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>
bootstrap.sh clones from a local mirror and extracts framework
files into the working directory. update-cached-repository.sh
maintains the mirror under ~/.cache/diachron/v1/repositories/.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>