Feat: enables cross-project file access by storing absolute paths and project names in all graph nodes

.env.example

@@ -76,3 +76,6 @@ TARGET_REPO_PATH=.
 
 # Ollama base URL (without /v1 suffix)
 OLLAMA_BASE_URL=http://localhost:11434
+
+ALLOWED_PROJECT_ROOTS=/path/to/project/root
+MCP_MODE=query

.gitignore

@@ -23,3 +23,4 @@ PROJECT.md
 .DS_Store
 .pypi_cache.json
 .omc
+openspec

README.md

@@ -513,17 +513,70 @@ The agent will incorporate the guidance from your reference documents when sugge
 
 Code-Graph-RAG can run as an MCP (Model Context Protocol) server, enabling seamless integration with Claude Code and other MCP clients.
 
+### MCP Dual Mode System (v0.0.60+)
+
+The MCP server now supports two distinct modes with different capabilities and security profiles:
+
+#### Query Mode (Production Recommended)
+**Read-only access** for safe codebase exploration and analysis.
+
+**Available Tools:**
+- `list_projects` - List all indexed projects
+- `query_code_graph` - Natural language graph queries
+- `get_code_snippet` - Retrieve source code by qualified name
+- `list_directory` - Browse directory structure
+
+**Use Cases:**
+- Production environments where code modification is not allowed
+- Code review and exploration
+- Documentation generation
+- Architecture analysis
+
+#### Edit Mode (Development)
+**Full access** including file editing and database management.
+
+**Additional Tools (beyond Query mode):**
+- `read_file` / `write_file` - File operations
+- `surgical_replace_code` - Precise code editing
+- `delete_project` - Remove projects from graph
+- `wipe_database` - Complete database reset (dangerous!)
+- `index_repository` - Build/update knowledge graph
+
+**Use Cases:**
+- Local development environments
+- Code refactoring assistance
+- Automated code generation
+- Database maintenance
+
 ### Quick Setup
 
+#### Query Mode (Recommended for Production)
+
+```bash
+claude mcp add --transport stdio code-graph-rag \
+  --env TARGET_REPO_PATH="$(pwd)" \
+  --env MCP_MODE=query \
+  --env CYPHER_PROVIDER=openai \
+  --env CYPHER_MODEL=gpt-4 \
+  --env CYPHER_API_KEY=your-api-key \
+  -- uv run --directory /path/to/code-graph-rag code-graph-rag mcp-server
+```
+
+#### Edit Mode (For Development)
+
 ```bash
 claude mcp add --transport stdio code-graph-rag \
-  --env TARGET_REPO_PATH=/absolute/path/to/your/project \
+  --env TARGET_REPO_PATH="$(pwd)" \
+  --env MCP_MODE=edit \
+  --env ALLOWED_PROJECT_ROOTS="$(pwd)" \
   --env CYPHER_PROVIDER=openai \
   --env CYPHER_MODEL=gpt-4 \
   --env CYPHER_API_KEY=your-api-key \
   -- uv run --directory /path/to/code-graph-rag code-graph-rag mcp-server
 ```
 
+**Important:** Always set `ALLOWED_PROJECT_ROOTS` in Edit mode to restrict file operations to specific directories.
+
 ### Available Tools
 
 <!-- SECTION:mcp_tools -->
@@ -543,13 +596,48 @@ claude mcp add --transport stdio code-graph-rag \
 
 ### Example Usage
 
+#### Query Mode
 ```
-> Index this repository
 > What functions call UserService.create_user?
+> Show me all classes that implement Repository
+> List all modules in the utils package
+> Get the source code for AuthService.login
+```
+
+#### Edit Mode
+```
+> Index this repository
 > Update the login function to add rate limiting
+> Refactor this class to use dependency injection
+> Delete the deprecated project from the graph
 ```
 
-For detailed setup, see [Claude Code Setup Guide](docs/claude-code-setup.md).
+### Security Configuration
+
+For Edit mode, always restrict access with `ALLOWED_PROJECT_ROOTS`:
+
+```bash
+# Single project
+--env ALLOWED_PROJECT_ROOTS="/path/to/project"
+
+# Multiple projects (comma-separated)
+--env ALLOWED_PROJECT_ROOTS="/path/to/project1,/path/to/project2"
+```
+
+This ensures file operations cannot modify files outside the specified directories.
+
+### Mode Selection Guide
+
+| Scenario | Recommended Mode | Reasoning |
+|----------|-----------------|-----------|
+| Production code review | Query | Prevents accidental modifications |
+| Development work | Edit | Allows code generation and editing |
+| CI/CD pipelines | Query | Read-only analysis is sufficient |
+| Local experimentation | Edit | Full control for testing |
+| Multi-project analysis | Query | Safe exploration across projects |
+| Code refactoring | Edit | Requires write access |
+
+For detailed setup and configuration examples, see [Claude Code Setup Guide](docs/claude-code-setup.md) and [Security Best Practices](docs/security-best-practices.md).
 
 ## 📊 Graph Schema
 
@@ -560,20 +648,20 @@ The knowledge graph uses the following node types and relationships:
 <!-- SECTION:node_schemas -->
 | Label | Properties |
 |-----|----------|
-| Project | `{name: string}` |
-| Package | `{qualified_name: string, name: string, path: string}` |
-| Folder | `{path: string, name: string}` |
-| File | `{path: string, name: string, extension: string}` |
-| Module | `{qualified_name: string, name: string, path: string}` |
-| Class | `{qualified_name: string, name: string, decorators: list[string]}` |
-| Function | `{qualified_name: string, name: string, decorators: list[string]}` |
-| Method | `{qualified_name: string, name: string, decorators: list[string]}` |
-| Interface | `{qualified_name: string, name: string}` |
-| Enum | `{qualified_name: string, name: string}` |
-| Type | `{qualified_name: string, name: string}` |
-| Union | `{qualified_name: string, name: string}` |
-| ModuleInterface | `{qualified_name: string, name: string, path: string}` |
-| ModuleImplementation | `{qualified_name: string, name: string, path: string, implements_module: string}` |
+| Project | `{name: string, absolute_path: string, project_name: string}` |
+| Package | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string}` |
+| Folder | `{path: string, name: string, absolute_path: string, project_name: string}` |
+| File | `{path: string, name: string, extension: string, absolute_path: string, project_name: string}` |
+| Module | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string}` |
+| Class | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string, decorators: list[string]}` |
+| Function | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string, decorators: list[string]}` |
+| Method | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string, decorators: list[string]}` |
+| Interface | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string}` |
+| Enum | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string}` |
+| Type | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string}` |
+| Union | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string}` |
+| ModuleInterface | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string}` |
+| ModuleImplementation | `{qualified_name: string, name: string, path: string, absolute_path: string, project_name: string, implements_module: string}` |
 | ExternalPackage | `{name: string, version_spec: string}` |
 <!-- /SECTION:node_schemas -->
 
@@ -653,6 +741,10 @@ Configuration is managed through environment variables in `.env` file:
 - `TARGET_REPO_PATH`: Default repository path (default: `.`)
 - `LOCAL_MODEL_ENDPOINT`: Fallback endpoint for Ollama (default: `http://localhost:11434/v1`)
 
+### MCP Server Configuration
+- `MCP_MODE`: MCP server operation mode - `query` (read-only) or `edit` (full access). Default: `edit`. **Recommended: Use `query` mode for production environments.**
+- `ALLOWED_PROJECT_ROOTS`: Comma-separated list of allowed project root paths for file operations in Edit mode. This is a critical security setting that restricts file read/write operations to specified directories. Example: `/path/to/project1,/path/to/project2`
+
 ### Custom Ignore Patterns
 
 You can specify additional directories to exclude by creating a `.cgrignore` file in your repository root:

codebase_rag/config.py

@@ -6,7 +6,7 @@
 
 from dotenv import load_dotenv
 from loguru import logger
-from pydantic import Field
+from pydantic import Field, field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from . import constants as cs
@@ -17,6 +17,19 @@
 load_dotenv()
 
 
+def _parse_frozenset_of_strings(value: str | frozenset[str] | None) -> frozenset[Path]:
+    if value is None:
+        return frozenset()
+    if isinstance(value, frozenset):
+        return frozenset(Path(path) for path in value)
+    if isinstance(value, str):
+        if value.strip():
+            return frozenset(
+                Path(path.strip()) for path in value.split(",") if path.strip()
+            )
+    return frozenset()
+
+
 class ApiKeyInfoEntry(TypedDict):
     env_var: str
     url: str
@@ -171,7 +184,21 @@ def ollama_endpoint(self) -> str:
         return f"{self.OLLAMA_BASE_URL.rstrip('/')}/v1"
 
     TARGET_REPO_PATH: str = "."
+    ALLOWED_PROJECT_ROOTS: str = ""
     SHELL_COMMAND_TIMEOUT: int = 30
+    MCP_MODE: str = "edit"
+
+    @field_validator("MCP_MODE")
+    @classmethod
+    def _validate_mcp_mode(cls, v: str) -> str:
+        if v not in ("query", "edit"):
+            raise ValueError("MCP_MODE must be 'query' or 'edit'")
+        return v
+
+    @property
+    def allowed_project_roots_set(self) -> frozenset[Path]:
+        return _parse_frozenset_of_strings(self.ALLOWED_PROJECT_ROOTS)
+
     SHELL_COMMAND_ALLOWLIST: frozenset[str] = frozenset(
         {
             "ls",

codebase_rag/constants.py

@@ -181,6 +181,8 @@ class GoogleProviderType(StrEnum):
 KEY_VERSION_SPEC = "version_spec"
 KEY_PREFIX = "prefix"
 KEY_PROJECT_NAME = "project_name"
+KEY_ABSOLUTE_PATH = "absolute_path"
+EXTERNAL_PROJECT_NAME = "__external__"
 KEY_IS_EXTERNAL = "is_external"
 
 ERR_SUBSTR_ALREADY_EXISTS = "already exists"
@@ -419,11 +421,10 @@ class RelationshipType(StrEnum):
 
 CYPHER_QUERY_EMBEDDINGS = """
 MATCH (m:Module)-[:DEFINES]->(n)
-WHERE (n:Function OR n:Method)
-  AND m.qualified_name STARTS WITH $project_name + '.'
+WHERE n.project_name = $project_name
 RETURN id(n) AS node_id, n.qualified_name AS qualified_name,
        n.start_line AS start_line, n.end_line AS end_line,
-       m.path AS path
+       n.path AS path
 """
 
 

codebase_rag/cypher_queries.py

@@ -13,47 +13,58 @@
 
 CYPHER_EXAMPLE_DECORATED_FUNCTIONS = f"""MATCH (n:Function|Method)
 WHERE ANY(d IN n.decorators WHERE toLower(d) IN ['flow', 'task'])
-RETURN n.name AS name, n.qualified_name AS qualified_name, labels(n) AS type
+RETURN n.name AS name, n.qualified_name AS qualified_name, labels(n) AS type,
+       n.path AS relative_path, n.absolute_path AS absolute_path, n.project_name AS project_name
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
 CYPHER_EXAMPLE_CONTENT_BY_PATH = f"""MATCH (n)
 WHERE n.path IS NOT NULL AND n.path STARTS WITH 'workflows'
-RETURN n.name AS name, n.path AS path, labels(n) AS type
+RETURN n.name AS name, n.path AS relative_path, n.absolute_path AS absolute_path,
+       n.project_name AS project_name, labels(n) AS type
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
 CYPHER_EXAMPLE_KEYWORD_SEARCH = f"""MATCH (n)
 WHERE toLower(n.name) CONTAINS 'database' OR (n.qualified_name IS NOT NULL AND toLower(n.qualified_name) CONTAINS 'database')
-RETURN n.name AS name, n.qualified_name AS qualified_name, labels(n) AS type
+RETURN n.name AS name, n.qualified_name AS qualified_name, labels(n) AS type,
+       n.path AS relative_path, n.absolute_path AS absolute_path, n.project_name AS project_name
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
 CYPHER_EXAMPLE_FIND_FILE = """MATCH (f:File) WHERE toLower(f.name) = 'readme.md' AND f.path = 'README.md'
-RETURN f.path as path, f.name as name, labels(f) as type"""
+RETURN f.path AS relative_path, f.absolute_path AS absolute_path, f.project_name AS project_name,
+       f.name as name, labels(f) as type"""
 
 CYPHER_EXAMPLE_README = f"""MATCH (f:File)
 WHERE toLower(f.name) CONTAINS 'readme'
-RETURN f.path AS path, f.name AS name, labels(f) AS type
+RETURN f.path AS relative_path, f.absolute_path AS absolute_path, f.project_name AS project_name,
+       f.name AS name, labels(f) AS type
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
 CYPHER_EXAMPLE_PYTHON_FILES = f"""MATCH (f:File)
 WHERE f.extension = '.py'
-RETURN f.path AS path, f.name AS name, labels(f) AS type
+RETURN f.path AS relative_path, f.absolute_path AS absolute_path, f.project_name AS project_name,
+       f.name AS name, labels(f) AS type
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
 CYPHER_EXAMPLE_TASKS = f"""MATCH (n:Function|Method)
 WHERE 'task' IN n.decorators
-RETURN n.qualified_name AS qualified_name, n.name AS name, labels(n) AS type
+RETURN n.qualified_name AS qualified_name, n.name AS name, labels(n) AS type,
+       n.path AS relative_path, n.absolute_path AS absolute_path, n.project_name AS project_name
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
 CYPHER_EXAMPLE_FILES_IN_FOLDER = f"""MATCH (f:File)
 WHERE f.path STARTS WITH 'services'
-RETURN f.path AS path, f.name AS name, labels(f) AS type
+RETURN f.path AS relative_path, f.absolute_path AS absolute_path, f.project_name AS project_name,
+       f.name AS name, labels(f) AS type
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
-CYPHER_EXAMPLE_LIMIT_ONE = """MATCH (f:File) RETURN f.path as path, f.name as name, labels(f) as type LIMIT 1"""
+CYPHER_EXAMPLE_LIMIT_ONE = """MATCH (f:File)
+RETURN f.path AS relative_path, f.absolute_path AS absolute_path, f.project_name AS project_name,
+       f.name as name, labels(f) as type LIMIT 1"""
 
 CYPHER_EXAMPLE_CLASS_METHODS = f"""MATCH (c:Class)-[:DEFINES_METHOD]->(m:Method)
 WHERE c.qualified_name ENDS WITH '.UserService'
-RETURN m.name AS name, m.qualified_name AS qualified_name, labels(m) AS type
+RETURN m.name AS name, m.qualified_name AS qualified_name, labels(m) AS type,
+       m.path AS relative_path, m.absolute_path AS absolute_path, m.project_name AS project_name
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
 CYPHER_EXPORT_NODES = """
@@ -70,16 +81,18 @@
 CYPHER_SET_PROPS_RETURN_COUNT = "SET r += row.props\nRETURN count(r) as created"
 
 CYPHER_GET_FUNCTION_SOURCE_LOCATION = """
-MATCH (m:Module)-[:DEFINES]->(n)
+MATCH (n)
 WHERE id(n) = $node_id
 RETURN n.qualified_name AS qualified_name, n.start_line AS start_line,
-       n.end_line AS end_line, m.path AS path
+       n.end_line AS end_line, n.path AS relative_path,
+       n.absolute_path AS absolute_path, n.project_name AS project_name
 """
 
 CYPHER_FIND_BY_QUALIFIED_NAME = """
 MATCH (n) WHERE n.qualified_name = $qn
-OPTIONAL MATCH (m:Module)-[*]-(n)
-RETURN n.name AS name, n.start_line AS start, n.end_line AS end, m.path AS path, n.docstring AS docstring
+RETURN n.name AS name, n.start_line AS start, n.end_line AS end,
+       n.path AS relative_path, n.absolute_path AS absolute_path,
+       n.project_name AS project_name, n.docstring AS docstring
 LIMIT 1
 """
 
@@ -94,7 +107,9 @@ def build_nodes_by_ids_query(node_ids: list[int]) -> str:
 MATCH (n)
 WHERE id(n) IN [{placeholders}]
 RETURN id(n) AS node_id, n.qualified_name AS qualified_name,
-       labels(n) AS type, n.name AS name
+       labels(n) AS type, n.name AS name,
+       n.path AS relative_path, n.absolute_path AS absolute_path,
+       n.project_name AS project_name
 ORDER BY n.qualified_name
 """
 
@@ -126,3 +141,11 @@ def build_merge_relationship_query(
     )
     query += CYPHER_SET_PROPS_RETURN_COUNT if has_props else CYPHER_RETURN_COUNT
     return query
+
+
+def build_project_name_indexes() -> list[str]:
+    return [
+        build_index_query("Function", "project_name"),
+        build_index_query("Method", "project_name"),
+        build_index_query("Class", "project_name"),
+    ]

codebase_rag/decorators.py

@@ -13,6 +13,7 @@
     LoadableProtocol,
     PathValidatorProtocol,
 )
+from .utils.path_utils import validate_allowed_path
 
 
 def ensure_loaded[T](func: Callable[..., T]) -> Callable[..., T]:
@@ -70,10 +71,10 @@ async def wrapper(self: PathValidatorProtocol, *args, **kwargs) -> T:
                     file_path=str(file_path_str), error_message=ex.ACCESS_DENIED
                 )
             try:
-                full_path = (self.project_root / file_path_str).resolve()
-                project_root = self.project_root.resolve()
-                full_path.relative_to(project_root)
-            except (ValueError, RuntimeError):
+                full_path = validate_allowed_path(
+                    file_path_str, self.project_root, self.allowed_roots
+                )
+            except PermissionError:
                 return result_factory(
                     file_path=file_path_str,
                     error_message=ls.FILE_OUTSIDE_ROOT.format(action="access"),