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>

diff-upstream.sh

@@ -50,12 +50,12 @@ if ! git -C "$cached_repo" rev-parse --verify "$ref^{commit}" >/dev/null 2>&1; t
     exit 1
 fi
 
-# Read file-list
+# Read file-list (strip ? prefix from sample entries)
 files=()
 while IFS= read -r line; do
     [[ "$line" =~ ^[[:space:]]*# ]] && continue
     [[ -z "$line" ]] && continue
-    files+=("$line")
+    files+=("${line#\?}")
 done < "$DIR/file-list"
 
 # Check out upstream into a temp directory