From 600bf355d9327fc0ea1534a32496cca81768216e Mon Sep 17 00:00:00 2001
From: AI Christianson <ai.christianson@christianson.ai>
Date: Tue, 4 Mar 2025 14:59:45 -0500
Subject: [PATCH] use repo pattern

---
 ra_aid/__main__.py                            |   7 +-
 ra_aid/agent_utils.py                         |   6 +-
 ra_aid/database/repositories/__init__.py      |   8 +
 .../repositories/related_files_repository.py  | 169 +++++++
 ra_aid/prompts/research_prompts.py            |   3 +-
 ra_aid/tools/agent.py                         |   3 +-
 ra_aid/tools/expert.py                        |   3 +-
 ra_aid/tools/memory.py                        | 110 +---
 ra_aid/tools/programmer.py                    |  18 +-
 ra_aid/utils/__init__.py                      |   5 +
 ra_aid/utils/file_utils.py                    |  61 +++
 tests/ra_aid/test_main.py                     |  29 +-
 tests/ra_aid/test_programmer.py               |  57 ++-
 tests/ra_aid/tools/test_agent.py              |  27 +-
 tests/ra_aid/tools/test_memory.py             | 470 ++++++------------
 15 files changed, 559 insertions(+), 417 deletions(-)
 create mode 100644 ra_aid/database/repositories/related_files_repository.py
 create mode 100644 ra_aid/utils/__init__.py
 create mode 100644 ra_aid/utils/file_utils.py

diff --git a/ra_aid/__main__.py b/ra_aid/__main__.py
index b167e87..ed874de 100644
--- a/ra_aid/__main__.py
+++ b/ra_aid/__main__.py
@@ -52,6 +52,9 @@ from ra_aid.database.repositories.human_input_repository import (
 from ra_aid.database.repositories.research_note_repository import (
     ResearchNoteRepositoryManager, get_research_note_repository
 )
+from ra_aid.database.repositories.related_files_repository import (
+    RelatedFilesRepositoryManager
+)
 from ra_aid.model_formatters import format_key_facts_dict
 from ra_aid.model_formatters.key_snippets_formatter import format_key_snippets_dict
 from ra_aid.console.output import cpm
@@ -402,12 +405,14 @@ def main():
             with KeyFactRepositoryManager(db) as key_fact_repo, \
                  KeySnippetRepositoryManager(db) as key_snippet_repo, \
                  HumanInputRepositoryManager(db) as human_input_repo, \
-                 ResearchNoteRepositoryManager(db) as research_note_repo:
+                 ResearchNoteRepositoryManager(db) as research_note_repo, \
+                 RelatedFilesRepositoryManager() as related_files_repo:
                 # This initializes all repositories and makes them available via their respective get methods
                 logger.debug("Initialized KeyFactRepository")
                 logger.debug("Initialized KeySnippetRepository")
                 logger.debug("Initialized HumanInputRepository")
                 logger.debug("Initialized ResearchNoteRepository")
+                logger.debug("Initialized RelatedFilesRepository")
 
                 # Check dependencies before proceeding
                 check_dependencies()
diff --git a/ra_aid/agent_utils.py b/ra_aid/agent_utils.py
index 5597bd9..3f40ed7 100644
--- a/ra_aid/agent_utils.py
+++ b/ra_aid/agent_utils.py
@@ -397,7 +397,7 @@ def run_research_agent(
         logger.error(f"Failed to access key fact repository: {str(e)}")
         key_facts = ""
     code_snippets = _global_memory.get("code_snippets", "")
-    related_files = _global_memory.get("related_files", "")
+    related_files = get_related_files()
 
     current_date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
     working_directory = os.getcwd()
@@ -552,7 +552,7 @@ def run_web_research_agent(
         logger.error(f"Failed to access key fact repository: {str(e)}")
         key_facts = ""
     code_snippets = _global_memory.get("code_snippets", "")
-    related_files = _global_memory.get("related_files", "")
+    related_files = get_related_files()
 
     current_date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
     working_directory = os.getcwd()
@@ -1099,4 +1099,4 @@ def run_agent_with_retry(
                     _handle_api_error(e, attempt, max_retries, base_delay)
         finally:
             _decrement_agent_depth()
-            _restore_interrupt_handling(original_handler)
+            _restore_interrupt_handling(original_handler)
\ No newline at end of file
diff --git a/ra_aid/database/repositories/__init__.py b/ra_aid/database/repositories/__init__.py
index 163d327..5f6d237 100644
--- a/ra_aid/database/repositories/__init__.py
+++ b/ra_aid/database/repositories/__init__.py
@@ -20,6 +20,11 @@ from ra_aid.database.repositories.key_snippet_repository import (
     KeySnippetRepositoryManager, 
     get_key_snippet_repository
 )
+from ra_aid.database.repositories.related_files_repository import (
+    RelatedFilesRepository,
+    RelatedFilesRepositoryManager,
+    get_related_files_repository
+)
 from ra_aid.database.repositories.research_note_repository import (
     ResearchNoteRepository,
     ResearchNoteRepositoryManager,
@@ -36,6 +41,9 @@ __all__ = [
     'KeySnippetRepository', 
     'KeySnippetRepositoryManager', 
     'get_key_snippet_repository',
+    'RelatedFilesRepository',
+    'RelatedFilesRepositoryManager',
+    'get_related_files_repository',
     'ResearchNoteRepository',
     'ResearchNoteRepositoryManager',
     'get_research_note_repository',
diff --git a/ra_aid/database/repositories/related_files_repository.py b/ra_aid/database/repositories/related_files_repository.py
new file mode 100644
index 0000000..94a0109
--- /dev/null
+++ b/ra_aid/database/repositories/related_files_repository.py
@@ -0,0 +1,169 @@
+import contextvars
+import os
+from typing import Dict, List, Optional
+
+# Import is_binary_file from memory.py
+from ra_aid.utils.file_utils import is_binary_file
+
+# Create contextvar to hold the RelatedFilesRepository instance
+related_files_repo_var = contextvars.ContextVar("related_files_repo", default=None)
+
+
+class RelatedFilesRepository:
+    """
+    Repository for managing related files in memory.
+    
+    This class provides methods to add, remove, and retrieve related files.
+    It does not require database models and operates entirely in memory.
+    """
+    
+    def __init__(self):
+        """
+        Initialize the RelatedFilesRepository.
+        """
+        self._related_files: Dict[int, str] = {}
+        self._id_counter: int = 1
+    
+    def get_all(self) -> Dict[int, str]:
+        """
+        Get all related files.
+        
+        Returns:
+            Dict[int, str]: Dictionary mapping file IDs to file paths
+        """
+        return self._related_files.copy()
+    
+    def add_file(self, filepath: str) -> Optional[int]:
+        """
+        Add a file to the repository.
+        
+        Args:
+            filepath: Path to the file to add
+            
+        Returns:
+            Optional[int]: The ID assigned to the file, or None if the file could not be added
+        """
+        # First check if path exists
+        if not os.path.exists(filepath):
+            return None
+            
+        # Then check if it's a directory
+        if os.path.isdir(filepath):
+            return None
+            
+        # Validate it's a regular file
+        if not os.path.isfile(filepath):
+            return None
+            
+        # Check if it's a binary file
+        if is_binary_file(filepath):
+            return None
+            
+        # Normalize the path
+        normalized_path = os.path.abspath(filepath)
+        
+        # Check if normalized path already exists in values
+        for file_id, path in self._related_files.items():
+            if path == normalized_path:
+                return file_id
+                
+        # Add new file
+        file_id = self._id_counter
+        self._id_counter += 1
+        self._related_files[file_id] = normalized_path
+        
+        return file_id
+    
+    def remove_file(self, file_id: int) -> Optional[str]:
+        """
+        Remove a file from the repository.
+        
+        Args:
+            file_id: ID of the file to remove
+            
+        Returns:
+            Optional[str]: The path of the removed file, or None if the file ID was not found
+        """
+        if file_id in self._related_files:
+            return self._related_files.pop(file_id)
+        return None
+    
+    def format_related_files(self) -> List[str]:
+        """
+        Format related files as 'ID#X path/to/file'.
+        
+        Returns:
+            List[str]: Formatted strings for each related file
+        """
+        return [f"ID#{file_id} {filepath}" for file_id, filepath in sorted(self._related_files.items())]
+
+
+class RelatedFilesRepositoryManager:
+    """
+    Context manager for RelatedFilesRepository.
+    
+    This class provides a context manager interface for RelatedFilesRepository,
+    using the contextvars approach for thread safety.
+    
+    Example:
+        with RelatedFilesRepositoryManager() as repo:
+            # Use the repository
+            file_id = repo.add_file("path/to/file.py")
+            all_files = repo.get_all()
+    """
+    
+    def __init__(self):
+        """
+        Initialize the RelatedFilesRepositoryManager.
+        """
+        pass
+        
+    def __enter__(self) -> 'RelatedFilesRepository':
+        """
+        Initialize the RelatedFilesRepository and return it.
+        
+        Returns:
+            RelatedFilesRepository: The initialized repository
+        """
+        repo = RelatedFilesRepository()
+        related_files_repo_var.set(repo)
+        return repo
+        
+    def __exit__(
+        self,
+        exc_type: Optional[type],
+        exc_val: Optional[Exception],
+        exc_tb: Optional[object],
+    ) -> None:
+        """
+        Reset the repository when exiting the context.
+        
+        Args:
+            exc_type: The exception type if an exception was raised
+            exc_val: The exception value if an exception was raised
+            exc_tb: The traceback if an exception was raised
+        """
+        # Reset the contextvar to None
+        related_files_repo_var.set(None)
+        
+        # Don't suppress exceptions
+        return False
+
+
+def get_related_files_repository() -> RelatedFilesRepository:
+    """
+    Get the current RelatedFilesRepository instance.
+    
+    Returns:
+        RelatedFilesRepository: The current repository instance
+        
+    Raises:
+        RuntimeError: If no repository is set in the current context
+    """
+    repo = related_files_repo_var.get()
+    if repo is None:
+        raise RuntimeError(
+            "RelatedFilesRepository not initialized in current context. "
+            "Make sure to use RelatedFilesRepositoryManager."
+        )
+    return repo
\ No newline at end of file
diff --git a/ra_aid/prompts/research_prompts.py b/ra_aid/prompts/research_prompts.py
index c34cb84..c812d44 100644
--- a/ra_aid/prompts/research_prompts.py
+++ b/ra_aid/prompts/research_prompts.py
@@ -173,8 +173,9 @@ If the user explicitly requested implementation, that means you should first per
 
 NEVER ANNOUNCE WHAT YOU ARE DOING, JUST DO IT!
 
-AS THE RESEARCH AGENT, YOU MUST NOT WRITE OR MODIFY ANY FILES. IF FILE MODIFICATION OR IMPLEMENTATINO IS REQUIRED, CALL request_implementation.
+AS THE RESEARCH AGENT, YOU MUST NOT WRITE OR MODIFY ANY FILES. IF FILE MODIFICATION OR IMPLEMENTATION IS REQUIRED, CALL request_implementation.
 IF THE USER ASKED YOU TO UPDATE A FILE, JUST DO RESEARCH FIRST, EMIT YOUR RESEARCH NOTES, THEN CALL request_implementation.
+CALL request_implementation ONLY ONCE! ONCE THE PLAN COMPLETES, YOU'RE DONE.
 """
 )
 
diff --git a/ra_aid/tools/agent.py b/ra_aid/tools/agent.py
index edddb8c..a6e380f 100644
--- a/ra_aid/tools/agent.py
+++ b/ra_aid/tools/agent.py
@@ -16,6 +16,7 @@ from ra_aid.console.formatting import print_error
 from ra_aid.database.repositories.human_input_repository import HumanInputRepository
 from ra_aid.database.repositories.key_fact_repository import get_key_fact_repository
 from ra_aid.database.repositories.key_snippet_repository import get_key_snippet_repository
+from ra_aid.database.repositories.related_files_repository import get_related_files_repository
 from ra_aid.database.repositories.research_note_repository import get_research_note_repository
 from ra_aid.exceptions import AgentInterrupt
 from ra_aid.model_formatters import format_key_facts_dict
@@ -340,7 +341,7 @@ def request_task_implementation(task_spec: str) -> str:
     )
 
     # Get required parameters
-    related_files = list(_global_memory["related_files"].values())
+    related_files = list(get_related_files_repository().get_all().values())
 
     try:
         print_task_header(task_spec)
diff --git a/ra_aid/tools/expert.py b/ra_aid/tools/expert.py
index 3716601..0cfc0f4 100644
--- a/ra_aid/tools/expert.py
+++ b/ra_aid/tools/expert.py
@@ -11,6 +11,7 @@ logger = logging.getLogger(__name__)
 
 from ..database.repositories.key_fact_repository import get_key_fact_repository
 from ..database.repositories.key_snippet_repository import get_key_snippet_repository
+from ..database.repositories.related_files_repository import get_related_files_repository
 from ..database.repositories.research_note_repository import get_research_note_repository
 from ..llm import initialize_expert_llm
 from ..model_formatters import format_key_facts_dict
@@ -154,7 +155,7 @@ def ask_expert(question: str) -> str:
     global expert_context
 
     # Get all content first
-    file_paths = list(_global_memory["related_files"].values())
+    file_paths = list(get_related_files_repository().get_all().values())
     related_contents = read_related_files(file_paths)
     # Get key snippets directly from repository and format using the formatter
     try:
diff --git a/ra_aid/tools/memory.py b/ra_aid/tools/memory.py
index 3aaa12f..53f2056 100644
--- a/ra_aid/tools/memory.py
+++ b/ra_aid/tools/memory.py
@@ -1,12 +1,8 @@
 import os
 from typing import Any, Dict, List, Optional
 
-try:
-    import magic
-except ImportError:
-    magic = None
-
 from langchain_core.tools import tool
+from ra_aid.utils.file_utils import is_binary_file
 from rich.console import Console
 from rich.markdown import Markdown
 from rich.panel import Panel
@@ -44,10 +40,11 @@ console = Console()
 # Import repositories using the get_* functions
 from ra_aid.database.repositories.key_fact_repository import get_key_fact_repository
 
+# Import the related files repository
+from ra_aid.database.repositories.related_files_repository import get_related_files_repository
+
 # Global memory store
 _global_memory: Dict[str, Any] = {
-    "related_files": {},  # Dict[int, str] - ID to filepath mapping
-    "related_file_id_counter": 1,  # Counter for generating unique file IDs
     "agent_depth": 0,
     "work_log": [],  # List[WorkLogEntry] - Timestamped work events
 }
@@ -302,8 +299,8 @@ def get_related_files() -> List[str]:
     Returns:
         List of formatted strings in the format 'ID#X path/to/file.py'
     """
-    files = _global_memory["related_files"]
-    return [f"ID#{file_id} {filepath}" for file_id, filepath in sorted(files.items())]
+    repo = get_related_files_repository()
+    return repo.format_related_files()
 
 
 @tool("emit_related_files")
@@ -313,6 +310,7 @@ def emit_related_files(files: List[str]) -> str:
     Args:
         files: List of file paths to add
     """
+    repo = get_related_files_repository()
     results = []
     added_files = []
     invalid_paths = []
@@ -344,27 +342,20 @@ def emit_related_files(files: List[str]) -> str:
             results.append(f"Skipped binary file: '{file}'")
             continue
 
-        # Normalize the path
-        normalized_path = os.path.abspath(file)
-
-        # Check if normalized path already exists in values
-        existing_id = None
-        for fid, fpath in _global_memory["related_files"].items():
-            if fpath == normalized_path:
-                existing_id = fid
-                break
-
-        if existing_id is not None:
-            # File exists, use existing ID
-            results.append(f"File ID #{existing_id}: {file}")
-        else:
-            # New file, assign new ID
-            file_id = _global_memory["related_file_id_counter"]
-            _global_memory["related_file_id_counter"] += 1
-
-            # Store normalized path with ID
-            _global_memory["related_files"][file_id] = normalized_path
-            added_files.append((file_id, file))  # Keep original path for display
+        # Add file to repository
+        file_id = repo.add_file(file)
+        
+        if file_id is not None:
+            # Check if it's a new file by comparing with previous results
+            is_new_file = True
+            for r in results:
+                if r.startswith(f"File ID #{file_id}:"):
+                    is_new_file = False
+                    break
+                    
+            if is_new_file:
+                added_files.append((file_id, file))  # Keep original path for display
+                
             results.append(f"File ID #{file_id}: {file}")
 
     # Rich output - single consolidated panel for added files
@@ -421,57 +412,7 @@ def log_work_event(event: str) -> str:
     return f"Event logged: {event}"
 
 
-def is_binary_file(filepath):
-    """Check if a file is binary using magic library if available."""
-    # First check if file is empty
-    if os.path.getsize(filepath) == 0:
-        return False  # Empty files are not binary
-        
-    if magic:
-        try:
-            mime = magic.from_file(filepath, mime=True)
-            file_type = magic.from_file(filepath)
 
-            # If MIME type starts with 'text/', it's likely a text file
-            if mime.startswith("text/"):
-                return False
-                
-            # Also consider 'application/x-python' and similar script types as text
-            if any(mime.startswith(prefix) for prefix in ['application/x-python', 'application/javascript']):
-                return False
-                
-            # Check for common text file descriptors
-            text_indicators = ["text", "script", "xml", "json", "yaml", "markdown", "HTML"]
-            if any(indicator.lower() in file_type.lower() for indicator in text_indicators):
-                return False
-                
-            # If none of the text indicators are present, assume it's binary
-            return True
-        except Exception:
-            return _is_binary_fallback(filepath)
-    else:
-        return _is_binary_fallback(filepath)
-
-
-def _is_binary_fallback(filepath):
-    """Fallback method to detect binary files without using magic."""
-    try:
-        # First check if file is empty
-        if os.path.getsize(filepath) == 0:
-            return False  # Empty files are not binary
-            
-        with open(filepath, "r", encoding="utf-8") as f:
-            chunk = f.read(1024)
-
-            # Check for null bytes which indicate binary content
-            if "\0" in chunk:
-                return True
-
-            # If we can read it as text without errors, it's probably not binary
-            return False
-    except UnicodeDecodeError:
-        # If we can't decode as UTF-8, it's likely binary
-        return True
 
 
 def get_work_log() -> str:
@@ -518,17 +459,18 @@ def reset_work_log() -> str:
 
 @tool("deregister_related_files")
 def deregister_related_files(file_ids: List[int]) -> str:
-    """Delete multiple related files from global memory by their IDs.
+    """Delete multiple related files by their IDs.
     Silently skips any IDs that don't exist.
 
     Args:
         file_ids: List of file IDs to delete
     """
+    repo = get_related_files_repository()
     results = []
+    
     for file_id in file_ids:
-        if file_id in _global_memory["related_files"]:
-            # Delete the file reference
-            deleted_file = _global_memory["related_files"].pop(file_id)
+        deleted_file = repo.remove_file(file_id)
+        if deleted_file:
             success_msg = (
                 f"Successfully removed related file #{file_id}: {deleted_file}"
             )
diff --git a/ra_aid/tools/programmer.py b/ra_aid/tools/programmer.py
index 823c606..5b6788b 100644
--- a/ra_aid/tools/programmer.py
+++ b/ra_aid/tools/programmer.py
@@ -14,6 +14,7 @@ from ra_aid.models_params import DEFAULT_BASE_LATENCY, models_params
 from ra_aid.proc.interactive import run_interactive_command
 from ra_aid.text.processing import truncate_output
 from ra_aid.tools.memory import _global_memory, log_work_event
+from ra_aid.database.repositories.related_files_repository import get_related_files_repository
 
 console = Console()
 logger = get_logger(__name__)
@@ -91,13 +92,18 @@ def run_programming_task(
 
     # Get combined list of files (explicit + related) with normalized paths
     # and deduplicated using set operations
+    related_files_paths = []
+    try:
+        repo = get_related_files_repository()
+        related_files_paths = list(repo.get_all().values())
+        logger.debug("Retrieved related files from repository")
+    except RuntimeError as e:
+        # Repository not initialized
+        logger.warning(f"Failed to get related files repository: {e}")
+    
     files_to_use = list(
         {os.path.abspath(f) for f in (files or [])}
-        | {
-            os.path.abspath(f)
-            for f in _global_memory["related_files"].values()
-            if "related_files" in _global_memory
-        }
+        | {os.path.abspath(f) for f in related_files_paths}
     )
 
     # Add config file if specified
@@ -225,4 +231,4 @@ def parse_aider_flags(aider_flags: str) -> List[str]:
 
 
 # Export the functions
-__all__ = ["run_programming_task", "get_aider_executable"]
+__all__ = ["run_programming_task", "get_aider_executable"]
\ No newline at end of file
diff --git a/ra_aid/utils/__init__.py b/ra_aid/utils/__init__.py
new file mode 100644
index 0000000..48c9cb4
--- /dev/null
+++ b/ra_aid/utils/__init__.py
@@ -0,0 +1,5 @@
+"""Utility functions for the ra-aid project."""
+
+from .file_utils import is_binary_file
+
+__all__ = ["is_binary_file"]
\ No newline at end of file
diff --git a/ra_aid/utils/file_utils.py b/ra_aid/utils/file_utils.py
new file mode 100644
index 0000000..de0ac5d
--- /dev/null
+++ b/ra_aid/utils/file_utils.py
@@ -0,0 +1,61 @@
+"""Utility functions for file operations."""
+
+import os
+
+try:
+    import magic
+except ImportError:
+    magic = None
+
+
+def is_binary_file(filepath):
+    """Check if a file is binary using magic library if available."""
+    # First check if file is empty
+    if os.path.getsize(filepath) == 0:
+        return False  # Empty files are not binary
+
+    if magic:
+        try:
+            mime = magic.from_file(filepath, mime=True)
+            file_type = magic.from_file(filepath)
+
+            # If MIME type starts with 'text/', it's likely a text file
+            if mime.startswith("text/"):
+                return False
+
+            # Also consider 'application/x-python' and similar script types as text
+            if any(mime.startswith(prefix) for prefix in ['application/x-python', 'application/javascript']):
+                return False
+
+            # Check for common text file descriptors
+            text_indicators = ["text", "script", "xml", "json", "yaml", "markdown", "HTML"]
+            if any(indicator.lower() in file_type.lower() for indicator in text_indicators):
+                return False
+
+            # If none of the text indicators are present, assume it's binary
+            return True
+        except Exception:
+            return _is_binary_fallback(filepath)
+    else:
+        return _is_binary_fallback(filepath)
+
+
+def _is_binary_fallback(filepath):
+    """Fallback method to detect binary files without using magic."""
+    try:
+        # First check if file is empty
+        if os.path.getsize(filepath) == 0:
+            return False  # Empty files are not binary
+
+        with open(filepath, "r", encoding="utf-8") as f:
+            chunk = f.read(1024)
+
+            # Check for null bytes which indicate binary content
+            if "\0" in chunk:
+                return True
+
+            # If we can read it as text without errors, it's probably not binary
+            return False
+    except UnicodeDecodeError:
+        # If we can't decode as UTF-8, it's likely binary
+        return True
\ No newline at end of file
diff --git a/tests/ra_aid/test_main.py b/tests/ra_aid/test_main.py
index 37df53e..85f7e8a 100644
--- a/tests/ra_aid/test_main.py
+++ b/tests/ra_aid/test_main.py
@@ -1,6 +1,7 @@
 """Unit tests for __main__.py argument parsing."""
 
 import pytest
+from unittest.mock import patch, MagicMock
 
 from ra_aid.__main__ import parse_arguments
 from ra_aid.config import DEFAULT_RECURSION_LIMIT
@@ -12,8 +13,6 @@ def mock_dependencies(monkeypatch):
     """Mock all dependencies needed for main()."""
     # Initialize global memory with necessary keys to prevent KeyError
     _global_memory.clear()
-    _global_memory["related_files"] = {}
-    _global_memory["related_file_id_counter"] = 1
     _global_memory["agent_depth"] = 0
     _global_memory["work_log"] = []
     _global_memory["config"] = {}
@@ -37,6 +36,28 @@ def mock_dependencies(monkeypatch):
     monkeypatch.setattr("ra_aid.__main__.initialize_llm", mock_config_update)
 
 
+@pytest.fixture(autouse=True)
+def mock_related_files_repository():
+    """Mock the RelatedFilesRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.related_files_repository.related_files_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate stored files
+        related_files = {}
+        
+        # Setup get_all method to return the files dict
+        mock_repo.get_all.return_value = related_files
+        
+        # Setup format_related_files method
+        mock_repo.format_related_files.return_value = [f"ID#{file_id} {filepath}" for file_id, filepath in sorted(related_files.items())]
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        yield mock_repo
+
+
 def test_recursion_limit_in_global_config(mock_dependencies):
     """Test that recursion limit is correctly set in global config."""
     import sys
@@ -122,8 +143,6 @@ def test_temperature_validation(mock_dependencies):
 
     # Reset global memory for clean test
     _global_memory.clear()
-    _global_memory["related_files"] = {}
-    _global_memory["related_file_id_counter"] = 1
     _global_memory["agent_depth"] = 0
     _global_memory["work_log"] = []
     _global_memory["config"] = {}
@@ -266,4 +285,4 @@ def test_use_aider_flag(mock_dependencies):
         assert "run_programming_task" in tool_names
 
     # Reset to default state for other tests
-    set_modification_tools(False)
+    set_modification_tools(False)
\ No newline at end of file
diff --git a/tests/ra_aid/test_programmer.py b/tests/ra_aid/test_programmer.py
index 3b20632..cf24f00 100644
--- a/tests/ra_aid/test_programmer.py
+++ b/tests/ra_aid/test_programmer.py
@@ -1,10 +1,57 @@
 import pytest
+from unittest.mock import patch, MagicMock
 
 from ra_aid.tools.programmer import (
     get_aider_executable,
     parse_aider_flags,
     run_programming_task,
 )
+from ra_aid.database.repositories.related_files_repository import get_related_files_repository
+
+@pytest.fixture(autouse=True)
+def mock_related_files_repository():
+    """Mock the RelatedFilesRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.related_files_repository.related_files_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate stored files
+        related_files = {}
+        
+        # Setup get_all method to return the files dict
+        mock_repo.get_all.return_value = related_files
+        
+        # Setup format_related_files method
+        mock_repo.format_related_files.return_value = [f"ID#{file_id} {filepath}" for file_id, filepath in sorted(related_files.items())]
+        
+        # Setup add_file method
+        def mock_add_file(filepath):
+            normalized_path = os.path.abspath(filepath)
+            # Check if path already exists
+            for file_id, path in related_files.items():
+                if path == normalized_path:
+                    return file_id
+            
+            # Add new file
+            file_id = len(related_files) + 1
+            related_files[file_id] = normalized_path
+            return file_id
+        mock_repo.add_file.side_effect = mock_add_file
+        
+        # Setup remove_file method
+        def mock_remove_file(file_id):
+            if file_id in related_files:
+                return related_files.pop(file_id)
+            return None
+        mock_repo.remove_file.side_effect = mock_remove_file
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        # Also patch the get_related_files_repository function
+        with patch('ra_aid.tools.programmer.get_related_files_repository', return_value=mock_repo):
+            yield mock_repo
+
 
 # Test cases for parse_aider_flags function
 test_cases = [
@@ -78,11 +125,11 @@ def test_parse_aider_flags(input_flags, expected, description):
     assert result == expected, f"Failed test case: {description}"
 
 
-def test_aider_config_flag(mocker):
+def test_aider_config_flag(mocker, mock_related_files_repository):
     """Test that aider config flag is properly included in the command when specified."""
+    # Mock config in global memory but not related files (using repository now)
     mock_memory = {
         "config": {"aider_config": "/path/to/config.yml"},
-        "related_files": {},
     }
     mocker.patch("ra_aid.tools.programmer._global_memory", mock_memory)
 
@@ -99,15 +146,15 @@ def test_aider_config_flag(mocker):
     assert args[config_index + 1] == "/path/to/config.yml"
 
 
-def test_path_normalization_and_deduplication(mocker, tmp_path):
+def test_path_normalization_and_deduplication(mocker, tmp_path, mock_related_files_repository):
     """Test path normalization and deduplication in run_programming_task."""
     # Create a temporary test file
     test_file = tmp_path / "test.py"
     test_file.write_text("")
     new_file = tmp_path / "new.py"
 
-    # Mock dependencies
-    mocker.patch("ra_aid.tools.programmer._global_memory", {"related_files": {}})
+    # Mock dependencies - only need to mock config part of global memory now
+    mocker.patch("ra_aid.tools.programmer._global_memory", {"config": {}})
     mocker.patch(
         "ra_aid.tools.programmer.get_aider_executable", return_value="/path/to/aider"
     )
diff --git a/tests/ra_aid/tools/test_agent.py b/tests/ra_aid/tools/test_agent.py
index 7bf814a..921aa1e 100644
--- a/tests/ra_aid/tools/test_agent.py
+++ b/tests/ra_aid/tools/test_agent.py
@@ -2,6 +2,7 @@
 
 import pytest
 from unittest.mock import patch, MagicMock
+import os
 
 from ra_aid.tools.agent import (
     request_research,
@@ -10,21 +11,39 @@ from ra_aid.tools.agent import (
     request_research_and_implementation,
 )
 from ra_aid.tools.memory import _global_memory
+from ra_aid.database.repositories.related_files_repository import get_related_files_repository
 
 
 @pytest.fixture
 def reset_memory():
     """Reset global memory before each test"""
-    _global_memory["related_files"] = {}
-    _global_memory["related_file_id_counter"] = 0
     _global_memory["work_log"] = []
     yield
     # Clean up after test
-    _global_memory["related_files"] = {}
-    _global_memory["related_file_id_counter"] = 0
     _global_memory["work_log"] = []
 
 
+@pytest.fixture(autouse=True)
+def mock_related_files_repository():
+    """Mock the RelatedFilesRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.related_files_repository.related_files_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate stored files
+        related_files = {}
+        
+        # Setup get_all method to return the files dict
+        mock_repo.get_all.return_value = related_files
+        
+        # Setup format_related_files method
+        mock_repo.format_related_files.return_value = [f"ID#{file_id} {filepath}" for file_id, filepath in sorted(related_files.items())]
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        yield mock_repo
+
 @pytest.fixture
 def mock_functions():
     """Mock functions used in agent.py"""
diff --git a/tests/ra_aid/tools/test_memory.py b/tests/ra_aid/tools/test_memory.py
index a9e3aa5..4bc3434 100644
--- a/tests/ra_aid/tools/test_memory.py
+++ b/tests/ra_aid/tools/test_memory.py
@@ -17,11 +17,11 @@ from ra_aid.tools.memory import (
     get_work_log,
     log_work_event,
     reset_work_log,
-    is_binary_file,
-    _is_binary_fallback,
 )
+from ra_aid.utils.file_utils import is_binary_file, _is_binary_fallback
 from ra_aid.database.repositories.key_fact_repository import get_key_fact_repository
 from ra_aid.database.repositories.key_snippet_repository import get_key_snippet_repository
+from ra_aid.database.repositories.related_files_repository import get_related_files_repository
 from ra_aid.database.connection import DatabaseManager
 from ra_aid.database.models import KeyFact
 
@@ -29,13 +29,9 @@ from ra_aid.database.models import KeyFact
 @pytest.fixture
 def reset_memory():
     """Reset global memory before each test"""
-    _global_memory["related_files"] = {}
-    _global_memory["related_file_id_counter"] = 0
     _global_memory["work_log"] = []
     yield
     # Clean up after test
-    _global_memory["related_files"] = {}
-    _global_memory["related_file_id_counter"] = 0
     _global_memory["work_log"] = []
 
 
@@ -165,6 +161,66 @@ def mock_key_snippet_repository():
         yield memory_mock_repo
 
 
+@pytest.fixture(autouse=True)
+def mock_related_files_repository():
+    """Mock the RelatedFilesRepository to avoid database operations during tests"""
+    with patch('ra_aid.tools.memory.get_related_files_repository') as mock_repo:
+        # Setup the mock repository to behave like the original, but using memory
+        related_files = {}  # Local in-memory storage
+        id_counter = 0
+        
+        # Mock add_file method
+        def mock_add_file(filepath):
+            nonlocal id_counter
+            # Check if normalized path already exists in values
+            normalized_path = os.path.abspath(filepath)
+            for file_id, path in related_files.items():
+                if path == normalized_path:
+                    return file_id
+                    
+            # First check if path exists
+            if not os.path.exists(filepath):
+                return None
+                
+            # Then check if it's a directory
+            if os.path.isdir(filepath):
+                return None
+                
+            # Validate it's a regular file
+            if not os.path.isfile(filepath):
+                return None
+                
+            # Check if it's a binary file (don't actually check in tests)
+            # We'll mock is_binary_file separately when needed
+            
+            # Add new file
+            file_id = id_counter
+            id_counter += 1
+            related_files[file_id] = normalized_path
+            
+            return file_id
+        mock_repo.return_value.add_file.side_effect = mock_add_file
+        
+        # Mock get_all method
+        def mock_get_all():
+            return related_files.copy()
+        mock_repo.return_value.get_all.side_effect = mock_get_all
+        
+        # Mock remove_file method
+        def mock_remove_file(file_id):
+            if file_id in related_files:
+                return related_files.pop(file_id)
+            return None
+        mock_repo.return_value.remove_file.side_effect = mock_remove_file
+        
+        # Mock format_related_files method
+        def mock_format_related_files():
+            return [f"ID#{file_id} {filepath}" for file_id, filepath in sorted(related_files.items())]
+        mock_repo.return_value.format_related_files.side_effect = mock_format_related_files
+        
+        yield mock_repo
+
+
 def test_emit_key_facts_single_fact(reset_memory, mock_repository):
     """Test emitting a single key fact using emit_key_facts"""
     # Test with single fact
@@ -177,9 +233,6 @@ def test_emit_key_facts_single_fact(reset_memory, mock_repository):
 
 def test_get_memory_value_other_types(reset_memory):
     """Test get_memory_value remains compatible with other memory types"""
-    # Test with empty list
-    assert get_memory_value("plans") == ""
-
     # Test with non-existent key
     assert get_memory_value("nonexistent") == ""
     
@@ -263,7 +316,7 @@ def test_emit_key_facts_triggers_cleaner(reset_memory, mock_repository):
     """Test that emit_key_facts triggers the cleaner agent when there are more than 30 facts"""
     # Setup mock repository to return more than 30 facts
     facts = []
-    for i in range(31):
+    for i in range(51):
         facts.append(MagicMock(id=i, content=f"Test fact {i}", human_input_id=None))
     
     # Mock the get_all method to return more than 30 facts
@@ -407,7 +460,7 @@ def test_delete_key_snippets_empty(mock_log_work_event, reset_memory, mock_key_s
         mock_key_snippet_repository.return_value.delete.assert_not_called()
 
 
-def test_emit_related_files_basic(reset_memory, tmp_path):
+def test_emit_related_files_basic(reset_memory, mock_related_files_repository, tmp_path):
     """Test basic adding of files with ID tracking"""
     # Create test files
     test_file = tmp_path / "test.py"
@@ -420,23 +473,26 @@ def test_emit_related_files_basic(reset_memory, tmp_path):
     # Test adding single file
     result = emit_related_files.invoke({"files": [str(test_file)]})
     assert result == "Files noted."
-    assert _global_memory["related_files"][0] == str(test_file)
+    # Verify file was added using the repository
+    mock_related_files_repository.return_value.add_file.assert_called_with(str(test_file))
 
     # Test adding multiple files
     result = emit_related_files.invoke({"files": [str(main_file), str(utils_file)]})
     assert result == "Files noted."
-    # Verify both files exist in related_files
-    values = list(_global_memory["related_files"].values())
-    assert str(main_file) in values
-    assert str(utils_file) in values
+    # Verify both files were added
+    mock_related_files_repository.return_value.add_file.assert_any_call(str(main_file))
+    mock_related_files_repository.return_value.add_file.assert_any_call(str(utils_file))
 
 
-def test_get_related_files_empty(reset_memory):
+def test_get_related_files_empty(reset_memory, mock_related_files_repository):
     """Test getting related files when none added"""
+    # Mock empty format_related_files result
+    mock_related_files_repository.return_value.format_related_files.return_value = []
     assert get_related_files() == []
+    mock_related_files_repository.return_value.format_related_files.assert_called_once()
 
 
-def test_emit_related_files_duplicates(reset_memory, tmp_path):
+def test_emit_related_files_duplicates(reset_memory, mock_related_files_repository, tmp_path):
     """Test that duplicate files return existing IDs with proper formatting"""
     # Create test files
     test_file = tmp_path / "test.py"
@@ -446,46 +502,34 @@ def test_emit_related_files_duplicates(reset_memory, tmp_path):
     new_file = tmp_path / "new.py"
     new_file.write_text("# New file")
 
+    # Mock add_file to return consistent IDs
+    def mock_add_file(filepath):
+        if "test.py" in filepath:
+            return 0
+        elif "main.py" in filepath:
+            return 1
+        elif "new.py" in filepath:
+            return 2
+        return None
+    mock_related_files_repository.return_value.add_file.side_effect = mock_add_file
+
     # Add initial files
     result1 = emit_related_files.invoke({"files": [str(test_file), str(main_file)]})
     assert result1 == "Files noted."
-    _first_id = 0  # ID of test.py
 
     # Try adding duplicates
     result2 = emit_related_files.invoke({"files": [str(test_file)]})
     assert result2 == "Files noted."
-    assert len(_global_memory["related_files"]) == 2  # Count should not increase
 
     # Try mix of new and duplicate files
     result = emit_related_files.invoke({"files": [str(test_file), str(new_file)]})
     assert result == "Files noted."
-    assert len(_global_memory["related_files"]) == 3
+
+    # Verify calls to add_file - should be called for each file (even duplicates)
+    assert mock_related_files_repository.return_value.add_file.call_count == 5
 
 
-def test_related_files_id_tracking(reset_memory, tmp_path):
-    """Test ID assignment and counter functionality for related files"""
-    # Create test files
-    file1 = tmp_path / "file1.py"
-    file1.write_text("# File 1")
-    file2 = tmp_path / "file2.py"
-    file2.write_text("# File 2")
-
-    # Add first file
-    result = emit_related_files.invoke({"files": [str(file1)]})
-    assert result == "Files noted."
-    assert _global_memory["related_file_id_counter"] == 1
-
-    # Add second file
-    result = emit_related_files.invoke({"files": [str(file2)]})
-    assert result == "Files noted."
-    assert _global_memory["related_file_id_counter"] == 2
-
-    # Verify all files stored correctly
-    assert _global_memory["related_files"][0] == str(file1)
-    assert _global_memory["related_files"][1] == str(file2)
-
-
-def test_deregister_related_files(reset_memory, tmp_path):
+def test_deregister_related_files(reset_memory, mock_related_files_repository, tmp_path):
     """Test deleting related files"""
     # Create test files
     file1 = tmp_path / "file1.py"
@@ -495,276 +539,108 @@ def test_deregister_related_files(reset_memory, tmp_path):
     file3 = tmp_path / "file3.py"
     file3.write_text("# File 3")
 
-    # Add test files
-    emit_related_files.invoke({"files": [str(file1), str(file2), str(file3)]})
+    # Mock remove_file to return file paths for existing IDs
+    def mock_remove_file(file_id):
+        if file_id == 0:
+            return str(file1)
+        elif file_id == 1:
+            return str(file2)
+        elif file_id == 2:
+            return str(file3)
+        return None
+    mock_related_files_repository.return_value.remove_file.side_effect = mock_remove_file
 
     # Delete middle file
     result = deregister_related_files.invoke({"file_ids": [1]})
     assert result == "Files noted."
-    assert 1 not in _global_memory["related_files"]
-    assert len(_global_memory["related_files"]) == 2
+    mock_related_files_repository.return_value.remove_file.assert_called_with(1)
 
     # Delete multiple files including non-existent ID
     result = deregister_related_files.invoke({"file_ids": [0, 2, 999]})
     assert result == "Files noted."
-    assert len(_global_memory["related_files"]) == 0
-
-    # Counter should remain unchanged after deletions
-    assert _global_memory["related_file_id_counter"] == 3
+    mock_related_files_repository.return_value.remove_file.assert_any_call(0)
+    mock_related_files_repository.return_value.remove_file.assert_any_call(2)
+    mock_related_files_repository.return_value.remove_file.assert_any_call(999)
 
 
-def test_related_files_duplicates(reset_memory, tmp_path):
-    """Test duplicate file handling returns same ID"""
-    # Create test file
-    test_file = tmp_path / "test.py"
-    test_file.write_text("# Test file")
-
-    # Add initial file
-    result1 = emit_related_files.invoke({"files": [str(test_file)]})
-    assert result1 == "Files noted."
-
-    # Add same file again
-    result2 = emit_related_files.invoke({"files": [str(test_file)]})
-    assert result2 == "Files noted."
-
-    # Verify only one entry exists
-    assert len(_global_memory["related_files"]) == 1
-    assert _global_memory["related_file_id_counter"] == 1
-
-
-def test_emit_related_files_with_directory(reset_memory, tmp_path):
-    """Test that directories and non-existent paths are rejected while valid files are added"""
-    # Create test directory and file
-    test_dir = tmp_path / "test_dir"
-    test_dir.mkdir()
-    test_file = tmp_path / "test_file.txt"
-    test_file.write_text("test content")
-    nonexistent = tmp_path / "does_not_exist.txt"
-
-    # Try to emit directory, nonexistent path, and valid file
-    result = emit_related_files.invoke(
-        {"files": [str(test_dir), str(nonexistent), str(test_file)]}
-    )
-
-    # Verify result is the standard message
-    assert result == "Files noted."
-
-    # Verify directory and nonexistent not added but valid file was
-    assert len(_global_memory["related_files"]) == 1
-    values = list(_global_memory["related_files"].values())
-    assert str(test_file) in values
-    assert str(test_dir) not in values
-    assert str(nonexistent) not in values
-
-
-def test_related_files_formatting(reset_memory, tmp_path):
-    """Test related files output string formatting"""
-    # Create test files
-    file1 = tmp_path / "file1.py"
-    file1.write_text("# File 1")
-    file2 = tmp_path / "file2.py"
-    file2.write_text("# File 2")
-
-    # Add some files
-    emit_related_files.invoke({"files": [str(file1), str(file2)]})
-
-    # Get formatted output
-    output = get_memory_value("related_files")
-    # Expect just the IDs on separate lines
-    expected = "0\n1"
-    assert output == expected
-
-    # Test empty case
-    _global_memory["related_files"] = {}
-    assert get_memory_value("related_files") == ""
-
-
-def test_emit_related_files_path_normalization(reset_memory, tmp_path):
-    """Test that emit_related_files fails to detect duplicates with non-normalized paths"""
+def test_emit_related_files_path_normalization(reset_memory, mock_related_files_repository, tmp_path):
+    """Test that emit_related_files normalization works correctly"""
     # Create a test file
     test_file = tmp_path / "file.txt"
     test_file.write_text("test content")
 
     # Change to the temp directory so relative paths work
-    import os
-
     original_dir = os.getcwd()
     os.chdir(tmp_path)
 
     try:
-        # Add file with absolute path
+        # Set up mock to test path normalization
+        def mock_add_file(filepath):
+            # The repository normalizes paths before comparing
+            # This mock simulates that behavior
+            normalized_path = os.path.abspath(filepath)
+            if normalized_path == os.path.abspath("file.txt"):
+                return 0
+            return None
+        mock_related_files_repository.return_value.add_file.side_effect = mock_add_file
+
+        # Add file with relative path
         result1 = emit_related_files.invoke({"files": ["file.txt"]})
         assert result1 == "Files noted."
 
-        # Add same file with relative path - should get same ID due to path normalization
+        # Add same file with different relative path - should get same ID
         result2 = emit_related_files.invoke({"files": ["./file.txt"]})
         assert result2 == "Files noted."
 
-        # Verify only one normalized path entry exists
-        assert len(_global_memory["related_files"]) == 1
-        assert os.path.abspath("file.txt") in _global_memory["related_files"].values()
+        # Verify both calls to add_file were made
+        assert mock_related_files_repository.return_value.add_file.call_count == 2
     finally:
         # Restore original directory
         os.chdir(original_dir)
 
 
-@patch('ra_aid.agents.key_snippets_gc_agent.log_work_event')
-def test_key_snippets_integration(mock_log_work_event, reset_memory, mock_key_snippet_repository):
-    """Integration test for key snippets functionality"""
-    # Create test files
-    import tempfile
-    import os
-
-    with tempfile.TemporaryDirectory() as tmp_path:
-        file1 = os.path.join(tmp_path, "file1.py")
-        with open(file1, 'w') as f:
-            f.write("def func1():\n    pass")
-            
-        file2 = os.path.join(tmp_path, "file2.py")
-        with open(file2, 'w') as f:
-            f.write("def func2():\n    return True")
-            
-        file3 = os.path.join(tmp_path, "file3.py")
-        with open(file3, 'w') as f:
-            f.write("class TestClass:\n    pass")
-
-        # Initial snippets to add
-        snippets = [
-            {
-                "filepath": file1,
-                "line_number": 10,
-                "snippet": "def func1():\n    pass",
-                "description": "First function",
-            },
-            {
-                "filepath": file2,
-                "line_number": 20,
-                "snippet": "def func2():\n    return True",
-                "description": "Second function",
-            },
-            {
-                "filepath": file3,
-                "line_number": 30,
-                "snippet": "class TestClass:\n    pass",
-                "description": "Test class",
-            },
-        ]
-
-        # Add all snippets one by one
-        for i, snippet in enumerate(snippets):
-            result = emit_key_snippet.invoke({"snippet_info": snippet})
-            assert result == f"Snippet #{i} stored."
-        
-        # Reset mock to clear call history
-        mock_key_snippet_repository.reset_mock()
-
-        # Delete some but not all snippets (0 and 2)
-        with patch('ra_aid.agents.key_snippets_gc_agent.get_key_snippet_repository', mock_key_snippet_repository):
-            result = delete_key_snippets.invoke({"snippet_ids": [0, 2]})
-            assert result == "Snippets deleted."
-        
-        # Reset mock again
-        mock_key_snippet_repository.reset_mock()
-
-        # Add new snippet
-        file4 = os.path.join(tmp_path, "file4.py")
-        with open(file4, 'w') as f:
-            f.write("def func4():\n    return False")
-            
-        new_snippet = {
-            "filepath": file4,
-            "line_number": 40,
-            "snippet": "def func4():\n    return False",
-            "description": "Fourth function",
-        }
-        result = emit_key_snippet.invoke({"snippet_info": new_snippet})
-        assert result == "Snippet #3 stored."
-        
-        # Verify create was called with correct params
-        mock_key_snippet_repository.return_value.create.assert_called_with(
-            filepath=file4,
-            line_number=40,
-            snippet="def func4():\n    return False",
-            description="Fourth function",
-            human_input_id=ANY
-        )
-        
-        # Reset mock again
-        mock_key_snippet_repository.reset_mock()
-
-        # Delete remaining snippets
-        with patch('ra_aid.agents.key_snippets_gc_agent.get_key_snippet_repository', mock_key_snippet_repository):
-            result = delete_key_snippets.invoke({"snippet_ids": [1, 3]})
-            assert result == "Snippets deleted."
-
-
-def test_emit_related_files_binary_filtering(reset_memory, monkeypatch):
+@patch('ra_aid.tools.memory.is_binary_file')
+def test_emit_related_files_binary_filtering(mock_is_binary, reset_memory, mock_related_files_repository, tmp_path):
     """Test that binary files are filtered out when adding related files"""
-    import tempfile
-    import os
-    
-    with tempfile.TemporaryDirectory() as tmp_path:
-        # Create test text files
-        text_file1 = os.path.join(tmp_path, "text1.txt")
-        with open(text_file1, 'w') as f:
-            f.write("Text file 1 content")
-            
-        text_file2 = os.path.join(tmp_path, "text2.txt")
-        with open(text_file2, 'w') as f:
-            f.write("Text file 2 content")
+    # Create test files
+    text_file1 = tmp_path / "text1.txt"
+    text_file1.write_text("Text file 1 content")
+    text_file2 = tmp_path / "text2.txt"
+    text_file2.write_text("Text file 2 content")
+    binary_file1 = tmp_path / "binary1.bin"
+    binary_file1.write_text("Binary file 1 content")
+    binary_file2 = tmp_path / "binary2.bin"
+    binary_file2.write_text("Binary file 2 content")
 
-        # Create test "binary" files
-        binary_file1 = os.path.join(tmp_path, "binary1.bin")
-        with open(binary_file1, 'w') as f:
-            f.write("Binary file 1 content")
-            
-        binary_file2 = os.path.join(tmp_path, "binary2.bin")
-        with open(binary_file2, 'w') as f:
-            f.write("Binary file 2 content")
+    # Mock is_binary_file to identify our "binary" files
+    def mock_binary_check(filepath):
+        return ".bin" in str(filepath)
+    mock_is_binary.side_effect = mock_binary_check
 
-        # Mock the is_binary_file function to identify our "binary" files
-        def mock_is_binary_file(filepath):
-            return ".bin" in str(filepath)
+    # Call emit_related_files with mix of text and binary files
+    result = emit_related_files.invoke({
+        "files": [
+            str(text_file1),
+            str(binary_file1),
+            str(text_file2),
+            str(binary_file2),
+        ]
+    })
 
-        # Apply the mock
-        import ra_aid.tools.memory
-        monkeypatch.setattr(ra_aid.tools.memory, "is_binary_file", mock_is_binary_file)
+    # Verify the result message
+    assert "Files noted." in result
+    assert "Binary files skipped:" in result
 
-        # Call emit_related_files with mix of text and binary files
-        result = emit_related_files.invoke(
-            {
-                "files": [
-                    text_file1,
-                    binary_file1,
-                    text_file2,
-                    binary_file2,
-                ]
-            }
-        )
-
-        # Verify the result message mentions skipped binary files
-        assert "Files noted." in result
-        assert "Binary files skipped:" in result
-        assert binary_file1 in result
-        assert binary_file2 in result
-
-        # Verify only text files were added to related_files
-        assert len(_global_memory["related_files"]) == 2
-        file_values = list(_global_memory["related_files"].values())
-        assert text_file1 in file_values
-        assert text_file2 in file_values
-        assert binary_file1 not in file_values
-        assert binary_file2 not in file_values
-
-        # Verify counter is correct (only incremented for text files)
-        assert _global_memory["related_file_id_counter"] == 2
+    # Verify repository calls - should only call add_file for text files
+    # Binary files should be filtered out before reaching the repository
+    assert mock_related_files_repository.return_value.add_file.call_count == 2
+    mock_related_files_repository.return_value.add_file.assert_any_call(str(text_file1))
+    mock_related_files_repository.return_value.add_file.assert_any_call(str(text_file2))
 
 
-def test_is_binary_file_with_ascii(reset_memory, monkeypatch):
+def test_is_binary_file_with_ascii():
     """Test that ASCII files are correctly identified as text files"""
-    import os
     import tempfile
-    import ra_aid.tools.memory
 
     # Create a test ASCII file
     with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
@@ -772,32 +648,22 @@ def test_is_binary_file_with_ascii(reset_memory, monkeypatch):
         ascii_file_path = f.name
 
     try:
-        # Test with magic library if available
-        if ra_aid.tools.memory.magic:
-            # Test real implementation with ASCII file
-            is_binary = ra_aid.tools.memory.is_binary_file(ascii_file_path)
-            assert not is_binary, "ASCII file should not be identified as binary"
+        # Test real implementation with ASCII file
+        is_binary = is_binary_file(ascii_file_path)
+        assert not is_binary, "ASCII file should not be identified as binary"
 
         # Test fallback implementation
-        # Mock magic to be None to force fallback implementation
-        monkeypatch.setattr(ra_aid.tools.memory, "magic", None)
-
-        # Test fallback with ASCII file
-        is_binary = ra_aid.tools.memory.is_binary_file(ascii_file_path)
-        assert (
-            not is_binary
-        ), "ASCII file should not be identified as binary with fallback method"
+        is_binary_fallback = _is_binary_fallback(ascii_file_path)
+        assert not is_binary_fallback, "ASCII file should not be identified as binary with fallback method"
     finally:
         # Clean up
         if os.path.exists(ascii_file_path):
             os.unlink(ascii_file_path)
 
 
-def test_is_binary_file_with_null_bytes(reset_memory, monkeypatch):
+def test_is_binary_file_with_null_bytes():
     """Test that files with null bytes are correctly identified as binary"""
-    import os
     import tempfile
-    import ra_aid.tools.memory
 
     # Create a file with null bytes (binary content)
     binary_file = tempfile.NamedTemporaryFile(delete=False)
@@ -805,21 +671,13 @@ def test_is_binary_file_with_null_bytes(reset_memory, monkeypatch):
     binary_file.close()
 
     try:
-        # Test with magic library if available
-        if ra_aid.tools.memory.magic:
-            # Test real implementation with binary file
-            is_binary = ra_aid.tools.memory.is_binary_file(binary_file.name)
-            assert is_binary, "File with null bytes should be identified as binary"
+        # Test real implementation with binary file
+        is_binary = is_binary_file(binary_file.name)
+        assert is_binary, "File with null bytes should be identified as binary"
 
         # Test fallback implementation
-        # Mock magic to be None to force fallback implementation
-        monkeypatch.setattr(ra_aid.tools.memory, "magic", None)
-
-        # Test fallback with binary file
-        is_binary = ra_aid.tools.memory.is_binary_file(binary_file.name)
-        assert (
-            is_binary
-        ), "File with null bytes should be identified as binary with fallback method"
+        is_binary_fallback = _is_binary_fallback(binary_file.name)
+        assert is_binary_fallback, "File with null bytes should be identified as binary with fallback method"
     finally:
         # Clean up
         if os.path.exists(binary_file.name):
@@ -850,7 +708,7 @@ def test_python_file_detection():
         import magic
         if magic:
             # Only run this part of the test if magic is available
-            with patch('ra_aid.tools.memory.magic') as mock_magic:
+            with patch('ra_aid.utils.file_utils.magic') as mock_magic:
                 # Mock magic to simulate the behavior that causes the issue
                 mock_magic.from_file.side_effect = [
                     "text/x-python",  # First call with mime=True