Add ? prefix for sample files in file-list; fix bootstrap/upgrade

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

@@ -42,8 +42,8 @@ echo working dir: $PWD
 
 # exit 0
 
-tar cvf - $(cat "$PWD/file-list" | grep -v '^#') | (cd "$here" && tar xf -)
+tar cvf - $(cat "$PWD/file-list" | grep -v '^#' | sed 's/^?//') | (cd "$here" && tar xf -)
 
-echo "$ref" > .diachron-version
+echo "$ref" > "$here/.diachron-version"
 
 echo "Now, run the command ./sync.sh"