feat: add multi-project support to MCP tools

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,19 @@
+---
+name: Question
+about: Ask a question about the project
+title: ''
+labels: 'question'
+assignees: ''
+---
+
+## Question
+
+Describe your question clearly
+
+## Context
+
+Any relevant context or background information
+
+## What I've Tried
+
+Steps or research you've already done

.github/ISSUE_TEMPLATE/todo.md

@@ -1,32 +1,24 @@
 ---
-name: TODO/Task
+name: Task/Enhancement
 about: Track development tasks and improvements
-title: '[TODO] '
-labels: 'enhancement, todo'
+title: ''
+labels: 'enhancement'
 assignees: ''
 ---
 
-## 📋 Task Description
+## Description
+
 Brief description of what needs to be done
 
-## 🎯 Acceptance Criteria
+## Acceptance Criteria
+
 - [ ] Criterion 1
 - [ ] Criterion 2
-- [ ] Criterion 3
 
-## 🔗 Related Files/Components
-- File: `path/to/file.py`
-- Component: Service/Tool name
+## Related Files
 
-## 📝 Additional Context
-Any additional information, screenshots, or context
+- `path/to/file.py`
 
-## 🚦 Priority
-- [ ] High
-- [ ] Medium
-- [ ] Low
+## Additional Context
 
-## 📊 Estimated Effort
-- [ ] Small (< 2 hours)
-- [ ] Medium (2-8 hours)
-- [ ] Large (> 8 hours)
+Any additional information or context

README.md

@@ -519,7 +519,10 @@ claude mcp add --transport stdio graph-code \
 <!-- SECTION:mcp_tools -->
 | Tool | Description |
 |----|-----------|
-| `index_repository` | Parse and ingest the repository into the Memgraph knowledge graph. This builds a comprehensive graph of functions, classes, dependencies, and relationships. |
+| `list_projects` | List all indexed projects in the knowledge graph database. Returns a list of project names that have been indexed. |
+| `delete_project` | Delete a specific project from the knowledge graph database. This removes all nodes associated with the project while preserving other projects. Use list_projects first to see available projects. |
+| `wipe_database` | WARNING: Completely wipe the entire database, removing ALL indexed projects. This cannot be undone. Use delete_project for removing individual projects. |
+| `index_repository` | Parse and ingest the repository into the Memgraph knowledge graph. This builds a comprehensive graph of functions, classes, dependencies, and relationships. Note: This preserves other projects - only the current project is re-indexed. |
 | `query_code_graph` | Query the codebase knowledge graph using natural language. Ask questions like 'What functions call UserService.create_user?' or 'Show me all classes that implement the Repository interface'. |
 | `get_code_snippet` | Retrieve source code for a function, class, or method by its qualified name. Returns the source code, file path, line numbers, and docstring. |
 | `surgical_replace_code` | Surgically replace an exact code block in a file using diff-match-patch. Only modifies the exact target block, leaving the rest unchanged. |

codebase_rag/constants.py

@@ -169,6 +169,8 @@ class GoogleProviderType(StrEnum):
 KEY_FROM_VAL = "from_val"
 KEY_TO_VAL = "to_val"
 KEY_VERSION_SPEC = "version_spec"
+KEY_PREFIX = "prefix"
+KEY_PROJECT_NAME = "project_name"
 
 ERR_SUBSTR_ALREADY_EXISTS = "already exists"
 ERR_SUBSTR_CONSTRAINT = "constraint"
@@ -362,6 +364,8 @@ class RelationshipType(StrEnum):
 CSPROJ_SUFFIX = ".csproj"
 
 # (H) Cypher queries
+CYPHER_DEFAULT_LIMIT = 50
+
 CYPHER_QUERY_EMBEDDINGS = """
 MATCH (m:Module)-[:DEFINES]->(n)
 WHERE n:Function OR n:Method
@@ -2298,6 +2302,9 @@ class CppNodeType(StrEnum):
 
 # (H) MCP tool names
 class MCPToolName(StrEnum):
+    LIST_PROJECTS = "list_projects"
+    DELETE_PROJECT = "delete_project"
+    WIPE_DATABASE = "wipe_database"
     INDEX_REPOSITORY = "index_repository"
     QUERY_CODE_GRAPH = "query_code_graph"
     GET_CODE_SNIPPET = "get_code_snippet"
@@ -2319,6 +2326,7 @@ class MCPSchemaType(StrEnum):
     OBJECT = "object"
     STRING = "string"
     INTEGER = "integer"
+    BOOLEAN = "boolean"
 
 
 # (H) MCP schema fields
@@ -2332,6 +2340,8 @@ class MCPSchemaField(StrEnum):
 
 # (H) MCP parameter names
 class MCPParamName(StrEnum):
+    PROJECT_NAME = "project_name"
+    CONFIRM = "confirm"
     NATURAL_LANGUAGE_QUERY = "natural_language_query"
     QUALIFIED_NAME = "qualified_name"
     FILE_PATH = "file_path"
@@ -2354,10 +2364,15 @@ class MCPParamName(StrEnum):
 
 # (H) MCP response messages
 MCP_INDEX_SUCCESS = "Successfully indexed repository at {path}. Knowledge graph has been updated (previous data cleared)."
+MCP_INDEX_SUCCESS_PROJECT = "Successfully indexed repository at {path}. Project '{project_name}' has been updated."
 MCP_INDEX_ERROR = "Error indexing repository: {error}"
 MCP_WRITE_SUCCESS = "Successfully wrote file: {path}"
 MCP_UNKNOWN_TOOL_ERROR = "Unknown tool: {name}"
 MCP_TOOL_EXEC_ERROR = "Error executing tool '{name}': {error}"
+MCP_PROJECT_DELETED = "Successfully deleted project '{project_name}'."
+MCP_WIPE_CANCELLED = "Database wipe cancelled. Set confirm=true to proceed."
+MCP_WIPE_SUCCESS = "Database completely wiped. All projects have been removed."
+MCP_WIPE_ERROR = "Error wiping database: {error}"
 
 # (H) MCP dict keys and values
 MCP_KEY_RESULTS = "results"

codebase_rag/cypher_queries.py

@@ -1,27 +1,53 @@
+from .constants import CYPHER_DEFAULT_LIMIT
+
 CYPHER_DELETE_ALL = "MATCH (n) DETACH DELETE n;"
 
-CYPHER_EXAMPLE_DECORATED_FUNCTIONS = """MATCH (n:Function|Method)
+CYPHER_LIST_PROJECTS = "MATCH (p:Project) RETURN p.name AS name ORDER BY p.name"
+
+CYPHER_DELETE_PROJECT = """
+MATCH (p:Project {name: $project_name})
+OPTIONAL MATCH (p)-[:CONTAINS_PACKAGE|CONTAINS_FOLDER|CONTAINS_FILE|CONTAINS_MODULE*]->(container)
+OPTIONAL MATCH (container)-[:DEFINES|DEFINES_METHOD*]->(defined)
+DETACH DELETE p, container, defined
+"""
+
+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
+LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
-CYPHER_EXAMPLE_CONTENT_BY_PATH = """MATCH (n)
+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 path, labels(n) AS type
+LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
-CYPHER_EXAMPLE_KEYWORD_SEARCH = """MATCH (n)
+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
+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"""
 
-CYPHER_EXAMPLE_README = """MATCH (f:File) WHERE toLower(f.name) CONTAINS 'readme' RETURN f.path AS path, f.name AS name, labels(f) AS type"""
-
-CYPHER_EXAMPLE_PYTHON_FILES = """MATCH (f:File) WHERE f.extension = '.py' RETURN f.path AS path, f.name AS name, labels(f) AS type"""
-
-CYPHER_EXAMPLE_TASKS = """MATCH (n:Function|Method) WHERE 'task' IN n.decorators RETURN n.qualified_name AS qualified_name, n.name AS name, labels(n) AS type"""
-
-CYPHER_EXAMPLE_FILES_IN_FOLDER = """MATCH (f:File) WHERE f.path STARTS WITH 'services' RETURN f.path AS path, 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
+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
+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
+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
+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"""
 

codebase_rag/graph_updater.py

@@ -234,7 +234,7 @@ def __init__(
         self.repo_path = repo_path
         self.parsers = parsers
         self.queries = queries
-        self.project_name = repo_path.name
+        self.project_name = repo_path.resolve().name
         self.simple_name_lookup: SimpleNameLookup = defaultdict(set)
         self.function_registry = FunctionRegistryTrie(
             simple_name_lookup=self.simple_name_lookup

codebase_rag/logs.py

@@ -164,6 +164,8 @@
 MG_BATCH_PARAMS_TRUNCATED = "    Params (first 10 of {count}): {params}..."
 MG_CLEANING_DB = "--- Cleaning database... ---"
 MG_DB_CLEANED = "--- Database cleaned. ---"
+MG_DELETING_PROJECT = "--- Deleting project: {project_name} ---"
+MG_PROJECT_DELETED = "--- Project {project_name} deleted. ---"
 MG_ENSURING_CONSTRAINTS = "Ensuring constraints..."
 MG_CONSTRAINTS_DONE = "Constraints checked/created."
 MG_NODE_BUFFER_FLUSH = (
@@ -568,7 +570,14 @@
 MCP_INDEXING_REPO = "[MCP] Indexing repository at: {path}"
 MCP_CLEARING_DB = "[MCP] Clearing existing database to avoid conflicts..."
 MCP_DB_CLEARED = "[MCP] Database cleared. Starting fresh indexing..."
+MCP_CLEARING_PROJECT = "[MCP] Clearing existing data for project '{project_name}'..."
 MCP_ERROR_INDEXING = "[MCP] Error indexing repository: {error}"
+MCP_LISTING_PROJECTS = "[MCP] Listing all projects..."
+MCP_ERROR_LIST_PROJECTS = "[MCP] Error listing projects: {error}"
+MCP_DELETING_PROJECT = "[MCP] Deleting project: {project_name}"
+MCP_ERROR_DELETE_PROJECT = "[MCP] Error deleting project: {error}"
+MCP_WIPING_DATABASE = "[MCP] Wiping entire database!"
+MCP_ERROR_WIPE = "[MCP] Error wiping database: {error}"
 MCP_QUERY_CODE_GRAPH = "[MCP] query_code_graph: {query}"
 MCP_QUERY_RESULTS = "[MCP] Query returned {count} results"
 MCP_ERROR_QUERY = "[MCP] Error querying code graph: {error}"

codebase_rag/mcp/tools.py

@@ -23,6 +23,12 @@
 from codebase_rag.tools.file_writer import FileWriter, create_file_writer_tool
 from codebase_rag.types_defs import (
     CodeSnippetResultDict,
+    DeleteProjectErrorResult,
+    DeleteProjectResult,
+    DeleteProjectSuccessResult,
+    ListProjectsErrorResult,
+    ListProjectsResult,
+    ListProjectsSuccessResult,
     MCPHandlerType,
     MCPInputSchema,
     MCPInputSchemaProperty,
@@ -62,6 +68,49 @@ def __init__(
         )
 
         self._tools: dict[str, ToolMetadata] = {
+            cs.MCPToolName.LIST_PROJECTS: ToolMetadata(
+                name=cs.MCPToolName.LIST_PROJECTS,
+                description=td.MCP_TOOLS[cs.MCPToolName.LIST_PROJECTS],
+                input_schema=MCPInputSchema(
+                    type=cs.MCPSchemaType.OBJECT,
+                    properties={},
+                    required=[],
+                ),
+                handler=self.list_projects,
+                returns_json=True,
+            ),
+            cs.MCPToolName.DELETE_PROJECT: ToolMetadata(
+                name=cs.MCPToolName.DELETE_PROJECT,
+                description=td.MCP_TOOLS[cs.MCPToolName.DELETE_PROJECT],
+                input_schema=MCPInputSchema(
+                    type=cs.MCPSchemaType.OBJECT,
+                    properties={
+                        cs.MCPParamName.PROJECT_NAME: MCPInputSchemaProperty(
+                            type=cs.MCPSchemaType.STRING,
+                            description=td.MCP_PARAM_PROJECT_NAME,
+                        )
+                    },
+                    required=[cs.MCPParamName.PROJECT_NAME],
+                ),
+                handler=self.delete_project,
+                returns_json=True,
+            ),
+            cs.MCPToolName.WIPE_DATABASE: ToolMetadata(
+                name=cs.MCPToolName.WIPE_DATABASE,
+                description=td.MCP_TOOLS[cs.MCPToolName.WIPE_DATABASE],
+                input_schema=MCPInputSchema(
+                    type=cs.MCPSchemaType.OBJECT,
+                    properties={
+                        cs.MCPParamName.CONFIRM: MCPInputSchemaProperty(
+                            type=cs.MCPSchemaType.BOOLEAN,
+                            description=td.MCP_PARAM_CONFIRM,
+                        )
+                    },
+                    required=[cs.MCPParamName.CONFIRM],
+                ),
+                handler=self.wipe_database,
+                returns_json=False,
+            ),
             cs.MCPToolName.INDEX_REPOSITORY: ToolMetadata(
                 name=cs.MCPToolName.INDEX_REPOSITORY,
                 description=td.MCP_TOOLS[cs.MCPToolName.INDEX_REPOSITORY],
@@ -199,13 +248,53 @@ def __init__(
             ),
         }
 
-    async def index_repository(self) -> str:
-        logger.info(lg.MCP_INDEXING_REPO.format(path=self.project_root))
+    async def list_projects(self) -> ListProjectsResult:
+        logger.info(lg.MCP_LISTING_PROJECTS)
+        try:
+            projects = self.ingestor.list_projects()
+            return ListProjectsSuccessResult(projects=projects, count=len(projects))
+        except Exception as e:
+            logger.error(lg.MCP_ERROR_LIST_PROJECTS.format(error=e))
+            return ListProjectsErrorResult(error=str(e), projects=[], count=0)
 
+    async def delete_project(self, project_name: str) -> DeleteProjectResult:
+        logger.info(lg.MCP_DELETING_PROJECT.format(project_name=project_name))
+        try:
+            projects = self.ingestor.list_projects()
+            if project_name not in projects:
+                return DeleteProjectErrorResult(
+                    success=False,
+                    error=te.MCP_PROJECT_NOT_FOUND.format(
+                        project_name=project_name, projects=projects
+                    ),
+                )
+            self.ingestor.delete_project(project_name)
+            return DeleteProjectSuccessResult(
+                success=True,
+                project=project_name,
+                message=cs.MCP_PROJECT_DELETED.format(project_name=project_name),
+            )
+        except Exception as e:
+            logger.error(lg.MCP_ERROR_DELETE_PROJECT.format(error=e))
+            return DeleteProjectErrorResult(success=False, error=str(e))
+
+    async def wipe_database(self, confirm: bool) -> str:
+        if not confirm:
+            return cs.MCP_WIPE_CANCELLED
+        logger.warning(lg.MCP_WIPING_DATABASE)
         try:
-            logger.info(lg.MCP_CLEARING_DB)
             self.ingestor.clean_database()
-            logger.info(lg.MCP_DB_CLEARED)
+            return cs.MCP_WIPE_SUCCESS
+        except Exception as e:
+            logger.error(lg.MCP_ERROR_WIPE.format(error=e))
+            return cs.MCP_WIPE_ERROR.format(error=e)
+
+    async def index_repository(self) -> str:
+        logger.info(lg.MCP_INDEXING_REPO.format(path=self.project_root))
+        project_name = Path(self.project_root).resolve().name
+        try:
+            logger.info(lg.MCP_CLEARING_PROJECT.format(project_name=project_name))
+            self.ingestor.delete_project(project_name)
 
             updater = GraphUpdater(
                 ingestor=self.ingestor,
@@ -215,7 +304,9 @@ async def index_repository(self) -> str:
             )
             updater.run()
 
-            return cs.MCP_INDEX_SUCCESS.format(path=self.project_root)
+            return cs.MCP_INDEX_SUCCESS_PROJECT.format(
+                path=self.project_root, project_name=project_name
+            )
         except Exception as e:
             logger.error(lg.MCP_ERROR_INDEXING.format(error=e))
             return cs.MCP_INDEX_ERROR.format(error=e)