refactor: Fix mcp migrations

[dexters1]

Description

• Include alembic migrations with Cognee library
• Use alembic migrations from Cognee library in Cognee MCP

Type of Change

• 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)

Pre-submission Checklist

• 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.

[pull-checklist]

Please make sure all the checkboxes are checked:

• I have tested these changes locally.
• I have reviewed the code changes.
• I have added end-to-end and unit tests (if applicable).
• I have updated the documentation and README.md file (if necessary).
• I have removed unnecessary code and debug statements.
• PR title is clear and follows the convention.
• I have tagged reviewers or team members for feedback.

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✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix-mcp-migrations

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[dexters1]

UV lock can be either removed or regenerated when new Cognee version is released

[dexters1]

Cognee v0.5.0 doesn't exist, but we need to set this to a version that has the changes from this PR when they become available

[borisarzentar]

Moving everything to cognee directory means that we can't call alembic upgrade head from cognee repo root like we used to do. We need to update docs if it is mentioned somewhere.

[dexters1]

Note: The location change of alembic migrations requires a Docker update as well along with workflow and docs updates