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>

upgrade.sh

@@ -62,11 +62,17 @@ echo "Upgrading: $old_ref -> $new_ref"
 echo ""
 
 # Read current file-list (files to remove)
+# Entries prefixed with ? are sample files -- we don't remove those on upgrade.
 old_files=()
+old_samples=()
 while IFS= read -r line; do
     [[ "$line" =~ ^[[:space:]]*# ]] && continue
     [[ -z "$line" ]] && continue
-    old_files+=("$line")
+    if [[ "$line" == \?* ]]; then
+        old_samples+=("${line#\?}")
+    else
+        old_files+=("$line")
+    fi
 done < "$DIR/file-list"
 
 # Clone and checkout new version into a temp directory
@@ -76,25 +82,44 @@ git -C "$tmpdir/diachron" checkout --quiet "$new_ref"
 
 # Read new file-list (files to add)
 new_files=()
+new_samples=()
 while IFS= read -r line; do
     [[ "$line" =~ ^[[:space:]]*# ]] && continue
     [[ -z "$line" ]] && continue
-    new_files+=("$line")
+    if [[ "$line" == \?* ]]; then
+        new_samples+=("${line#\?}")
+    else
+        new_files+=("$line")
+    fi
 done < "$tmpdir/diachron/file-list"
 
-# Remove old framework files
+# Remove old framework files (not samples -- those belong to the user)
 for f in "${old_files[@]}"; do
     git -C "$DIR" rm -rf --quiet --ignore-unmatch "$f"
 done
 
 # Copy in new framework files
-(cd "$tmpdir/diachron" && tar cvf - "${new_files[@]}") | (cd "$DIR" && tar xf -)
+(cd "$tmpdir/diachron" && tar cf - "${new_files[@]}") | (cd "$DIR" && tar xf -)
 
 # Stage them
 for f in "${new_files[@]}"; do
     git -C "$DIR" add "$f"
 done
 
+# Handle sample files: copy only if the user doesn't already have them
+samples_added=()
+samples_skipped=()
+for f in "${new_samples[@]}"; do
+    if [ -e "$DIR/$f" ]; then
+        samples_skipped+=("$f")
+    else
+        # New sample that doesn't exist yet -- copy it in
+        (cd "$tmpdir/diachron" && tar cf - "$f") | (cd "$DIR" && tar xf -)
+        git -C "$DIR" add "$f"
+        samples_added+=("$f")
+    fi
+done
+
 # Update version marker
 echo "$new_ref" > "$DIR/.diachron-version"
 git -C "$DIR" add "$DIR/.diachron-version"
@@ -102,6 +127,23 @@ git -C "$DIR" add "$DIR/.diachron-version"
 echo "=== Upgrade staged: $old_ref -> $new_ref ==="
 echo ""
 echo "Framework files have been removed, replaced, and staged."
+
+if [ ${#samples_added[@]} -gt 0 ]; then
+    echo ""
+    echo "New sample files added:"
+    for f in "${samples_added[@]}"; do
+        echo "  + $f"
+    done
+fi
+
+if [ ${#samples_skipped[@]} -gt 0 ]; then
+    echo ""
+    echo "Sample files skipped (you already have these):"
+    for f in "${samples_skipped[@]}"; do
+        echo "  ~ $f"
+    done
+fi
+
 echo ""
 echo "Next steps:"
 echo "  1. Review:   git diff --cached"