⚙️ Upgrade dependencies and synchronize documentation

[Miyamura80]

Summary

• Upgraded project dependencies to latest stable versions (DSPy 3.1.2, Pydantic 2.12.5, Google GenAI 1.60.0, etc.).
• Synchronized CLAUDE.md and README.md with the actual project structure of the main branch.
• Fixed tool.hatch wheel packaging configuration in pyproject.toml.
• Resolved type-checking errors surfaced by dependency upgrades.
• Cleaned up outdated items in TODO.md.
• Verified stability with a full CI run and test suite execution.

[greptile-apps]

Greptile Overview

Greptile Summary

This PR upgrades project dependencies to their latest stable versions (DSPy 3.1.2, Pydantic 2.10.6, Langfuse 3.12.1, etc.) and synchronizes documentation with the actual project structure on the main branch.

Key changes:

• Upgraded 20+ dependencies in pyproject.toml to latest stable versions
• Fixed tool.hatch.build.targets.wheel.packages configuration to correctly include ["src", "common", "utils"] instead of the non-existent ["src/python_template"]
• Synchronized CLAUDE.md and README.md to accurately reflect the current project structure (removed references to non-existent alembic/, api/, db/, stripe/ directories)
• Removed unnecessary type: ignore comments in test files and utils/llm/dspy_langfuse.py that are no longer needed after dependency upgrades improved type checking
• Added isinstance(message, str) assertions in tests/test_logging_security.py to satisfy type checker requirements
• Updated uv.lock to reflect new dependency versions

The changes are straightforward and well-tested according to the PR description. All modifications improve code quality by removing outdated type ignore comments and fixing documentation accuracy.

Confidence Score: 5/5

• This PR is safe to merge with minimal risk
• All changes are maintenance-oriented (dependency upgrades, documentation synchronization, and type-checking improvements). The dependency upgrades follow semantic versioning with minor/patch bumps. Type ignore comment removals indicate improved typing from newer library versions. Documentation changes accurately reflect the current codebase structure. The PR author verified stability with a full CI run and test suite execution.
• No files require special attention

Important Files Changed

Filename	Overview
CLAUDE.md	Updated documentation to reflect current project structure and CI targets
README.md	Updated make command descriptions to be more accurate
pyproject.toml	Upgraded dependencies to latest stable versions and fixed wheel packaging configuration
tests/test_logging_security.py	Added type assertions to fix type-checking errors from dependency upgrades
utils/llm/dspy_langfuse.py	Removed unnecessary type ignore comments after dependency upgrades improved typing