From 5bd8c76a222e8021a34ee4740744cab9797d0d08 Mon Sep 17 00:00:00 2001
From: AI Christianson <ai.christianson@christianson.ai>
Date: Tue, 4 Mar 2025 21:01:08 -0500
Subject: [PATCH] config repository

---
 ra_aid/__main__.py                            |  59 +--
 ra_aid/agent_utils.py                         |  16 +-
 ra_aid/agents/key_facts_gc_agent.py           |   5 +-
 ra_aid/agents/key_snippets_gc_agent.py        |   5 +-
 ra_aid/agents/research_notes_gc_agent.py      |   5 +-
 .../repositories/config_repository.py         | 165 ++++++++
 ra_aid/tool_configs.py                        |  29 +-
 ra_aid/tools/agent.py                         |  12 +-
 ra_aid/tools/expert.py                        |   9 +-
 ra_aid/tools/human.py                         |   4 +-
 ra_aid/tools/programmer.py                    |  13 +-
 ra_aid/tools/shell.py                         |   7 +-
 tests/conftest.py                             |  15 +
 tests/ra_aid/test_agent_utils.py              |  91 +++--
 tests/ra_aid/test_info_query.py               |  36 +-
 tests/ra_aid/test_main.py                     | 382 +++++++++++-------
 tests/ra_aid/test_programmer.py               |  44 +-
 tests/ra_aid/tools/test_agent.py              |  29 ++
 tests/ra_aid/tools/test_shell.py              |  59 ++-
 19 files changed, 695 insertions(+), 290 deletions(-)
 create mode 100644 ra_aid/database/repositories/config_repository.py

diff --git a/ra_aid/__main__.py b/ra_aid/__main__.py
index d18c90a..3d02851 100644
--- a/ra_aid/__main__.py
+++ b/ra_aid/__main__.py
@@ -58,6 +58,10 @@ from ra_aid.database.repositories.related_files_repository import (
 from ra_aid.database.repositories.work_log_repository import (
     WorkLogRepositoryManager
 )
+from ra_aid.database.repositories.config_repository import (
+    ConfigRepositoryManager,
+    get_config_repository
+)
 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
@@ -77,7 +81,7 @@ from ra_aid.prompts.chat_prompts import CHAT_PROMPT
 from ra_aid.prompts.web_research_prompts import WEB_RESEARCH_PROMPT_SECTION_CHAT
 from ra_aid.tool_configs import get_chat_tools, set_modification_tools
 from ra_aid.tools.human import ask_human
-from ra_aid.tools.memory import _global_memory, get_memory_value
+from ra_aid.tools.memory import get_memory_value
 
 logger = get_logger(__name__)
 
@@ -338,7 +342,7 @@ implementation_memory = MemorySaver()
 
 def is_informational_query() -> bool:
     """Determine if the current query is informational based on config settings."""
-    return _global_memory.get("config", {}).get("research_only", False)
+    return get_config_repository().get("research_only", False)
 
 
 def is_stage_requested(stage: str) -> bool:
@@ -404,13 +408,17 @@ def main():
             except Exception as e:
                 logger.error(f"Database migration error: {str(e)}")
 
+            # Initialize empty config dictionary to be populated later
+            config = {}
+            
             # Initialize repositories with database connection
             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, \
                  RelatedFilesRepositoryManager() as related_files_repo, \
-                 WorkLogRepositoryManager() as work_log_repo:
+                 WorkLogRepositoryManager() as work_log_repo, \
+                 ConfigRepositoryManager(config) as config_repo:
                 # This initializes all repositories and makes them available via their respective get methods
                 logger.debug("Initialized KeyFactRepository")
                 logger.debug("Initialized KeySnippetRepository")
@@ -418,6 +426,7 @@ def main():
                 logger.debug("Initialized ResearchNoteRepository")
                 logger.debug("Initialized RelatedFilesRepository")
                 logger.debug("Initialized WorkLogRepository")
+                logger.debug("Initialized ConfigRepository")
 
                 # Check dependencies before proceeding
                 check_dependencies()
@@ -520,13 +529,13 @@ def main():
                         "limit_tokens": args.disable_limit_tokens,
                     }
 
-                    # Store config in global memory
-                    _global_memory["config"] = config
-                    _global_memory["config"]["provider"] = args.provider
-                    _global_memory["config"]["model"] = args.model
-                    _global_memory["config"]["expert_provider"] = args.expert_provider
-                    _global_memory["config"]["expert_model"] = args.expert_model
-                    _global_memory["config"]["temperature"] = args.temperature
+                    # Store config in repository
+                    config_repo.update(config)
+                    config_repo.set("provider", args.provider)
+                    config_repo.set("model", args.model)
+                    config_repo.set("expert_provider", args.expert_provider)
+                    config_repo.set("expert_model", args.expert_model)
+                    config_repo.set("temperature", args.temperature)
 
                     # Set modification tools based on use_aider flag
                     set_modification_tools(args.use_aider)
@@ -594,33 +603,27 @@ def main():
                     "test_cmd_timeout": args.test_cmd_timeout,
                 }
 
-                # Store config in global memory for access by is_informational_query
-                _global_memory["config"] = config
+                # Store config in repository
+                config_repo.update(config)
 
                 # Store base provider/model configuration
-                _global_memory["config"]["provider"] = args.provider
-                _global_memory["config"]["model"] = args.model
+                config_repo.set("provider", args.provider)
+                config_repo.set("model", args.model)
 
                 # Store expert provider/model (no fallback)
-                _global_memory["config"]["expert_provider"] = args.expert_provider
-                _global_memory["config"]["expert_model"] = args.expert_model
+                config_repo.set("expert_provider", args.expert_provider)
+                config_repo.set("expert_model", args.expert_model)
 
                 # Store planner config with fallback to base values
-                _global_memory["config"]["planner_provider"] = (
-                    args.planner_provider or args.provider
-                )
-                _global_memory["config"]["planner_model"] = args.planner_model or args.model
+                config_repo.set("planner_provider", args.planner_provider or args.provider)
+                config_repo.set("planner_model", args.planner_model or args.model)
 
                 # Store research config with fallback to base values
-                _global_memory["config"]["research_provider"] = (
-                    args.research_provider or args.provider
-                )
-                _global_memory["config"]["research_model"] = (
-                    args.research_model or args.model
-                )
+                config_repo.set("research_provider", args.research_provider or args.provider)
+                config_repo.set("research_model", args.research_model or args.model)
 
-                # Store temperature in global config
-                _global_memory["config"]["temperature"] = args.temperature
+                # Store temperature in config
+                config_repo.set("temperature", args.temperature)
 
                 # Set modification tools based on use_aider flag
                 set_modification_tools(args.use_aider)
diff --git a/ra_aid/agent_utils.py b/ra_aid/agent_utils.py
index 7ef9efa..3460acb 100644
--- a/ra_aid/agent_utils.py
+++ b/ra_aid/agent_utils.py
@@ -94,11 +94,11 @@ 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.model_formatters.research_notes_formatter import format_research_notes_dict
 from ra_aid.tools.memory import (
-    _global_memory,
     get_memory_value,
     get_related_files,
     log_work_event,
 )
+from ra_aid.database.repositories.config_repository import get_config_repository
 
 console = Console()
 
@@ -302,7 +302,7 @@ def create_agent(
     config['limit_tokens'] = False.
     """
     try:
-        config = _global_memory.get("config", {})
+        config = get_config_repository().get_all()
         max_input_tokens = (
             get_model_token_limit(config, agent_type) or DEFAULT_TOKEN_LIMIT
         )
@@ -319,7 +319,7 @@ def create_agent(
     except Exception as e:
         # Default to REACT agent if provider/model detection fails
         logger.warning(f"Failed to detect model type: {e}. Defaulting to REACT agent.")
-        config = _global_memory.get("config", {})
+        config = get_config_repository().get_all()
         max_input_tokens = get_model_token_limit(config, agent_type)
         agent_kwargs = build_agent_kwargs(checkpointer, config, max_input_tokens)
         return create_react_agent(model, tools, **agent_kwargs)
@@ -443,7 +443,7 @@ def run_research_agent(
         new_project_hints=NEW_PROJECT_HINTS if project_info.is_new else "",
     )
 
-    config = _global_memory.get("config", {}) if not config else config
+    config = get_config_repository().get_all() if not config else config
     recursion_limit = config.get("recursion_limit", DEFAULT_RECURSION_LIMIT)
     run_config = {
         "configurable": {"thread_id": thread_id},
@@ -575,7 +575,7 @@ def run_web_research_agent(
         related_files=related_files,
     )
 
-    config = _global_memory.get("config", {}) if not config else config
+    config = get_config_repository().get_all() if not config else config
 
     recursion_limit = config.get("recursion_limit", DEFAULT_RECURSION_LIMIT)
     run_config = {
@@ -709,7 +709,7 @@ def run_planning_agent(
         ),
     )
 
-    config = _global_memory.get("config", {}) if not config else config
+    config = get_config_repository().get_all() if not config else config
     recursion_limit = config.get("recursion_limit", DEFAULT_RECURSION_LIMIT)
     run_config = {
         "configurable": {"thread_id": thread_id},
@@ -824,7 +824,7 @@ def run_task_implementation_agent(
         expert_section=EXPERT_PROMPT_SECTION_IMPLEMENTATION if expert_enabled else "",
         human_section=(
             HUMAN_PROMPT_SECTION_IMPLEMENTATION
-            if _global_memory.get("config", {}).get("hil", False)
+            if get_config_repository().get("hil", False)
             else ""
         ),
         web_research_section=(
@@ -834,7 +834,7 @@ def run_task_implementation_agent(
         ),
     )
 
-    config = _global_memory.get("config", {}) if not config else config
+    config = get_config_repository().get_all() if not config else config
     recursion_limit = config.get("recursion_limit", DEFAULT_RECURSION_LIMIT)
     run_config = {
         "configurable": {"thread_id": thread_id},
diff --git a/ra_aid/agents/key_facts_gc_agent.py b/ra_aid/agents/key_facts_gc_agent.py
index e8eae2c..ece3c3d 100644
--- a/ra_aid/agents/key_facts_gc_agent.py
+++ b/ra_aid/agents/key_facts_gc_agent.py
@@ -19,9 +19,10 @@ logger = logging.getLogger(__name__)
 from ra_aid.agent_utils import create_agent, run_agent_with_retry
 from ra_aid.database.repositories.key_fact_repository import get_key_fact_repository
 from ra_aid.database.repositories.human_input_repository import get_human_input_repository
+from ra_aid.database.repositories.config_repository import get_config_repository
 from ra_aid.llm import initialize_llm
 from ra_aid.prompts.key_facts_gc_prompts import KEY_FACTS_GC_PROMPT
-from ra_aid.tools.memory import log_work_event, _global_memory
+from ra_aid.tools.memory import log_work_event
 
 
 console = Console()
@@ -149,7 +150,7 @@ def run_key_facts_gc_agent() -> None:
             formatted_facts = "\n".join([f"Fact #{k}: {v}" for k, v in facts_dict.items()])
             
             # Retrieve configuration
-            llm_config = _global_memory.get("config", {})
+            llm_config = get_config_repository().get_all()
 
             # Initialize the LLM model
             model = initialize_llm(
diff --git a/ra_aid/agents/key_snippets_gc_agent.py b/ra_aid/agents/key_snippets_gc_agent.py
index 120d6e6..72e4c38 100644
--- a/ra_aid/agents/key_snippets_gc_agent.py
+++ b/ra_aid/agents/key_snippets_gc_agent.py
@@ -16,9 +16,10 @@ from rich.panel import Panel
 from ra_aid.agent_utils import create_agent, run_agent_with_retry
 from ra_aid.database.repositories.key_snippet_repository import get_key_snippet_repository
 from ra_aid.database.repositories.human_input_repository import get_human_input_repository
+from ra_aid.database.repositories.config_repository import get_config_repository
 from ra_aid.llm import initialize_llm
 from ra_aid.prompts.key_snippets_gc_prompts import KEY_SNIPPETS_GC_PROMPT
-from ra_aid.tools.memory import log_work_event, _global_memory
+from ra_aid.tools.memory import log_work_event
 
 
 console = Console()
@@ -153,7 +154,7 @@ def run_key_snippets_gc_agent() -> None:
             ])
             
             # Retrieve configuration
-            llm_config = _global_memory.get("config", {})
+            llm_config = get_config_repository().get_all()
 
             # Initialize the LLM model
             model = initialize_llm(
diff --git a/ra_aid/agents/research_notes_gc_agent.py b/ra_aid/agents/research_notes_gc_agent.py
index d992137..9fe168e 100644
--- a/ra_aid/agents/research_notes_gc_agent.py
+++ b/ra_aid/agents/research_notes_gc_agent.py
@@ -19,9 +19,10 @@ logger = logging.getLogger(__name__)
 from ra_aid.agent_utils import create_agent, run_agent_with_retry
 from ra_aid.database.repositories.research_note_repository import get_research_note_repository
 from ra_aid.database.repositories.human_input_repository import get_human_input_repository
+from ra_aid.database.repositories.config_repository import get_config_repository
 from ra_aid.llm import initialize_llm
 from ra_aid.model_formatters.research_notes_formatter import format_research_note
-from ra_aid.tools.memory import log_work_event, _global_memory
+from ra_aid.tools.memory import log_work_event
 
 
 console = Console()
@@ -154,7 +155,7 @@ def run_research_notes_gc_agent(threshold: int = 30) -> None:
             formatted_notes = "\n".join([f"Note #{k}: {v}" for k, v in notes_dict.items()])
             
             # Retrieve configuration
-            llm_config = _global_memory.get("config", {})
+            llm_config = get_config_repository().get_all()
 
             # Initialize the LLM model
             model = initialize_llm(
diff --git a/ra_aid/database/repositories/config_repository.py b/ra_aid/database/repositories/config_repository.py
new file mode 100644
index 0000000..70be4cc
--- /dev/null
+++ b/ra_aid/database/repositories/config_repository.py
@@ -0,0 +1,165 @@
+"""Repository for managing configuration values."""
+
+import contextvars
+from typing import Any, Dict, Optional
+
+# Create contextvar to hold the ConfigRepository instance
+config_repo_var = contextvars.ContextVar("config_repo", default=None)
+
+
+class ConfigRepository:
+    """
+    Repository for managing configuration values in memory.
+    
+    This class provides methods to get, set, update, and retrieve all configuration values.
+    It does not require database models and operates entirely in memory.
+    """
+    
+    def __init__(self, initial_config: Optional[Dict[str, Any]] = None):
+        """
+        Initialize the ConfigRepository.
+        
+        Args:
+            initial_config: Optional dictionary of initial configuration values
+        """
+        self._config: Dict[str, Any] = {}
+        
+        # Initialize with default values from config.py
+        from ra_aid.config import (
+            DEFAULT_RECURSION_LIMIT,
+            DEFAULT_MAX_TEST_CMD_RETRIES,
+            DEFAULT_MAX_TOOL_FAILURES,
+            FALLBACK_TOOL_MODEL_LIMIT,
+            RETRY_FALLBACK_COUNT,
+            DEFAULT_TEST_CMD_TIMEOUT,
+            VALID_PROVIDERS,
+        )
+        
+        self._config = {
+            "recursion_limit": DEFAULT_RECURSION_LIMIT,
+            "max_test_cmd_retries": DEFAULT_MAX_TEST_CMD_RETRIES,
+            "max_tool_failures": DEFAULT_MAX_TOOL_FAILURES,
+            "fallback_tool_model_limit": FALLBACK_TOOL_MODEL_LIMIT,
+            "retry_fallback_count": RETRY_FALLBACK_COUNT,
+            "test_cmd_timeout": DEFAULT_TEST_CMD_TIMEOUT,
+            "valid_providers": VALID_PROVIDERS,
+        }
+        
+        # Update with any provided initial configuration
+        if initial_config:
+            self._config.update(initial_config)
+    
+    def get(self, key: str, default: Any = None) -> Any:
+        """
+        Get a configuration value by key.
+        
+        Args:
+            key: Configuration key to retrieve
+            default: Default value to return if key is not found
+            
+        Returns:
+            The configuration value or default if not found
+        """
+        return self._config.get(key, default)
+    
+    def set(self, key: str, value: Any) -> None:
+        """
+        Set a configuration value by key.
+        
+        Args:
+            key: Configuration key to set
+            value: Value to set for the key
+        """
+        self._config[key] = value
+    
+    def update(self, config_dict: Dict[str, Any]) -> None:
+        """
+        Update multiple configuration values at once.
+        
+        Args:
+            config_dict: Dictionary of configuration key-value pairs to update
+        """
+        self._config.update(config_dict)
+    
+    def get_all(self) -> Dict[str, Any]:
+        """
+        Get all configuration values.
+        
+        Returns:
+            Dictionary containing all configuration values
+        """
+        return self._config.copy()
+
+
+class ConfigRepositoryManager:
+    """
+    Context manager for ConfigRepository.
+    
+    This class provides a context manager interface for ConfigRepository,
+    using the contextvars approach for thread safety.
+    
+    Example:
+        with ConfigRepositoryManager() as repo:
+            # Use the repository
+            value = repo.get("key")
+            repo.set("key", new_value)
+    """
+    
+    def __init__(self, initial_config: Optional[Dict[str, Any]] = None):
+        """
+        Initialize the ConfigRepositoryManager.
+        
+        Args:
+            initial_config: Optional dictionary of initial configuration values
+        """
+        self.initial_config = initial_config
+        
+    def __enter__(self) -> 'ConfigRepository':
+        """
+        Initialize the ConfigRepository and return it.
+        
+        Returns:
+            ConfigRepository: The initialized repository
+        """
+        repo = ConfigRepository(self.initial_config)
+        config_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
+        config_repo_var.set(None)
+        
+        # Don't suppress exceptions
+        return False
+
+
+def get_config_repository() -> ConfigRepository:
+    """
+    Get the current ConfigRepository instance.
+    
+    Returns:
+        ConfigRepository: The current repository instance
+        
+    Raises:
+        RuntimeError: If no repository is set in the current context
+    """
+    repo = config_repo_var.get()
+    if repo is None:
+        raise RuntimeError(
+            "ConfigRepository not initialized in current context. "
+            "Make sure to use ConfigRepositoryManager."
+        )
+    return repo
\ No newline at end of file
diff --git a/ra_aid/tool_configs.py b/ra_aid/tool_configs.py
index 0de5553..6eba30e 100644
--- a/ra_aid/tool_configs.py
+++ b/ra_aid/tool_configs.py
@@ -27,6 +27,7 @@ from ra_aid.tools.agent import (
     request_web_research,
 )
 from ra_aid.tools.memory import plan_implementation_completed
+from ra_aid.database.repositories.config_repository import get_config_repository
 
 
 def set_modification_tools(use_aider=False):
@@ -98,13 +99,11 @@ def get_all_tools() -> list[BaseTool]:
 
 
 # Define constant tool groups
-# Get config from global memory for use_aider value
+# Get config from repository for use_aider value
 _config = {}
 try:
-    from ra_aid.tools.memory import _global_memory
-
-    _config = _global_memory.get("config", {})
-except ImportError:
+    _config = get_config_repository().get_all()
+except (ImportError, RuntimeError):
     pass
 
 READ_ONLY_TOOLS = get_read_only_tools(use_aider=_config.get("use_aider", False))
@@ -139,10 +138,8 @@ def get_research_tools(
     # Get config for use_aider value
     use_aider = False
     try:
-        from ra_aid.tools.memory import _global_memory
-
-        use_aider = _global_memory.get("config", {}).get("use_aider", False)
-    except ImportError:
+        use_aider = get_config_repository().get("use_aider", False)
+    except (ImportError, RuntimeError):
         pass
 
     # Start with read-only tools
@@ -180,10 +177,8 @@ def get_planning_tools(
     # Get config for use_aider value
     use_aider = False
     try:
-        from ra_aid.tools.memory import _global_memory
-
-        use_aider = _global_memory.get("config", {}).get("use_aider", False)
-    except ImportError:
+        use_aider = get_config_repository().get("use_aider", False)
+    except (ImportError, RuntimeError):
         pass
 
     # Start with read-only tools
@@ -219,10 +214,8 @@ def get_implementation_tools(
     # Get config for use_aider value
     use_aider = False
     try:
-        from ra_aid.tools.memory import _global_memory
-
-        use_aider = _global_memory.get("config", {}).get("use_aider", False)
-    except ImportError:
+        use_aider = get_config_repository().get("use_aider", False)
+    except (ImportError, RuntimeError):
         pass
 
     # Start with read-only tools
@@ -285,4 +278,4 @@ def get_chat_tools(expert_enabled: bool = True, web_research_enabled: bool = Fal
     if web_research_enabled:
         tools.append(request_web_research)
 
-    return tools
+    return tools
\ No newline at end of file
diff --git a/ra_aid/tools/agent.py b/ra_aid/tools/agent.py
index a87841f..7e32afb 100644
--- a/ra_aid/tools/agent.py
+++ b/ra_aid/tools/agent.py
@@ -18,13 +18,13 @@ 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.config_repository import get_config_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
 from ra_aid.model_formatters.key_snippets_formatter import format_key_snippets_dict
 from ra_aid.model_formatters.research_notes_formatter import format_research_notes_dict
-from ra_aid.tools.memory import _global_memory
 
 from ..console import print_task_header
 from ..llm import initialize_llm
@@ -52,7 +52,7 @@ def request_research(query: str) -> ResearchResult:
         query: The research question or project description
     """
     # Initialize model from config
-    config = _global_memory.get("config", {})
+    config = get_config_repository().get_all()
     model = initialize_llm(
         config.get("provider", "anthropic"),
         config.get("model", "claude-3-7-sonnet-20250219"),
@@ -165,7 +165,7 @@ def request_web_research(query: str) -> ResearchResult:
         query: The research question or project description
     """
     # Initialize model from config
-    config = _global_memory.get("config", {})
+    config = get_config_repository().get_all()
     model = initialize_llm(
         config.get("provider", "anthropic"),
         config.get("model", "claude-3-7-sonnet-20250219"),
@@ -246,7 +246,7 @@ def request_research_and_implementation(query: str) -> Dict[str, Any]:
         query: The research question or project description
     """
     # Initialize model from config
-    config = _global_memory.get("config", {})
+    config = get_config_repository().get_all()
     model = initialize_llm(
         config.get("provider", "anthropic"),
         config.get("model", "claude-3-7-sonnet-20250219"),
@@ -335,7 +335,7 @@ def request_task_implementation(task_spec: str) -> str:
         task_spec: REQUIRED The full task specification (markdown format, typically one part of the overall plan)
     """
     # Initialize model from config
-    config = _global_memory.get("config", {})
+    config = get_config_repository().get_all()
     model = initialize_llm(
         config.get("provider", "anthropic"),
         config.get("model", "claude-3-5-sonnet-20241022"),
@@ -474,7 +474,7 @@ def request_implementation(task_spec: str) -> str:
         task_spec: The task specification to plan implementation for
     """
     # Initialize model from config
-    config = _global_memory.get("config", {})
+    config = get_config_repository().get_all()
     model = initialize_llm(
         config.get("provider", "anthropic"),
         config.get("model", "claude-3-5-sonnet-20241022"),
diff --git a/ra_aid/tools/expert.py b/ra_aid/tools/expert.py
index 0cfc0f4..3b563d6 100644
--- a/ra_aid/tools/expert.py
+++ b/ra_aid/tools/expert.py
@@ -13,11 +13,12 @@ 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 ..database.repositories.config_repository import get_config_repository
 from ..llm import initialize_expert_llm
 from ..model_formatters import format_key_facts_dict
 from ..model_formatters.key_snippets_formatter import format_key_snippets_dict
 from ..model_formatters.research_notes_formatter import format_research_notes_dict
-from .memory import _global_memory, get_memory_value
+from .memory import get_memory_value
 
 console = Console()
 _model = None
@@ -27,9 +28,9 @@ def get_model():
     global _model
     try:
         if _model is None:
-            config = _global_memory["config"]
-            provider = config.get("expert_provider") or config.get("provider")
-            model = config.get("expert_model") or config.get("model")
+            config_repo = get_config_repository()
+            provider = config_repo.get("expert_provider") or config_repo.get("provider")
+            model = config_repo.get("expert_model") or config_repo.get("model")
             _model = initialize_expert_llm(provider, model)
     except Exception as e:
         _model = None
diff --git a/ra_aid/tools/human.py b/ra_aid/tools/human.py
index dc77937..ec275c3 100644
--- a/ra_aid/tools/human.py
+++ b/ra_aid/tools/human.py
@@ -58,10 +58,10 @@ def ask_human(question: str) -> str:
     # Record human response in database
     try:
         from ra_aid.database.repositories.human_input_repository import get_human_input_repository
-        from ra_aid.tools.memory import _global_memory
+        from ra_aid.database.repositories.config_repository import get_config_repository
         
         # Determine the source based on context
-        config = _global_memory.get("config", {})
+        config = get_config_repository().get_all()
         # If chat_mode is enabled, use 'chat', otherwise determine if hil mode is active
         if config.get("chat_mode", False):
             source = "chat"
diff --git a/ra_aid/tools/programmer.py b/ra_aid/tools/programmer.py
index 5b6788b..1a5d99c 100644
--- a/ra_aid/tools/programmer.py
+++ b/ra_aid/tools/programmer.py
@@ -13,7 +13,8 @@ from ra_aid.logging_config import get_logger
 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.tools.memory import log_work_event
+from ra_aid.database.repositories.config_repository import get_config_repository
 from ra_aid.database.repositories.related_files_repository import get_related_files_repository
 
 console = Console()
@@ -107,8 +108,9 @@ def run_programming_task(
     )
 
     # Add config file if specified
-    if "config" in _global_memory and _global_memory["config"].get("aider_config"):
-        command.extend(["--config", _global_memory["config"]["aider_config"]])
+    config = get_config_repository().get_all()
+    if config.get("aider_config"):
+        command.extend(["--config", config["aider_config"]])
 
     # if environment variable AIDER_FLAGS exists then parse
     if "AIDER_FLAGS" in os.environ:
@@ -147,8 +149,9 @@ def run_programming_task(
         # Run the command interactively
         print()
         # Get provider/model specific latency coefficient
-        provider = _global_memory.get("config", {}).get("provider", "")
-        model = _global_memory.get("config", {}).get("model", "")
+        config = get_config_repository().get_all()
+        provider = config.get("provider", "")
+        model = config.get("model", "")
         latency = (
             models_params.get(provider, {})
             .get(model, {})
diff --git a/ra_aid/tools/shell.py b/ra_aid/tools/shell.py
index 48b6247..21733db 100644
--- a/ra_aid/tools/shell.py
+++ b/ra_aid/tools/shell.py
@@ -9,6 +9,7 @@ from ra_aid.console.cowboy_messages import get_cowboy_message
 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.config_repository import get_config_repository
 
 console = Console()
 
@@ -46,7 +47,7 @@ def run_shell_command(
     4. Add flags e.g. git --no-pager in order to reduce interaction required by the human.
     """
     # Check if we need approval
-    cowboy_mode = _global_memory.get("config", {}).get("cowboy_mode", False)
+    cowboy_mode = get_config_repository().get("cowboy_mode", False)
 
     if cowboy_mode:
         console.print("")
@@ -74,7 +75,7 @@ def run_shell_command(
                 "success": False,
             }
         elif response == "c":
-            _global_memory["config"]["cowboy_mode"] = True
+            get_config_repository().set("cowboy_mode", True)
             console.print("")
             console.print(" " + get_cowboy_message())
             console.print("")
@@ -96,4 +97,4 @@ def run_shell_command(
     except Exception as e:
         print()
         console.print(Panel(str(e), title="❌ Error", border_style="red"))
-        return {"output": str(e), "return_code": 1, "success": False}
+        return {"output": str(e), "return_code": 1, "success": False}
\ No newline at end of file
diff --git a/tests/conftest.py b/tests/conftest.py
index 08fbadb..76c4524 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -7,10 +7,25 @@ ensuring consistent test environments and proper isolation.
 
 import os
 from pathlib import Path
+from unittest.mock import MagicMock
 
 import pytest
 
 
+@pytest.fixture()
+def mock_config_repository():
+    """Mock the config repository."""
+    from ra_aid.database.repositories.config_repository import get_config_repository
+
+    repo = MagicMock()
+    # Default config values
+    config_values = {"recursion_limit": 2}
+    repo.get_all.return_value = config_values
+    repo.get.side_effect = lambda key, default=None: config_values.get(key, default)
+    get_config_repository.return_value = repo
+    yield repo
+
+
 @pytest.fixture(autouse=True)
 def isolated_db_environment(tmp_path, monkeypatch):
     """
diff --git a/tests/ra_aid/test_agent_utils.py b/tests/ra_aid/test_agent_utils.py
index 591c0db..3927321 100644
--- a/tests/ra_aid/test_agent_utils.py
+++ b/tests/ra_aid/test_agent_utils.py
@@ -1,7 +1,7 @@
 """Unit tests for agent_utils.py."""
 
 from typing import Any, Dict, Literal
-from unittest.mock import Mock, patch
+from unittest.mock import Mock, patch, MagicMock
 
 import litellm
 import pytest
@@ -19,6 +19,7 @@ from ra_aid.agent_utils import (
     state_modifier,
 )
 from ra_aid.models_params import DEFAULT_TOKEN_LIMIT, models_params
+from ra_aid.database.repositories.config_repository import ConfigRepositoryManager, get_config_repository, config_repo_var
 
 
 @pytest.fixture
@@ -29,40 +30,70 @@ def mock_model():
 
 
 @pytest.fixture
-def mock_memory():
-    """Fixture providing a mock global memory store."""
-    with patch("ra_aid.agent_utils._global_memory") as mock_mem:
-        mock_mem.get.return_value = {}
-        yield mock_mem
+def mock_config_repository():
+    """Mock the ConfigRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.config_repository.config_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate config
+        config = {}
+        
+        # Setup get method to return config values
+        def get_config(key, default=None):
+            return config.get(key, default)
+        mock_repo.get.side_effect = get_config
+        
+        # Setup get_all method to return all config values
+        mock_repo.get_all.return_value = config
+        
+        # Setup set method to update config values
+        def set_config(key, value):
+            config[key] = value
+        mock_repo.set.side_effect = set_config
+        
+        # Setup update method to update multiple config values
+        def update_config(update_dict):
+            config.update(update_dict)
+        mock_repo.update.side_effect = update_config
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        yield mock_repo
 
 
-def test_get_model_token_limit_anthropic(mock_memory):
+def test_get_model_token_limit_anthropic(mock_config_repository):
     """Test get_model_token_limit with Anthropic model."""
     config = {"provider": "anthropic", "model": "claude2"}
+    mock_config_repository.update(config)
 
     token_limit = get_model_token_limit(config, "default")
     assert token_limit == models_params["anthropic"]["claude2"]["token_limit"]
 
 
-def test_get_model_token_limit_openai(mock_memory):
+def test_get_model_token_limit_openai(mock_config_repository):
     """Test get_model_token_limit with OpenAI model."""
     config = {"provider": "openai", "model": "gpt-4"}
+    mock_config_repository.update(config)
 
     token_limit = get_model_token_limit(config, "default")
     assert token_limit == models_params["openai"]["gpt-4"]["token_limit"]
 
 
-def test_get_model_token_limit_unknown(mock_memory):
+def test_get_model_token_limit_unknown(mock_config_repository):
     """Test get_model_token_limit with unknown provider/model."""
     config = {"provider": "unknown", "model": "unknown-model"}
+    mock_config_repository.update(config)
 
     token_limit = get_model_token_limit(config, "default")
     assert token_limit is None
 
 
-def test_get_model_token_limit_missing_config(mock_memory):
+def test_get_model_token_limit_missing_config(mock_config_repository):
     """Test get_model_token_limit with missing configuration."""
     config = {}
+    mock_config_repository.update(config)
 
     token_limit = get_model_token_limit(config, "default")
     assert token_limit is None
@@ -108,9 +139,9 @@ def test_get_model_token_limit_unexpected_error():
     assert token_limit is None
 
 
-def test_create_agent_anthropic(mock_model, mock_memory):
+def test_create_agent_anthropic(mock_model, mock_config_repository):
     """Test create_agent with Anthropic Claude model."""
-    mock_memory.get.return_value = {"provider": "anthropic", "model": "claude-2"}
+    mock_config_repository.update({"provider": "anthropic", "model": "claude-2"})
 
     with patch("ra_aid.agent_utils.create_react_agent") as mock_react:
         mock_react.return_value = "react_agent"
@@ -125,9 +156,9 @@ def test_create_agent_anthropic(mock_model, mock_memory):
         )
 
 
-def test_create_agent_openai(mock_model, mock_memory):
+def test_create_agent_openai(mock_model, mock_config_repository):
     """Test create_agent with OpenAI model."""
-    mock_memory.get.return_value = {"provider": "openai", "model": "gpt-4"}
+    mock_config_repository.update({"provider": "openai", "model": "gpt-4"})
 
     with patch("ra_aid.agent_utils.CiaynAgent") as mock_ciayn:
         mock_ciayn.return_value = "ciayn_agent"
@@ -142,9 +173,9 @@ def test_create_agent_openai(mock_model, mock_memory):
         )
 
 
-def test_create_agent_no_token_limit(mock_model, mock_memory):
+def test_create_agent_no_token_limit(mock_model, mock_config_repository):
     """Test create_agent when no token limit is found."""
-    mock_memory.get.return_value = {"provider": "unknown", "model": "unknown-model"}
+    mock_config_repository.update({"provider": "unknown", "model": "unknown-model"})
 
     with patch("ra_aid.agent_utils.CiaynAgent") as mock_ciayn:
         mock_ciayn.return_value = "ciayn_agent"
@@ -159,9 +190,9 @@ def test_create_agent_no_token_limit(mock_model, mock_memory):
         )
 
 
-def test_create_agent_missing_config(mock_model, mock_memory):
+def test_create_agent_missing_config(mock_model, mock_config_repository):
     """Test create_agent with missing configuration."""
-    mock_memory.get.return_value = {"provider": "openai"}
+    mock_config_repository.update({"provider": "openai"})
 
     with patch("ra_aid.agent_utils.CiaynAgent") as mock_ciayn:
         mock_ciayn.return_value = "ciayn_agent"
@@ -205,9 +236,9 @@ def test_state_modifier(mock_messages):
         assert result[-1] == mock_messages[-1]
 
 
-def test_create_agent_with_checkpointer(mock_model, mock_memory):
+def test_create_agent_with_checkpointer(mock_model, mock_config_repository):
     """Test create_agent with checkpointer argument."""
-    mock_memory.get.return_value = {"provider": "openai", "model": "gpt-4"}
+    mock_config_repository.update({"provider": "openai", "model": "gpt-4"})
     mock_checkpointer = Mock()
 
     with patch("ra_aid.agent_utils.CiaynAgent") as mock_ciayn:
@@ -223,13 +254,13 @@ def test_create_agent_with_checkpointer(mock_model, mock_memory):
         )
 
 
-def test_create_agent_anthropic_token_limiting_enabled(mock_model, mock_memory):
+def test_create_agent_anthropic_token_limiting_enabled(mock_model, mock_config_repository):
     """Test create_agent sets up token limiting for Claude models when enabled."""
-    mock_memory.get.return_value = {
+    mock_config_repository.update({
         "provider": "anthropic",
         "model": "claude-2",
         "limit_tokens": True,
-    }
+    })
 
     with (
         patch("ra_aid.agent_utils.create_react_agent") as mock_react,
@@ -246,13 +277,13 @@ def test_create_agent_anthropic_token_limiting_enabled(mock_model, mock_memory):
         assert callable(args[1]["state_modifier"])
 
 
-def test_create_agent_anthropic_token_limiting_disabled(mock_model, mock_memory):
+def test_create_agent_anthropic_token_limiting_disabled(mock_model, mock_config_repository):
     """Test create_agent doesn't set up token limiting for Claude models when disabled."""
-    mock_memory.get.return_value = {
+    mock_config_repository.update({
         "provider": "anthropic",
         "model": "claude-2",
         "limit_tokens": False,
-    }
+    })
 
     with (
         patch("ra_aid.agent_utils.create_react_agent") as mock_react,
@@ -267,7 +298,7 @@ def test_create_agent_anthropic_token_limiting_disabled(mock_model, mock_memory)
         mock_react.assert_called_once_with(mock_model, [], version="v2")
 
 
-def test_get_model_token_limit_research(mock_memory):
+def test_get_model_token_limit_research(mock_config_repository):
     """Test get_model_token_limit with research provider and model."""
     config = {
         "provider": "openai",
@@ -275,13 +306,15 @@ def test_get_model_token_limit_research(mock_memory):
         "research_provider": "anthropic",
         "research_model": "claude-2",
     }
+    mock_config_repository.update(config)
+    
     with patch("ra_aid.agent_utils.get_model_info") as mock_get_info:
         mock_get_info.return_value = {"max_input_tokens": 150000}
         token_limit = get_model_token_limit(config, "research")
         assert token_limit == 150000
 
 
-def test_get_model_token_limit_planner(mock_memory):
+def test_get_model_token_limit_planner(mock_config_repository):
     """Test get_model_token_limit with planner provider and model."""
     config = {
         "provider": "openai",
@@ -289,6 +322,8 @@ def test_get_model_token_limit_planner(mock_memory):
         "planner_provider": "deepseek",
         "planner_model": "dsm-1",
     }
+    mock_config_repository.update(config)
+    
     with patch("ra_aid.agent_utils.get_model_info") as mock_get_info:
         mock_get_info.return_value = {"max_input_tokens": 120000}
         token_limit = get_model_token_limit(config, "planner")
diff --git a/tests/ra_aid/test_info_query.py b/tests/ra_aid/test_info_query.py
index d54f443..c8b8ef2 100644
--- a/tests/ra_aid/test_info_query.py
+++ b/tests/ra_aid/test_info_query.py
@@ -1,41 +1,35 @@
 """Tests for the is_informational_query and is_stage_requested functions."""
 
+import pytest
+
 from ra_aid.__main__ import is_informational_query, is_stage_requested
-from ra_aid.tools.memory import _global_memory
+from ra_aid.database.repositories.config_repository import ConfigRepositoryManager
 
 
-def test_is_informational_query():
+@pytest.fixture
+def config_repo():
+    """Fixture for config repository."""
+    with ConfigRepositoryManager() as repo:
+        yield repo
+
+
+def test_is_informational_query(config_repo):
     """Test that is_informational_query only depends on research_only config setting."""
-    # Clear global memory to ensure clean state
-    _global_memory.clear()
-    
     # When research_only is True, should return True
-    _global_memory["config"] = {"research_only": True}
+    config_repo.set("research_only", True)
     assert is_informational_query() is True
     
     # When research_only is False, should return False
-    _global_memory["config"] = {"research_only": False}
+    config_repo.set("research_only", False)
     assert is_informational_query() is False
     
     # When config is empty, should return False (default)
-    _global_memory.clear()
-    _global_memory["config"] = {}
-    assert is_informational_query() is False
-    
-    # When global memory is empty, should return False (default)
-    _global_memory.clear()
+    config_repo.update({})
     assert is_informational_query() is False
 
 
 def test_is_stage_requested():
     """Test that is_stage_requested always returns False now."""
-    # Clear global memory to ensure clean state
-    _global_memory.clear()
-    
     # Should always return False regardless of input
     assert is_stage_requested("implementation") is False
-    assert is_stage_requested("anything_else") is False
-    
-    # Even if we set implementation_requested in global memory
-    _global_memory["implementation_requested"] = True
-    assert is_stage_requested("implementation") is False
\ No newline at end of file
+    assert is_stage_requested("anything_else") is False
\ No newline at end of file
diff --git a/tests/ra_aid/test_main.py b/tests/ra_aid/test_main.py
index 2787b8f..e7a1846 100644
--- a/tests/ra_aid/test_main.py
+++ b/tests/ra_aid/test_main.py
@@ -7,14 +7,50 @@ from ra_aid.__main__ import parse_arguments
 from ra_aid.config import DEFAULT_RECURSION_LIMIT
 from ra_aid.tools.memory import _global_memory
 from ra_aid.database.repositories.work_log_repository import WorkLogEntry
+from ra_aid.database.repositories.config_repository import ConfigRepositoryManager, get_config_repository
+
+
+@pytest.fixture(autouse=True)
+def mock_config_repository():
+    """Mock the ConfigRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.config_repository.config_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate config
+        config = {}
+        
+        # Setup get method to return config values
+        def get_config(key, default=None):
+            return config.get(key, default)
+        mock_repo.get.side_effect = get_config
+        
+        # Setup set method to update config values
+        def set_config(key, value):
+            config[key] = value
+        mock_repo.set.side_effect = set_config
+        
+        # Setup update method to update multiple config values
+        def update_config(config_dict):
+            config.update(config_dict)
+        mock_repo.update.side_effect = update_config
+        
+        # Setup get_all method to return the config dict
+        def get_all_config():
+            return config.copy()
+        mock_repo.get_all.side_effect = get_all_config
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        yield mock_repo
 
 
 @pytest.fixture
 def mock_dependencies(monkeypatch):
     """Mock all dependencies needed for main()."""
-    # Initialize global memory with necessary keys to prevent KeyError
+    # Initialize global memory 
     _global_memory.clear()
-    _global_memory["config"] = {}
     
     # Mock dependencies that interact with external systems
     monkeypatch.setattr("ra_aid.__main__.check_dependencies", lambda: None)
@@ -26,10 +62,9 @@ def mock_dependencies(monkeypatch):
     
     # Mock LLM initialization
     def mock_config_update(*args, **kwargs):
-        config = _global_memory.get("config", {})
+        config_repo = get_config_repository()
         if kwargs.get("temperature"):
-            config["temperature"] = kwargs["temperature"]
-        _global_memory["config"] = config
+            config_repo.set("temperature", kwargs["temperature"])
         return None
 
     monkeypatch.setattr("ra_aid.__main__.initialize_llm", mock_config_update)
@@ -107,26 +142,52 @@ def mock_work_log_repository():
         yield mock_repo
 
 
-def test_recursion_limit_in_global_config(mock_dependencies):
+def test_recursion_limit_in_global_config(mock_dependencies, mock_config_repository):
     """Test that recursion limit is correctly set in global config."""
     import sys
     from unittest.mock import patch
 
     from ra_aid.__main__ import main
 
-    _global_memory.clear()
+    # Clear the mock repository before each test
+    mock_config_repository.update.reset_mock()
+    
+    # For testing, we need to patch ConfigRepositoryManager.__enter__ to return our mock
+    with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__', return_value=mock_config_repository):
+        # Test default recursion limit
+        with patch.object(sys, "argv", ["ra-aid", "-m", "test message"]):
+            main()
+            # Check that the recursion_limit value was included in the update call
+            mock_config_repository.update.assert_called()
+            # Get the call arguments
+            call_args = mock_config_repository.update.call_args_list
+            # Find the call that includes recursion_limit
+            recursion_limit_found = False
+            for args, _ in call_args:
+                config_dict = args[0]
+                if "recursion_limit" in config_dict and config_dict["recursion_limit"] == DEFAULT_RECURSION_LIMIT:
+                    recursion_limit_found = True
+                    break
+            assert recursion_limit_found, f"recursion_limit not found in update calls: {call_args}"
 
-    with patch.object(sys, "argv", ["ra-aid", "-m", "test message"]):
-        main()
-        assert _global_memory["config"]["recursion_limit"] == DEFAULT_RECURSION_LIMIT
-
-    _global_memory.clear()
-
-    with patch.object(
-        sys, "argv", ["ra-aid", "-m", "test message", "--recursion-limit", "50"]
-    ):
-        main()
-        assert _global_memory["config"]["recursion_limit"] == 50
+        # Reset mock to clear call history
+        mock_config_repository.update.reset_mock()
+        
+        # Test custom recursion limit
+        with patch.object(sys, "argv", ["ra-aid", "-m", "test message", "--recursion-limit", "50"]):
+            main()
+            # Check that the recursion_limit value was included in the update call
+            mock_config_repository.update.assert_called()
+            # Get the call arguments
+            call_args = mock_config_repository.update.call_args_list
+            # Find the call that includes recursion_limit with value 50
+            recursion_limit_found = False
+            for args, _ in call_args:
+                config_dict = args[0]
+                if "recursion_limit" in config_dict and config_dict["recursion_limit"] == 50:
+                    recursion_limit_found = True
+                    break
+            assert recursion_limit_found, f"recursion_limit=50 not found in update calls: {call_args}"
 
 
 def test_negative_recursion_limit():
@@ -141,70 +202,83 @@ def test_zero_recursion_limit():
         parse_arguments(["-m", "test message", "--recursion-limit", "0"])
 
 
-def test_config_settings(mock_dependencies):
+def test_config_settings(mock_dependencies, mock_config_repository):
     """Test that various settings are correctly applied in global config."""
     import sys
     from unittest.mock import patch
 
     from ra_aid.__main__ import main
-
-    _global_memory.clear()
-
-    with patch.object(
-        sys,
-        "argv",
-        [
-            "ra-aid",
-            "-m",
-            "test message",
-            "--cowboy-mode",
-            "--research-only",
-            "--provider",
-            "anthropic",
-            "--model",
-            "claude-3-7-sonnet-20250219",
-            "--expert-provider",
-            "openai",
-            "--expert-model",
-            "gpt-4",
-            "--temperature",
-            "0.7",
-            "--disable-limit-tokens",
-        ],
-    ):
-        main()
-        config = _global_memory["config"]
-        assert config["cowboy_mode"] is True
-        assert config["research_only"] is True
-        assert config["provider"] == "anthropic"
-        assert config["model"] == "claude-3-7-sonnet-20250219"
-        assert config["expert_provider"] == "openai"
-        assert config["expert_model"] == "gpt-4"
-        assert config["limit_tokens"] is False
+    
+    # Clear the mock repository before each test
+    mock_config_repository.update.reset_mock()
+    
+    # For testing, we need to patch ConfigRepositoryManager.__enter__ to return our mock
+    with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__', return_value=mock_config_repository):
+        with patch.object(
+            sys,
+            "argv",
+            [
+                "ra-aid",
+                "-m",
+                "test message",
+                "--cowboy-mode",
+                "--research-only",
+                "--provider",
+                "anthropic",
+                "--model",
+                "claude-3-7-sonnet-20250219",
+                "--expert-provider",
+                "openai",
+                "--expert-model",
+                "gpt-4",
+                "--temperature",
+                "0.7",
+                "--disable-limit-tokens",
+            ],
+        ):
+            main()
+            # Verify config values are set via the update method
+            mock_config_repository.update.assert_called()
+            # Get the call arguments
+            call_args = mock_config_repository.update.call_args_list
+            
+            # Check for config values in the update calls
+            for args, _ in call_args:
+                config_dict = args[0]
+                if "cowboy_mode" in config_dict:
+                    assert config_dict["cowboy_mode"] is True
+                if "research_only" in config_dict:
+                    assert config_dict["research_only"] is True
+                if "limit_tokens" in config_dict:
+                    assert config_dict["limit_tokens"] is False
+            
+            # Check provider and model settings via set method
+            mock_config_repository.set.assert_any_call("provider", "anthropic")
+            mock_config_repository.set.assert_any_call("model", "claude-3-7-sonnet-20250219")
+            mock_config_repository.set.assert_any_call("expert_provider", "openai")
+            mock_config_repository.set.assert_any_call("expert_model", "gpt-4")
 
 
-def test_temperature_validation(mock_dependencies):
+def test_temperature_validation(mock_dependencies, mock_config_repository):
     """Test that temperature argument is correctly passed to initialize_llm."""
     import sys
     from unittest.mock import patch, ANY
 
     from ra_aid.__main__ import main
 
-    # Reset global memory for clean test
-    _global_memory.clear()
-    _global_memory["config"] = {}
-
-    # Test valid temperature (0.7)
-    with patch("ra_aid.__main__.initialize_llm", return_value=None) as mock_init_llm:
-        # Also patch any calls that would actually use the mocked initialize_llm function
-        with patch("ra_aid.__main__.run_research_agent", return_value=None):
-            with patch("ra_aid.__main__.run_planning_agent", return_value=None):
-                with patch.object(
-                    sys, "argv", ["ra-aid", "-m", "test", "--temperature", "0.7"]
-                ):
-                    main()
-                    # Check if temperature was stored in config correctly
-                    assert _global_memory["config"]["temperature"] == 0.7
+    # For testing, we need to patch ConfigRepositoryManager.__enter__ to return our mock
+    with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__', return_value=mock_config_repository):
+        # Test valid temperature (0.7)
+        with patch("ra_aid.__main__.initialize_llm", return_value=None) as mock_init_llm:
+            # Also patch any calls that would actually use the mocked initialize_llm function
+            with patch("ra_aid.__main__.run_research_agent", return_value=None):
+                with patch("ra_aid.__main__.run_planning_agent", return_value=None):
+                    with patch.object(
+                        sys, "argv", ["ra-aid", "-m", "test", "--temperature", "0.7"]
+                    ):
+                        main()
+                        # Verify that the temperature was set in the config repository
+                        mock_config_repository.set.assert_any_call("temperature", 0.7)
 
     # Test invalid temperature (2.1)
     with pytest.raises(SystemExit):
@@ -230,61 +304,67 @@ def test_missing_message():
     assert args.message == "test"
 
 
-def test_research_model_provider_args(mock_dependencies):
+def test_research_model_provider_args(mock_dependencies, mock_config_repository):
     """Test that research-specific model/provider args are correctly stored in config."""
     import sys
     from unittest.mock import patch
 
     from ra_aid.__main__ import main
 
-    _global_memory.clear()
-
-    with patch.object(
-        sys,
-        "argv",
-        [
-            "ra-aid",
-            "-m",
-            "test message",
-            "--research-provider",
-            "anthropic",
-            "--research-model",
-            "claude-3-haiku-20240307",
-            "--planner-provider",
-            "openai",
-            "--planner-model",
-            "gpt-4",
-        ],
-    ):
-        main()
-        config = _global_memory["config"]
-        assert config["research_provider"] == "anthropic"
-        assert config["research_model"] == "claude-3-haiku-20240307"
-        assert config["planner_provider"] == "openai"
-        assert config["planner_model"] == "gpt-4"
+    # Reset mocks
+    mock_config_repository.set.reset_mock()
+    
+    # For testing, we need to patch ConfigRepositoryManager.__enter__ to return our mock
+    with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__', return_value=mock_config_repository):
+        with patch.object(
+            sys,
+            "argv",
+            [
+                "ra-aid",
+                "-m",
+                "test message",
+                "--research-provider",
+                "anthropic",
+                "--research-model",
+                "claude-3-haiku-20240307",
+                "--planner-provider",
+                "openai",
+                "--planner-model",
+                "gpt-4",
+            ],
+        ):
+            main()
+            # Verify the mock repo's set method was called with the expected values
+            mock_config_repository.set.assert_any_call("research_provider", "anthropic")
+            mock_config_repository.set.assert_any_call("research_model", "claude-3-haiku-20240307")
+            mock_config_repository.set.assert_any_call("planner_provider", "openai")
+            mock_config_repository.set.assert_any_call("planner_model", "gpt-4")
 
 
-def test_planner_model_provider_args(mock_dependencies):
+def test_planner_model_provider_args(mock_dependencies, mock_config_repository):
     """Test that planner provider/model args fall back to main config when not specified."""
     import sys
     from unittest.mock import patch
 
     from ra_aid.__main__ import main
 
-    _global_memory.clear()
-
-    with patch.object(
-        sys,
-        "argv",
-        ["ra-aid", "-m", "test message", "--provider", "openai", "--model", "gpt-4"],
-    ):
-        main()
-        config = _global_memory["config"]
-        assert config["planner_provider"] == "openai"
-        assert config["planner_model"] == "gpt-4"
+    # Reset mocks
+    mock_config_repository.set.reset_mock()
+    
+    # For testing, we need to patch ConfigRepositoryManager.__enter__ to return our mock
+    with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__', return_value=mock_config_repository):
+        with patch.object(
+            sys,
+            "argv",
+            ["ra-aid", "-m", "test message", "--provider", "openai", "--model", "gpt-4"],
+        ):
+            main()
+            # Verify the mock repo's set method was called with the expected values
+            mock_config_repository.set.assert_any_call("planner_provider", "openai")
+            mock_config_repository.set.assert_any_call("planner_model", "gpt-4")
 
 
-def test_use_aider_flag(mock_dependencies):
+def test_use_aider_flag(mock_dependencies, mock_config_repository):
     """Test that use-aider flag is correctly stored in config."""
     import sys
     from unittest.mock import patch
@@ -292,44 +372,68 @@ def test_use_aider_flag(mock_dependencies):
     from ra_aid.__main__ import main
     from ra_aid.tool_configs import MODIFICATION_TOOLS, set_modification_tools
 
-    _global_memory.clear()
-
+    # Reset mocks
+    mock_config_repository.update.reset_mock()
+    
     # Reset to default state
     set_modification_tools(False)
 
-    # Check default behavior (use_aider=False)
-    with patch.object(
-        sys,
-        "argv",
-        ["ra-aid", "-m", "test message"],
-    ):
-        main()
-        config = _global_memory["config"]
-        assert config.get("use_aider") is False
+    # For testing, we need to patch ConfigRepositoryManager.__enter__ to return our mock
+    with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__', return_value=mock_config_repository):
+        # Check default behavior (use_aider=False)
+        with patch.object(
+            sys,
+            "argv",
+            ["ra-aid", "-m", "test message"],
+        ):
+            main()
+            # Verify use_aider is set to False in the update call
+            mock_config_repository.update.assert_called()
+            # Get the call arguments
+            call_args = mock_config_repository.update.call_args_list
+            # Find the call that includes use_aider
+            use_aider_found = False
+            for args, _ in call_args:
+                config_dict = args[0]
+                if "use_aider" in config_dict and config_dict["use_aider"] is False:
+                    use_aider_found = True
+                    break
+            assert use_aider_found, f"use_aider=False not found in update calls: {call_args}"
 
-        # Check that file tools are enabled by default
-        tool_names = [tool.name for tool in MODIFICATION_TOOLS]
-        assert "file_str_replace" in tool_names
-        assert "put_complete_file_contents" in tool_names
-        assert "run_programming_task" not in tool_names
+            # Check that file tools are enabled by default
+            tool_names = [tool.name for tool in MODIFICATION_TOOLS]
+            assert "file_str_replace" in tool_names
+            assert "put_complete_file_contents" in tool_names
+            assert "run_programming_task" not in tool_names
 
-    _global_memory.clear()
+        # Reset mocks
+        mock_config_repository.update.reset_mock()
 
-    # Check with --use-aider flag
-    with patch.object(
-        sys,
-        "argv",
-        ["ra-aid", "-m", "test message", "--use-aider"],
-    ):
-        main()
-        config = _global_memory["config"]
-        assert config.get("use_aider") is True
+        # Check with --use-aider flag
+        with patch.object(
+            sys,
+            "argv",
+            ["ra-aid", "-m", "test message", "--use-aider"],
+        ):
+            main()
+            # Verify use_aider is set to True in the update call
+            mock_config_repository.update.assert_called()
+            # Get the call arguments
+            call_args = mock_config_repository.update.call_args_list
+            # Find the call that includes use_aider
+            use_aider_found = False
+            for args, _ in call_args:
+                config_dict = args[0]
+                if "use_aider" in config_dict and config_dict["use_aider"] is True:
+                    use_aider_found = True
+                    break
+            assert use_aider_found, f"use_aider=True not found in update calls: {call_args}"
 
-        # Check that run_programming_task is enabled
-        tool_names = [tool.name for tool in MODIFICATION_TOOLS]
-        assert "file_str_replace" not in tool_names
-        assert "put_complete_file_contents" not in tool_names
-        assert "run_programming_task" in tool_names
+            # Check that run_programming_task is enabled
+            tool_names = [tool.name for tool in MODIFICATION_TOOLS]
+            assert "file_str_replace" not in tool_names
+            assert "put_complete_file_contents" not in tool_names
+            assert "run_programming_task" in tool_names
 
     # Reset to default state for other tests
     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 cf24f00..82e9a36 100644
--- a/tests/ra_aid/test_programmer.py
+++ b/tests/ra_aid/test_programmer.py
@@ -1,3 +1,4 @@
+import os
 import pytest
 from unittest.mock import patch, MagicMock
 
@@ -7,6 +8,36 @@ from ra_aid.tools.programmer import (
     run_programming_task,
 )
 from ra_aid.database.repositories.related_files_repository import get_related_files_repository
+from ra_aid.database.repositories.config_repository import get_config_repository
+
+@pytest.fixture(autouse=True)
+def mock_config_repository():
+    """Mock the ConfigRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.config_repository.config_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate config
+        config = {
+            "recursion_limit": 2,
+            "provider": "anthropic",
+            "model": "claude-3-5-sonnet-20241022",
+            "temperature": 0.01,
+            "aider_config": "/path/to/config.yml"
+        }
+        
+        # Setup get_all method to return the config dict
+        mock_repo.get_all.return_value = config
+        
+        # Setup get method to return config values
+        def get_config(key, default=None):
+            return config.get(key, default)
+        mock_repo.get.side_effect = get_config
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        yield mock_repo
 
 @pytest.fixture(autouse=True)
 def mock_related_files_repository():
@@ -125,13 +156,9 @@ def test_parse_aider_flags(input_flags, expected, description):
     assert result == expected, f"Failed test case: {description}"
 
 
-def test_aider_config_flag(mocker, mock_related_files_repository):
+def test_aider_config_flag(mocker, mock_config_repository, 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"},
-    }
-    mocker.patch("ra_aid.tools.programmer._global_memory", mock_memory)
+    # Config is mocked by mock_config_repository fixture
 
     # Mock the run_interactive_command to capture the command that would be run
     mock_run = mocker.patch(
@@ -146,15 +173,14 @@ def test_aider_config_flag(mocker, mock_related_files_repository):
     assert args[config_index + 1] == "/path/to/config.yml"
 
 
-def test_path_normalization_and_deduplication(mocker, tmp_path, mock_related_files_repository):
+def test_path_normalization_and_deduplication(mocker, tmp_path, mock_config_repository, 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 - only need to mock config part of global memory now
-    mocker.patch("ra_aid.tools.programmer._global_memory", {"config": {}})
+    # Config is mocked by mock_config_repository fixture
     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 fdb36df..e371dfc 100644
--- a/tests/ra_aid/tools/test_agent.py
+++ b/tests/ra_aid/tools/test_agent.py
@@ -13,6 +13,7 @@ from ra_aid.tools.agent import (
 from ra_aid.tools.memory import _global_memory
 from ra_aid.database.repositories.related_files_repository import get_related_files_repository
 from ra_aid.database.repositories.work_log_repository import get_work_log_repository, WorkLogEntry
+from ra_aid.database.repositories.config_repository import get_config_repository
 
 
 @pytest.fixture
@@ -43,6 +44,34 @@ def mock_related_files_repository():
         
         yield mock_repo
 
+@pytest.fixture(autouse=True)
+def mock_config_repository():
+    """Mock the ConfigRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.config_repository.config_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate config
+        config = {
+            "recursion_limit": 2,
+            "provider": "anthropic",
+            "model": "claude-3-5-sonnet-20241022",
+            "temperature": 0.01
+        }
+        
+        # Setup get_all method to return the config dict
+        mock_repo.get_all.return_value = config
+        
+        # Setup get method to return config values
+        def get_config(key, default=None):
+            return config.get(key, default)
+        mock_repo.get.side_effect = get_config
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        yield mock_repo
+
 @pytest.fixture(autouse=True)
 def mock_work_log_repository():
     """Mock the WorkLogRepository to avoid database operations during tests"""
diff --git a/tests/ra_aid/tools/test_shell.py b/tests/ra_aid/tools/test_shell.py
index 3636ae6..6d2e410 100644
--- a/tests/ra_aid/tools/test_shell.py
+++ b/tests/ra_aid/tools/test_shell.py
@@ -1,8 +1,8 @@
-from unittest.mock import patch
+from unittest.mock import patch, MagicMock
 
 import pytest
 
-from ra_aid.tools.memory import _global_memory
+from ra_aid.database.repositories.config_repository import ConfigRepositoryManager
 from ra_aid.tools.shell import run_shell_command
 
 
@@ -25,9 +25,38 @@ def mock_run_interactive():
         yield mock
 
 
-def test_shell_command_cowboy_mode(mock_console, mock_prompt, mock_run_interactive):
+@pytest.fixture(autouse=True)
+def mock_config_repository():
+    """Mock the ConfigRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.config_repository.config_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate config
+        config = {
+            "cowboy_mode": False
+        }
+        
+        # Setup get method to return config values
+        def get_config(key, default=None):
+            return config.get(key, default)
+        mock_repo.get.side_effect = get_config
+        
+        # Setup set method to update config values
+        def set_config(key, value):
+            config[key] = value
+        mock_repo.set.side_effect = set_config
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        yield mock_repo
+
+
+def test_shell_command_cowboy_mode(mock_console, mock_prompt, mock_run_interactive, mock_config_repository):
     """Test shell command execution in cowboy mode (no approval)"""
-    _global_memory["config"] = {"cowboy_mode": True}
+    # Set cowboy mode to True using the repository
+    mock_config_repository.set("cowboy_mode", True)
 
     result = run_shell_command.invoke({"command": "echo test"})
 
@@ -37,9 +66,10 @@ def test_shell_command_cowboy_mode(mock_console, mock_prompt, mock_run_interacti
     mock_prompt.ask.assert_not_called()
 
 
-def test_shell_command_cowboy_message(mock_console, mock_prompt, mock_run_interactive):
+def test_shell_command_cowboy_message(mock_console, mock_prompt, mock_run_interactive, mock_config_repository):
     """Test that cowboy mode displays a properly formatted cowboy message with correct spacing"""
-    _global_memory["config"] = {"cowboy_mode": True}
+    # Set cowboy mode to True using the repository
+    mock_config_repository.set("cowboy_mode", True)
 
     with patch("ra_aid.tools.shell.get_cowboy_message") as mock_get_message:
         mock_get_message.return_value = "🤠 Test cowboy message!"
@@ -53,10 +83,11 @@ def test_shell_command_cowboy_message(mock_console, mock_prompt, mock_run_intera
 
 
 def test_shell_command_interactive_approved(
-    mock_console, mock_prompt, mock_run_interactive
+    mock_console, mock_prompt, mock_run_interactive, mock_config_repository
 ):
     """Test shell command execution with interactive approval"""
-    _global_memory["config"] = {"cowboy_mode": False}
+    # Set cowboy mode to False using the repository
+    mock_config_repository.set("cowboy_mode", False)
     mock_prompt.ask.return_value = "y"
 
     result = run_shell_command.invoke({"command": "echo test"})
@@ -74,10 +105,11 @@ def test_shell_command_interactive_approved(
 
 
 def test_shell_command_interactive_rejected(
-    mock_console, mock_prompt, mock_run_interactive
+    mock_console, mock_prompt, mock_run_interactive, mock_config_repository
 ):
     """Test shell command rejection in interactive mode"""
-    _global_memory["config"] = {"cowboy_mode": False}
+    # Set cowboy mode to False using the repository
+    mock_config_repository.set("cowboy_mode", False)
     mock_prompt.ask.return_value = "n"
 
     result = run_shell_command.invoke({"command": "echo test"})
@@ -95,13 +127,14 @@ def test_shell_command_interactive_rejected(
     mock_run_interactive.assert_not_called()
 
 
-def test_shell_command_execution_error(mock_console, mock_prompt, mock_run_interactive):
+def test_shell_command_execution_error(mock_console, mock_prompt, mock_run_interactive, mock_config_repository):
     """Test handling of shell command execution errors"""
-    _global_memory["config"] = {"cowboy_mode": True}
+    # Set cowboy mode to True using the repository
+    mock_config_repository.set("cowboy_mode", True)
     mock_run_interactive.side_effect = Exception("Command failed")
 
     result = run_shell_command.invoke({"command": "invalid command"})
 
     assert result["success"] is False
     assert result["return_code"] == 1
-    assert "Command failed" in result["output"]
+    assert "Command failed" in result["output"]
\ No newline at end of file