diff --git a/reme_cli/component/component_registry.py b/reme_cli/component/component_registry.py
new file mode 100644
index 00000000..ab0cbd9c
--- /dev/null
+++ b/reme_cli/component/component_registry.py
@@ -0,0 +1,128 @@
+"""
+Component registry module.
+
+Provides a global registry for managing component class registration and lookup.
+Supports two registration methods:
+1. Direct registration: R.register(MyClass, "name")
+2. Decorator registration: @R.register("name")
+"""
+
+from typing import Callable, TypeVar, cast
+
+from .base_component import BaseComponent
+from ..enumeration import ComponentEnum
+
+T = TypeVar("T", bound=BaseComponent)
+
+
+class ComponentRegistry:
+    """Registry for managing component class registration and lookup.
+
+    Components are organized by type (ComponentEnum), with each type
+    containing multiple named component implementations.
+
+    Attributes:
+        _registry: Internal storage structure, format: {ComponentEnum: {name: component_class}}
+
+    Usage:
+        # Direct registration
+        R.register(OpenAIChatModel, "openai")
+
+        # Decorator registration
+        @R.register("openai")
+        class OpenAIChatModel(BaseComponent):
+            ...
+
+        # Get registered component
+        cls = R.get(ComponentEnum.LLM, "openai")
+    """
+
+    def __init__(self) -> None:
+        """Initialize the component registry."""
+        self._registry: dict[ComponentEnum, dict[str, type[BaseComponent]]] = {}
+
+    def _do_register(self, cls: type[T], name: str) -> type[T]:
+        """Internal method to register a class.
+
+        Args:
+            cls: The component class to register.
+            name: The name identifier for the component.
+
+        Returns:
+            The registered class.
+        """
+        component_type = cls.component_type
+        if component_type not in self._registry:
+            self._registry[component_type] = {}
+        self._registry[component_type][name] = cls
+        return cls
+
+    def register(
+        self, cls_or_name: type[T] | str, name: str | None = None
+    ) -> Callable[[type[T]], type[T]] | type[T]:
+        """Register a component class.
+
+        Supports two calling patterns:
+        - Direct: R.register(MyClass, "name") -> returns MyClass
+        - Decorator: @R.register("name") -> returns decorator function
+
+        Args:
+            cls_or_name: Either a class to register (direct mode), or a name string
+                for decorator mode.
+            name: Optional name when using direct registration with a class.
+                If not provided, the class name will be used.
+
+        Returns:
+            Either the registered class (direct mode) or a decorator function.
+
+        Example:
+            # Direct registration
+            R.register(OpenAIChatModel, "openai")
+
+            # Decorator registration
+            @R.register("openai")
+            class OpenAIChatModel(BaseComponent):
+                ...
+        """
+        # Direct registration: R.register(MyClass, "name")
+        if isinstance(cls_or_name, type):
+            cls = cast(type[T], cls_or_name)
+            _key = name or cls.__name__
+            return self._do_register(cls, _key)
+
+        # Decorator mode: @R.register("name")
+        _decorator_name = cls_or_name
+
+        def decorator(decorated_cls: type[T]) -> type[T]:
+            key = _decorator_name or decorated_cls.__name__
+            return self._do_register(decorated_cls, key)
+
+        return decorator
+
+    def get(self, component_type: ComponentEnum, name: str) -> type[BaseComponent] | None:
+        """Get a registered component by type and name.
+
+        Args:
+            component_type: The component type enum value.
+            name: The registered name of the component.
+
+        Returns:
+            The component class if found, None otherwise.
+        """
+        return self._registry.get(component_type, {}).get(name)
+
+    def get_all(self, component_type: ComponentEnum) -> dict[str, type[BaseComponent]]:
+        """Get all registered components for a given type.
+
+        Args:
+            component_type: The component type enum value.
+
+        Returns:
+            Dictionary mapping component names to their classes.
+            Returns empty dict if no components registered for the type.
+        """
+        return self._registry.get(component_type, {})
+
+
+# Global registry instance
+R = ComponentRegistry()
\ No newline at end of file
diff --git a/reme_cli/component/file_store/__init__.py b/reme_cli/component/file_store/__init__.py
new file mode 100644
index 00000000..a84d7b1a
--- /dev/null
+++ b/reme_cli/component/file_store/__init__.py
@@ -0,0 +1,13 @@
+"""File store module for persistent memory management.
+
+This module provides storage backends for memory chunks and file metadata,
+including pure-Python local implementations with vector and full-text search.
+"""
+
+from .base_file_store import BaseFileStore
+from .local_file_store import LocalFileStore
+
+__all__ = [
+    "BaseFileStore",
+    "LocalFileStore",
+]
\ No newline at end of file
diff --git a/reme_cli/component/file_store/base_file_store.py b/reme_cli/component/file_store/base_file_store.py
new file mode 100644
index 00000000..0d0f06f5
--- /dev/null
+++ b/reme_cli/component/file_store/base_file_store.py
@@ -0,0 +1,168 @@
+"""Base storage interface for file store."""
+
+import re
+from abc import abstractmethod
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+from ..base_component import BaseComponent
+from ..embedding import BaseEmbeddingModel
+from ...enumeration import ComponentEnum
+from ...schema import FileChunk, FileMetadata
+
+if TYPE_CHECKING:
+    from ..application_context import ApplicationContext
+
+
+class BaseFileStore(BaseComponent):
+    """Abstract base class for file storage backends."""
+
+    def __init__(
+            self,
+            store_name: str,
+            db_path: str | Path,
+            embedding_model: str = "default",
+            fts_enabled: bool = True,
+            **kwargs,
+    ):
+        super().__init__(**kwargs)
+        self._embedding_model_name: str = embedding_model
+        self.embedding_model: BaseEmbeddingModel | None = None
+        self.store_name: str = store_name
+        self.db_path: Path = Path(db_path)
+        self.db_path.mkdir(parents=True, exist_ok=True)
+        self.vector_enabled: bool = bool(embedding_model)
+        self.fts_enabled: bool = fts_enabled
+
+        if not re.match(r"^[a-zA-Z0-9_]+$", store_name):
+            raise ValueError(f"Invalid '{store_name}'. Only alphanumeric characters and underscores are allowed.")
+        if not self.vector_enabled and not self.fts_enabled:
+            raise ValueError("At least one of embedding_model or fts_enabled must be set.")
+
+    async def _start(self, app_context: ApplicationContext | None = None):
+        """Initialize the storage backend and resolve embedding_model from app_context."""
+        if not self._embedding_model_name:
+            return
+        models = app_context.components.get(ComponentEnum.EMBEDDING_MODEL, {})
+        if self._embedding_model_name not in models:
+            raise ValueError(f"Embedding model '{self._embedding_model_name}' not found.")
+        model = models[self._embedding_model_name]
+        if not isinstance(model, BaseEmbeddingModel):
+            raise TypeError(f"Expected BaseEmbeddingModel, got {type(model).__name__}")
+        self.embedding_model = model
+
+    async def _close(self):
+        """Close storage and release resources."""
+        self.embedding_model = None
+
+    @property
+    def embedding_dim(self) -> int:
+        """Get the embedding model's dimensionality."""
+        return self.embedding_model.dimensions if self.embedding_model else 1024
+
+    def _disable_vector_search(self, reason: str = "embedding API error") -> None:
+        """Disable vector search and log a warning."""
+        if self.vector_enabled:
+            self.logger.warning(f"[{self.store_name}] Disabling vector search: {reason}")
+            self.vector_enabled = False
+
+    async def _get_embeddings_safe(self, texts: list[str], **kwargs) -> list[list[float]] | None:
+        """Get embeddings, return None if vector search is disabled or failed."""
+        if not self.vector_enabled:
+            return None
+        try:
+            return await self.embedding_model.get_embeddings(texts, **kwargs)
+        except Exception as e:
+            self._disable_vector_search(str(e))
+            return None
+
+    async def get_embedding(self, query: str, **kwargs) -> list[float] | None:
+        """Get embedding for a single query string."""
+        result = await self._get_embeddings_safe([query], **kwargs)
+        return result[0] if result else None
+
+    async def get_embeddings(self, queries: list[str], **kwargs) -> list[list[float]] | None:
+        """Get embeddings for a batch of query strings."""
+        return await self._get_embeddings_safe(queries, **kwargs)
+
+    async def get_chunk_embedding(self, chunk: FileChunk, **kwargs) -> FileChunk:
+        """Generate embedding for a single FileChunk."""
+        chunk.embedding = await self.get_embedding(chunk.text, **kwargs)
+        return chunk
+
+    async def get_chunk_embeddings(self, chunks: list[FileChunk], **kwargs) -> list[FileChunk]:
+        """Generate embeddings for a batch of FileChunk."""
+        if not chunks:
+            return chunks
+        embeddings = await self.get_embeddings([c.text for c in chunks], **kwargs)
+        if embeddings and len(embeddings) == len(chunks):
+            for chunk, emb in zip(chunks, embeddings):
+                chunk.embedding = emb
+        else:
+            for chunk in chunks:
+                chunk.embedding = None
+        return chunks
+
+    @abstractmethod
+    async def clear_all(self):
+        """Clear all indexed data."""
+
+    @abstractmethod
+    async def upsert_file(self, file_meta: FileMetadata, chunks: list[FileChunk]):
+        """Insert or update a file and its chunks."""
+
+    @abstractmethod
+    async def delete_file(self, path: str):
+        """Delete a file and all its chunks."""
+
+    @abstractmethod
+    async def delete_file_chunks(self, path: str, chunk_ids: list[str]):
+        """Delete chunks for a file."""
+
+    @abstractmethod
+    async def upsert_chunks(self, chunks: list[FileChunk]):
+        """Insert or update specific chunks without affecting other chunks."""
+
+    @abstractmethod
+    async def list_files(self) -> list[str]:
+        """List all indexed file paths."""
+
+    @abstractmethod
+    async def get_file_metadata(self, path: str) -> FileMetadata | None:
+        """Get full file metadata with statistics."""
+
+    @abstractmethod
+    async def update_file_metadata(self, file_meta: FileMetadata) -> None:
+        """Update file metadata without affecting chunks."""
+
+    @abstractmethod
+    async def get_file_chunks(self, path: str) -> list[FileChunk]:
+        """Get all chunks for a file."""
+
+    @abstractmethod
+    async def vector_search(self, query: str, limit: int) -> list[FileChunk]:
+        """Perform vector similarity search."""
+
+    @abstractmethod
+    async def keyword_search(self, query: str, limit: int) -> list[FileChunk]:
+        """Perform keyword/full-text search."""
+
+    @abstractmethod
+    async def hybrid_search(
+        self,
+        query: str,
+        limit: int,
+        vector_weight: float = 0.7,
+        candidate_multiplier: float = 3.0,
+    ) -> list[FileChunk]:
+        """Perform hybrid search combining vector and keyword search.
+
+        Args:
+            query: Search query text
+            limit: Maximum number of results
+            vector_weight: Weight for vector search results (0.0-1.0)
+            candidate_multiplier: Multiplier for candidate pool size
+
+        Returns:
+            List of FileChunk with score populated, sorted by combined relevance
+        """
diff --git a/reme_cli/component/file_store/local_file_store.py b/reme_cli/component/file_store/local_file_store.py
new file mode 100644
index 00000000..713a4cc8
--- /dev/null
+++ b/reme_cli/component/file_store/local_file_store.py
@@ -0,0 +1,392 @@
+"""Pure-Python in-memory storage backend for file store, with JSON file persistence."""
+
+import json
+from pathlib import Path
+
+import numpy as np
+
+from .base_file_store import BaseFileStore
+from ...schema import FileChunk, FileMetadata
+from ...utils import batch_cosine_similarity
+
+
+class LocalFileStore(BaseFileStore):
+    """Pure-Python in-memory file storage with JSONL file persistence.
+
+    No external dependencies required. All data lives in Python dicts;
+    writes are persisted to JSONL files on disk so state survives restarts.
+
+    Inherits embedding methods from BaseFileStore:
+    - get_chunk_embedding / get_chunk_embeddings (async)
+    - get_embedding / get_embeddings (async)
+
+    Provides:
+    - Vector similarity search (cosine similarity, pure Python)
+    - Full-text / keyword search (Python substring matching)
+    - Efficient chunk and file metadata management
+    """
+
+    def __init__(self, encoding: str = "utf-8", **kwargs):
+        super().__init__(**kwargs)
+        self._encoding: str = encoding
+        self._chunks: dict[str, FileChunk] = {}
+        self._files: dict[str, FileMetadata] = {}
+        self._chunks_file: Path = self.db_path / f"{self.store_name}_chunks.jsonl"
+        self._metadata_file: Path = self.db_path / f"{self.store_name}_file_metadata.json"
+
+    # ------------------------------------------------------------------
+    # Persistence helpers
+    # ------------------------------------------------------------------
+
+    async def _load_chunks(self) -> None:
+        """Load chunks from JSONL file into memory."""
+        if not self._chunks_file.exists():
+            return
+        try:
+            data = self._chunks_file.read_text(encoding=self._encoding)
+            self._chunks = {}
+            for line in data.strip().split("\n"):
+                if not line:
+                    continue
+                chunk = FileChunk.model_validate(json.loads(line))
+                self._chunks[chunk.id] = chunk
+        except Exception as e:
+            self.logger.warning(f"Failed to load chunks: {e}")
+
+    async def _save_chunks(self) -> None:
+        """Persist chunks to JSONL file with atomic write."""
+        lines = [json.dumps(c.model_dump(mode="json"), ensure_ascii=False) for c in self._chunks.values()]
+        content = "\n".join(lines)
+        temp_path = self._chunks_file.with_suffix('.tmp')
+        try:
+            temp_path.write_text(content, encoding=self._encoding)
+            temp_path.replace(self._chunks_file)
+        except Exception as e:
+            self.logger.error(f"Failed to save chunks: {e}")
+            raise
+        finally:
+            if temp_path.exists():
+                temp_path.unlink()
+
+    async def _load_metadata(self) -> None:
+        """Load file metadata from JSON file into memory."""
+        if not self._metadata_file.exists():
+            return
+        try:
+            data = self._metadata_file.read_text(encoding=self._encoding)
+            raw: dict = json.loads(data)
+            self._files = {path: FileMetadata(**meta) for path, meta in raw.items()}
+        except Exception as e:
+            self.logger.warning(f"Failed to load metadata: {e}")
+
+    async def _save_metadata(self) -> None:
+        """Persist file metadata to JSON file with atomic write."""
+        raw = {path: meta.model_dump(exclude={"content", "metadata"}, mode="json")
+               for path, meta in self._files.items()}
+        content = json.dumps(raw, indent=2, ensure_ascii=False)
+        temp_path = self._metadata_file.with_suffix('.tmp')
+        try:
+            temp_path.write_text(content, encoding=self._encoding)
+            temp_path.replace(self._metadata_file)
+        except Exception as e:
+            self.logger.error(f"Failed to save metadata: {e}")
+            raise
+        finally:
+            if temp_path.exists():
+                temp_path.unlink()
+
+    # ------------------------------------------------------------------
+    # Lifecycle
+    # ------------------------------------------------------------------
+
+    async def _start(self, app_context=None) -> None:
+        """Load persisted data into memory."""
+        await self._load_metadata()
+        await self._load_chunks()
+        self.logger.info(
+            f"LocalFileStore '{self.store_name}' ready: "
+            f"{len(self._chunks)} chunks, metadata at {self._metadata_file}",
+        )
+        await super()._start()
+
+    async def _close(self) -> None:
+        """Flush state to disk and release memory."""
+        await self._save_metadata()
+        await self._save_chunks()
+        self._chunks.clear()
+        self._files.clear()
+        await super()._close()
+
+    # ------------------------------------------------------------------
+    # Write operations
+    # ------------------------------------------------------------------
+
+    async def upsert_file(
+            self,
+            file_meta: FileMetadata,
+            chunks: list[FileChunk],
+    ) -> None:
+        """Insert or update file and its chunks."""
+        if not chunks:
+            return
+
+        # Remove existing chunks for this file first
+        await self.delete_file(file_meta.path)
+
+        # Batch generate embeddings (base class returns mock embeddings when vector_enabled=False)
+        chunks = await self.get_chunk_embeddings(chunks)
+
+        for chunk in chunks:
+            self._chunks[chunk.id] = chunk
+
+        self._files[file_meta.path] = FileMetadata(
+            hash=file_meta.hash,
+            mtime_ms=file_meta.mtime_ms,
+            size=file_meta.size,
+            path=file_meta.path,
+            chunk_count=len(chunks),
+        )
+
+    async def delete_file(self, path: str) -> None:
+        """Delete file and all its chunks."""
+        to_delete = [cid for cid, chunk in self._chunks.items() if chunk.path == path]
+        for cid in to_delete:
+            del self._chunks[cid]
+
+        self._files.pop(path, None)
+
+    async def delete_file_chunks(self, path: str, chunk_ids: list[str]) -> None:
+        """Delete specific chunks for a file."""
+        if not chunk_ids:
+            return
+
+        for cid in chunk_ids:
+            self._chunks.pop(cid, None)
+
+        # Recalculate chunk_count in file metadata
+        if path in self._files:
+            self._files[path].chunk_count = sum(
+                1 for chunk in self._chunks.values() if chunk.path == path
+            )
+
+    async def upsert_chunks(
+            self,
+            chunks: list[FileChunk],
+    ) -> None:
+        """Insert or update specific chunks without affecting other chunks."""
+        if not chunks:
+            return
+
+        chunks = await self.get_chunk_embeddings(chunks)
+
+        for chunk in chunks:
+            self._chunks[chunk.id] = chunk
+
+    # ------------------------------------------------------------------
+    # Read operations
+    # ------------------------------------------------------------------
+
+    async def list_files(self) -> list[str]:
+        """List all indexed files."""
+        return list(self._files.keys())
+
+    async def get_file_metadata(
+            self,
+            path: str,
+    ) -> FileMetadata | None:
+        """Get file metadata."""
+        return self._files.get(path)
+
+    async def update_file_metadata(self, file_meta: FileMetadata) -> None:
+        """Update file metadata without affecting chunks."""
+        self._files[file_meta.path] = FileMetadata(
+            hash=file_meta.hash,
+            mtime_ms=file_meta.mtime_ms,
+            size=file_meta.size,
+            path=file_meta.path,
+            chunk_count=file_meta.chunk_count,
+        )
+
+    async def get_file_chunks(
+            self,
+            path: str,
+    ) -> list[FileChunk]:
+        """Get all chunks for a file, sorted by start_line."""
+        chunks = [chunk for chunk in self._chunks.values() if chunk.path == path]
+        chunks.sort(key=lambda c: c.start_line)
+        return chunks
+
+    # ------------------------------------------------------------------
+    # Search
+    # ------------------------------------------------------------------
+
+    async def vector_search(
+            self,
+            query: str,
+            limit: int,
+    ) -> list[FileChunk]:
+        """Perform cosine-similarity vector search over in-memory embeddings."""
+        if not self.vector_enabled or not query:
+            return []
+
+        query_embedding = await self.get_embedding(query)
+        if not query_embedding:
+            return []
+
+        expected_dim = self.embedding_dim
+
+        # Collect candidate chunks with embeddings
+        candidates = [c for c in self._chunks.values() if c.embedding]
+        if not candidates:
+            return []
+
+        # Validate and fix chunk embedding dimensions
+        valid_embeddings = []
+        for chunk in candidates:
+            emb = chunk.embedding
+            emb_len = len(emb)
+            if emb_len != expected_dim:
+                if emb_len < expected_dim:
+                    emb = emb + [0.0] * (expected_dim - emb_len)
+                else:
+                    emb = emb[:expected_dim]
+            valid_embeddings.append(emb)
+
+        # Compute similarities
+        query_array = np.array([query_embedding])
+        chunk_embeddings = np.array(valid_embeddings)
+        similarities = batch_cosine_similarity(query_array, chunk_embeddings)[0]
+
+        # Build results
+        results = []
+        for chunk, sim in zip(candidates, similarities):
+            results.append(
+                FileChunk(
+                    id=chunk.id,
+                    path=chunk.path,
+                    start_line=chunk.start_line,
+                    end_line=chunk.end_line,
+                    hash=chunk.hash,
+                    text=chunk.text,
+                    embedding=chunk.embedding,
+                    scores={"vector": float(sim), "score": float(sim)},
+                )
+            )
+
+        results.sort(key=lambda r: r.score, reverse=True)
+        return results[:limit]
+
+    async def keyword_search(
+            self,
+            query: str,
+            limit: int,
+    ) -> list[FileChunk]:
+        """Perform keyword/full-text search via Python substring matching."""
+        if not self.fts_enabled or not query:
+            return []
+
+        words = query.split()
+        if not words:
+            return []
+
+        query_lower = query.lower()
+        words_lower = [w.lower() for w in words]
+        n_words = len(words)
+
+        results = []
+        for chunk in self._chunks.values():
+            text_lower = chunk.text.lower()
+            match_count = sum(1 for w in words_lower if w in text_lower)
+            if match_count == 0:
+                continue
+
+            base_score = match_count / n_words
+            phrase_bonus = 0.2 if n_words > 1 and query_lower in text_lower else 0.0
+            score = min(1.0, base_score + phrase_bonus)
+
+            results.append(
+                FileChunk(
+                    id=chunk.id,
+                    path=chunk.path,
+                    start_line=chunk.start_line,
+                    end_line=chunk.end_line,
+                    hash=chunk.hash,
+                    text=chunk.text,
+                    scores={"keyword": score, "score": score},
+                )
+            )
+
+        results.sort(key=lambda r: r.score, reverse=True)
+        return results[:limit]
+
+    async def hybrid_search(
+            self,
+            query: str,
+            limit: int,
+            vector_weight: float = 0.7,
+            candidate_multiplier: float = 3.0,
+    ) -> list[FileChunk]:
+        """Perform hybrid search combining vector and keyword search."""
+        assert 0.0 <= vector_weight <= 1.0
+
+        candidates = min(200, max(1, int(limit * candidate_multiplier)))
+        text_weight = 1.0 - vector_weight
+
+        if self.vector_enabled and self.fts_enabled:
+            keyword_results = await self.keyword_search(query, candidates)
+            vector_results = await self.vector_search(query, candidates)
+
+            if not keyword_results:
+                return vector_results[:limit]
+            elif not vector_results:
+                return keyword_results[:limit]
+
+            merged = self._merge_hybrid_results(
+                vector=vector_results,
+                keyword=keyword_results,
+                vector_weight=vector_weight,
+                text_weight=text_weight,
+            )
+            return merged[:limit]
+        elif self.vector_enabled:
+            return await self.vector_search(query, limit)
+        elif self.fts_enabled:
+            return await self.keyword_search(query, limit)
+        else:
+            return []
+
+    @staticmethod
+    def _merge_hybrid_results(
+            vector: list[FileChunk],
+            keyword: list[FileChunk],
+            vector_weight: float,
+            text_weight: float,
+    ) -> list[FileChunk]:
+        """Merge vector and keyword search results with weighted scoring."""
+        merged: dict[str, FileChunk] = {}
+
+        for result in vector:
+            v_score = result.scores.get("vector", 0)
+            result.scores["score"] = v_score * vector_weight
+            merged[result.merge_key] = result
+
+        for result in keyword:
+            key = result.merge_key
+            k_score = result.scores.get("keyword", 0)
+            if key in merged:
+                merged[key].scores["score"] += k_score * text_weight
+            else:
+                result.scores["score"] = k_score * text_weight
+                merged[key] = result
+
+        results = list(merged.values())
+        results.sort(key=lambda r: r.score, reverse=True)
+        return results
+
+    async def clear_all(self) -> None:
+        """Clear all indexed data from memory and disk."""
+        self._chunks.clear()
+        self._files.clear()
+        await self._save_chunks()
+        await self._save_metadata()
+        self.logger.info(f"Cleared all data from LocalFileStore '{self.store_name}'")
diff --git a/reme_cli/component/file_watcher/__init__.py b/reme_cli/component/file_watcher/__init__.py
new file mode 100644
index 00000000..c0485c71
--- /dev/null
+++ b/reme_cli/component/file_watcher/__init__.py
@@ -0,0 +1,13 @@
+"""File watcher module for monitoring file system changes.
+
+This module provides file watcher implementations for monitoring file changes
+and updating memory stores accordingly.
+"""
+
+from .base_file_watcher import BaseFileWatcher
+from .md_file_watcher import MdFileWatcher
+
+__all__ = [
+    "BaseFileWatcher",
+    "MdFileWatcher",
+]
\ No newline at end of file
diff --git a/reme_cli/component/file_watcher/base_file_watcher.py b/reme_cli/component/file_watcher/base_file_watcher.py
new file mode 100644
index 00000000..0919517a
--- /dev/null
+++ b/reme_cli/component/file_watcher/base_file_watcher.py
@@ -0,0 +1,223 @@
+"""Base file watcher implementation.
+
+This module provides the base class for file watcher implementations
+that monitor file system changes and trigger callbacks.
+"""
+
+import asyncio
+from abc import abstractmethod
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+from watchfiles import Change, awatch
+
+from ..base_component import BaseComponent
+from ..file_store import BaseFileStore
+from ...enumeration import ComponentEnum
+
+if TYPE_CHECKING:
+    from ..application_context import ApplicationContext
+
+
+class BaseFileWatcher(BaseComponent):
+    """Abstract base class for file watcher implementations.
+
+    This base class provides file monitoring functionality that can be extended
+    to implement specific file monitoring requirements.
+    """
+
+    def __init__(
+            self,
+            watch_paths: list[str] | str,
+            suffix_filters: list[str] | None = None,
+            recursive: bool = False,
+            debounce: int = 2000,
+            chunk_tokens: int = 400,
+            chunk_overlap: int = 80,
+            file_store: str = "default",
+            rebuild_index_on_start: bool = True,
+            poll_delay_ms: int = 2000,
+            **kwargs,
+    ):
+        """Initialize the file watcher.
+
+        Args:
+            watch_paths: Paths to watch for changes
+            suffix_filters: File suffix filters (e.g., ['.py', '.txt'])
+            recursive: Whether to watch directories recursively
+            debounce: Debounce time in milliseconds
+            chunk_tokens: Token size for chunking
+            chunk_overlap: Overlap size for chunks
+            file_store: Name of the file store component to use
+            rebuild_index_on_start: If True, clear all indexed data on start and rescan existing files.
+                           If False, only monitor new changes without initialization.
+            poll_delay_ms: Polling delay in milliseconds.
+            **kwargs: Additional keyword arguments
+        """
+        super().__init__(**kwargs)
+        self._file_store_name: str = file_store
+        self.file_store: BaseFileStore | None = None
+        self.watch_paths: list[str] = [watch_paths] if isinstance(watch_paths, str) else watch_paths
+        self.suffix_filters: list[str] = suffix_filters or []
+        self.recursive: bool = recursive
+        self.debounce: int = debounce
+        self.chunk_tokens: int = chunk_tokens
+        self.chunk_overlap: int = chunk_overlap
+        self.rebuild_index_on_start: bool = rebuild_index_on_start
+        self.poll_delay_ms: int = poll_delay_ms
+
+        self._stop_event = asyncio.Event()
+        self._watch_task: asyncio.Task | None = None
+
+    async def _start(self, app_context: ApplicationContext | None = None):
+        """Initialize the file watcher and resolve file_store from app_context."""
+        # Resolve file_store from app_context
+        if self._file_store_name:
+            stores = app_context.components.get(ComponentEnum.FILE_STORE, {})
+            if self._file_store_name not in stores:
+                raise ValueError(f"File store '{self._file_store_name}' not found.")
+            store = stores[self._file_store_name]
+            if not isinstance(store, BaseFileStore):
+                raise TypeError(f"Expected BaseFileStore, got {type(store).__name__}")
+            self.file_store = store
+
+        # Start watching task
+        async def _initialize_and_watch():
+            if self.rebuild_index_on_start and self.file_store:
+                await self.file_store.clear_all()
+                self.logger.info("Cleared all indexed data on start")
+                await self._scan_existing_files()
+            await self._watch_loop()
+
+        self._stop_event.clear()
+        self._watch_task = asyncio.create_task(_initialize_and_watch())
+        self.logger.info(f"Started watching: {self.watch_paths}")
+
+    async def _close(self):
+        """Stop the file watcher and release resources."""
+        # Signal stop and cancel watch task
+        self._stop_event.set()
+        if self._watch_task and not self._watch_task.done():
+            self._watch_task.cancel()
+            try:
+                await self._watch_task
+            except asyncio.CancelledError:
+                pass
+
+        self._watch_task = None
+        self._stop_event.clear()
+        self.file_store = None
+        self.logger.info("Stopped watching")
+
+    def watch_filter(self, _change: Change, path: str) -> bool:
+        """Filter function for file watching."""
+        if not self.suffix_filters:
+            return True
+
+        for suffix in self.suffix_filters:
+            if path.endswith("." + suffix.strip(".")):
+                return True
+
+        return False
+
+    async def _scan_existing_files(self):
+        """Scan existing files matching watch criteria and trigger on_changes with Change.added."""
+        if not self.file_store:
+            return
+
+        existing_files: set[tuple[Change, str]] = set()
+
+        for watch_path_str in self.watch_paths:
+            watch_path = Path(watch_path_str)
+
+            if not watch_path.exists():
+                self.logger.warning(f"Watch path does not exist: {watch_path}")
+                continue
+
+            if watch_path.is_file():
+                if self.watch_filter(Change.added, str(watch_path)):
+                    existing_files.add((Change.added, str(watch_path)))
+            elif watch_path.is_dir():
+                if self.recursive:
+                    for file_path in watch_path.rglob("*"):
+                        if file_path.is_file() and self.watch_filter(Change.added, str(file_path)):
+                            existing_files.add((Change.added, str(file_path)))
+                else:
+                    for file_path in watch_path.iterdir():
+                        if file_path.is_file() and self.watch_filter(Change.added, str(file_path)):
+                            existing_files.add((Change.added, str(file_path)))
+
+        if existing_files:
+            self.logger.info(f"[SCAN_ON_START] Found {len(existing_files)} existing files matching watch criteria")
+            await self.on_changes(existing_files)
+            self.logger.info(f"[SCAN_ON_START] Added {len(existing_files)} files to memory store")
+        else:
+            self.logger.info("[SCAN_ON_START] No existing files found matching watch criteria")
+
+        files: list[str] = await self.file_store.list_files()
+        for file_path in files:
+            chunks = await self.file_store.get_file_chunks(file_path)
+            self.logger.info(f"Found existing file: {file_path}, {len(chunks)} chunks")
+
+    async def _interruptible_sleep(self, seconds: float):
+        """Sleep that can be interrupted by stop_event."""
+        try:
+            await asyncio.wait_for(self._stop_event.wait(), timeout=seconds)
+        except asyncio.TimeoutError:
+            pass
+
+    async def _watch_loop(self):
+        """Core monitoring loop with auto-restart on failure."""
+        if not self.watch_paths:
+            self.logger.warning("No watch paths specified")
+            return
+
+        while not self._stop_event.is_set():
+            valid_paths = [p for p in self.watch_paths if Path(p).exists()]
+
+            if not valid_paths:
+                self.logger.warning("No valid watch paths exist, waiting 10 seconds before retry...")
+                await self._interruptible_sleep(10)
+                continue
+
+            invalid_paths = set(self.watch_paths) - set(valid_paths)
+            if invalid_paths:
+                self.logger.warning(f"Skipping non-existent paths: {invalid_paths}")
+
+            try:
+                self.logger.info(f"Starting watch on valid paths: {valid_paths}")
+                async for changes in awatch(
+                        *valid_paths,
+                        watch_filter=self.watch_filter,
+                        recursive=self.recursive,
+                        debounce=self.debounce,
+                        poll_delay_ms=self.poll_delay_ms,
+                        stop_event=self._stop_event,
+                ):
+                    if self._stop_event.is_set():
+                        break
+
+                    await self.on_changes(changes)
+
+            except FileNotFoundError as e:
+                self.logger.error(f"Watch path no longer exists: {e}, restarting in 10 seconds...")
+                if not self._stop_event.is_set():
+                    await self._interruptible_sleep(10)
+
+            except Exception as e:
+                self.logger.error(f"Error in watch loop: {e}, restarting in 10 seconds...", exc_info=True)
+                if not self._stop_event.is_set():
+                    await self._interruptible_sleep(10)
+
+    async def on_changes(self, changes: set[tuple[Change, str]]):
+        """Hook method to handle file changes."""
+        await self._on_changes(changes)
+        self.logger.info(f"[{self.__class__.__name__}] on_changes: {changes}")
+
+    @abstractmethod
+    async def _on_changes(self, changes: set[tuple[Change, str]]):
+        """Callback method to handle file changes.
+
+        Args:
+            changes: Set of (Change, path) tuples representing file changes
+        """
diff --git a/reme_cli/component/file_watcher/md_file_watcher.py b/reme_cli/component/file_watcher/md_file_watcher.py
new file mode 100644
index 00000000..7ee0fb18
--- /dev/null
+++ b/reme_cli/component/file_watcher/md_file_watcher.py
@@ -0,0 +1,89 @@
+"""Markdown file watcher for Markdown file synchronization.
+
+This module provides a file watcher that processes Markdown files
+on any change, ensuring complete synchronization.
+"""
+
+import asyncio
+from pathlib import Path
+
+from watchfiles import Change
+
+from .base_file_watcher import BaseFileWatcher
+from ...schema import FileMetadata
+from ...utils import hash_text, chunk_markdown
+
+
+class MdFileWatcher(BaseFileWatcher):
+    """Markdown file watcher implementation for Markdown file synchronization."""
+
+    def __init__(self, encoding: str = "utf-8", **kwargs):
+        """Initialize Markdown file watcher.
+
+        Args:
+            encoding: File encoding (default: "utf-8")
+            **kwargs: Additional keyword arguments passed to BaseFileWatcher
+        """
+        super().__init__(**kwargs)
+        self.encoding = encoding
+
+    async def _on_changes(self, changes: set[tuple[Change, str]]):
+        """Handle file changes with full synchronization."""
+        if not self.file_store:
+            self.logger.warning("File store not initialized, skipping changes")
+            return
+
+        for change_type, path in changes:
+            try:
+                if change_type in [Change.added, Change.modified]:
+                    file_meta = await self._build_file_metadata(path)
+                    chunks = (
+                            chunk_markdown(
+                                file_meta.content,
+                                file_meta.path,
+                                self.chunk_tokens,
+                                self.chunk_overlap,
+                            )
+                            or []
+                    )
+                    if chunks:
+                        chunks = await self.file_store.get_chunk_embeddings(chunks)
+                    file_meta.chunk_count = len(chunks)
+
+                    await self.file_store.delete_file(file_meta.path)
+                    self.logger.info(f"delete_file {file_meta.path}")
+
+                    await self.file_store.upsert_file(file_meta, chunks)
+                    self.logger.info(f"Upserted {file_meta.chunk_count} chunks for {file_meta.path}")
+
+                elif change_type == Change.deleted:
+                    await self.file_store.delete_file(path)
+                    self.logger.info(f"Deleted {path}")
+
+                else:
+                    self.logger.warning(f"Unknown change type: {change_type}")
+
+                self.logger.info(f"File {change_type} changed: {path}")
+
+            except FileNotFoundError:
+                self.logger.warning(f"File not found: {path}, skipping")
+            except PermissionError:
+                self.logger.warning(f"Permission denied: {path}, skipping")
+            except Exception as e:
+                self.logger.error(f"Error processing {path}: {e}", exc_info=True)
+
+    async def _build_file_metadata(self, path: str) -> FileMetadata:
+        """Build file metadata from path."""
+        file_path = Path(path)
+
+        def _read_file_sync():
+            return file_path.stat(), file_path.read_text(encoding=self.encoding)
+
+        stat, content = await asyncio.to_thread(_read_file_sync)
+        return FileMetadata(
+            hash=hash_text(content),
+            mtime_ms=stat.st_mtime * 1000,
+            size=stat.st_size,
+            path=str(file_path.absolute()),
+            content=content,
+        )
diff --git a/reme_cli/enumeration/component_enum.py b/reme_cli/enumeration/component_enum.py
index 46f7ee3f..a5eded0c 100644
--- a/reme_cli/enumeration/component_enum.py
+++ b/reme_cli/enumeration/component_enum.py
@@ -6,6 +6,8 @@ class ComponentEnum(str, Enum):
 
     BASE = "base"
 
+    EMBEDDING_MODEL = "embedding_model"
+
     AS_LLM = "as_llm"
 
     AS_LLM_FORMATTER = "as_llm_formatter"
diff --git a/reme_cli/schema/__init__.py b/reme_cli/schema/__init__.py
index ed4b2c12..3bab477e 100644
--- a/reme_cli/schema/__init__.py
+++ b/reme_cli/schema/__init__.py
@@ -1,7 +1,11 @@
 from .application_config import ApplicationConfig
 from .base_node import BaseNode
+from .file_chunk import FileChunk
+from .file_metadata import FileMetadata
 
 __all__ = [
     "ApplicationConfig",
     "BaseNode",
+    "FileChunk",
+    "FileMetadata",
 ]
diff --git a/reme_cli/schema/file_chunk.py b/reme_cli/schema/file_chunk.py
new file mode 100644
index 00000000..d5195c76
--- /dev/null
+++ b/reme_cli/schema/file_chunk.py
@@ -0,0 +1,24 @@
+"""File chunk schema."""
+
+from pydantic import Field
+from .base_node import BaseNode
+
+
+class FileChunk(BaseNode):
+    """A chunk of file content with metadata."""
+
+    path: str = Field(..., description="File path relative to workspace")
+    start_line: int = Field(..., description="Starting line number in the source file")
+    end_line: int = Field(..., description="Ending line number in the source file")
+    hash: str = Field(..., description="Hash of the chunk content")
+    scores: dict[str, float] = Field(default_factory=dict, description="Search scores by type")
+
+    @property
+    def score(self) -> float:
+        """Final score for search result."""
+        return self.scores.get("score", 0.0)
+
+    @property
+    def merge_key(self) -> str:
+        """Key for merging search results."""
+        return f"{self.path}:{self.start_line}:{self.end_line}"
\ No newline at end of file
diff --git a/reme_cli/schema/file_metadata.py b/reme_cli/schema/file_metadata.py
new file mode 100644
index 00000000..672e9c27
--- /dev/null
+++ b/reme_cli/schema/file_metadata.py
@@ -0,0 +1,15 @@
+"""File metadata schema."""
+
+from pydantic import BaseModel, Field
+
+
+class FileMetadata(BaseModel):
+    """File metadata with optional extended fields for various use cases."""
+
+    hash: str = Field(default=..., description="Hash of the file content")
+    mtime_ms: float = Field(default=..., description="Last modification time in milliseconds")
+    size: int = Field(default=..., description="File size in bytes")
+    path: str | None = Field(default=None, description="Relative path to the session file")
+    content: str | None = Field(default=None, description="Parsed content from the session file")
+    chunk_count: int | None = Field(default=None, description="Number of chunks in the file")
+    metadata: dict = Field(default_factory=dict, description="Additional metadata")
diff --git a/reme_cli/utils/__init__.py b/reme_cli/utils/__init__.py
index f2fdaa87..b0ca8dbe 100644
--- a/reme_cli/utils/__init__.py
+++ b/reme_cli/utils/__init__.py
@@ -1,9 +1,15 @@
+from .chunking_utils import chunk_markdown
+from .common_utils import hash_text
 from .logger_utils import get_logger
 from .pydantic_config_parser import PydanticConfigParser
+from .similarity_utils import batch_cosine_similarity
 from .singleton import singleton
 
 __all__ = [
+    "chunk_markdown",
+    "hash_text",
     "get_logger",
     "PydanticConfigParser",
+    "batch_cosine_similarity",
     "singleton",
 ]
diff --git a/reme_cli/utils/chunking_utils.py b/reme_cli/utils/chunking_utils.py
new file mode 100644
index 00000000..bfd1f556
--- /dev/null
+++ b/reme_cli/utils/chunking_utils.py
@@ -0,0 +1,121 @@
+"""Chunking logic for Markdown files."""
+
+from .common_utils import hash_text
+from ..schema import FileChunk
+
+
+def chunk_markdown(
+    text: str,
+    path: str,
+    chunk_tokens: int,
+    overlap: int,
+) -> list[FileChunk]:
+    """
+    Markdown chunking logic implemented based on the TypeScript version.
+
+    Args:
+        text: Input text
+        path: File path
+        chunk_tokens: Maximum tokens per chunk
+        overlap: Overlap tokens between chunks
+
+    Returns:
+        List of FileChunk objects
+    """
+    if not text.strip():
+        return []
+
+    lines = text.split("\n")
+
+    # Convert tokens to characters (~1 token = 4 chars)
+    max_chars = max(32, chunk_tokens * 4)
+    overlap_chars = max(0, overlap * 4)
+
+    chunks: list[FileChunk] = []
+
+    # Currently building chunk
+    current: list[dict] = []  # [{'line': str, 'line_no': int}]
+    current_chars = 0
+
+    def flush():
+        """Add current chunk to results list"""
+        if not current:
+            return
+
+        first_entry = current[0]
+        last_entry = current[-1]
+
+        if not first_entry or not last_entry:
+            return
+
+        chunk_text = "\n".join([entry["line"] for entry in current])
+        start_line = first_entry["line_no"]
+        end_line = last_entry["line_no"]
+
+        chunk_hash = hash_text(chunk_text)
+
+        chunks.append(
+            FileChunk(
+                id=hash_text(f"{path}:{start_line}:{end_line}:{chunk_hash}:{len(chunks)}"),
+                path=path,
+                start_line=start_line,
+                end_line=end_line,
+                text=chunk_text,
+                hash=chunk_hash,
+            ),
+        )
+
+    def carry_overlap():
+        """Keep overlapping part and clear the rest"""
+        nonlocal current, current_chars
+
+        if overlap_chars <= 0 or not current:
+            current = []
+            current_chars = 0
+            return
+
+        acc = 0
+        kept = []
+
+        # Collect lines from the end until reaching overlap size
+        for j in range(len(current) - 1, -1, -1):
+            entry = current[j]
+            if not entry:
+                continue
+
+            acc += len(entry["line"]) + 1  # +1 for newline
+            kept.insert(0, entry)  # Insert at the beginning to maintain order
+
+            if acc >= overlap_chars:
+                break
+
+        current = kept
+        current_chars = sum(len(entry["line"]) + 1 for entry in kept)
+
+    for i, line in enumerate(lines):
+        line_no = i + 1
+
+        # Split long lines into multiple segments
+        segments = []
+        if not line:  # Empty line
+            segments.append("")
+        else:
+            # If line is too long, split by maximum character count
+            for start in range(0, len(line), max_chars):
+                segments.append(line[start : start + max_chars])
+
+        for segment in segments:
+            line_size = len(segment) + 1  # +1 for newline
+
+            # If adding current segment would exceed the limit, flush current chunk
+            if current_chars + line_size > max_chars and current:
+                flush()
+                carry_overlap()
+
+            current.append({"line": segment, "line_no": line_no})
+            current_chars += line_size
+
+    # Process the final chunk
+    flush()
+
+    return [c for c in chunks if c.text.strip()]
diff --git a/reme_cli/utils/common_utils.py b/reme_cli/utils/common_utils.py
new file mode 100644
index 00000000..c4b1dce3
--- /dev/null
+++ b/reme_cli/utils/common_utils.py
@@ -0,0 +1,14 @@
+import hashlib
+
+
+def hash_text(text: str, encoding: str = "utf-8") -> str:
+    """Generate SHA-256 hash of text content.
+
+    Args:
+        text: Input text to hash
+        encoding: Encoding of the text (default: "utf-8")
+
+    Returns:
+        Hexadecimal representation of the SHA-256 hash
+    """
+    return hashlib.sha256(text.encode(encoding)).hexdigest()
diff --git a/reme_cli/utils/similarity_utils.py b/reme_cli/utils/similarity_utils.py
new file mode 100644
index 00000000..4550404b
--- /dev/null
+++ b/reme_cli/utils/similarity_utils.py
@@ -0,0 +1,52 @@
+import numpy as np
+
+
+def cosine_similarity(vec1: list[float], vec2: list[float]) -> float:
+    """Calculate the cosine similarity between two numeric vectors."""
+    if len(vec1) != len(vec2):
+        raise ValueError(f"Vectors must have same length: {len(vec1)} != {len(vec2)}")
+
+    dot_product = sum(a * b for a, b in zip(vec1, vec2))
+    magnitude1 = sum(a * a for a in vec1) ** 0.5
+    magnitude2 = sum(b * b for b in vec2) ** 0.5
+
+    if magnitude1 == 0 or magnitude2 == 0:
+        return 0.0
+
+    return dot_product / (magnitude1 * magnitude2)
+
+
+def batch_cosine_similarity(nd_array1: np.ndarray, nd_array2: np.ndarray) -> np.ndarray:
+    """Calculate cosine similarity matrix between two batches of vectors.
+
+    Args:
+        nd_array1: Matrix of shape (batch_size1, emb_size)
+        nd_array2: Matrix of shape (batch_size2, emb_size)
+
+    Returns:
+        Similarity matrix of shape (batch_size1, batch_size2) where
+        result[i, j] is the cosine similarity between nd_array1[i] and nd_array2[j]
+
+    Raises:
+        ValueError: If embedding dimensions don't match
+    """
+    if nd_array1.shape[1] != nd_array2.shape[1]:
+        raise ValueError(f"Embedding dimensions must match: {nd_array1.shape[1]} != {nd_array2.shape[1]}")
+
+    # Compute dot products: (batch_size1, emb_size) @ (emb_size, batch_size2)
+    # Result shape: (batch_size1, batch_size2)
+    dot_products = np.dot(nd_array1, nd_array2.T)
+
+    # Compute L2 norms for each vector
+    norms1 = np.linalg.norm(nd_array1, axis=1)  # Shape: (batch_size1,)
+    norms2 = np.linalg.norm(nd_array2, axis=1)  # Shape: (batch_size2,)
+
+    # Compute outer product of norms: (batch_size1, 1) @ (1, batch_size2)
+    # Result shape: (batch_size1, batch_size2)
+    norm_products = np.outer(norms1, norms2)
+
+    # Avoid division by zero
+    norm_products = np.where(norm_products == 0, 1e-10, norm_products)
+
+    # Compute cosine similarities
+    return dot_products / norm_products