,
+# generated by tools/skillgen and guarded by `skillgen --check`. Reading them at
+# load keeps the install-string / issue-#580 contract byte-for-byte while letting
+# a human edit one fragment instead of a triple-quoted literal here.
+
+_CLAUDE_MD_MARKER = "## graphify"
+
+_CODEBUDDY_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_MARKER = "## graphify"
+
+
+_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, *, project: bool = False) -> None:
+    """Copy skill file, write GEMINI.md section, and install BeforeTool hook."""
+    project_dir = project_dir or Path(".")
+    skill_dst = _copy_skill_file("gemini", project=project, project_dir=project_dir)
+
+    target = project_dir / "GEMINI.md"
+
+    if target.exists():
+        content = target.read_text(encoding="utf-8")
+        new_content = _replace_or_append_section(
+            content, _GEMINI_MD_MARKER, _always_on("gemini-md")
+        )
+    else:
+        new_content = _always_on("gemini-md")
+
+    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)
+    if project:
+        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / "GEMINI.md", project_dir / ".gemini"])
+    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, *, project: bool = False) -> None:
+    """Remove the graphify section from GEMINI.md, uninstall hook, and remove skill file."""
+    project_dir = project_dir or Path(".")
+    _remove_skill_file("gemini", project=project, project_dir=project_dir)
+
+    target = project_dir / "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)
+
+
+_VSCODE_INSTRUCTIONS_MARKER = "## graphify"
+
+
+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"
+    refs_bundle = "vscode"
+    if not skill_src.exists():
+        skill_src = Path(__file__).parent / "skill-copilot.md"
+        refs_bundle = "copilot"
+    skill_dst = Path.home() / ".copilot" / "skills" / "graphify" / "SKILL.md"
+    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
+    # Progressive-capable: install the packaged references/ sidecar when present.
+    refs_src = Path(__file__).parent / "skills" / refs_bundle / "references"
+    if refs_src.exists():
+        _install_skill_references(skill_dst, refs_src)
+        print(f"  references       ->  {skill_dst.parent / 'references'}")
+    else:
+        orphan_refs = skill_dst.parent / "references"
+        if orphan_refs.exists():
+            shutil.rmtree(orphan_refs)
+    (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, _always_on("vscode-instructions")
+        )
+        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(_always_on("vscode-instructions"), 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()
+    refs_dir = skill_dst.parent / "references"
+    if refs_dir.exists():
+        shutil.rmtree(refs_dir)
+    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_WORKFLOW = """\
+---
+name: graphify
+description: Turn any folder of files into a navigable knowledge graph
+---
+
+# Workflow: graphify
+
+Follow the graphify skill installed at ~/.gemini/config/skills/graphify/SKILL.md to run the full pipeline.
+
+If no path argument is given, use `.` (current directory).
+"""
+
+
+
+_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 + references/ sidecar + .graphify_version stamp via the shared
+    # progressive-disclosure helper.  Previously this used a bare write_text that
+    # bypassed _copy_skill_file, so the references/ dir and version stamp were
+    # never written even though kiro declares skill_refs: "kiro" (#1142).
+    _copy_skill_file("kiro", project=True, project_dir=project_dir)
+
+    # 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") == _always_on("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(_always_on("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 + .graphify_version + references/ sidecar + empty-dir walk.
+    skill_dst = _platform_skill_destination("kiro", project=True, project_dir=project_dir)
+    if _remove_skill_file("kiro", project=True, project_dir=project_dir):
+        removed.append(str(skill_dst.relative_to(project_dir)))
+
+    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_finalize(skill_dst: Path, project_dir: Path) -> None:
+    """Write Antigravity's always-on layer next to an installed skill.
+
+    Injects the native tool-discovery YAML frontmatter into *skill_dst*, then
+    writes ``.agents/rules/graphify.md`` and ``.agents/workflows/graphify.md``
+    under *project_dir*. Shared by the global ``antigravity install`` and the
+    project-scoped ``install --project --platform antigravity`` paths, so both lay
+    down the rules/workflows that the uninstall path already expects to remove.
+    """
+    # Inject YAML frontmatter for native Antigravity tool discovery.
+    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")
+
+    # .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 _always_on("antigravity-rules").strip() != existing.strip():
+            rules_path.write_text(_always_on("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(_always_on("antigravity-rules"), encoding="utf-8")
+        print(f"graphify rule written to {rules_path.resolve()}")
+
+    # .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()}")
+
+
+def _antigravity_install(project_dir: Path) -> None:
+    """Install graphify for Google Antigravity (global skill + .agents/rules + .agents/workflows)."""
+    # Copy the skill to ~/.gemini/config/skills/graphify/SKILL.md (global), then
+    # lay down the always-on rules/workflows under the project dir.
+    install(platform="antigravity")
+    _antigravity_finalize(_platform_skill_destination("antigravity"), project_dir)
+
+    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, *, project: bool = False) -> 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_skill_destination("antigravity", project=project, project_dir=project_dir)
+    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()
+    refs_dir = skill_dst.parent / "references"
+    if refs_dir.exists():
+        shutil.rmtree(refs_dir)
+    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()}")
+
+
+# Devin CLI — .windsurf/rules/graphify.md (always-on context)
+# Devin reads .windsurf/rules/*.md files the same way Windsurf IDE does.
+_DEVIN_RULES_PATH = Path(".windsurf") / "rules" / "graphify.md"
+_DEVIN_RULES = """\
+## 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>"` (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 _devin_rules_install(project_dir: Path) -> None:
+    """Write .windsurf/rules/graphify.md for always-on Devin context."""
+    rules_path = (project_dir or Path(".")) / _DEVIN_RULES_PATH
+    rules_path.parent.mkdir(parents=True, exist_ok=True)
+    if rules_path.exists() and rules_path.read_text(encoding="utf-8") == _DEVIN_RULES:
+        print(f"  {rules_path}  ->  already configured (no change)")
+        return
+    action = "updated" if rules_path.exists() else "written"
+    rules_path.write_text(_DEVIN_RULES, encoding="utf-8")
+    print(f"  rules {action}  ->  {rules_path}")
+
+
+def _devin_rules_uninstall(project_dir: Path) -> None:
+    """Remove .windsurf/rules/graphify.md."""
+    rules_path = (project_dir or Path(".")) / _DEVIN_RULES_PATH
+    if not rules_path.exists():
+        return
+    rules_path.unlink()
+    print(f"  rules removed  ->  {rules_path}")
+
+
+_KILO_PLUGIN_JS = """\
+// graphify Kilo 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 available. Read graphify-out/GRAPH_REPORT.md for god nodes and architecture context before searching files." && ' +
+          output.args.command;
+        reminded = true;
+      }
+    },
+  };
+};
+"""
+
+_KILO_PLUGIN_PATH = Path(".kilo") / "plugins" / "graphify.js"
+_KILO_CONFIG_JSON_PATH = Path(".kilo") / "kilo.json"
+_KILO_CONFIG_JSONC_PATH = Path(".kilo") / "kilo.jsonc"
+
+
+def _strip_json_comments(raw: str) -> str:
+    """Remove JSONC-style comments while leaving string content intact."""
+    result: list[str] = []
+    in_string = False
+    escaped = False
+    line_comment = False
+    block_comment = False
+    i = 0
+
+    while i < len(raw):
+        ch = raw[i]
+        nxt = raw[i + 1] if i + 1 < len(raw) else ""
+
+        if line_comment:
+            if ch == "\n":
+                line_comment = False
+                result.append(ch)
+            i += 1
+            continue
+
+        if block_comment:
+            if ch == "*" and nxt == "/":
+                block_comment = False
+                i += 2
+            else:
+                i += 1
+            continue
+
+        if in_string:
+            result.append(ch)
+            if escaped:
+                escaped = False
+            elif ch == "\\":
+                escaped = True
+            elif ch == '"':
+                in_string = False
+            i += 1
+            continue
+
+        if ch == "/" and nxt == "/":
+            line_comment = True
+            i += 2
+            continue
+        if ch == "/" and nxt == "*":
+            block_comment = True
+            i += 2
+            continue
+
+        result.append(ch)
+        if ch == '"':
+            in_string = True
+        i += 1
+
+    return re.sub(r",(\s*[}\]])", r"\1", "".join(result))
+
+
+def _load_json_like(config_file: Path) -> dict:
+    if not config_file.exists():
+        return {}
+    try:
+        raw = config_file.read_text(encoding="utf-8")
+        if config_file.suffix == ".jsonc":
+            raw = _strip_json_comments(raw)
+        loaded = json.loads(raw)
+    except (OSError, json.JSONDecodeError):
+        return {}
+    return loaded if isinstance(loaded, dict) else {}
+
+
+def _kilo_config_path(project_dir: Path) -> Path:
+    kilo_dir = (project_dir or Path(".")) / ".kilo"
+    json_path = kilo_dir / _KILO_CONFIG_JSON_PATH.name
+    if json_path.exists():
+        return json_path
+    jsonc_path = kilo_dir / _KILO_CONFIG_JSONC_PATH.name
+    if jsonc_path.exists():
+        return jsonc_path
+    return json_path
+
+
+def _kilo_config_write_path(project_dir: Path) -> Path:
+    """Write automated Kilo edits to kilo.json so existing JSONC stays untouched."""
+    kilo_dir = (project_dir or Path(".")) / ".kilo"
+    return kilo_dir / _KILO_CONFIG_JSON_PATH.name
+
+
+def _install_kilo_plugin(project_dir: Path) -> None:
+    """Write graphify.js plugin and register it without rewriting user JSONC."""
+    plugin_file = project_dir / _KILO_PLUGIN_PATH
+    plugin_file.parent.mkdir(parents=True, exist_ok=True)
+    plugin_file.write_text(_KILO_PLUGIN_JS, encoding="utf-8")
+    print(f"  {_KILO_PLUGIN_PATH}  ->  tool.execute.before hook written")
+
+    config_file = _kilo_config_path(project_dir)
+    write_config_file = _kilo_config_write_path(project_dir)
+    write_config_file.parent.mkdir(parents=True, exist_ok=True)
+    config = _load_json_like(config_file)
+    plugins = config.get("plugin")
+    if not isinstance(plugins, list):
+        plugins = []
+        config["plugin"] = plugins
+    entry = plugin_file.resolve().as_uri()
+    if entry not in plugins:
+        plugins.append(entry)
+        write_config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
+        print(f"  {write_config_file.relative_to(project_dir)}  ->  plugin registered")
+    else:
+        print(
+            f"  {config_file.relative_to(project_dir)}  ->  plugin already registered (no change)"
+        )
+
+
+def _uninstall_kilo_plugin(project_dir: Path) -> None:
+    """Remove graphify.js plugin and deregister it without rewriting user JSONC."""
+    plugin_file = project_dir / _KILO_PLUGIN_PATH
+    if plugin_file.exists():
+        plugin_file.unlink()
+        print(f"  {_KILO_PLUGIN_PATH}  ->  removed")
+
+    config_file = _kilo_config_path(project_dir)
+    if not config_file.exists():
+        return
+    write_config_file = _kilo_config_write_path(project_dir)
+    config = _load_json_like(config_file)
+    plugins = config.get("plugin", [])
+    if not isinstance(plugins, list):
+        plugins = []
+    entry = plugin_file.resolve().as_uri()
+    if entry in plugins:
+        config["plugin"] = [plugin for plugin in plugins if plugin != entry]
+        if not config["plugin"]:
+            config.pop("plugin")
+        write_config_file.parent.mkdir(parents=True, exist_ok=True)
+        write_config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
+        print(
+            f"  {write_config_file.relative_to(project_dir)}  ->  plugin deregistered"
+        )
+
+
+# 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 for always-on platforms."""
+    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, _always_on("agents-md")
+        )
+    else:
+        new_content = _always_on("agents-md")
+
+    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("."))
+    elif platform == "kilo":
+        _install_kilo_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", "kilo"):
+        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 _amp_legacy_cleanup() -> None:
+    """Best-effort removal of the pre-fix ~/.amp/skills/graphify install dir.
+
+    Older graphify versions wrote the Amp skill to ~/.amp/skills, which Amp does
+    not search. Clean it up on install so a stale, never-loaded copy does not
+    linger. Failures are ignored (the new path is what matters).
+    """
+    legacy = Path.home() / ".amp" / "skills" / "graphify"
+    if legacy.exists():
+        shutil.rmtree(legacy, ignore_errors=True)
+        if not legacy.exists():
+            print(f"  legacy removed   ->  {legacy}")
+
+
+def _amp_install(project_dir: Path | None = None) -> None:
+    """User-scope Amp install: skill into ~/.config/agents/skills + AGENTS.md."""
+    _amp_legacy_cleanup()
+    _copy_skill_file("amp")
+    _agents_install(project_dir or Path("."), "amp")
+
+
+def _amp_uninstall(project_dir: Path | None = None) -> None:
+    """User-scope Amp uninstall: remove the skill and the AGENTS.md section."""
+    removed = _remove_skill_file("amp")
+    if removed:
+        print("skill removed")
+    _agents_uninstall(project_dir or Path("."), platform="amp")
+
+
+def _project_install(platform_name: str, project_dir: Path | None = None) -> None:
+    """Install platform skill/config files in the current project."""
+    project_dir = project_dir or Path(".")
+    if platform_name in ("claude", "windows"):
+        install(platform=platform_name, project=True, project_dir=project_dir)
+        claude_install(project_dir)
+        _print_project_git_add_hint([project_dir / ".claude", project_dir / "CLAUDE.md"])
+    elif platform_name == "gemini":
+        gemini_install(project_dir, project=True)
+    elif platform_name == "cursor":
+        _cursor_install(project_dir)
+        _print_project_git_add_hint([project_dir / ".cursor"])
+    elif platform_name == "kiro":
+        _kiro_install(project_dir)
+        _print_project_git_add_hint([project_dir / ".kiro"])
+    elif platform_name in ("aider", "amp", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
+        skill_dst = _copy_skill_file(platform_name, project=True, project_dir=project_dir)
+        _agents_install(project_dir, platform_name)
+        hint_paths = [_project_scope_root(skill_dst, project_dir), project_dir / "AGENTS.md"]
+        if platform_name == "opencode":
+            hint_paths.append(project_dir / ".opencode")
+        elif platform_name == "codex":
+            hint_paths.append(project_dir / ".codex")
+        _print_project_git_add_hint(hint_paths)
+    elif platform_name == "devin":
+        skill_dst = _copy_skill_file("devin", project=True, project_dir=project_dir)
+        _devin_rules_install(project_dir)
+        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / ".windsurf"])
+    elif platform_name == "antigravity":
+        # Project-scoped: skill in .agents/skills/ PLUS the .agents/rules +
+        # .agents/workflows always-on layer (previously this path wrote only the
+        # skill, leaving the rules/workflows the uninstall path removes unset).
+        skill_dst = _copy_skill_file("antigravity", project=True, project_dir=project_dir)
+        _antigravity_finalize(skill_dst, project_dir)
+        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / ".agents"])
+    elif platform_name in ("copilot", "pi", "kimi"):
+        skill_dst = _copy_skill_file(platform_name, project=True, project_dir=project_dir)
+        _print_project_git_add_hint([_project_scope_root(skill_dst, project_dir)])
+    else:
+        install(platform=platform_name, project=True, project_dir=project_dir)
+
+
+def _project_uninstall(platform_name: str, project_dir: Path | None = None) -> None:
+    """Remove project-scoped platform skill/config files only."""
+    project_dir = project_dir or Path(".")
+    if platform_name in ("claude", "windows"):
+        _remove_skill_file(platform_name, project=True, project_dir=project_dir)
+        _remove_claude_skill_registration(project_dir)
+        claude_uninstall(project_dir, project=True)
+    elif platform_name == "gemini":
+        gemini_uninstall(project_dir, project=True)
+    elif platform_name == "cursor":
+        _cursor_uninstall(project_dir)
+    elif platform_name == "kiro":
+        _kiro_uninstall(project_dir)
+    elif platform_name in ("aider", "amp", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
+        _remove_skill_file(platform_name, project=True, project_dir=project_dir)
+        _agents_uninstall(project_dir, platform=platform_name)
+        if platform_name == "codex":
+            _uninstall_codex_hook(project_dir)
+    elif platform_name == "antigravity":
+        _antigravity_uninstall(project_dir, project=True)
+    elif platform_name == "devin":
+        removed = _remove_skill_file("devin", project=True, project_dir=project_dir)
+        _devin_rules_uninstall(project_dir)
+        if not removed:
+            print("nothing to remove")
+    elif platform_name in ("copilot", "pi", "kimi"):
+        removed = _remove_skill_file(platform_name, project=True, project_dir=project_dir)
+        if not removed:
+            print("nothing to remove")
+    elif platform_name == "codebuddy":
+        codebuddy_uninstall(project_dir)
+    else:
+        _remove_skill_file(platform_name, project=True, project_dir=project_dir)
+
+
+def _project_uninstall_all(project_dir: Path | None = None) -> None:
+    """Remove project-scoped install files without touching user-scope installs."""
+    project_dir = project_dir or Path(".")
+    print("Uninstalling project-scoped graphify files...\n")
+    for platform_name in _PLATFORM_CONFIG:
+        _project_uninstall(platform_name, project_dir)
+    for platform_name in ("gemini", "cursor"):
+        _project_uninstall(platform_name, project_dir)
+    print("\nDone.")
+
+
+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")
+        if platform == "opencode":
+            _uninstall_opencode_plugin(project_dir or Path("."))
+        elif platform == "kilo":
+            _uninstall_kilo_plugin(project_dir or Path("."))
+        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")
+        if platform == "opencode":
+            _uninstall_opencode_plugin(project_dir or Path("."))
+        elif platform == "kilo":
+            _uninstall_kilo_plugin(project_dir or Path("."))
+        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("."))
+    elif platform == "kilo":
+        _uninstall_kilo_plugin(project_dir or Path("."))
+
+
+def _kilo_uninstall_global() -> list[str]:
+    removed = []
+    command_dst = Path.home() / ".config" / "kilo" / "command" / "graphify.md"
+    if command_dst.exists():
+        command_dst.unlink()
+        removed.append(f"command removed: {command_dst}")
+    try:
+        command_dst.parent.rmdir()
+    except OSError:
+        pass
+
+    skill_dst = Path.home() / _PLATFORM_CONFIG["kilo"]["skill_dst"]
+    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
+
+    return removed
+
+
+def _kilo_install(project_dir: Path) -> None:
+    """Install native Kilo skill + command globally and always-on project wiring locally."""
+    install(platform="kilo")
+    _agents_install(project_dir or Path("."), "kilo")
+
+
+def _kilo_uninstall(project_dir: Path) -> None:
+    """Remove Kilo always-on project wiring and global skill/command files."""
+    _agents_uninstall(project_dir or Path("."), platform="kilo")
+    removed = _kilo_uninstall_global()
+    print("; ".join(removed) if removed else "nothing to remove")
+
+
+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, _always_on("claude-md")
+        )
+    else:
+        new_content = _always_on("claude-md")
+
+    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", "Read|Glob") and "graphify" in str(h))]
+    hooks["PreToolUse"].append(_SETTINGS_HOOK)
+    hooks["PreToolUse"].append(_READ_SETTINGS_HOOK)
+    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
+    print(f"  .claude/settings.json  ->  PreToolUse hooks registered (Bash search + Read/Glob)")
+
+
+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", "Read|Glob") 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)
+    codebuddy_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)
+    # Amp also drops a user-scope skill at ~/.config/agents/skills, which the
+    # AGENTS.md cleanup above does not touch.
+    _remove_skill_file("amp")
+    _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, *, project: bool = False) -> None:
+    """Remove the graphify skill tree (SKILL.md + references/) and the CLAUDE.md section.
+
+    Mirrors gemini_uninstall: the bare `graphify uninstall` and `graphify claude
+    uninstall` must remove the installed skill, not just strip CLAUDE.md, or the
+    progressive-disclosure tree (SKILL.md + references/) is orphaned (#1121).
+    """
+    project_dir = project_dir or Path(".")
+    _remove_skill_file("claude", project=project, project_dir=project_dir)
+    target = project_dir / "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 codebuddy_install(project_dir: Path | None = None) -> None:
+    """Install the graphify skill and CODEBUDDY.md section for CodeBuddy."""
+    _copy_skill_file("codebuddy", project=bool(project_dir), project_dir=project_dir)
+    target = (project_dir or Path(".")) / "CODEBUDDY.md"
+
+    if target.exists():
+        content = target.read_text(encoding="utf-8")
+        new_content = _replace_or_append_section(
+            content, _CODEBUDDY_MD_MARKER, _always_on("claude-md")
+        )
+    else:
+        new_content = _always_on("claude-md")
+
+    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()}")
+
+    # Also write CodeBuddy PreToolUse hook to .codebuddy/settings.json
+    _install_codebuddy_hook(project_dir or Path("."))
+
+    print()
+    print("CodeBuddy will now check the knowledge graph before answering")
+    print("codebase questions and rebuild it after code changes.")
+
+
+def _install_codebuddy_hook(project_dir: Path) -> None:
+    """Add graphify PreToolUse hook to .codebuddy/settings.json."""
+    settings_path = project_dir / ".codebuddy" / "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", "Read|Glob") and "graphify" in str(h))]
+    hooks["PreToolUse"].append(_SETTINGS_HOOK)
+    hooks["PreToolUse"].append(_READ_SETTINGS_HOOK)
+    settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
+    print(f"  .codebuddy/settings.json  ->  PreToolUse hooks registered")
+
+
+def _uninstall_codebuddy_hook(project_dir: Path) -> None:
+    """Remove graphify PreToolUse hook from .codebuddy/settings.json."""
+    settings_path = project_dir / ".codebuddy" / "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", "Read|Glob") 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"  .codebuddy/settings.json  ->  PreToolUse hook removed")
+
+
+def codebuddy_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
+    """Remove the graphify skill tree (SKILL.md + references/) and the CODEBUDDY.md section."""
+    project_dir = project_dir or Path(".")
+    _remove_skill_file("codebuddy", project=project, project_dir=project_dir)
+    target = project_dir / "CODEBUDDY.md"
+
+    if not target.exists():
+        print("No CODEBUDDY.md found in current directory - nothing to do")
+        return
+
+    content = target.read_text(encoding="utf-8")
+    if _CODEBUDDY_MD_MARKER not in content:
+        print("graphify section not found in CODEBUDDY.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"CODEBUDDY.md was empty after removal - deleted {target.resolve()}")
+
+    _uninstall_codebuddy_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:
+    for _stream in (sys.stdout, sys.stderr):
+        if _stream is not None and hasattr(_stream, "reconfigure"):
+            try:
+                _stream.reconfigure(encoding="utf-8", errors="replace")
+            except Exception:
+                pass
+    # 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):
+        # Resolve each platform's real user-scope destination so per-platform
+        # overrides (gemini, opencode, devin, antigravity, amp) check the dir
+        # they actually install into, not the bare cfg['skill_dst'].
+        for skill_dst in {_platform_skill_destination(name) for name in _PLATFORM_CONFIG}:
+            _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|codebuddy|codex|opencode|aider|amp|claw|droid|trae|trae-cn|gemini|cursor|antigravity|hermes|kiro|pi|devin)")
+        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("    --no-label              keep 'Community N' placeholders (skip LLM community naming)")
+        print("    --backend=<name>        backend to use for community naming (default: auto-detect)")
+        print("  label <path>            (re)name communities with the configured LLM backend, regenerate report")
+        print("    --backend=<name>        backend to use (default: auto-detect from API keys)")
+        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("  affected \"X\"             reverse traversal to find nodes impacted by X")
+        print("    --relation R            edge relation to traverse in reverse (repeatable)")
+        print("    --depth N               reverse traversal depth (default 2)")
+        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("    --mode deep             aggressive INFERRED-edge semantic extraction")
+        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("    --postgres DSN          extract schema from a live PostgreSQL database")
+        print("                            maps tables, views, functions + FK relationships;")
+        print("                            column-level detail is not represented in the graph")
+        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("  codebuddy install       write graphify section to CODEBUDDY.md + PreToolUse hook (CodeBuddy)")
+        print("  codebuddy uninstall     remove graphify section from CODEBUDDY.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(
+            "  kilo install            install native Kilo skill + command + AGENTS.md + .kilo plugin"
+        )
+        print(
+            "  kilo uninstall          remove native Kilo skill + command + AGENTS.md + .kilo 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("  devin install           write skill to ~/.config/devin/skills/graphify/ (Devin CLI)")
+        print("  devin uninstall         remove skill from ~/.config/devin/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
+        project_scope = False
+        args = sys.argv[2:]
+        i = 0
+        while i < len(args):
+            arg = args[i]
+            if arg in ("-h", "--help"):
+                _print_install_usage()
+                return
+            if arg == "--project":
+                project_scope = True
+                i += 1
+            elif 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
+        if project_scope:
+            _project_install(chosen_platform, Path("."))
+        else:
+            install(platform=chosen_platform)
+    elif cmd == "uninstall":
+        args = sys.argv[2:]
+        purge = "--purge" in args
+        project_scope = "--project" in args
+        selected_platform = None
+        i = 0
+        while i < len(args):
+            arg = args[i]
+            if arg in ("--purge", "--project"):
+                i += 1
+            elif arg.startswith("--platform="):
+                selected_platform = arg.split("=", 1)[1]
+                i += 1
+            elif arg == "--platform":
+                if i + 1 >= len(args):
+                    print("error: --platform requires a value", file=sys.stderr)
+                    sys.exit(1)
+                selected_platform = args[i + 1]
+                i += 2
+            elif arg.startswith("-"):
+                print(f"error: unknown uninstall option '{arg}'", file=sys.stderr)
+                sys.exit(1)
+            else:
+                selected_platform = arg
+                i += 1
+        if project_scope:
+            if selected_platform:
+                _project_uninstall(selected_platform, Path("."))
+            else:
+                _project_uninstall_all(Path("."))
+        else:
+            uninstall_all(purge=purge)
+    elif cmd == "claude":
+        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
+        if subcmd == "install":
+            if "--project" in sys.argv[3:]:
+                _project_install("claude", Path("."))
+            else:
+                claude_install()
+        elif subcmd == "uninstall":
+            if "--project" in sys.argv[3:]:
+                _project_uninstall("claude", Path("."))
+            else:
+                claude_uninstall()
+        else:
+            print("Usage: graphify claude [install|uninstall]", file=sys.stderr)
+            sys.exit(1)
+    elif cmd == "codebuddy":
+        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
+        if subcmd == "install":
+            codebuddy_install()
+        elif subcmd == "uninstall":
+            codebuddy_uninstall()
+        else:
+            print("Usage: graphify codebuddy [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(project=("--project" in sys.argv[3:]))
+        elif subcmd == "uninstall":
+            gemini_uninstall(project=("--project" in sys.argv[3:]))
+        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":
+            if "--project" in sys.argv[3:]:
+                _project_install("copilot", Path("."))
+            else:
+                install(platform="copilot")
+        elif subcmd == "uninstall":
+            if "--project" in sys.argv[3:]:
+                _project_uninstall("copilot", Path("."))
+            else:
+                removed = _remove_skill_file("copilot")
+                print("skill removed" if removed else "nothing to remove")
+        else:
+            print("Usage: graphify copilot [install|uninstall]", file=sys.stderr)
+            sys.exit(1)
+    elif cmd == "kilo":
+        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
+        if subcmd == "install":
+            _kilo_install(Path("."))
+        elif subcmd == "uninstall":
+            _kilo_uninstall(Path("."))
+        else:
+            print("Usage: graphify kilo [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 == "devin":
+        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
+        if subcmd == "install":
+            if "--project" in sys.argv[3:]:
+                _project_install("devin", Path("."))
+            else:
+                install(platform="devin")
+        elif subcmd == "uninstall":
+            if "--project" in sys.argv[3:]:
+                _project_uninstall("devin", Path("."))
+            else:
+                removed = _remove_skill_file("devin")
+                print("skill removed" if removed else "nothing to remove")
+        else:
+            print("Usage: graphify devin [install|uninstall]", file=sys.stderr)
+            sys.exit(1)
+    elif cmd == "pi":
+        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
+        if subcmd == "install":
+            if "--project" in sys.argv[3:]:
+                _project_install("pi", Path("."))
+            else:
+                install("pi")
+        elif subcmd == "uninstall":
+            if "--project" in sys.argv[3:]:
+                _project_uninstall("pi", Path("."))
+            else:
+                _remove_skill_file("pi")
+        else:
+            print("Usage: graphify pi [install|uninstall]", file=sys.stderr)
+            sys.exit(1)
+    elif cmd == "amp":
+        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
+        if subcmd == "install":
+            if "--project" in sys.argv[3:]:
+                _project_install("amp", Path("."))
+            else:
+                _amp_install(Path("."))
+        elif subcmd == "uninstall":
+            if "--project" in sys.argv[3:]:
+                _project_uninstall("amp", Path("."))
+            else:
+                _amp_uninstall(Path("."))
+        else:
+            print("Usage: graphify amp [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":
+            if "--project" in sys.argv[3:]:
+                _project_install(cmd, Path("."))
+            else:
+                _agents_install(Path("."), cmd)
+        elif subcmd == "uninstall":
+            if "--project" in sys.argv[3:]:
+                _project_uninstall(cmd, Path("."))
+            else:
+                _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":
+            if "--project" in sys.argv[3:]:
+                _project_install("antigravity", Path("."))
+            else:
+                _antigravity_install(Path("."))
+        elif subcmd == "uninstall":
+            if "--project" in sys.argv[3:]:
+                _project_uninstall("antigravity", Path("."))
+            else:
+                _antigravity_uninstall(Path("."))
+        else:
+            print("Usage: graphify antigravity [install|uninstall]", file=sys.stderr)
+            sys.exit(1)
+    elif cmd == "provider":
+        from graphify.llm import _custom_providers_path, BACKENDS
+        import json as _json
+        subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
+        global_path = _custom_providers_path(global_=True)
+
+        if subcmd == "list":
+            global_path.parent.mkdir(parents=True, exist_ok=True)
+            existing: dict = {}
+            if global_path.is_file():
+                try:
+                    existing = _json.loads(global_path.read_text(encoding="utf-8"))
+                except Exception:
+                    pass
+            if not existing:
+                print("No custom providers registered.")
+            else:
+                for name in existing:
+                    print(f"  {name}  ({existing[name].get('base_url', '')})")
+
+        elif subcmd == "show":
+            name = sys.argv[3] if len(sys.argv) > 3 else ""
+            if not name:
+                print("Usage: graphify provider show <name>", file=sys.stderr)
+                sys.exit(1)
+            existing = {}
+            if global_path.is_file():
+                try:
+                    existing = _json.loads(global_path.read_text(encoding="utf-8"))
+                except Exception:
+                    pass
+            if name not in existing:
+                print(f"Provider '{name}' not found.", file=sys.stderr)
+                sys.exit(1)
+            print(_json.dumps({name: existing[name]}, indent=2))
+
+        elif subcmd == "add":
+            args = sys.argv[3:]
+            name = args[0] if args and not args[0].startswith("-") else ""
+            if not name:
+                print("Usage: graphify provider add <name> --base-url URL --default-model MODEL --env-key KEY", file=sys.stderr)
+                sys.exit(1)
+            if name in BACKENDS:
+                print(f"Error: '{name}' is a built-in provider and cannot be overridden.", file=sys.stderr)
+                sys.exit(1)
+            base_url = ""
+            default_model = ""
+            env_key = ""
+            pricing_input = 0.0
+            pricing_output = 0.0
+            i = 1
+            while i < len(args):
+                a = args[i]
+                if a == "--base-url" and i + 1 < len(args):
+                    base_url = args[i + 1]; i += 2
+                elif a.startswith("--base-url="):
+                    base_url = a.split("=", 1)[1]; i += 1
+                elif a == "--default-model" and i + 1 < len(args):
+                    default_model = args[i + 1]; i += 2
+                elif a.startswith("--default-model="):
+                    default_model = a.split("=", 1)[1]; i += 1
+                elif a == "--env-key" and i + 1 < len(args):
+                    env_key = args[i + 1]; i += 2
+                elif a.startswith("--env-key="):
+                    env_key = a.split("=", 1)[1]; i += 1
+                elif a == "--pricing-input" and i + 1 < len(args):
+                    pricing_input = float(args[i + 1]); i += 2
+                elif a == "--pricing-output" and i + 1 < len(args):
+                    pricing_output = float(args[i + 1]); i += 2
+                else:
+                    i += 1
+            if not base_url or not default_model or not env_key:
+                print("Error: --base-url, --default-model, and --env-key are required.", file=sys.stderr)
+                sys.exit(1)
+            from graphify.llm import provider_base_url_ok
+            if not provider_base_url_ok(base_url, name):
+                print(f"Error: refusing to add provider with unsafe base_url {base_url!r}.", file=sys.stderr)
+                sys.exit(1)
+            global_path.parent.mkdir(parents=True, exist_ok=True)
+            existing = {}
+            if global_path.is_file():
+                try:
+                    existing = _json.loads(global_path.read_text(encoding="utf-8"))
+                except Exception:
+                    pass
+            existing[name] = {
+                "base_url": base_url,
+                "default_model": default_model,
+                "env_key": env_key,
+                "pricing": {"input": pricing_input, "output": pricing_output},
+                "temperature": 0,
+            }
+            global_path.write_text(_json.dumps(existing, indent=2) + "\n", encoding="utf-8")
+            print(f"Provider '{name}' added. Use with: graphify extract . --backend {name}")
+
+        elif subcmd == "remove":
+            name = sys.argv[3] if len(sys.argv) > 3 else ""
+            if not name:
+                print("Usage: graphify provider remove <name>", file=sys.stderr)
+                sys.exit(1)
+            existing = {}
+            if global_path.is_file():
+                try:
+                    existing = _json.loads(global_path.read_text(encoding="utf-8"))
+                except Exception:
+                    pass
+            if name not in existing:
+                print(f"Provider '{name}' not found.", file=sys.stderr)
+                sys.exit(1)
+            del existing[name]
+            global_path.write_text(_json.dumps(existing, indent=2) + "\n", encoding="utf-8")
+            print(f"Provider '{name}' removed.")
+
+        else:
+            print("Usage: graphify provider [add|list|show|remove]", file=sys.stderr)
+            if subcmd:
+                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
+        from graphify import querylog
+
+        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)
+        import time as _time
+        _t0 = _time.perf_counter()
+        _mode = "dfs" if use_dfs else "bfs"
+        _result = _query_graph_text(
+            G,
+            question,
+            mode=_mode,
+            depth=2,
+            token_budget=budget,
+            context_filters=context_filters,
+        )
+        querylog.log_query(
+            kind="query",
+            question=question,
+            corpus=str(gp),
+            result=_result,
+            mode=_mode,
+            depth=2,
+            token_budget=budget,
+            duration_ms=(_time.perf_counter() - _t0) * 1000,
+        )
+        print(_result)
+    elif cmd == "affected":
+        if len(sys.argv) < 3:
+            print("Usage: graphify affected \"<node-or-label>\" [--relation R] [--depth N] [--graph path]", file=sys.stderr)
+            sys.exit(1)
+        from graphify.affected import DEFAULT_AFFECTED_RELATIONS, format_affected, load_graph
+        query = sys.argv[2]
+        graph_path = "graphify-out/graph.json"
+        depth = 2
+        relations: list[str] = []
+        args = sys.argv[3:]
+        i = 0
+        while i < len(args):
+            if args[i] == "--graph" and i + 1 < len(args):
+                graph_path = args[i + 1]
+                i += 2
+            elif args[i].startswith("--graph="):
+                graph_path = args[i].split("=", 1)[1]
+                i += 1
+            elif args[i] == "--depth" and i + 1 < len(args):
+                try:
+                    depth = int(args[i + 1])
+                except ValueError:
+                    print("error: --depth must be an integer", file=sys.stderr)
+                    sys.exit(1)
+                i += 2
+            elif args[i].startswith("--depth="):
+                try:
+                    depth = int(args[i].split("=", 1)[1])
+                except ValueError:
+                    print("error: --depth must be an integer", file=sys.stderr)
+                    sys.exit(1)
+                i += 1
+            elif args[i] == "--relation" and i + 1 < len(args):
+                relations.append(args[i + 1])
+                i += 2
+            elif args[i].startswith("--relation="):
+                relations.append(args[i].split("=", 1)[1])
+                i += 1
+            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("error: graph file must be a .json file", file=sys.stderr)
+            sys.exit(1)
+        try:
+            graph = load_graph(gp)
+        except Exception as exc:
+            print(f"error: could not load graph: {exc}", file=sys.stderr)
+            sys.exit(1)
+        print(
+            format_affected(
+                graph,
+                query,
+                relations=relations or DEFAULT_AFFECTED_RELATIONS,
+                depth=depth,
+            )
+        )
+    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))
+        from graphify import querylog
+        querylog.log_query(
+            kind="path",
+            question=f"{sys.argv[2]} -> {sys.argv[3]}",
+            corpus=str(gp),
+            nodes_returned=hops,
+        )
+
+    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")
+        from graphify import querylog
+        querylog.log_query(
+            kind="explain",
+            question=sys.argv[2],
+            corpus=str(gp),
+            nodes_returned=len(connections),
+        )
+
+    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 in ("cluster-only", "label"):
+        # `label` is `cluster-only` that always (re)generates community names with
+        # the configured backend, even when a .graphify_labels.json already exists.
+        force_relabel = cmd == "label"
+        # 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
+        no_label = "--no-label" in sys.argv
+        _backend_arg = next((a for a in sys.argv if a.startswith("--backend=")), None)
+        label_backend = _backend_arg.split("=", 1)[1] if _backend_arg else None
+        _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, remap_communities_to_previous
+        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)
+        # Mirror the watch/update path (#822): map new cids to prior ones by
+        # node-overlap so the existing .graphify_labels.json keeps attaching
+        # to the same conceptual community after re-clustering. Without this,
+        # labels follow raw cid index and become misaligned whenever the
+        # graph has changed between labeling and cluster-only (#1027).
+        previous_node_community = {
+            n["id"]: n["community"]
+            for n in _raw.get("nodes", [])
+            if n.get("community") is not None and n.get("id") is not None
+        }
+        if previous_node_community:
+            communities = remap_communities_to_previous(communities, previous_node_community)
+        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() and not force_relabel:
+            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}
+        elif no_label and not force_relabel:
+            labels = {cid: f"Community {cid}" for cid in communities}
+        else:
+            # No labels file yet (or `graphify label` forced a refresh). When run
+            # standalone there is no orchestrating agent to do skill.md Step 5, so
+            # auto-name communities with the configured backend rather than leave
+            # "Community N" (#1097). Degrades to placeholders if no backend/on error.
+            from graphify.llm import generate_community_labels
+            print("Labeling communities...")
+            # The final labels (LLM or placeholder fallback) are persisted to
+            # .graphify_labels.json by the unconditional write below.
+            labels, _ = generate_community_labels(
+                G, communities, backend=label_backend, gods=gods
+            )
+        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 = []
+
+        # Fallback: graph.json carries the per-node community as a node attribute
+        # (`to_json` writes it on every node). The analysis sidecar is the
+        # canonical source — but the post-commit / watch rebuild path doesn't
+        # regenerate it, and `extract` may have its temp files cleaned up. When
+        # that happens, `graphify export html` previously bailed with
+        # "Single community - aggregated view not useful." even though the
+        # per-node attribute had the right data all along. Reconstruct from
+        # the graph itself so downstream subcommands (html, obsidian, wiki,
+        # svg, graphml, neo4j) don't silently produce a degraded artifact.
+        if not communities:
+            reconstructed: dict[int, list[str]] = {}
+            for node_id, data in G.nodes(data=True):
+                cid_raw = data.get("community")
+                if cid_raw is None:
+                    continue
+                try:
+                    cid = int(cid_raw)
+                except (TypeError, ValueError):
+                    continue
+                reconstructed.setdefault(cid, []).append(str(node_id))
+            if reconstructed:
+                communities = reconstructed
+
+        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] [--mode deep] [--out DIR] [--google-workspace] [--no-cluster] "
+                "[--max-workers N] [--token-budget N] [--max-concurrency N] "
+                "[--api-timeout S] [--postgres DSN]",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+
+        has_path = True
+        if sys.argv[2].startswith("-"):
+            has_path = False
+            target = Path(".").resolve()
+        else:
+            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
+        extract_mode: str | None = None
+        out_dir: Path | None = None
+        cli_postgres_dsn: str | 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:] if has_path else sys.argv[2:]
+        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 == "--mode" and i + 1 < len(args):
+                extract_mode = args[i + 1]; i += 2
+            elif a.startswith("--mode="):
+                extract_mode = 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
+            elif a == "--postgres" and i + 1 < len(args):
+                cli_postgres_dsn = args[i + 1]; i += 2
+            elif a.startswith("--postgres="):
+                cli_postgres_dsn = a.split("=", 1)[1]; i += 1
+            else:
+                i += 1
+
+        if not has_path and cli_postgres_dsn is None:
+            print("error: must specify a path to scan or a --postgres DSN", file=sys.stderr)
+            sys.exit(1)
+
+        _VALID_MODES = {"deep"}
+        if extract_mode is not None and extract_mode not in _VALID_MODES:
+            print(
+                f"error: unknown --mode '{extract_mode}'. "
+                f"Available: {', '.join(sorted(_VALID_MODES))}",
+                file=sys.stderr,
+            )
+            sys.exit(2)
+        deep_mode = extract_mode == "deep"
+        if deep_mode:
+            print("[graphify extract] deep mode enabled: richer semantic extraction")
+
+        # 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)
+
+        # 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 has_path else False
+
+        if not has_path:
+            code_files = []
+            doc_files = []
+            paper_files = []
+            image_files = []
+            deleted_files = []
+            unchanged_total = 0
+            files_by_type = {}
+        elif 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,
+            )
+            files_by_type = detection.get("files", {})
+            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:
+            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", {})
+            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"
+            )
+
+        # Resolve the LLM backend only now that we know whether the corpus
+        # needs one. A code-only corpus is pure local AST and must not require
+        # an API key; the key is enforced below only when there's LLM work.
+        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,
+        )
+        needs_llm = bool(semantic_files) or dedup_llm
+        if backend is None and needs_llm:
+            backend = _detect_backend()
+        if backend is not None and backend not in _BACKENDS:
+            print(
+                f"error: unknown backend '{backend}'. "
+                f"Available: {', '.join(sorted(_BACKENDS))}",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+        if needs_llm:
+            if backend is None:
+                reasons = []
+                if semantic_files:
+                    reasons.append(
+                        f"{len(semantic_files)} doc/paper/image file(s) need semantic extraction"
+                    )
+                if dedup_llm:
+                    reasons.append("--dedup-llm was passed")
+                print(
+                    "error: no LLM API key found (" + "; ".join(reasons) + "). "
+                    "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. A code-only "
+                    "corpus needs no key.",
+                    file=sys.stderr,
+                )
+                sys.exit(1)
+            if backend == "ollama":
+                from graphify.llm import _validate_ollama_base_url
+                _oll_url = os.environ.get("OLLAMA_BASE_URL", _BACKENDS["ollama"].get("base_url", ""))
+                try:
+                    _validate_ollama_base_url(_oll_url, warn=False)
+                except ValueError as exc:
+                    print(f"error: {exc}", file=sys.stderr)
+                    sys.exit(2)
+            if not _get_backend_api_key(backend):
+                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)
+
+        # 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 deep_mode:
+                    corpus_kwargs["deep_mode"] = True
+                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).
+                # Also track per-chunk success so we can fail loudly when
+                # every chunk errors (e.g. missing backend SDK package).
+                _chunk_stats = {"total": 0, "succeeded": 0}
+                def _progress(idx: int, total: int, _result: dict) -> None:
+                    _chunk_stats["total"] = total
+                    _chunk_stats["succeeded"] += 1
+                    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}
+
+                # on_chunk_done only fires after a chunk succeeds. If fresh
+                # semantic extraction was requested and no chunks completed,
+                # fail instead of writing an AST-only graph with exit 0.
+                if uncached_paths and _chunk_stats["succeeded"] == 0:
+                    print(
+                        f"[graphify extract] error: all semantic chunks failed "
+                        f"for backend '{backend}' ({len(uncached_paths)} uncached files) - "
+                        f"see per-chunk errors above. If you see 'requires the X package', "
+                        f"run `pip install X` and retry.",
+                        file=sys.stderr,
+                    )
+                    sys.exit(1)
+                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)
+
+        pg_result: dict = {"nodes": [], "edges": []}
+        if cli_postgres_dsn is not None:
+            from graphify.pg_introspect import introspect_postgres
+            print(f"[graphify extract] introspecting PostgreSQL schema...")
+            try:
+                pg_result = introspect_postgres(cli_postgres_dsn)
+            except (ConnectionError, ImportError) as exc:
+                print(f"error: {exc}", file=sys.stderr)
+                sys.exit(1)
+            print(f"[graphify extract] PostgreSQL: {len(pg_result['nodes'])} nodes, "
+                  f"{len(pg_result['edges'])} edges")
+
+        # Merge AST + semantic + pg_result. 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", [])) + list(pg_result.get("nodes", [])),
+            "edges": list(ast_result.get("edges", [])) + list(sem_result.get("edges", [])) + list(pg_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", root=target)
+            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", root=target)
+        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}"
+            )
+        # extract intentionally stops at graph.json + analysis; the report and
+        # community labels are produced by `cluster-only` (or an agent's Step 5).
+        # Point standalone users at it so communities get named (#1097).
+        print(
+            "[graphify extract] next: run "
+            f"`graphify cluster-only {graphify_out.parent}` "
+            "to generate GRAPH_REPORT.md and name communities"
+        )
+
+    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()