audit clean-env install/runtime deps for user-rag CLI

[HumanBean17]

Context

PR-V2-4 extracted operational commands into the user-rag CLI and fixed packaging/import wiring for installed usage. There is still a non-blocking residual risk that pip install . may not be fully self-sufficient in a brand-new environment due to pre-existing dependency metadata gaps.

Problem

In a fresh environment, some user-rag subcommands may fail at runtime if transitive/imported dependencies are not fully declared in pyproject.toml.

Goal

Validate and tighten install/runtime dependency metadata so a fresh environment can run all CLI subcommands reliably.

Proposed scope

• Create a brand-new virtual environment (no preinstalled project deps).
• Install with pip install . (and separately verify pip install -e .).
• Run and verify each command path:
  • user-rag --help
  • user-rag meta
  • user-rag tables
  • user-rag diagnose-ignore <path>
  • user-rag analyze-pr --diff-file <file>
  • user-rag refresh --source-root <fixture> --kuzu-path <tmp> --quiet
• Record any ModuleNotFoundError / missing runtime dependency failures.
• Add missing runtime dependencies to pyproject.toml only as needed.
• Add/adjust tests if necessary to prevent regressions.

Acceptance criteria

• Fresh-venv pip install . succeeds.
• All user-rag subcommands execute without missing-dependency errors (for valid inputs).
• Dependency declarations reflect actual runtime requirements for CLI paths.
• No unrelated refactors.