fix: preserve user config when init cannot parse existing JSON (#94)

Fixes #93.

Add a shared _load_existing_config helper so existing config files that fail to parse raise a clear ClickException instead of being treated as empty objects.

Migrate save_root_mcp_config, _merge_mcp_entry, and install_claude_code_hooks to the shared loader, preserving missing-file initialization while preventing silent overwrites of malformed user settings.

Co-authored-by: Raghav Chamadiya <65403859+RaghavChamadiya@users.noreply.github.com>

Author: CyanoTex

packages/cli/src/repowise/cli/mcp_config.py

@@ -6,6 +6,8 @@
 import sys
 from pathlib import Path
 
+import click
+
 
 def _claude_desktop_config_path() -> Path | None:
     """Return the Claude Desktop config path for this OS, or None if unsupported."""
@@ -66,10 +68,7 @@ def save_root_mcp_config(repo_path: Path) -> Path:
     new_entry = generate_mcp_config(repo_path)["mcpServers"]
 
     if config_path.exists():
-        try:
-            existing = json.loads(config_path.read_text(encoding="utf-8"))
-        except (json.JSONDecodeError, OSError):
-            existing = {}
+        existing = _load_existing_config(config_path)
         servers = dict(existing.get("mcpServers", {}))
         servers.update(new_entry)
         existing["mcpServers"] = servers
@@ -88,10 +87,7 @@ def _merge_mcp_entry(config_path: Path, new_entry: dict) -> bool:
     """
     try:
         if config_path.exists():
-            try:
-                existing = json.loads(config_path.read_text(encoding="utf-8"))
-            except (json.JSONDecodeError, OSError):
-                existing = {}
+            existing = _load_existing_config(config_path)
         else:
             config_path.parent.mkdir(parents=True, exist_ok=True)
             existing = {}
@@ -105,6 +101,28 @@ def _merge_mcp_entry(config_path: Path, new_entry: dict) -> bool:
         return False
 
 
+def _load_existing_config(config_path: Path) -> dict:
+    """Load an existing JSON config without silently replacing bad content."""
+    try:
+        existing = json.loads(config_path.read_text(encoding="utf-8"))
+    except json.JSONDecodeError as exc:
+        raise click.ClickException(
+            f"Cannot update {config_path}: existing file is not valid JSON. "
+            "Fix or remove it and retry; no changes were written."
+        ) from exc
+    except OSError as exc:
+        raise click.ClickException(
+            f"Cannot update {config_path}: existing file could not be read. "
+            "Fix the file permissions and retry; no changes were written."
+        ) from exc
+    if not isinstance(existing, dict):
+        raise click.ClickException(
+            f"Cannot update {config_path}: existing file must contain a JSON object. "
+            "Fix or remove it and retry; no changes were written."
+        )
+    return existing
+
+
 def register_with_claude_desktop(repo_path: Path) -> Path | None:
     """Add repowise MCP server to Claude Desktop's config.
 
@@ -171,10 +189,7 @@ def install_claude_code_hooks() -> Path | None:
 
     try:
         if settings_path.exists():
-            try:
-                existing = json.loads(settings_path.read_text(encoding="utf-8"))
-            except (json.JSONDecodeError, OSError):
-                existing = {}
+            existing = _load_existing_config(settings_path)
         else:
             settings_path.parent.mkdir(parents=True, exist_ok=True)
             existing = {}
@@ -191,9 +206,7 @@ def install_claude_code_hooks() -> Path | None:
         if not _has_repowise_hook(post_hooks):
             post_hooks.append(post_hook_entry)
 
-        settings_path.write_text(
-            json.dumps(existing, indent=2) + "\n", encoding="utf-8"
-        )
+        settings_path.write_text(json.dumps(existing, indent=2) + "\n", encoding="utf-8")
         return settings_path
     except OSError:
         return None

tests/unit/cli/test_mcp_config.py

@@ -0,0 +1,154 @@
+import json
+import re
+from pathlib import Path
+
+import click
+import pytest
+
+from repowise.cli import mcp_config
+
+
+def _repowise_entry(repo_path: Path) -> dict:
+    return mcp_config.generate_mcp_config(repo_path)["mcpServers"]
+
+
+def test_save_root_mcp_config_creates_missing_file(tmp_path: Path) -> None:
+    config_path = mcp_config.save_root_mcp_config(tmp_path)
+
+    saved = json.loads(config_path.read_text(encoding="utf-8"))
+    assert "repowise" in saved["mcpServers"]
+
+
+def test_save_root_mcp_config_merges_valid_existing_file(tmp_path: Path) -> None:
+    config_path = tmp_path / ".mcp.json"
+    config_path.write_text(
+        json.dumps(
+            {
+                "mcpServers": {"other": {"command": "other"}},
+                "custom": {"preserved": True},
+            }
+        ),
+        encoding="utf-8",
+    )
+
+    mcp_config.save_root_mcp_config(tmp_path)
+
+    saved = json.loads(config_path.read_text(encoding="utf-8"))
+    assert saved["mcpServers"]["other"] == {"command": "other"}
+    assert "repowise" in saved["mcpServers"]
+    assert saved["custom"] == {"preserved": True}
+
+
+def test_save_root_mcp_config_rejects_invalid_existing_file(tmp_path: Path) -> None:
+    config_path = tmp_path / ".mcp.json"
+    original = '{\n  "mcpServers": {},\n}\n'
+    config_path.write_text(original, encoding="utf-8")
+
+    with pytest.raises(click.ClickException, match=re.escape(str(config_path))):
+        mcp_config.save_root_mcp_config(tmp_path)
+
+    assert config_path.read_text(encoding="utf-8") == original
+
+
+def test_merge_mcp_entry_creates_missing_file(tmp_path: Path) -> None:
+    config_path = tmp_path / "settings.json"
+
+    assert mcp_config._merge_mcp_entry(config_path, _repowise_entry(tmp_path))
+
+    saved = json.loads(config_path.read_text(encoding="utf-8"))
+    assert "repowise" in saved["mcpServers"]
+
+
+def test_merge_mcp_entry_merges_valid_existing_file(tmp_path: Path) -> None:
+    config_path = tmp_path / "settings.json"
+    config_path.write_text(
+        json.dumps(
+            {
+                "mcpServers": {"existing": {"command": "existing"}},
+                "permissions": {"allow": ["Bash(git status:*)"]},
+            }
+        ),
+        encoding="utf-8",
+    )
+
+    assert mcp_config._merge_mcp_entry(config_path, _repowise_entry(tmp_path))
+
+    saved = json.loads(config_path.read_text(encoding="utf-8"))
+    assert saved["mcpServers"]["existing"] == {"command": "existing"}
+    assert "repowise" in saved["mcpServers"]
+    assert saved["permissions"] == {"allow": ["Bash(git status:*)"]}
+
+
+def test_merge_mcp_entry_rejects_invalid_existing_file(tmp_path: Path) -> None:
+    config_path = tmp_path / "settings.json"
+    original = '{\n  "permissions": {},\n}\n'
+    config_path.write_text(original, encoding="utf-8")
+
+    with pytest.raises(click.ClickException, match=re.escape(str(config_path))):
+        mcp_config._merge_mcp_entry(config_path, _repowise_entry(tmp_path))
+
+    assert config_path.read_text(encoding="utf-8") == original
+
+
+def test_install_claude_code_hooks_creates_missing_file(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    monkeypatch.setattr(Path, "home", lambda: tmp_path)
+
+    settings_path = mcp_config.install_claude_code_hooks()
+
+    assert settings_path == tmp_path / ".claude" / "settings.json"
+    saved = json.loads(settings_path.read_text(encoding="utf-8"))
+    assert "PreToolUse" in saved["hooks"]
+    assert "PostToolUse" in saved["hooks"]
+
+
+def test_install_claude_code_hooks_merges_valid_existing_file(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    monkeypatch.setattr(Path, "home", lambda: tmp_path)
+    settings_path = tmp_path / ".claude" / "settings.json"
+    settings_path.parent.mkdir(parents=True)
+    settings_path.write_text(
+        json.dumps(
+            {
+                "permissions": {"allow": ["Bash(git status:*)"]},
+                "hooks": {
+                    "PreToolUse": [
+                        {
+                            "matcher": "Read",
+                            "hooks": [{"type": "command", "command": "echo read"}],
+                        }
+                    ]
+                },
+            }
+        ),
+        encoding="utf-8",
+    )
+
+    assert mcp_config.install_claude_code_hooks() == settings_path
+
+    saved = json.loads(settings_path.read_text(encoding="utf-8"))
+    assert saved["permissions"] == {"allow": ["Bash(git status:*)"]}
+    assert saved["hooks"]["PreToolUse"][0]["matcher"] == "Read"
+    assert any(
+        hook["command"] == "repowise augment"
+        for entry in saved["hooks"]["PreToolUse"]
+        for hook in entry["hooks"]
+    )
+    assert "PostToolUse" in saved["hooks"]
+
+
+def test_install_claude_code_hooks_rejects_invalid_existing_file(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    monkeypatch.setattr(Path, "home", lambda: tmp_path)
+    settings_path = tmp_path / ".claude" / "settings.json"
+    settings_path.parent.mkdir(parents=True)
+    original = '{\n  "permissions": {},\n}\n'
+    settings_path.write_text(original, encoding="utf-8")
+
+    with pytest.raises(click.ClickException, match=re.escape(str(settings_path))):
+        mcp_config.install_claude_code_hooks()
+
+    assert settings_path.read_text(encoding="utf-8") == original