chore: fix lint errors and modernize python syntax

[Cipher208]

This PR fixes over 300 linting errors and modernizes type annotations to use Python 3.10+ syntax (| None, list, dict).

[coderabbitai]

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📥 Commits

Reviewing files that changed from the base of the PR and between d08d27a and a5e41fe.

⛔ Files ignored due to path filters (1)

• uv.lock is excluded by !**/*.lock

📒 Files selected for processing (84)

• .claude/CLAUDE.md
• .pytest_cache/v/cache/lastfailed
• .pytest_cache/v/cache/nodeids
• core/__init__.py
• core/episodic.py
• core/memory.py
• core/reflex.py
• core/session.py
• demo.py
• docs/research/RESEARCH-ideas.md
• features/audit_trail.py
• features/auth.py
• features/backup.py
• features/backup_cron.py
• features/compression.py
• features/dashboard.py
• features/import_export.py
• features/rate_limiting.py
• features/secrets.py
• graph/epistemic.py
• graph/temporal.py
• hooks/registry.py
• hooks/shared.py
• hooks/user_hooks.py
• lifecycle/consolidation.py
• lifecycle/emotion_trigger.py
• lifecycle/forgetting.py
• lifecycle/importance_scheduler.py
• mcp_server/registry.py
• mcp_server/server.py
• mcp_server/tools_layer.py
• mcp_server/tools_ops.py
• mcp_server/utils/circuit_breaker.py
• mcp_server/utils/privacy.py
• rag/conflict.py
• rag/engine.py
• rag/multi_source.py
• rag/quantize.py
• rag/router.py
• rag/scoring.py
• rag/search.py
• shared/archived_memories.py
• shared/dream_buffer.py
• shared/embeddings.py
• shared/importance.py
• shared/memory_types.py
• shared/middleware.py
• shared/migrations.py
• shared/read_only.py
• shared/saga.py
• shared/saga_crypto.py
• shared/План перехода на aiosqlite.md
• tests/benchmark_memory.py
• tests/benchmark_perf.py
• tests/test_auth_crypto.py
• tests/test_conflict_bm25.py
• tests/test_features/test_backup_path_safety.py
• tests/test_features/test_import_export_path_safety.py
• tests/test_features_coverage.py
• tests/test_hypothesis.py
• tests/test_importance_middleware.py
• tests/test_importance_scheduler.py
• tests/test_importance_v2.py
• tests/test_mcp/test_tools_e2e.py
• tests/test_mcp/test_tools_unit.py
• tests/test_memory_types.py
• tests/test_rag_chunking.py
• tests/test_rag_no_legacy_api.py
• tests/test_rag_scoring.py
• tests/test_saga_behavior.py
• tests/test_shared/test_connection.py
• tests/test_shared/test_embeddings_unit.py
• tests/test_shared/test_middleware_unit.py
• tests/test_shared/test_migrations_coverage.py
• tests/test_shared/test_read_only_coverage.py
• tests/test_shared/test_saga_crypto_coverage.py
• tests/test_shared/test_saga_crypto_wiring.py
• tests/test_shared/test_saga_unit.py
• tests/test_threshold_training.py
• tests/test_typed_consolidation.py
• tests/test_typed_forgetting.py
• tests/test_wiki/test_manager.py
• tests/test_wiki/test_path_safety.py
• wiki/manager.py

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[greptile-apps]

Greptile Summary

This PR modernizes Python annotations and lint-sensitive constructs while preserving existing runtime behavior.

• Replaces legacy typing aliases with built-in generics and union syntax.
• Simplifies equivalent control flow, formatting, and exception suppression.
• Reorders imports and updates lint-generated lock and test files.
• Accidentally adds local pytest cache artifacts that should remain untracked.

Confidence Score: 4/5

The PR appears safe to merge after removing the accidentally committed pytest cache artifacts.

The production-code changes preserve existing behavior; the only accepted issue is non-blocking repository churn from tracking generated pytest cache state.

Files Needing Attention: .pytest_cache/v/cache/lastfailed and .pytest_cache/v/cache/nodeids

Important Files Changed

Filename	Overview
shared/saga.py	Modernizes formatting, annotations, conditionals, and exception suppression without changing saga persistence or recovery behavior.
mcp_server/tools_layer.py	Applies typing and lint modernization while preserving tool signatures, filtering, hook invocation, and response shapes.
rag/engine.py	Uses modern annotations, explicit non-strict zip behavior, and equivalent exception suppression without changing retrieval semantics.
features/auth.py	Replaces legacy typing and equivalent OSError suppression without changing authentication behavior.
shared/migrations.py	Rewrites ignored OperationalError handlers using contextlib.suppress with equivalent migration behavior.
.pytest_cache/v/cache/lastfailed	Adds generated local failure metadata that should be removed from version control.
.pytest_cache/v/cache/nodeids	Adds generated pytest collection state that will produce ongoing repository churn.

Prompt To Fix All With AI

### Issue 1
.pytest_cache/v/cache/lastfailed:1-6
**Generated pytest cache tracked**

This adds local pytest failure and collection state to version control; subsequent test runs rewrite these generated files, creating unrelated repository churn. Remove both `.pytest_cache/v/cache/lastfailed` and `.pytest_cache/v/cache/nodeids` from the change and keep the cache ignored.

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (1): Last reviewed commit: "chore: fix 300+ lint errors and moderniz..." | Re-trigger Greptile}

[greptile-apps]

Generated pytest cache tracked

This adds local pytest failure and collection state to version control; subsequent test runs rewrite these generated files, creating unrelated repository churn. Remove both .pytest_cache/v/cache/lastfailed and .pytest_cache/v/cache/nodeids from the change and keep the cache ignored.

Prompt To Fix With AI

This is a comment left during a code review.
Path: .pytest_cache/v/cache/lastfailed
Line: 1-6

Comment:
**Generated pytest cache tracked**

This adds local pytest failure and collection state to version control; subsequent test runs rewrite these generated files, creating unrelated repository churn. Remove both `.pytest_cache/v/cache/lastfailed` and `.pytest_cache/v/cache/nodeids` from the change and keep the cache ignored.

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!