diff --git a/doc/VectorCode-cli.txt b/doc/VectorCode-cli.txt
index c56228db..08d58b1d 100644
--- a/doc/VectorCode-cli.txt
+++ b/doc/VectorCode-cli.txt
@@ -781,7 +781,8 @@ features:
 
 - `ls`list local collections, similar to the `ls` subcommand in the CLI;
 - `query`query from a given collection, similar to the `query` subcommand in
-    the CLI.
+    the CLI;
+- `vectorise`vectorise files into a given project.
 
 To try it out, install the `vectorcode[mcp]` dependency group and the MCP
 server is available in the shell as `vectorcode-mcp-server`, and make sure
diff --git a/docs/cli.md b/docs/cli.md
index 49e7e1ba..688c4f8a 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -706,7 +706,8 @@ features:
 
 - `ls`: list local collections, similar to the `ls` subcommand in the CLI;
 - `query`: query from a given collection, similar to the `query` subcommand in
-  the CLI.
+  the CLI;
+- `vectorise`: vectorise files into a given project.
 
 To try it out, install the `vectorcode[mcp]` dependency group and the MCP server 
 is available in the shell as `vectorcode-mcp-server`, and make sure you're using 
diff --git a/src/vectorcode/mcp_main.py b/src/vectorcode/mcp_main.py
index da97a69a..e9a9812c 100644
--- a/src/vectorcode/mcp_main.py
+++ b/src/vectorcode/mcp_main.py
@@ -12,6 +12,13 @@
 from chromadb.api.models.AsyncCollection import AsyncCollection
 from chromadb.errors import InvalidCollectionException
 
+from vectorcode.subcommands.vectorise import (
+    VectoriseStats,
+    chunked_add,
+    exclude_paths_by_spec,
+    find_exclude_specs,
+)
+
 try:  # pragma: nocover
     from mcp import ErrorData, McpError
     from mcp.server.fastmcp import FastMCP
@@ -26,6 +33,7 @@
     Config,
     cleanup_path,
     config_logging,
+    expand_globs,
     find_project_config_dir,
     get_project_config,
     load_config_file,
@@ -89,6 +97,69 @@ async def list_collections() -> list[str]:
     return names
 
 
+async def vectorise_files(paths: list[str], project_root: str) -> dict[str, int]:
+    logger.info(
+        f"vectorise tool called with the following args: {paths=}, {project_root=}"
+    )
+    project_root = os.path.expanduser(project_root)
+    if not os.path.isdir(project_root):
+        logger.error(f"Invalid project root: {project_root}")
+        raise McpError(
+            ErrorData(code=1, message=f"{project_root} is not a valid path.")
+        )
+    config = await get_project_config(project_root)
+    try:
+        client = await get_client(config)
+        collection = await get_collection(client, config, True)
+    except Exception as e:
+        logger.error("Failed to access collection at %s", project_root)
+        raise McpError(
+            ErrorData(
+                code=1,
+                message=f"{e.__class__.__name__}: Failed to create the collection at {project_root}.",
+            )
+        )
+    if collection is None:  # pragma: nocover
+        raise McpError(
+            ErrorData(
+                code=1,
+                message=f"Failed to access the collection at {project_root}. Use `list_collections` tool to get a list of valid paths for this field.",
+            )
+        )
+
+    paths = [os.path.expanduser(i) for i in await expand_globs(paths)]
+    final_config = await config.merge_from(
+        Config(files=[i for i in paths if os.path.isfile(i)], project_root=project_root)
+    )
+    for ignore_spec in find_exclude_specs(final_config):
+        if os.path.isfile(ignore_spec):
+            logger.info(f"Loading ignore specs from {ignore_spec}.")
+            paths = exclude_paths_by_spec((str(i) for i in paths), ignore_spec)
+    stats = VectoriseStats()
+    collection_lock = asyncio.Lock()
+    stats_lock = asyncio.Lock()
+    max_batch_size = await client.get_max_batch_size()
+    semaphore = asyncio.Semaphore(os.cpu_count() or 1)
+    tasks = [
+        asyncio.create_task(
+            chunked_add(
+                str(file),
+                collection,
+                collection_lock,
+                stats,
+                stats_lock,
+                final_config,
+                max_batch_size,
+                semaphore,
+            )
+        )
+        for file in paths
+    ]
+    for i, task in enumerate(asyncio.as_completed(tasks), start=1):
+        await task
+    return stats.to_dict()
+
+
 async def query_tool(
     n_query: int, query_messages: list[str], project_root: str
 ) -> list[str]:
@@ -186,18 +257,25 @@ async def mcp_server():
     mcp.add_tool(
         fn=list_collections,
         name="ls",
-        description="List all projects indexed by VectorCode. Call this before making queries.",
+        description="\n".join(
+            prompt_by_categories["ls"] + prompt_by_categories["general"]
+        ),
     )
 
     mcp.add_tool(
         fn=query_tool,
         name="query",
-        description=f"""
-Use VectorCode to perform vector similarity search on repositories and return a list of relevant file paths and contents. 
-Make sure `project_root` is one of the values from the `ls` tool. 
-Unless the user requested otherwise, start your retrievals by {mcp_config.n_results} files.
-The result contains the relative paths for the files and their corresponding contents.
-""",
+        description="\n".join(
+            prompt_by_categories["query"] + prompt_by_categories["general"]
+        ),
+    )
+
+    mcp.add_tool(
+        fn=vectorise_files,
+        name="vectorise",
+        description="\n".join(
+            prompt_by_categories["vectorise"] + prompt_by_categories["general"]
+        ),
     )
 
     return mcp
diff --git a/src/vectorcode/subcommands/query/__init__.py b/src/vectorcode/subcommands/query/__init__.py
index 0341772b..4f4b507a 100644
--- a/src/vectorcode/subcommands/query/__init__.py
+++ b/src/vectorcode/subcommands/query/__init__.py
@@ -1,7 +1,7 @@
 import json
 import logging
 import os
-from typing import cast
+from typing import Any, cast
 
 from chromadb import GetResult, Where
 from chromadb.api.models.AsyncCollection import AsyncCollection
@@ -49,12 +49,15 @@ async def get_query_result_files(
     try:
         if len(configs.query_exclude):
             logger.info(f"Excluding {len(configs.query_exclude)} files from the query.")
-            filter: dict[str, dict] = {"path": {"$nin": configs.query_exclude}}
+            filter: dict[str, Any] = {"path": {"$nin": configs.query_exclude}}
         else:
             filter = {}
         num_query = configs.n_result
         if QueryInclude.chunk in configs.include:
-            filter["start"] = {"$gte": 0}
+            if filter:
+                filter = {"$and": [filter.copy(), {"$gte": 0}]}
+            else:
+                filter["start"] = {"$gte": 0}
         else:
             num_query = await collection.count()
             if configs.query_multiplier > 0:
diff --git a/tests/subcommands/query/test_query.py b/tests/subcommands/query/test_query.py
index 64463fca..a6b17689 100644
--- a/tests/subcommands/query/test_query.py
+++ b/tests/subcommands/query/test_query.py
@@ -205,6 +205,36 @@ async def test_get_query_result_files_with_query_exclude(mock_collection, mock_c
         assert kwargs["where"] == {"path": {"$nin": ["/excluded/path.py"]}}
 
 
+@pytest.mark.asyncio
+async def test_get_query_result_chunks_with_query_exclude(mock_collection, mock_config):
+    # Setup query_exclude
+    mock_config.query_exclude = ["/excluded/path.py"]
+    mock_config.include = [QueryInclude.chunk, QueryInclude.path]
+
+    with (
+        patch("vectorcode.subcommands.query.expand_path") as mock_expand_path,
+        patch("vectorcode.subcommands.query.expand_globs") as mock_expand_globs,
+        patch("vectorcode.subcommands.query.reranker.NaiveReranker") as MockReranker,
+        patch("os.path.isfile", return_value=True),  # Add this line to mock isfile
+    ):
+        mock_expand_globs.return_value = ["/excluded/path.py"]
+        mock_expand_path.return_value = "/excluded/path.py"
+
+        mock_reranker_instance = MagicMock()
+        mock_reranker_instance.rerank = AsyncMock(return_value=["file1.py", "file2.py"])
+        MockReranker.return_value = mock_reranker_instance
+
+        # Call the function
+        await get_query_result_files(mock_collection, mock_config)
+
+        # Check that query was called with the right parameters including the where clause
+        mock_collection.query.assert_called_once()
+        _, kwargs = mock_collection.query.call_args
+        assert kwargs["where"] == {
+            "$and": [{"path": {"$nin": ["/excluded/path.py"]}}, {"$gte": 0}]
+        }
+
+
 @pytest.mark.asyncio
 async def test_get_query_reranker_initialisation_error(mock_collection, mock_config):
     # Configure to use CrossEncoder reranker
diff --git a/tests/test_mcp.py b/tests/test_mcp.py
index 004e92dc..a9be2f11 100644
--- a/tests/test_mcp.py
+++ b/tests/test_mcp.py
@@ -1,5 +1,7 @@
+import os
+import tempfile
 from argparse import ArgumentParser
-from unittest.mock import AsyncMock, MagicMock, patch
+from unittest.mock import AsyncMock, MagicMock, mock_open, patch
 
 import pytest
 from mcp import McpError
@@ -11,6 +13,7 @@
     mcp_server,
     parse_cli_args,
     query_tool,
+    vectorise_files,
 )
 
 
@@ -168,6 +171,125 @@ async def test_query_tool_no_collection():
         )
 
 
+@pytest.mark.asyncio
+async def test_vectorise_tool_invalid_project_root():
+    with (
+        patch("os.path.isdir", return_value=False),
+    ):
+        with pytest.raises(McpError):
+            await vectorise_files(paths=["foo.bar"], project_root=".")
+
+
+@pytest.mark.asyncio
+async def test_vectorise_files_success():
+    with tempfile.TemporaryDirectory() as temp_dir:
+        file_path = f"{temp_dir}/test_file.py"
+        with open(file_path, "w") as f:
+            f.write("def func(): pass")
+
+        with (
+            patch("os.path.isdir", return_value=True),
+            patch("vectorcode.mcp_main.get_project_config") as mock_get_project_config,
+            patch("vectorcode.mcp_main.get_client") as mock_get_client,
+            patch("vectorcode.mcp_main.get_collection") as mock_get_collection,
+            patch("vectorcode.subcommands.vectorise.chunked_add"),
+            patch(
+                "vectorcode.subcommands.vectorise.hash_file", return_value="test_hash"
+            ),
+        ):
+            mock_config = Config(project_root=temp_dir)
+            mock_get_project_config.return_value = mock_config
+            mock_client = AsyncMock()
+            mock_get_client.return_value = mock_client
+            mock_collection = AsyncMock()
+            mock_collection.get.return_value = {"ids": [], "metadatas": []}
+            mock_get_collection.return_value = mock_collection
+            mock_client.get_max_batch_size.return_value = 100
+
+            result = await vectorise_files(paths=[file_path], project_root=temp_dir)
+
+            assert result["add"] == 1
+            mock_get_project_config.assert_called_once_with(temp_dir)
+            mock_get_client.assert_called_once_with(mock_config)
+            mock_get_collection.assert_called_once_with(mock_client, mock_config, True)
+
+
+@pytest.mark.asyncio
+async def test_vectorise_files_collection_access_failure():
+    with (
+        patch("os.path.isdir", return_value=True),
+        patch("vectorcode.mcp_main.get_project_config"),
+        patch("vectorcode.mcp_main.get_client", side_effect=Exception("Client error")),
+        patch("vectorcode.mcp_main.get_collection"),
+    ):
+        with pytest.raises(McpError) as exc_info:
+            await vectorise_files(paths=["file.py"], project_root="/valid/path")
+
+        assert exc_info.value.error.code == 1
+        assert (
+            "Failed to create the collection at /valid/path"
+            in exc_info.value.error.message
+        )
+
+
+@pytest.mark.asyncio
+async def test_vectorise_files_with_exclude_spec():
+    with tempfile.TemporaryDirectory() as temp_dir:
+        file1 = f"{temp_dir}/file1.py"
+        excluded_file = f"{temp_dir}/excluded.py"
+        exclude_spec_file = f"{temp_dir}/.vectorcode/vectorcode.exclude"
+
+        os.makedirs(f"{temp_dir}/.vectorcode")
+        with open(file1, "w") as f:
+            f.write("content1")
+        with open(excluded_file, "w") as f:
+            f.write("content_excluded")
+
+        # Create mock file handles for specific file contents
+        mock_exclude_file_handle = mock_open(read_data="excluded.py").return_value
+
+        def mock_open_side_effect(filename, *args, **kwargs):
+            if filename == exclude_spec_file:
+                return mock_exclude_file_handle
+            # For other files that might be opened, return a generic mock
+            return MagicMock()
+
+        with (
+            patch("os.path.isdir", return_value=True),
+            patch("vectorcode.mcp_main.get_project_config") as mock_get_project_config,
+            patch("vectorcode.mcp_main.get_client") as mock_get_client,
+            patch("vectorcode.mcp_main.get_collection") as mock_get_collection,
+            patch("vectorcode.subcommands.vectorise.chunked_add") as mock_chunked_add,
+            patch(
+                "vectorcode.subcommands.vectorise.hash_file", return_value="test_hash"
+            ),
+            # Patch builtins.open with the custom side effect
+            patch("builtins.open", side_effect=mock_open_side_effect),
+            # Patch os.path.isfile to control which files "exist"
+            patch(
+                "os.path.isfile",
+                side_effect=lambda x: x in [file1, excluded_file, exclude_spec_file],
+            ),
+        ):
+            mock_config = Config(project_root=temp_dir)
+            mock_get_project_config.return_value = mock_config
+            mock_client = AsyncMock()
+            mock_get_client.return_value = mock_client
+            mock_collection = AsyncMock()
+            mock_collection.get.return_value = {"ids": [], "metadatas": []}
+            mock_get_collection.return_value = mock_collection
+            mock_client.get_max_batch_size.return_value = 100
+
+            result = await vectorise_files(
+                paths=[file1, excluded_file], project_root=temp_dir
+            )
+
+            assert result["add"] == 0
+            assert mock_chunked_add.call_count == 0
+            call_args = [call[0][0] for call in mock_chunked_add.call_args_list]
+            assert excluded_file not in call_args
+
+
 @pytest.mark.asyncio
 async def test_mcp_server():
     with (
@@ -188,7 +310,7 @@ async def test_mcp_server():
 
         await mcp_server()
 
-        assert mock_add_tool.call_count == 2
+        assert mock_add_tool.call_count == 3
 
 
 @pytest.mark.asyncio
@@ -223,7 +345,7 @@ async def new_get_collections(clients):
 
         await mcp_server()
 
-        assert mock_add_tool.call_count == 2
+        assert mock_add_tool.call_count == 3
         mock_get_collections.assert_called()