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"

diachron/AGENTS.md

@@ -187,6 +187,21 @@ framework.  When you create or delete a file that is part of the project
 (not a scratch file or generated output), you must update `file-list` to
 match.  Keep it sorted alphabetically.
 
+Entries can have a `?` prefix (e.g. `?backend/app.ts`).  These are
+**sample files** -- starter code that `bootstrap.sh` copies into a new
+project but that `upgrade.sh` will not overwrite.  Once the user has the
+file, it belongs to them.  On upgrade, new sample files that don't exist
+yet in the project are copied in; existing ones are left untouched.
+
+Unprefixed entries are **framework-owned** and are always replaced on
+upgrade.  When adding a new file to `file-list`, decide which category
+it belongs to:
+
+- Framework-owned (no prefix): infrastructure scripts, framework
+  library code, build tooling, config that must stay in sync.
+- Sample (`?` prefix): application starter code the user is expected
+  to edit (routes, handlers, services, types, package.json, etc.).
+
 ## Things to avoid
 
 - Do not introduce `.env` files or `dotenv` without checking with the

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

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/group.ts
-backend/handlers.spec.ts
+?backend/handlers.spec.ts
-backend/handlers.ts
+?backend/handlers.ts
-backend/package.json
+?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

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
+    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
+    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"