From b06fe395b32e55a7a70349e8740e5911e9442f83 Mon Sep 17 00:00:00 2001
From: gneeraj2001 <gneeraj2001@gmail.com>
Date: Fri, 29 Aug 2025 02:06:43 -0700
Subject: [PATCH 1/9] Fix path handling consistency

Signed-off-by: gneeraj2001 <gneeraj2001@gmail.com>
---
 cognee/base_config.py                         |  15 ++-
 .../infrastructure/databases/graph/config.py  |  16 ++-
 .../infrastructure/databases/vector/config.py |  21 ++--
 cognee/root_dir.py                            |  28 +++++
 cognee/tests/test_path_config.py              | 114 ++++++++++++++++++
 5 files changed, 182 insertions(+), 12 deletions(-)
 create mode 100644 cognee/tests/test_path_config.py

diff --git a/cognee/base_config.py b/cognee/base_config.py
index aa0b14008..d80e6197f 100644
--- a/cognee/base_config.py
+++ b/cognee/base_config.py
@@ -1,15 +1,28 @@
 import os
 from typing import Optional
 from functools import lru_cache
-from cognee.root_dir import get_absolute_path
+from cognee.root_dir import get_absolute_path, ensure_absolute_path
 from cognee.modules.observability.observers import Observer
 from pydantic_settings import BaseSettings, SettingsConfigDict
+import pydantic
 
 
 class BaseConfig(BaseSettings):
     data_root_directory: str = get_absolute_path(".data_storage")
     system_root_directory: str = get_absolute_path(".cognee_system")
     monitoring_tool: object = Observer.LANGFUSE
+
+    @pydantic.model_validator(mode="after")
+    def validate_paths(cls, values):
+        # Require absolute paths for root directories
+        values.data_root_directory = ensure_absolute_path(
+            values.data_root_directory, allow_relative=False
+        )
+        values.system_root_directory = ensure_absolute_path(
+            values.system_root_directory, allow_relative=False
+        )
+        return values
+
     langfuse_public_key: Optional[str] = os.getenv("LANGFUSE_PUBLIC_KEY")
     langfuse_secret_key: Optional[str] = os.getenv("LANGFUSE_SECRET_KEY")
     langfuse_host: Optional[str] = os.getenv("LANGFUSE_HOST")
diff --git a/cognee/infrastructure/databases/graph/config.py b/cognee/infrastructure/databases/graph/config.py
index cdc001863..60c193d91 100644
--- a/cognee/infrastructure/databases/graph/config.py
+++ b/cognee/infrastructure/databases/graph/config.py
@@ -6,6 +6,7 @@ from pydantic_settings import BaseSettings, SettingsConfigDict
 import pydantic
 from pydantic import Field
 from cognee.base_config import get_base_config
+from cognee.root_dir import ensure_absolute_path
 from cognee.shared.data_models import KnowledgeGraph
 
 
@@ -51,15 +52,22 @@ class GraphConfig(BaseSettings):
     @pydantic.model_validator(mode="after")
     def fill_derived(cls, values):
         provider = values.graph_database_provider.lower()
+        base_config = get_base_config()
 
         # Set default filename if no filename is provided
         if not values.graph_filename:
             values.graph_filename = f"cognee_graph_{provider}"
 
-        # Set file path based on graph database provider if no file path is provided
-        if not values.graph_file_path:
-            base_config = get_base_config()
-
+        # Handle graph file path
+        if values.graph_file_path:
+            # Convert relative paths to absolute using system_root_directory as base
+            values.graph_file_path = ensure_absolute_path(
+                values.graph_file_path,
+                base_path=base_config.system_root_directory,
+                allow_relative=True
+            )
+        else:
+            # Default path
             databases_directory_path = os.path.join(base_config.system_root_directory, "databases")
             values.graph_file_path = os.path.join(databases_directory_path, values.graph_filename)
 
diff --git a/cognee/infrastructure/databases/vector/config.py b/cognee/infrastructure/databases/vector/config.py
index 07a3d1e05..ed846a54b 100644
--- a/cognee/infrastructure/databases/vector/config.py
+++ b/cognee/infrastructure/databases/vector/config.py
@@ -4,6 +4,7 @@ from functools import lru_cache
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from cognee.base_config import get_base_config
+from cognee.root_dir import ensure_absolute_path
 
 
 class VectorConfig(BaseSettings):
@@ -11,12 +12,10 @@ class VectorConfig(BaseSettings):
     Manage the configuration settings for the vector database.
 
     Public methods:
-
     - to_dict: Convert the configuration to a dictionary.
 
     Instance variables:
-
-    - vector_db_url: The URL of the vector database.
+    - vector_db_url: The URL of the vector database. Can be relative to system_root_directory.
     - vector_db_port: The port for the vector database.
     - vector_db_key: The key for accessing the vector database.
     - vector_db_provider: The provider for the vector database.
@@ -30,10 +29,18 @@ class VectorConfig(BaseSettings):
     model_config = SettingsConfigDict(env_file=".env", extra="allow")
 
     @pydantic.model_validator(mode="after")
-    def fill_derived(cls, values):
-        # Set file path based on graph database provider if no file path is provided
-        if not values.vector_db_url:
-            base_config = get_base_config()
+    def validate_paths(cls, values):
+        base_config = get_base_config()
+
+        if values.vector_db_url:
+            # Convert relative paths to absolute using system_root_directory as base
+            values.vector_db_url = ensure_absolute_path(
+                values.vector_db_url,
+                base_path=base_config.system_root_directory,
+                allow_relative=True,
+            )
+        else:
+            # Default path
             databases_directory_path = os.path.join(base_config.system_root_directory, "databases")
             values.vector_db_url = os.path.join(databases_directory_path, "cognee.lancedb")
 
diff --git a/cognee/root_dir.py b/cognee/root_dir.py
index 2e21d5ce3..73afd0c12 100644
--- a/cognee/root_dir.py
+++ b/cognee/root_dir.py
@@ -1,4 +1,5 @@
 from pathlib import Path
+from typing import Optional
 
 ROOT_DIR = Path(__file__).resolve().parent
 
@@ -6,3 +7,30 @@ ROOT_DIR = Path(__file__).resolve().parent
 def get_absolute_path(path_from_root: str) -> str:
     absolute_path = ROOT_DIR / path_from_root
     return str(absolute_path.resolve())
+
+
+def ensure_absolute_path(
+    path: str, base_path: Optional[str] = None, allow_relative: bool = False
+) -> str:
+    """Ensures a path is absolute, optionally converting relative paths.
+
+    Args:
+        path: The path to validate/convert
+        base_path: Optional base path for relative paths. If None, uses ROOT_DIR
+        allow_relative: If False, raises error for relative paths instead of converting
+
+    Returns:
+        Absolute path as string
+
+    Raises:
+        ValueError: If path is relative and allow_relative is False
+    """
+    path_obj = Path(path)
+    if path_obj.is_absolute():
+        return str(path_obj.resolve())
+
+    if not allow_relative:
+        raise ValueError(f"Path must be absolute. Got relative path: {path}")
+
+    base = Path(base_path) if base_path else ROOT_DIR
+    return str((base / path).resolve())
diff --git a/cognee/tests/test_path_config.py b/cognee/tests/test_path_config.py
new file mode 100644
index 000000000..ff1905c5e
--- /dev/null
+++ b/cognee/tests/test_path_config.py
@@ -0,0 +1,114 @@
+import os
+from pathlib import Path
+
+def ensure_absolute_path(path: str, base_path: str = None, allow_relative: bool = False) -> str:
+    """Ensures a path is absolute, optionally converting relative paths."""
+    if path is None:
+        raise ValueError("Path cannot be None")
+        
+    path_obj = Path(path)
+    if path_obj.is_absolute():
+        return str(path_obj.resolve())
+    
+    if not allow_relative:
+        raise ValueError(f"Path must be absolute. Got relative path: {path}")
+        
+    if base_path is None:
+        raise ValueError("base_path must be provided when converting relative paths")
+        
+    base = Path(base_path)
+    if not base.is_absolute():
+        raise ValueError("base_path must be absolute when converting relative paths")
+        
+    return str((base / path).resolve())
+
+def test_root_dir_absolute_paths():
+    """Test absolute path handling in root_dir.py"""
+    # Test with absolute path
+    abs_path = "C:/absolute/path" if os.name == 'nt' else "/absolute/path"
+    result = ensure_absolute_path(abs_path, allow_relative=False)
+    assert result == str(Path(abs_path).resolve())
+    
+    # Test with relative path (should fail)
+    rel_path = "relative/path"
+    try:
+        ensure_absolute_path(rel_path, allow_relative=False)
+        assert False, "Should fail with relative path when allow_relative=False"
+    except ValueError as e:
+        assert "must be absolute" in str(e)
+        
+    # Test with None path
+    try:
+        ensure_absolute_path(None)
+        assert False, "Should fail with None path"
+    except ValueError as e:
+        assert "cannot be None" in str(e)
+
+def test_database_relative_paths():
+    """Test relative path handling for vector and graph databases"""
+    system_root = "C:/system/root" if os.name == 'nt' else "/system/root"
+    
+    # Test with absolute path
+    abs_path = "C:/data/vector.db" if os.name == 'nt' else "/data/vector.db"
+    result = ensure_absolute_path(abs_path, base_path=system_root, allow_relative=True)
+    assert result == str(Path(abs_path).resolve())
+    
+    # Test with relative path (should convert to absolute)
+    rel_path = "data/vector.db"
+    result = ensure_absolute_path(rel_path, base_path=system_root, allow_relative=True)
+    expected = str((Path(system_root) / rel_path).resolve())
+    assert result == expected
+    
+    # Test with relative base_path (should fail)
+    try:
+        ensure_absolute_path(rel_path, base_path="relative/base", allow_relative=True)
+        assert False, "Should fail when base_path is relative"
+    except ValueError as e:
+        assert "base_path must be absolute" in str(e)
+    
+    # Test without base_path for relative path
+    try:
+        ensure_absolute_path(rel_path, allow_relative=True)
+        assert False, "Should fail when base_path is not provided for relative path"
+    except ValueError as e:
+        assert "base_path must be provided" in str(e)
+
+def test_path_consistency():
+    """Test that paths are handled consistently across configurations"""
+    system_root = "C:/system/root" if os.name == 'nt' else "/system/root"
+    
+    # Root directories must be absolute
+    data_root = "C:/data/root" if os.name == 'nt' else "/data/root"
+    assert ensure_absolute_path(data_root, allow_relative=False) == str(Path(data_root).resolve())
+    
+    # Database paths can be relative but must resolve against system_root
+    db_paths = [
+        # Vector DB paths
+        "vector.db",                    # Simple relative
+        "data/vector.db",              # Nested relative
+        "../vector.db",                # Parent relative
+        "./vector.db",                 # Current dir relative
+        # Graph DB paths
+        "graph.db",                    # Simple relative
+        "data/graph/db",              # Nested relative
+        "../graph.db",                # Parent relative
+        "./graph.db",                 # Current dir relative
+        # With different extensions
+        "data/vector.lancedb",        # Vector DB with extension
+        "data/graph/kuzu",           # Graph DB with extension
+    ]
+    
+    for rel_path in db_paths:
+        result = ensure_absolute_path(rel_path, base_path=system_root, allow_relative=True)
+        expected = str((Path(system_root) / rel_path).resolve())
+        assert result == expected, f"Failed to resolve {rel_path} correctly"
+
+if __name__ == "__main__":
+    print("Running path configuration tests...")
+    test_root_dir_absolute_paths()
+    print("✓ Root directory absolute path tests passed")
+    test_database_relative_paths()
+    print("✓ Database relative path tests passed")
+    test_path_consistency()
+    print("✓ Path consistency tests passed")
+    print("All tests passed successfully!")

From aa3d704adc6baa143309fc66fb0edc1450b0085a Mon Sep 17 00:00:00 2001
From: Neeraj Gopalakrishnan <91423180+gneeraj2001@users.noreply.github.com>
Date: Fri, 29 Aug 2025 02:31:58 -0700
Subject: [PATCH 2/9] Update cognee/base_config.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 cognee/base_config.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/cognee/base_config.py b/cognee/base_config.py
index d80e6197f..b3258dba9 100644
--- a/cognee/base_config.py
+++ b/cognee/base_config.py
@@ -13,15 +13,15 @@ class BaseConfig(BaseSettings):
     monitoring_tool: object = Observer.LANGFUSE
 
     @pydantic.model_validator(mode="after")
-    def validate_paths(cls, values):
+    def validate_paths(self):
         # Require absolute paths for root directories
-        values.data_root_directory = ensure_absolute_path(
-            values.data_root_directory, allow_relative=False
+        self.data_root_directory = ensure_absolute_path(
+            self.data_root_directory, allow_relative=False
         )
-        values.system_root_directory = ensure_absolute_path(
-            values.system_root_directory, allow_relative=False
+        self.system_root_directory = ensure_absolute_path(
+            self.system_root_directory, allow_relative=False
         )
-        return values
+        return self
 
     langfuse_public_key: Optional[str] = os.getenv("LANGFUSE_PUBLIC_KEY")
     langfuse_secret_key: Optional[str] = os.getenv("LANGFUSE_SECRET_KEY")

From 6e262d5eb3902c6839f071f78784f37c32f6934a Mon Sep 17 00:00:00 2001
From: Neeraj Gopalakrishnan <91423180+gneeraj2001@users.noreply.github.com>
Date: Fri, 29 Aug 2025 02:33:16 -0700
Subject: [PATCH 3/9] Update cognee/tests/test_path_config.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 cognee/tests/test_path_config.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/cognee/tests/test_path_config.py b/cognee/tests/test_path_config.py
index ff1905c5e..600f04579 100644
--- a/cognee/tests/test_path_config.py
+++ b/cognee/tests/test_path_config.py
@@ -103,12 +103,3 @@ def test_path_consistency():
         expected = str((Path(system_root) / rel_path).resolve())
         assert result == expected, f"Failed to resolve {rel_path} correctly"
 
-if __name__ == "__main__":
-    print("Running path configuration tests...")
-    test_root_dir_absolute_paths()
-    print("✓ Root directory absolute path tests passed")
-    test_database_relative_paths()
-    print("✓ Database relative path tests passed")
-    test_path_consistency()
-    print("✓ Path consistency tests passed")
-    print("All tests passed successfully!")

From 19e5980b50310dfa1f331911440b7591c1431689 Mon Sep 17 00:00:00 2001
From: Neeraj Gopalakrishnan <91423180+gneeraj2001@users.noreply.github.com>
Date: Fri, 29 Aug 2025 02:35:03 -0700
Subject: [PATCH 4/9] Update cognee/tests/test_path_config.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 cognee/tests/test_path_config.py | 25 +++++--------------------
 1 file changed, 5 insertions(+), 20 deletions(-)

diff --git a/cognee/tests/test_path_config.py b/cognee/tests/test_path_config.py
index 600f04579..7a3d57e5b 100644
--- a/cognee/tests/test_path_config.py
+++ b/cognee/tests/test_path_config.py
@@ -1,26 +1,11 @@
 import os
 from pathlib import Path
 
-def ensure_absolute_path(path: str, base_path: str = None, allow_relative: bool = False) -> str:
-    """Ensures a path is absolute, optionally converting relative paths."""
-    if path is None:
-        raise ValueError("Path cannot be None")
-        
-    path_obj = Path(path)
-    if path_obj.is_absolute():
-        return str(path_obj.resolve())
-    
-    if not allow_relative:
-        raise ValueError(f"Path must be absolute. Got relative path: {path}")
-        
-    if base_path is None:
-        raise ValueError("base_path must be provided when converting relative paths")
-        
-    base = Path(base_path)
-    if not base.is_absolute():
-        raise ValueError("base_path must be absolute when converting relative paths")
-        
-    return str((base / path).resolve())
+from pathlib import Path
+import pytest
+from cognee.root_dir import ensure_absolute_path
+
+# …rest of your test cases using ensure_absolute_path…
 
 def test_root_dir_absolute_paths():
     """Test absolute path handling in root_dir.py"""

From d385d7edba37fd7b8f177bc3ebe647a1d3aa2d17 Mon Sep 17 00:00:00 2001
From: Neeraj Gopalakrishnan <91423180+gneeraj2001@users.noreply.github.com>
Date: Fri, 29 Aug 2025 02:35:48 -0700
Subject: [PATCH 5/9] Update cognee/tests/test_path_config.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 cognee/tests/test_path_config.py | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/cognee/tests/test_path_config.py b/cognee/tests/test_path_config.py
index 7a3d57e5b..65201fc70 100644
--- a/cognee/tests/test_path_config.py
+++ b/cognee/tests/test_path_config.py
@@ -45,19 +45,12 @@ def test_database_relative_paths():
     assert result == expected
     
     # Test with relative base_path (should fail)
-    try:
+    with pytest.raises(ValueError, match="base_path must be absolute"):
         ensure_absolute_path(rel_path, base_path="relative/base", allow_relative=True)
-        assert False, "Should fail when base_path is relative"
-    except ValueError as e:
-        assert "base_path must be absolute" in str(e)
     
     # Test without base_path for relative path
-    try:
+    with pytest.raises(ValueError, match="base_path must be provided"):
         ensure_absolute_path(rel_path, allow_relative=True)
-        assert False, "Should fail when base_path is not provided for relative path"
-    except ValueError as e:
-        assert "base_path must be provided" in str(e)
-
 def test_path_consistency():
     """Test that paths are handled consistently across configurations"""
     system_root = "C:/system/root" if os.name == 'nt' else "/system/root"

From ded92862c7b5b21147bd344f5a2d254a4bab909b Mon Sep 17 00:00:00 2001
From: Neeraj Gopalakrishnan <91423180+gneeraj2001@users.noreply.github.com>
Date: Fri, 29 Aug 2025 02:38:39 -0700
Subject: [PATCH 6/9] Update cognee/root_dir.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 cognee/root_dir.py | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/cognee/root_dir.py b/cognee/root_dir.py
index 73afd0c12..4853acd02 100644
--- a/cognee/root_dir.py
+++ b/cognee/root_dir.py
@@ -15,22 +15,29 @@ def ensure_absolute_path(
     """Ensures a path is absolute, optionally converting relative paths.
 
     Args:
-        path: The path to validate/convert
-        base_path: Optional base path for relative paths. If None, uses ROOT_DIR
-        allow_relative: If False, raises error for relative paths instead of converting
+        path: The path to validate/convert.
+        base_path: Required base when converting relative paths (e.g., SYSTEM_ROOT_DIRECTORY).
+        allow_relative: If False, raises error for relative paths instead of converting.
 
     Returns:
         Absolute path as string
 
     Raises:
-        ValueError: If path is relative and allow_relative is False
+        ValueError: If path is None; or path is relative and allow_relative is False;
+                   or base_path is missing/non-absolute when converting.
     """
-    path_obj = Path(path)
+    if path is None:
+        raise ValueError("Path cannot be None")
+    path_obj = Path(path).expanduser()
     if path_obj.is_absolute():
         return str(path_obj.resolve())
 
     if not allow_relative:
         raise ValueError(f"Path must be absolute. Got relative path: {path}")
 
-    base = Path(base_path) if base_path else ROOT_DIR
-    return str((base / path).resolve())
+    if base_path is None:
+        raise ValueError("base_path must be provided when converting relative paths")
+    base = Path(base_path).expanduser()
+    if not base.is_absolute():
+        raise ValueError("base_path must be absolute when converting relative paths")
+    return str((base / path_obj).resolve())

From de939c154768e614022846d55977477f94e8b81e Mon Sep 17 00:00:00 2001
From: Neeraj Gopalakrishnan <91423180+gneeraj2001@users.noreply.github.com>
Date: Fri, 29 Aug 2025 02:39:04 -0700
Subject: [PATCH 7/9] Update cognee/tests/test_path_config.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 cognee/tests/test_path_config.py | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/cognee/tests/test_path_config.py b/cognee/tests/test_path_config.py
index 65201fc70..b90ce8cac 100644
--- a/cognee/tests/test_path_config.py
+++ b/cognee/tests/test_path_config.py
@@ -16,19 +16,12 @@ def test_root_dir_absolute_paths():
     
     # Test with relative path (should fail)
     rel_path = "relative/path"
-    try:
+    with pytest.raises(ValueError, match="must be absolute"):
         ensure_absolute_path(rel_path, allow_relative=False)
-        assert False, "Should fail with relative path when allow_relative=False"
-    except ValueError as e:
-        assert "must be absolute" in str(e)
-        
-    # Test with None path
-    try:
-        ensure_absolute_path(None)
-        assert False, "Should fail with None path"
-    except ValueError as e:
-        assert "cannot be None" in str(e)
 
+    # Test with None path
+    with pytest.raises(ValueError, match="cannot be None"):
+        ensure_absolute_path(None)
 def test_database_relative_paths():
     """Test relative path handling for vector and graph databases"""
     system_root = "C:/system/root" if os.name == 'nt' else "/system/root"

From 74cf56e1ce6db668f4019282c722965e7925d428 Mon Sep 17 00:00:00 2001
From: Igor Ilic <igorilic03@gmail.com>
Date: Mon, 1 Sep 2025 16:31:10 +0200
Subject: [PATCH 8/9] fix: Return coding rules to MCP

---
 cognee-mcp/pyproject.toml |  2 +-
 cognee-mcp/src/server.py  | 28 +++++++--------
 cognee-mcp/uv.lock        | 71 +++++++++++++++++++++++++++++++++------
 3 files changed, 75 insertions(+), 26 deletions(-)

diff --git a/cognee-mcp/pyproject.toml b/cognee-mcp/pyproject.toml
index a8596615b..8bde50841 100644
--- a/cognee-mcp/pyproject.toml
+++ b/cognee-mcp/pyproject.toml
@@ -8,7 +8,7 @@ requires-python = ">=3.10"
 dependencies = [
     # For local cognee repo usage remove comment bellow and add absolute path to cognee. Then run `uv sync --reinstall` in the mcp folder on local cognee changes.
 #    "cognee[postgres,codegraph,gemini,huggingface,docs,neo4j] @ file:/Users/vasilije/Projects/tiktok/cognee",
-    "cognee[postgres,codegraph,gemini,huggingface,docs,neo4j]==0.2.3",
+    "cognee[postgres,codegraph,gemini,huggingface,docs,neo4j]==0.2.4",
     "fastmcp>=2.10.0,<3.0.0",
     "mcp>=1.12.0,<2.0.0",
     "uv>=0.6.3,<1.0.0",
diff --git a/cognee-mcp/src/server.py b/cognee-mcp/src/server.py
index 5d11e0ce5..9e55b9707 100755
--- a/cognee-mcp/src/server.py
+++ b/cognee-mcp/src/server.py
@@ -21,16 +21,16 @@ from cognee.shared.data_models import KnowledgeGraph
 from cognee.modules.storage.utils import JSONEncoder
 
 
-# try:
-#     from codingagents.coding_rule_associations import (
-#         add_rule_associations,
-#         get_existing_rules,
-#     )
-# except ModuleNotFoundError:
-#     from .codingagents.coding_rule_associations import (
-#         add_rule_associations,
-#         get_existing_rules,
-#     )
+try:
+    from codingagents.coding_rule_associations import (
+        add_rule_associations,
+        get_existing_rules,
+    )
+except ModuleNotFoundError:
+    from .codingagents.coding_rule_associations import (
+        add_rule_associations,
+        get_existing_rules,
+    )
 
 
 mcp = FastMCP("Cognee")
@@ -310,7 +310,7 @@ async def save_interaction(data: str) -> list:
                 logger.info("Save interaction process finished.")
                 logger.info("Generating associated rules from interaction data.")
 
-                # await add_rule_associations(data=data, rules_nodeset_name="coding_agent_rules")
+                await add_rule_associations(data=data, rules_nodeset_name="coding_agent_rules")
 
                 logger.info("Associated rules generated from interaction data.")
 
@@ -572,10 +572,8 @@ async def get_developer_rules() -> list:
     async def fetch_rules_from_cognee() -> str:
         """Collect all developer rules from Cognee"""
         with redirect_stdout(sys.stderr):
-            note = "This is broken in 0.2.2"
-            return note
-            # developer_rules = await get_existing_rules(rules_nodeset_name="coding_agent_rules")
-            # return developer_rules
+            developer_rules = await get_existing_rules(rules_nodeset_name="coding_agent_rules")
+            return developer_rules
 
     rules_text = await fetch_rules_from_cognee()
 
diff --git a/cognee-mcp/uv.lock b/cognee-mcp/uv.lock
index bfa434b4f..dd2797519 100644
--- a/cognee-mcp/uv.lock
+++ b/cognee-mcp/uv.lock
@@ -332,6 +332,21 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/df/73/b6e24bd22e6720ca8ee9a85a0c4a2971af8497d8f3193fa05390cbd46e09/backoff-2.2.1-py3-none-any.whl", hash = "sha256:63579f9a0628e06278f7e47b7d7d5b6ce20dc65c5e96a6f3ca99a6adca0396e8", size = 15148, upload-time = "2022-10-05T19:19:30.546Z" },
 ]
 
+[[package]]
+name = "baml-py"
+version = "0.201.0"
+source = { registry = "https://pypi.org/simple" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/54/54/2b0edb3d22e95ce56f36610391c11108a4ef26ba2837736a32001687ae34/baml_py-0.201.0-cp38-abi3-macosx_10_12_x86_64.whl", hash = "sha256:83228d2af2b0e845bbbb4e14f7cbd3376cec385aee01210ac522ab6076e07bec", size = 17387971, upload-time = "2025-07-03T19:29:05.844Z" },
+    { url = "https://files.pythonhosted.org/packages/c9/08/1d48c28c63eadea2c04360cbb7f64968599e99cd6b8fc0ec0bd4424d3cf1/baml_py-0.201.0-cp38-abi3-macosx_11_0_arm64.whl", hash = "sha256:2a9d016139e3ae5b5ce98c7b05b5fbd53d5d38f04dc810ec4d70fb17dd6c10e4", size = 16191010, upload-time = "2025-07-03T19:29:09.323Z" },
+    { url = "https://files.pythonhosted.org/packages/73/1a/20b2d46501e3dd0648af339825106a6ac5eeb5d22d7e6a10cf16b9aa1cb8/baml_py-0.201.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b5058505b1a3c5f04fc1679aec4d730fa9bef2cbd96209b3ed50152f60b96baf", size = 19950249, upload-time = "2025-07-03T19:29:11.974Z" },
+    { url = "https://files.pythonhosted.org/packages/38/24/bc871059e905159ae1913c2e3032dd6ef2f5c3d0983999d2c2f1eebb65a4/baml_py-0.201.0-cp38-abi3-manylinux_2_24_aarch64.whl", hash = "sha256:36289d548581ba4accd5eaaab3246872542dd32dc6717e537654fa0cad884071", size = 19231310, upload-time = "2025-07-03T19:29:14.857Z" },
+    { url = "https://files.pythonhosted.org/packages/0e/11/4268a0b82b02c7202fe5aa0d7175712158d998c491cac723b2bac3d5d495/baml_py-0.201.0-cp38-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:5ab70e7bd6481d71edca8a33313347b29faccec78b9960138aa437522813ac9a", size = 19490012, upload-time = "2025-07-03T19:29:18.512Z" },
+    { url = "https://files.pythonhosted.org/packages/31/21/c9f9aea1adba2a5978ffab11ba0948a9f3f81ec6ed3056067713260e93a1/baml_py-0.201.0-cp38-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:7efc5c693a7142c230a4f3d6700415127fee0b9f5fdbb36db63e04e27ac4c0f1", size = 20090620, upload-time = "2025-07-03T19:29:21.072Z" },
+    { url = "https://files.pythonhosted.org/packages/99/cf/92123d8d753f1d1473e080c4c182139bfe3b9a6418e891cf1d96b6c33848/baml_py-0.201.0-cp38-abi3-win_amd64.whl", hash = "sha256:56499857b7a27ae61a661c8ce0dddd0fb567a45c0b826157e44048a14cf586f9", size = 17253005, upload-time = "2025-07-03T19:29:23.722Z" },
+    { url = "https://files.pythonhosted.org/packages/59/88/5056aa1bc9480f758cd6e210d63bd1f9ad90b44c87f4121285906526495e/baml_py-0.201.0-cp38-abi3-win_arm64.whl", hash = "sha256:1e52dc1151db84a302b746590fe2bc484bdd794f83fa5da7216d9394c559f33a", size = 15612701, upload-time = "2025-07-03T19:29:26.712Z" },
+]
+
 [[package]]
 name = "bcrypt"
 version = "4.3.0"
@@ -590,13 +605,14 @@ wheels = [
 
 [[package]]
 name = "cognee"
-version = "0.2.1"
+version = "0.2.4"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiofiles" },
     { name = "aiohttp" },
     { name = "aiosqlite" },
     { name = "alembic" },
+    { name = "baml-py" },
     { name = "dlt", extra = ["sqlalchemy"] },
     { name = "fastapi" },
     { name = "fastapi-users", extra = ["sqlalchemy"] },
@@ -624,6 +640,7 @@ dependencies = [
     { name = "pympler" },
     { name = "pypdf" },
     { name = "python-dotenv" },
+    { name = "python-magic-bin", marker = "sys_platform == 'win32'" },
     { name = "python-multipart" },
     { name = "rdflib" },
     { name = "s3fs", extra = ["boto3"] },
@@ -634,9 +651,9 @@ dependencies = [
     { name = "tiktoken" },
     { name = "typing-extensions" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/41/46/e7df1faebc92fa31ef8e33faf81feb435782727a789de5532d178e047224/cognee-0.2.1.tar.gz", hash = "sha256:bf5208383fc841981641c040e5b6588e58111af4d771f9eab6552f441e6a8e6c", size = 15497626, upload-time = "2025-07-25T15:53:57.009Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/da/b1/99c7f0c20cae101d4777bdc17b466bab58d0b4abfbb5d62c54d3babcc3ec/cognee-0.2.4.tar.gz", hash = "sha256:e8ac1c60cabb2e1d41db4f337a4dca3c7aa0c54d605d32e6087dba1c02b3beba", size = 13955686, upload-time = "2025-08-27T14:39:05.532Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/b3/0e/b705c6eeb538dcdd8fbbb331be25fe8e0bbc1af7d76e61566ec9845b29d3/cognee-0.2.1-py3-none-any.whl", hash = "sha256:6e9d437e0c58a16233841ebf19b1a3d8b67da069460a4f08d0c0e00301b1d36d", size = 1019851, upload-time = "2025-07-25T15:53:53.488Z" },
+    { url = "https://files.pythonhosted.org/packages/e8/78/24df77b88d719ba308281412ebeb17c37867333e16bd2d1da7e192c1dc5d/cognee-0.2.4-py3-none-any.whl", hash = "sha256:56ab83c18ec9d7b307dfa206fcef39bc036e893d13e5390212f730b5204e3ae1", size = 1433548, upload-time = "2025-08-27T14:38:56.986Z" },
 ]
 
 [package.optional-dependencies]
@@ -682,7 +699,7 @@ dev = [
 
 [package.metadata]
 requires-dist = [
-    { name = "cognee", extras = ["postgres", "codegraph", "gemini", "huggingface", "docs", "neo4j"], specifier = "==0.2.1" },
+    { name = "cognee", extras = ["postgres", "codegraph", "gemini", "huggingface", "docs", "neo4j"], specifier = "==0.2.4" },
     { name = "fastmcp", specifier = ">=2.10.0,<3.0.0" },
     { name = "mcp", specifier = ">=1.12.0,<2.0.0" },
     { name = "uv", specifier = ">=0.6.3,<1.0.0" },
@@ -1258,6 +1275,30 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/0c/9a/51108b68e77650a7289b5f1ceff8dc0929ab48a26d1d2015f22121a9d183/fastmcp-2.11.0-py3-none-any.whl", hash = "sha256:8709a04522e66fda407b469fbe4d3290651aa7b06097b91c097e9a973c9b9bb3", size = 256193, upload-time = "2025-08-01T21:30:09.905Z" },
 ]
 
+[[package]]
+name = "fastuuid"
+version = "0.12.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/19/17/13146a1e916bd2971d0a58db5e0a4ad23efdd49f78f33ac871c161f8007b/fastuuid-0.12.0.tar.gz", hash = "sha256:d0bd4e5b35aad2826403f4411937c89e7c88857b1513fe10f696544c03e9bd8e", size = 19180, upload-time = "2025-01-27T18:04:14.387Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/97/c3/9db9aee6f34e6dfd1f909d3d7432ac26e491a0471f8bb8b676c44b625b3f/fastuuid-0.12.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:22a900ef0956aacf862b460e20541fdae2d7c340594fe1bd6fdcb10d5f0791a9", size = 247356, upload-time = "2025-01-27T18:04:45.397Z" },
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+    { url = "https://files.pythonhosted.org/packages/c4/e6/beae8411cac5b3b0b9d59ee08405eb39c3abe81dad459114363eff55c14a/fastuuid-0.12.0-cp310-cp310-manylinux_2_34_x86_64.whl", hash = "sha256:7946b4a310cfc2d597dcba658019d72a2851612a2cebb949d809c0e2474cf0a6", size = 278480, upload-time = "2025-01-27T18:04:05.663Z" },
+    { url = "https://files.pythonhosted.org/packages/f1/f6/c598b9a052435716fc5a084ef17049edd35ca2c8241161269bfea4905ab4/fastuuid-0.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:a1b6764dd42bf0c46c858fb5ade7b7a3d93b7a27485a7a5c184909026694cd88", size = 156799, upload-time = "2025-01-27T18:05:41.867Z" },
+    { url = "https://files.pythonhosted.org/packages/d4/99/555eab31381c7912103d4c8654082611e5e82a7bb88ad5ab067e36b622d7/fastuuid-0.12.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:2bced35269315d16fe0c41003f8c9d63f2ee16a59295d90922cad5e6a67d0418", size = 247249, upload-time = "2025-01-27T18:03:23.092Z" },
+    { url = "https://files.pythonhosted.org/packages/6d/3b/d62ce7f2af3d50a8e787603d44809770f43a3f2ff708bf10c252bf479109/fastuuid-0.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:82106e4b0a24f4f2f73c88f89dadbc1533bb808900740ca5db9bbb17d3b0c824", size = 258369, upload-time = "2025-01-27T18:04:08.903Z" },
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+]
+
 [[package]]
 name = "filelock"
 version = "3.18.0"
@@ -2253,11 +2294,12 @@ wheels = [
 
 [[package]]
 name = "litellm"
-version = "1.70.4"
+version = "1.76.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohttp" },
     { name = "click" },
+    { name = "fastuuid" },
     { name = "httpx" },
     { name = "importlib-metadata" },
     { name = "jinja2" },
@@ -2268,9 +2310,9 @@ dependencies = [
     { name = "tiktoken" },
     { name = "tokenizers" },
 ]
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+sdist = { url = "https://files.pythonhosted.org/packages/f8/fd/aa87c0a598377786521bee585f4d525e846f5339b816903298bfbb9daef5/litellm-1.76.1.tar.gz", hash = "sha256:d5a3a3efda04999b60ec0d1c29c1eaaa12f89a7b29db4bda691c7fb55b4fa6ad", size = 10178100, upload-time = "2025-08-30T21:05:48.578Z" }
 wheels = [
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 ]
 
 [[package]]
@@ -3117,7 +3159,7 @@ wheels = [
 
 [[package]]
 name = "openai"
-version = "1.98.0"
+version = "1.99.8"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
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@@ -3129,9 +3171,9 @@ dependencies = [
     { name = "tqdm" },
     { name = "typing-extensions" },
 ]
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 [[package]]
@@ -4163,6 +4205,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/6c/73/9f872cb81fc5c3bb48f7227872c28975f998f3e7c2b1c16e95e6432bbb90/python_magic-0.4.27-py2.py3-none-any.whl", hash = "sha256:c212960ad306f700aa0d01e5d7a325d20548ff97eb9920dcd29513174f0294d3", size = 13840, upload-time = "2022-06-07T20:16:57.763Z" },
 ]
 
+[[package]]
+name = "python-magic-bin"
+version = "0.4.14"
+source = { registry = "https://pypi.org/simple" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/5a/5d/10b9ac745d9fd2f7151a2ab901e6bb6983dbd70e87c71111f54859d1ca2e/python_magic_bin-0.4.14-py2.py3-none-win32.whl", hash = "sha256:34a788c03adde7608028203e2dbb208f1f62225ad91518787ae26d603ae68892", size = 397784, upload-time = "2017-10-02T16:30:15.806Z" },
+    { url = "https://files.pythonhosted.org/packages/07/c2/094e3d62b906d952537196603a23aec4bcd7c6126bf80eb14e6f9f4be3a2/python_magic_bin-0.4.14-py2.py3-none-win_amd64.whl", hash = "sha256:90be6206ad31071a36065a2fc169c5afb5e0355cbe6030e87641c6c62edc2b69", size = 409299, upload-time = "2017-10-02T16:30:18.545Z" },
+]
+
 [[package]]
 name = "python-multipart"
 version = "0.0.20"

From d8326a7e3aad95d090739777d126b6cf4008a784 Mon Sep 17 00:00:00 2001
From: Igor Ilic <igorilic03@gmail.com>
Date: Tue, 2 Sep 2025 11:21:05 +0200
Subject: [PATCH 9/9] feat: path handling has to be absolute by gneeraj2001

---
 cognee/base_config.py                         |  8 +--
 .../infrastructure/databases/graph/config.py  |  6 +-
 .../infrastructure/databases/vector/config.py |  8 +--
 cognee/root_dir.py                            | 24 ++------
 cognee/tests/test_path_config.py              | 59 +------------------
 5 files changed, 14 insertions(+), 91 deletions(-)

diff --git a/cognee/base_config.py b/cognee/base_config.py
index b3258dba9..940846128 100644
--- a/cognee/base_config.py
+++ b/cognee/base_config.py
@@ -15,12 +15,8 @@ class BaseConfig(BaseSettings):
     @pydantic.model_validator(mode="after")
     def validate_paths(self):
         # Require absolute paths for root directories
-        self.data_root_directory = ensure_absolute_path(
-            self.data_root_directory, allow_relative=False
-        )
-        self.system_root_directory = ensure_absolute_path(
-            self.system_root_directory, allow_relative=False
-        )
+        self.data_root_directory = ensure_absolute_path(self.data_root_directory)
+        self.system_root_directory = ensure_absolute_path(self.system_root_directory)
         return self
 
     langfuse_public_key: Optional[str] = os.getenv("LANGFUSE_PUBLIC_KEY")
diff --git a/cognee/infrastructure/databases/graph/config.py b/cognee/infrastructure/databases/graph/config.py
index 60c193d91..d96de4520 100644
--- a/cognee/infrastructure/databases/graph/config.py
+++ b/cognee/infrastructure/databases/graph/config.py
@@ -60,11 +60,9 @@ class GraphConfig(BaseSettings):
 
         # Handle graph file path
         if values.graph_file_path:
-            # Convert relative paths to absolute using system_root_directory as base
+            # Check if absolute path is provided
             values.graph_file_path = ensure_absolute_path(
-                values.graph_file_path,
-                base_path=base_config.system_root_directory,
-                allow_relative=True
+                os.path.join(values.graph_file_path, values.graph_filename)
             )
         else:
             # Default path
diff --git a/cognee/infrastructure/databases/vector/config.py b/cognee/infrastructure/databases/vector/config.py
index ed846a54b..7a20130bd 100644
--- a/cognee/infrastructure/databases/vector/config.py
+++ b/cognee/infrastructure/databases/vector/config.py
@@ -1,5 +1,6 @@
 import os
 import pydantic
+from pathlib import Path
 from functools import lru_cache
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
@@ -32,12 +33,11 @@ class VectorConfig(BaseSettings):
     def validate_paths(cls, values):
         base_config = get_base_config()
 
-        if values.vector_db_url:
-            # Convert relative paths to absolute using system_root_directory as base
+        # If vector_db_url is provided and is not a path skip checking if path is absolute (as it can also be a url)
+        if values.vector_db_url and Path(values.vector_db_url).exists():
+            # Relative path to absolute
             values.vector_db_url = ensure_absolute_path(
                 values.vector_db_url,
-                base_path=base_config.system_root_directory,
-                allow_relative=True,
             )
         else:
             # Default path
diff --git a/cognee/root_dir.py b/cognee/root_dir.py
index 4853acd02..46d8fcb69 100644
--- a/cognee/root_dir.py
+++ b/cognee/root_dir.py
@@ -9,22 +9,14 @@ def get_absolute_path(path_from_root: str) -> str:
     return str(absolute_path.resolve())
 
 
-def ensure_absolute_path(
-    path: str, base_path: Optional[str] = None, allow_relative: bool = False
-) -> str:
-    """Ensures a path is absolute, optionally converting relative paths.
+def ensure_absolute_path(path: str) -> str:
+    """Ensures a path is absolute.
 
     Args:
-        path: The path to validate/convert.
-        base_path: Required base when converting relative paths (e.g., SYSTEM_ROOT_DIRECTORY).
-        allow_relative: If False, raises error for relative paths instead of converting.
+        path: The path to validate.
 
     Returns:
         Absolute path as string
-
-    Raises:
-        ValueError: If path is None; or path is relative and allow_relative is False;
-                   or base_path is missing/non-absolute when converting.
     """
     if path is None:
         raise ValueError("Path cannot be None")
@@ -32,12 +24,4 @@ def ensure_absolute_path(
     if path_obj.is_absolute():
         return str(path_obj.resolve())
 
-    if not allow_relative:
-        raise ValueError(f"Path must be absolute. Got relative path: {path}")
-
-    if base_path is None:
-        raise ValueError("base_path must be provided when converting relative paths")
-    base = Path(base_path).expanduser()
-    if not base.is_absolute():
-        raise ValueError("base_path must be absolute when converting relative paths")
-    return str((base / path_obj).resolve())
+    raise ValueError(f"Path must be absolute. Got relative path: {path}")
diff --git a/cognee/tests/test_path_config.py b/cognee/tests/test_path_config.py
index b90ce8cac..55f641479 100644
--- a/cognee/tests/test_path_config.py
+++ b/cognee/tests/test_path_config.py
@@ -1,19 +1,16 @@
 import os
-from pathlib import Path
-
 from pathlib import Path
 import pytest
 from cognee.root_dir import ensure_absolute_path
 
-# …rest of your test cases using ensure_absolute_path…
 
 def test_root_dir_absolute_paths():
     """Test absolute path handling in root_dir.py"""
     # Test with absolute path
-    abs_path = "C:/absolute/path" if os.name == 'nt' else "/absolute/path"
+    abs_path = "C:/absolute/path" if os.name == "nt" else "/absolute/path"
     result = ensure_absolute_path(abs_path, allow_relative=False)
     assert result == str(Path(abs_path).resolve())
-    
+
     # Test with relative path (should fail)
     rel_path = "relative/path"
     with pytest.raises(ValueError, match="must be absolute"):
@@ -22,55 +19,3 @@ def test_root_dir_absolute_paths():
     # Test with None path
     with pytest.raises(ValueError, match="cannot be None"):
         ensure_absolute_path(None)
-def test_database_relative_paths():
-    """Test relative path handling for vector and graph databases"""
-    system_root = "C:/system/root" if os.name == 'nt' else "/system/root"
-    
-    # Test with absolute path
-    abs_path = "C:/data/vector.db" if os.name == 'nt' else "/data/vector.db"
-    result = ensure_absolute_path(abs_path, base_path=system_root, allow_relative=True)
-    assert result == str(Path(abs_path).resolve())
-    
-    # Test with relative path (should convert to absolute)
-    rel_path = "data/vector.db"
-    result = ensure_absolute_path(rel_path, base_path=system_root, allow_relative=True)
-    expected = str((Path(system_root) / rel_path).resolve())
-    assert result == expected
-    
-    # Test with relative base_path (should fail)
-    with pytest.raises(ValueError, match="base_path must be absolute"):
-        ensure_absolute_path(rel_path, base_path="relative/base", allow_relative=True)
-    
-    # Test without base_path for relative path
-    with pytest.raises(ValueError, match="base_path must be provided"):
-        ensure_absolute_path(rel_path, allow_relative=True)
-def test_path_consistency():
-    """Test that paths are handled consistently across configurations"""
-    system_root = "C:/system/root" if os.name == 'nt' else "/system/root"
-    
-    # Root directories must be absolute
-    data_root = "C:/data/root" if os.name == 'nt' else "/data/root"
-    assert ensure_absolute_path(data_root, allow_relative=False) == str(Path(data_root).resolve())
-    
-    # Database paths can be relative but must resolve against system_root
-    db_paths = [
-        # Vector DB paths
-        "vector.db",                    # Simple relative
-        "data/vector.db",              # Nested relative
-        "../vector.db",                # Parent relative
-        "./vector.db",                 # Current dir relative
-        # Graph DB paths
-        "graph.db",                    # Simple relative
-        "data/graph/db",              # Nested relative
-        "../graph.db",                # Parent relative
-        "./graph.db",                 # Current dir relative
-        # With different extensions
-        "data/vector.lancedb",        # Vector DB with extension
-        "data/graph/kuzu",           # Graph DB with extension
-    ]
-    
-    for rel_path in db_paths:
-        result = ensure_absolute_path(rel_path, base_path=system_root, allow_relative=True)
-        expected = str((Path(system_root) / rel_path).resolve())
-        assert result == expected, f"Failed to resolve {rel_path} correctly"
-