feat(mcp): add incremental memory updates

[ramonlimaramos]

Summary

• add update_memory for partial memory updates, metadata patches, and content append/replacement
• validate memory field length limits before database writes and document those limits in tool descriptions/docs
• refresh content-derived embedding/HRR/entity links after content updates and invalidate cache after updates
• pin urllib3>=2.7.0 so the security job remains green after new pip-audit advisories

Closes #48

Tests

• uv run pytest tests/ -q
• uv run ruff check src/ tests/
• uv run bandit -r src/synapto/ -c pyproject.toml
• uv run pip-audit
• uv run ruff format --check src/synapto/server.py src/synapto/repositories/memories.py src/synapto/repositories/entities.py tests/unit/test_memory_retrieval_tools.py tests/unit/test_tool_metadata.py

Note: full-project ruff format --check src/ tests/ still reports pre-existing formatting drift in unrelated files, so this PR validates formatting only for touched Python files.