PR8: fix(inference): review follow-up in pipeline scripts

[SergeiNikolenko]

Summary

This PR contains targeted inference-pipeline fixes requested in review, plus a final cleanup pass in the same script area.

No new features are added.

Review Issues Addressed

1) Checkpoint root mismatch in v2 inference pipeline

File: matcha/utils/inference_utils.py

Issue:

• run_v2_inference_pipeline used conf.results_folder.
• YAML configs generally expose checkpoints_folder.

Fix:

• Added fallback resolution order:
  1. results_folder
  2. checkpoints_folder
• Added explicit error if neither key is available.

2) Duplicate stage save / script cleanup

File: scripts/run_inference_pipeline.py

Issue:

• duplicate stage-save behavior in legacy script path.

Fix:

• removed duplicate save behavior,
• simplified surrounding script logic in a follow-up cleanup.

File-Level Scope

• matcha/utils/inference_utils.py
• scripts/run_inference_pipeline.py

Quick Validation Command

uv run python scripts/run_inference_pipeline.py \
  -c configs/base.yaml \
  -p configs/default.yaml \
  -n pr8_pipeline_check \
  --n-samples 2

[SergeiNikolenko]

Superseded by #33 (restacked on #32, no codex/ branch names).