bootstrap.sh wrote .diachron-version to the temp clone directory
instead of the target project, causing upgrade.sh to fail. Fix that
and teach all three scripts (bootstrap, upgrade, diff-upstream) about
the new ? prefix convention in file-list.
Sample files (?-prefixed) are copied on bootstrap but left alone on
upgrade so user modifications are preserved. New samples introduced
in a newer framework version are still copied if absent.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Removes old framework files (per current file-list), copies in new
ones from the target ref, and stages everything for the user to
review before committing. Also adds file-list to itself so it
gets upgraded too.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
