fix: --from-stage without --output now finds existing run directory

[dennis-lynch-nv]

Summary

When using --from-stage without --output, the CLI generates a new empty run directory via _generate_run_id(). The StageContract.input_files check then fails immediately because prior stage artifacts (e.g., exp_plan.yaml from stage 9) don't exist in the fresh directory.

Fix

Extend the BUG-119 checkpoint-search logic (already working for --resume) to also apply when --from-stage is specified. One-line condition change:

# Before:
if resume and not output:

# After:
if (resume or from_stage_name) and not output:

Tests

5 new test cases in tests/test_from_stage_run_dir.py:

Test	Description
test_from_stage_without_output_finds_existing_run	Core fix — --from-stage finds existing run dir
test_from_stage_without_output_old_behavior_fails	Proves the bug existed before fix
test_resume_still_works	No regression for --resume
test_explicit_output_skips_search	--output bypasses search
test_picks_newest_run_when_multiple_exist	Multiple runs → picks newest

tests/test_from_stage_run_dir.py .....                     [100%]
tests/test_cli.py ...                                      [100%]
8 passed in 0.16s

Fixes #216

[Jiaaqiliu]

Merged manually via cherry-pick in commit 7b57457. Thank you @dennis-lynch-nv for the fix and tests!