Observe pyproject metadata in project diagnostics

[codeforester]

Summary

• Add read-only pyproject.toml diagnostics beside the active Base manifest.
• Report pyproject metadata, dependency metadata, malformed TOML, and unsupported [tool.base] through existing check/doctor output.
• Document the diagnostic finding IDs and source-of-truth boundary.

Validation

• PYTHONPATH=lib/python:cli/python /Users/rameshhp/.base.d/base/.venv/bin/python -m pytest cli/python/base_setup/tests/test_pyproject.py cli/python/base_setup/tests/test_diagnostics.py -q
• env -u BASE_HOME ./bin/base-test
• git diff --check

Demo Impact

• None. Diagnostics-only change.

Closes #358