diff --git a/code_review_graph/main.py b/code_review_graph/main.py
index 37c395b..4a5025e 100644
--- a/code_review_graph/main.py
+++ b/code_review_graph/main.py
@@ -292,6 +292,7 @@ def list_graph_stats_tool(
 @mcp.tool()
 def get_docs_section_tool(
     section_name: str,
+    repo_root: Optional[str] = None,
 ) -> dict:
     """Get a specific section from the LLM-optimized documentation reference.
 
@@ -303,8 +304,9 @@ def get_docs_section_tool(
 
     Args:
         section_name: The section to retrieve (e.g. "review-delta", "usage").
+        repo_root: Repository root path. Auto-detected if omitted.
     """
-    return get_docs_section(section_name=section_name, repo_root=_default_repo_root)
+    return get_docs_section(section_name=section_name, repo_root=repo_root)
 
 
 @mcp.tool()
diff --git a/code_review_graph/skills.py b/code_review_graph/skills.py
index 18c555c..ccfc8d6 100644
--- a/code_review_graph/skills.py
+++ b/code_review_graph/skills.py
@@ -331,7 +331,7 @@ def generate_skills(repo_root: Path, skills_dir: Path | None = None) -> Path:
     return skills_dir
 
 
-def generate_hooks_config() -> dict[str, Any]:
+def generate_hooks_config(repo_root: Path) -> dict[str, Any]:
     """Generate Claude Code hooks configuration.
 
     Returns a hooks config dict with PostToolUse, SessionStart, and
@@ -340,25 +340,34 @@ def generate_hooks_config() -> dict[str, Any]:
     Returns:
         Dict with hooks configuration suitable for .claude/settings.json.
     """
+    repo_arg = json.dumps(repo_root.resolve().as_posix())
     return {
         "hooks": {
             "PostToolUse": [
                 {
                     "matcher": "Edit|Write|Bash",
-                    "command": "code-review-graph update --skip-flows",
-                    "timeout": 5000,
+                    "hooks": [
+                        {
+                            "type": "command",
+                            "command": (
+                                f"code-review-graph update --skip-flows "
+                                f"--repo {repo_arg}"
+                            ),
+                            "timeout": 5000,
+                        }
+                    ],
                 },
             ],
             "SessionStart": [
                 {
-                    "command": "code-review-graph status",
-                    "timeout": 3000,
-                },
-            ],
-            "PreCommit": [
-                {
-                    "command": "code-review-graph detect-changes --brief",
-                    "timeout": 10000,
+                    "matcher": "",
+                    "hooks": [
+                        {
+                            "type": "command",
+                            "command": f"code-review-graph status --repo {repo_arg}",
+                            "timeout": 3000,
+                        }
+                    ],
                 },
             ],
         }
@@ -385,7 +394,7 @@ def install_hooks(repo_root: Path) -> None:
         except (json.JSONDecodeError, OSError) as exc:
             logger.warning("Could not read existing %s: %s", settings_path, exc)
 
-    hooks_config = generate_hooks_config()
+    hooks_config = generate_hooks_config(repo_root)
     existing.update(hooks_config)
 
     settings_path.write_text(json.dumps(existing, indent=2) + "\n", encoding="utf-8")
diff --git a/tests/test_skills.py b/tests/test_skills.py
index bad8b8b..b329ec8 100644
--- a/tests/test_skills.py
+++ b/tests/test_skills.py
@@ -1,11 +1,13 @@
 """Tests for skills and hooks auto-install."""
 
 import json
+from pathlib import Path
 from unittest.mock import patch
 
 from code_review_graph.skills import (
     _CLAUDE_MD_SECTION_MARKER,
     PLATFORMS,
+    _build_server_entry,
     generate_hooks_config,
     generate_skills,
     inject_claude_md,
@@ -78,38 +80,41 @@ def test_idempotent(self, tmp_path):
 
 class TestGenerateHooksConfig:
     def test_returns_dict_with_hooks(self):
-        config = generate_hooks_config()
+        config = generate_hooks_config(Path("/repo"))
         assert "hooks" in config
 
     def test_has_post_tool_use(self):
-        config = generate_hooks_config()
+        config = generate_hooks_config(Path("/repo"))
         assert "PostToolUse" in config["hooks"]
         hooks = config["hooks"]["PostToolUse"]
         assert len(hooks) >= 1
         assert hooks[0]["matcher"] == "Edit|Write|Bash"
-        assert "update" in hooks[0]["command"]
-        assert hooks[0]["timeout"] == 5000
+        assert hooks[0]["hooks"][0]["type"] == "command"
+        assert hooks[0]["hooks"][0]["command"].endswith('--repo "E:/repo"')
+        assert hooks[0]["hooks"][0]["timeout"] == 5000
 
     def test_has_session_start(self):
-        config = generate_hooks_config()
+        config = generate_hooks_config(Path("/repo"))
         assert "SessionStart" in config["hooks"]
         hooks = config["hooks"]["SessionStart"]
         assert len(hooks) >= 1
-        assert "status" in hooks[0]["command"]
-        assert hooks[0]["timeout"] == 3000
+        assert hooks[0]["matcher"] == ""
+        assert hooks[0]["hooks"][0]["command"].endswith('--repo "E:/repo"')
+        assert hooks[0]["hooks"][0]["timeout"] == 3000
 
-    def test_has_pre_commit(self):
-        config = generate_hooks_config()
-        assert "PreCommit" in config["hooks"]
-        hooks = config["hooks"]["PreCommit"]
-        assert len(hooks) >= 1
-        assert "detect-changes" in hooks[0]["command"]
-        assert hooks[0]["timeout"] == 10000
+    def test_quotes_repo_paths_with_spaces(self):
+        config = generate_hooks_config(Path("/repo with spaces"))
+        command = config["hooks"]["PostToolUse"][0]["hooks"][0]["command"]
+        assert '--repo "E:/repo with spaces"' in command
+
+    def test_does_not_emit_invalid_pre_commit_hook(self):
+        config = generate_hooks_config(Path("/repo"))
+        assert "PreCommit" not in config["hooks"]
 
-    def test_has_all_three_hook_types(self):
-        config = generate_hooks_config()
+    def test_has_only_valid_hook_types(self):
+        config = generate_hooks_config(Path("/repo"))
         hook_types = set(config["hooks"].keys())
-        assert hook_types == {"PostToolUse", "SessionStart", "PreCommit"}
+        assert hook_types == {"PostToolUse", "SessionStart"}
 
 
 class TestInstallHooks:
@@ -132,7 +137,7 @@ def test_merges_with_existing(self, tmp_path):
         assert data["customSetting"] is True
         assert "PostToolUse" in data["hooks"]
         assert "SessionStart" in data["hooks"]
-        assert "PreCommit" in data["hooks"]
+        assert "PreCommit" not in data["hooks"]
 
     def test_creates_claude_directory(self, tmp_path):
         install_hooks(tmp_path)
@@ -183,6 +188,14 @@ def test_idempotent_with_existing_content(self, tmp_path):
 
 
 class TestInstallPlatformConfigs:
+    def test_build_server_entry_includes_repo_target(self):
+        entry = _build_server_entry(
+            PLATFORMS["claude"],
+            key="claude",
+            repo_target="grimoirescribe",
+        )
+        assert entry["args"][-2:] == ["--repo", "grimoirescribe"]
+
     def test_install_cursor_config(self, tmp_path):
         with patch.dict(PLATFORMS, {
             "cursor": {**PLATFORMS["cursor"], "detect": lambda: True},
@@ -307,3 +320,23 @@ def test_continue_array_no_duplicate(self, tmp_path):
             install_platform_configs(tmp_path, target="continue")
         data = json.loads(config_path.read_text())
         assert len(data["mcpServers"]) == 1
+
+    def test_install_claude_user_scope_uses_cli(self, tmp_path):
+        with patch("code_review_graph.skills.shutil.which") as mock_which:
+            mock_which.side_effect = lambda name: name
+            with patch("code_review_graph.skills.subprocess.run") as mock_run:
+                configured = install_platform_configs(
+                    tmp_path,
+                    target="claude",
+                    scope="user",
+                    repo_target="grimoirescribe",
+                )
+
+        assert configured == ["Claude Code (user)"]
+        assert mock_run.call_count == 2
+        add_cmd = mock_run.call_args_list[1].args[0]
+        assert add_cmd[:6] == [
+            "claude", "mcp", "add-json", "--scope", "user", "code-review-graph",
+        ]
+        assert "--repo" in add_cmd[-1]
+        assert "grimoirescribe" in add_cmd[-1]
diff --git a/tests/test_tools.py b/tests/test_tools.py
index 7eede63..0b297b3 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -152,6 +152,19 @@ def test_search_edges_by_target_name(self):
 class TestGetDocsSection:
     """Tests for the get_docs_section tool."""
 
+    def test_explicit_repo_root_uses_that_docs_file(self, tmp_path):
+        docs_dir = tmp_path / "docs"
+        docs_dir.mkdir()
+        (docs_dir / "LLM-OPTIMIZED-REFERENCE.md").write_text(
+            '<section name="usage">hello</section>\n',
+            encoding="utf-8",
+        )
+
+        result = get_docs_section("usage", repo_root=str(tmp_path))
+
+        assert result["status"] == "ok"
+        assert result["content"] == "hello"
+
     def test_section_not_found(self):
         result = get_docs_section("nonexistent-section")
         assert result["status"] == "not_found"