[3.13] gh-131261: generate_sbom.py: Exclude the refresh script from SBOM (GH-131359) (GH-144625)

- generate_sbom.py: Exclude the refresh script from SBOM
- Modules/expat/refresh.sh: Expand the list of manual steps

(cherry picked from commit 51d309988b3041cae20cca89172b4fd825c9a1cc)