chore: v0.3.6 — dedup Claude Code registration + contradiction walk

- Extract register_with_claude_code(spec) helper. cli/main.py's
  install_mcp command and setup_wizard's claude registration step
  had near-identical blocks for ~/.claude/settings.json I/O. Each
  caller now constructs the spec dict (HTTP vs stdio) and delegates
  the load/setdefault/write to the shared helper.
- AlertPresenter._check_contradictions now delegates to
  GraphQueries.contradiction_map(). Removes ~25 lines of duplicated
  graph traversal. Alert message text now resolves titles consistently
  from the same source as the graph view.

No API change. Patch bump from v0.3.5.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: grayisnotacolor

CHANGELOG.md

@@ -7,6 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.3.6] — 2026-05-03
+
+### Changed
+
+- **Deduplicated Claude Code registration** — `cli/main.py::install_mcp` and `cli/setup_wizard.py` had near-identical blocks loading `~/.claude/settings.json`, setting `mcpServers["cortex"]`, and writing back. Extracted to `cli/_helpers.py::register_with_claude_code(spec)`. Each call site now constructs the `spec` dict (HTTP vs stdio) and delegates the file I/O. No behavior change.
+- **AlertPresenter delegates to GraphQueries for contradictions** — `AlertPresenter._check_contradictions` and `GraphQueries.contradiction_map` walked the graph identically; the alert version was just rewrapping the pair output. AlertPresenter now calls `GraphQueries.contradiction_map()` and formats the result. Removes ~25 lines of duplicated traversal logic; no behavior change beyond a cosmetic shift in alert message text wording (titles now resolved consistently from the same source as the graph view).
+
 ## [0.3.5] — 2026-05-03
 
 ### Fixed

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "abbacus-cortex"
-version = "0.3.5"
+version = "0.3.6"
 description = "Cognitive knowledge system with formal ontology, reasoning, and intelligence serving"
 readme = "README.md"
 authors = [

src/cortex/__init__.py

@@ -1,3 +1,3 @@
 """Cortex — Cognitive knowledge system."""
 
-__version__ = "0.3.5"
+__version__ = "0.3.6"

src/cortex/cli/_helpers.py

@@ -7,6 +7,10 @@
 
 from __future__ import annotations
 
+import json
+from pathlib import Path
+from typing import Any
+
 import typer
 
 from cortex.core.config import CortexConfig
@@ -21,3 +25,20 @@ def open_store_or_exit(config: CortexConfig) -> Store:
     except StoreLockedError as e:
         typer.secho(str(e), fg=typer.colors.RED, err=True)
         raise typer.Exit(1) from e
+
+
+def register_with_claude_code(spec: dict[str, Any]) -> Path:
+    """Set ``mcpServers["cortex"] = spec`` in ``~/.claude/settings.json``.
+
+    Preserves other entries in the file. Creates the file (and parent
+    directory) if missing. Returns the path written.
+    """
+    settings_path = Path.home() / ".claude" / "settings.json"
+    settings: dict[str, Any] = {}
+    if settings_path.exists():
+        settings = json.loads(settings_path.read_text())
+    mcp_servers = settings.setdefault("mcpServers", {})
+    mcp_servers["cortex"] = spec
+    settings_path.parent.mkdir(parents=True, exist_ok=True)
+    settings_path.write_text(json.dumps(settings, indent=2) + "\n")
+    return settings_path

src/cortex/cli/main.py

@@ -12,7 +12,7 @@
 
 import typer
 
-from cortex.cli._helpers import open_store_or_exit
+from cortex.cli._helpers import open_store_or_exit, register_with_claude_code
 from cortex.core.config import CortexConfig, load_config
 from cortex.core.constants import KNOWLEDGE_TYPES
 from cortex.core.errors import StoreLockedError
@@ -775,16 +775,6 @@ def register(
     this is the pre-Phase-2 behavior, where Claude Code spawns its own
     Cortex stdio child process per session.
     """
-    import json
-
-    settings_path = Path.home() / ".claude" / "settings.json"
-    settings: dict[str, Any] = {}
-
-    if settings_path.exists():
-        settings = json.loads(settings_path.read_text())
-
-    mcp_servers = settings.setdefault("mcpServers", {})
-
     if legacy_stdio:
         import shutil
 
@@ -796,25 +786,14 @@ def register(
             cmd = sys.executable
             args = ["-m", "cortex.transport.mcp"]
 
-        mcp_servers["cortex"] = {
-            "command": cmd,
-            "args": args,
-            "env": {},
-        }
-        settings_path.parent.mkdir(parents=True, exist_ok=True)
-        settings_path.write_text(json.dumps(settings, indent=2) + "\n")
-
+        spec = {"command": cmd, "args": args, "env": {}}
+        settings_path = register_with_claude_code(spec)
         typer.echo(f"Registered Cortex MCP (stdio) at {settings_path}")
         typer.echo(f"  Command: {cmd} {' '.join(args)}")
     else:
         config = load_config()
-        mcp_servers["cortex"] = {
-            "type": "http",
-            "url": config.mcp_server_url,
-        }
-        settings_path.parent.mkdir(parents=True, exist_ok=True)
-        settings_path.write_text(json.dumps(settings, indent=2) + "\n")
-
+        spec = {"type": "http", "url": config.mcp_server_url}
+        settings_path = register_with_claude_code(spec)
         typer.echo(f"Registered Cortex MCP (http) at {settings_path}")
         typer.echo(f"  URL: {config.mcp_server_url}")
         typer.echo(

src/cortex/cli/setup_wizard.py

@@ -17,7 +17,7 @@
 
 import typer
 
-from cortex.cli._helpers import open_store_or_exit
+from cortex.cli._helpers import open_store_or_exit, register_with_claude_code
 from cortex.core.config import CortexConfig, load_config
 from cortex.core.logging import setup_logging
 from cortex.db.store import Store
@@ -370,17 +370,7 @@ def _step_services(config: CortexConfig, env_updates: dict[str, str], auto: bool
     )
     if register_cc:
         try:
-            settings_path = Path.home() / ".claude" / "settings.json"
-            settings: dict[str, Any] = {}
-            if settings_path.exists():
-                settings = json.loads(settings_path.read_text())
-            mcp_servers = settings.setdefault("mcpServers", {})
-            mcp_servers["cortex"] = {
-                "type": "http",
-                "url": config.mcp_server_url,
-            }
-            settings_path.parent.mkdir(parents=True, exist_ok=True)
-            settings_path.write_text(json.dumps(settings, indent=2) + "\n")
+            register_with_claude_code({"type": "http", "url": config.mcp_server_url})
             _echo(f"      Registered with Claude Code ({config.mcp_server_url})")
         except Exception as e:
             _echo(f"      Registration failed: {e}")

src/cortex/retrieval/presenters.py

@@ -14,6 +14,7 @@
 
 from cortex.core.logging import get_logger
 from cortex.db.store import Store
+from cortex.retrieval.graph import GraphQueries
 from cortex.services.llm import LLMClient
 
 logger = get_logger("retrieval.presenters")
@@ -302,31 +303,20 @@ def render(self) -> list[dict[str, Any]]:
 
     def _check_contradictions(self) -> list[dict[str, Any]]:
         """Find active contradiction relationships."""
-        alerts = []
-        seen: set[tuple[str, str]] = set()
-
-        all_objects = self.store.list_objects(limit=500)
-        for obj in all_objects:
-            obj_id = obj.get("id", "")
-            rels = self.store.get_relationships(obj_id)
-            for rel in rels:
-                if rel["rel_type"] == "contradicts":
-                    pair = tuple(sorted([obj_id, rel["other_id"]]))
-                    if pair not in seen:
-                        seen.add(pair)
-                        alerts.append(
-                            {
-                                "type": "contradiction",
-                                "severity": "high",
-                                "message": (
-                                    f"Contradiction between "
-                                    f"'{obj.get('title', obj_id[:8])}' "
-                                    f"and object {rel['other_id'][:8]}"
-                                ),
-                                "object_ids": list(pair),
-                            }
-                        )
-        return alerts
+        pairs = GraphQueries(self.store).contradiction_map()
+        return [
+            {
+                "type": "contradiction",
+                "severity": "high",
+                "message": (
+                    f"Contradiction between "
+                    f"'{p['title_a'] or p['object_a'][:8]}' "
+                    f"and object {p['object_b'][:8]}"
+                ),
+                "object_ids": [p["object_a"], p["object_b"]],
+            }
+            for p in pairs
+        ]
 
     def _check_patterns(self) -> list[dict[str, Any]]:
         """Detect repeated entity mentions in fixes (systemic issues)."""