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>

file-list

@@ -1,27 +1,32 @@
 # please keep this file sorted alphabetically
+#
+# Files prefixed with ? are sample/starter files.  bootstrap.sh copies them
+# into a new project, but upgrade.sh will not overwrite them if the user has
+# already modified or replaced them.  Unprefixed files are framework-owned
+# and are always replaced on upgrade.
 
 .gitignore
 .go-version
 DIACHRON.md
 backend/.gitignore
 backend/.npmrc
-backend/app.ts
+?backend/app.ts
 backend/build.sh
 backend/check-deps.ts
 backend/check.sh
 backend/diachron
 backend/generated
-backend/group.ts
-backend/handlers.spec.ts
-backend/handlers.ts
-backend/package.json
+?backend/group.ts
+?backend/handlers.spec.ts
+?backend/handlers.ts
+?backend/package.json
 backend/pnpm-workspace.yaml
-backend/routes.ts
+?backend/routes.ts
 backend/run.sh
-backend/services.ts
+?backend/services.ts
 backend/show-config.sh
 backend/tsconfig.json
-backend/types.ts
+?backend/types.ts
 backend/watch.sh
 bootstrap.sh
 cmd