chore: Remove trailing whitespaces in the project, fix YAMLs (#1980)

<!-- .github/pull_request_template.md -->

## Description
Removes trailing whitespaces from all files in the project. Needed by
https://github.com/topoteretes/cognee/pull/1979

## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->

## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):

## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->

## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **I have tested my changes thoroughly before submitting this PR**
- [ ] **This PR contains minimal changes necessary to address the
issue/feature**
- [ ] My code follows the project's coding standards and style
guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
- [ ] I have linked any relevant issues in the description
- [ ] My commits have clear and descriptive messages

## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **New Features**
* Added `topK` parameter support in search functionality to control
result count (1-100).
  * Added Python tool configuration via mise.toml.

* **Documentation**
* Enhanced issue templates with improved UI metadata, labels, and
clearer guidance for bug reports, feature requests, and documentation
issues.
* Expanded CONTRIBUTING.md with comprehensive contribution guidelines
and community information.

* **Chores**
* Removed unused modules: `cognee.modules.retrieval` and
`cognee.tasks.temporal_graph`.
* Applied consistent formatting and whitespace normalization across
configuration files, workflows, and documentation.

<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

.github/ISSUE_TEMPLATE/documentation.yml

@@ -71,4 +71,3 @@ body:
           required: true
         - label: I have specified the location of the documentation issue
           required: true
-

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -75,4 +75,3 @@ body:
           required: true
         - label: I have described my specific use case
           required: true
-

.github/core-team.txt

@@ -8,5 +8,3 @@ lxobr
 pazone
 siillee
 vasilije1990
-
-

.github/workflows/label-core-team.yml

@@ -72,5 +72,3 @@ jobs:
             } catch (error) {
               core.warning(`Failed to add label: ${error.message}`);
             }
-
-

.github/workflows/load_tests.yml

@@ -66,5 +66,3 @@ jobs:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_S3_DEV_USER_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_S3_DEV_USER_SECRET_KEY }}
         run: uv run python ./cognee/tests/test_load.py
-  
-    

.github/workflows/release_test.yml

@@ -15,4 +15,3 @@ jobs:
     name: Load Tests
     uses: ./.github/workflows/load_tests.yml
     secrets: inherit
-

.pre-commit-config.yaml

@@ -7,6 +7,7 @@ repos:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
+        exclude: ^deployment/helm/templates/
     -   id: check-added-large-files
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.

AGENTS.md

@@ -128,5 +128,3 @@ MCP server and Frontend:
 ## CI Mirrors Local Commands
 
 Our GitHub Actions run the same ruff checks and pytest suites shown above (`.github/workflows/basic_tests.yml` and related workflows). Use the commands in this document locally to minimize CI surprises.
-
-

cognee-frontend/src/ui/elements/Modal/index.ts

@@ -1,3 +1,2 @@
 export { default as Modal } from "./Modal";
 export { default as useModal } from "./useModal";
-

cognee-frontend/src/ui/elements/Notebook/MarkdownPreview.tsx

@@ -74,4 +74,3 @@ function MarkdownPreview({ content, className = "" }: MarkdownPreviewProps) {
 }
 
 export default memo(MarkdownPreview);
-

cognee/modules/notebooks/tutorials/python-development-with-cognee/data/copilot_conversations.json

@@ -105,4 +105,3 @@
     }
   }
 }
-

cognee/modules/notebooks/tutorials/python-development-with-cognee/data/pep_style_guide.md

@@ -72,4 +72,3 @@ profile = "black"
 - E501: line too long -> break with parentheses
 - E225: missing whitespace around operator
 - E402: module import not at top of file
-

cognee/modules/notebooks/tutorials/python-development-with-cognee/data/zen_principles.md

@@ -72,4 +72,3 @@ Use modules/packages to separate concerns; avoid wildcard imports.
 - Is this the simplest working solution?
 - Are errors explicit and logged?
 - Are modules/namespaces used appropriately?
-

cognee/modules/retrieval/__init__.py

@@ -1 +0,0 @@
-

cognee/tasks/temporal_graph/__init__.py

@@ -1 +0,0 @@
-

deployment/helm/docker-compose-helm.yml

@@ -43,4 +43,3 @@ networks:
 
 volumes:
   postgres_data:
-

deployment/helm/templates/postgres_service.yaml

@@ -11,4 +11,3 @@ spec:
       targetPort: {{ .Values.postgres.port }}
   selector:
     app: {{ .Release.Name }}-postgres
-

examples/python/weighted_graph_visualization.html

@@ -209,4 +209,3 @@
         </svg>
     </body>
     </html>
-    

mise.toml

@@ -0,0 +1,2 @@
+[tools]
+python = "latest"

new-examples/custom_pipelines/organizational_hierarchy/data/companies.json

@@ -36,4 +36,3 @@
     ]
   }
 ]
-

new-examples/custom_pipelines/organizational_hierarchy/data/people.json

@@ -50,4 +50,3 @@
     "department": "HR"
   }
 ]
-

new-examples/custom_pipelines/product_recommendation/data/customers.json

@@ -106,4 +106,3 @@
     "action": "purchased"
   }]
 }]
-

tools/check-package.sh

@@ -58,4 +58,3 @@ fi
 
 # error in package
 exit 1
-