Keep Project Intake gh stderr out of JSON output

[codeforester]

Summary

• capture project_intake_gh stdout and stderr separately
• replay successful stderr notices on stderr without contaminating JSON stdout
• keep auth and retry diagnostics using combined failure output
• add a regression test for non-fatal gh stderr with valid JSON stdout

Fixes #1317

Tests

• PYTHONPATH=lib/python:cli/python /Users/rameshhp/.base.d/base/.venv/bin/python -m pytest tests/test_github_workflows.py::test_project_intake_keeps_success_stderr_out_of_json_stdout -q
• PYTHONPATH=lib/python:cli/python /Users/rameshhp/.base.d/base/.venv/bin/python -m pytest tests/test_github_workflows.py -q
• git diff --check