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>

AGENTS.md

@@ -0,0 +1,44 @@
+# Agent Instructions
+
+Read and follow the instructions in `diachron/AGENTS.md`.  That file
+contains framework conventions, commands, and structure that apply to
+all coding agents working on diachron-based projects.
+
+This project uses **bd** (beads) for issue tracking. Run `bd onboard` to get started.
+
+## Quick Reference
+
+```bash
+bd ready              # Find available work
+bd show <id>          # View issue details
+bd update <id> --status in_progress  # Claim work
+bd close <id>         # Complete work
+bd sync               # Sync with git
+```
+
+## Landing the Plane (Session Completion)
+
+**When ending a work session**, you MUST complete ALL steps below. Work is NOT complete until `git push` succeeds.
+
+**MANDATORY WORKFLOW:**
+
+1. **File issues for remaining work** - Create issues for anything that needs follow-up
+2. **Run quality gates** (if code changed) - Tests, linters, builds
+3. **Update issue status** - Close finished work, update in-progress items
+4. **PUSH TO REMOTE** - This is MANDATORY:
+   ```bash
+   git pull --rebase
+   bd sync
+   git push
+   git status  # MUST show "up to date with origin"
+   ```
+5. **Clean up** - Clear stashes, prune remote branches
+6. **Verify** - All changes committed AND pushed
+7. **Hand off** - Provide context for next session
+
+**CRITICAL RULES:**
+- Work is NOT complete until `git push` succeeds
+- NEVER stop before pushing - that leaves work stranded locally
+- NEVER say "ready to push when you are" - YOU must push
+- If push fails, resolve and retry until it succeeds
+

CLAUDE.md

@@ -3,6 +3,10 @@
 This file provides guidance to Claude Code (claude.ai/code) when working with
 code in this repository.
 
+Read and follow the instructions in `diachron/AGENTS.md`.  That file
+contains framework conventions, commands, and structure that apply to
+all coding agents working on diachron-based projects.
+
 ## Project Overview
 
 Diachron is an opinionated TypeScript/Node.js web framework with a Go-based

DIACHRON.md

@@ -88,8 +88,24 @@ There are two owners of files in a diachron project:
   `backend/diachron/`, and the top-level scripts (`cmd`, `develop`, `mgmt`,
   `sync.sh`, `check.sh`).
 
-Don't modify framework-owned files.  This separation keeps framework upgrades
+Don't modify framework-owned files unless you need to.  This separation
-clean.
+keeps framework upgrades clean.  If you do need to change framework files
+(especially early on, there are rough edges), you can extract your changes
+as a patch:
+
+```bash
+./diff-upstream.sh          # full diff against upstream
+./diff-upstream.sh --stat   # just list changed files
+```
+
+This diffs every file in `file-list` against the upstream ref recorded in
+`.diachron-version`.
+
+When you do change framework files, make each change in its own commit with
+a clear message explaining what the change is and why it's needed.  Mixing
+framework fixes with application work in a single commit makes it much
+harder to upstream later.  A clean history of discrete, well-explained
+framework commits is the easiest thing to turn into contributions.
 
 ## Getting started
 

backend/diachron/app.ts

@@ -61,7 +61,7 @@ const makeApp = ({routes, processTitle}: MakeAppArgs) => {
         console.log("DEBUG: trying pattern, match result =", match);
         if (match) {
             console.log("match", match);
-            const resp = await pr.handler(req);
+            const resp = await pr.handler(req, match.params);
 
             return resp;
         }

backend/diachron/routing.ts

@@ -29,6 +29,7 @@ const processRoutes=(routes:Route[]) :ProcessedRoutes => {
         
         const handler: InternalHandler = async (
             expressRequest: ExpressRequest,
+            params: Record<string, string>,
         ): Promise<Result> => {
             const method = massageMethod(expressRequest.method);
             
@@ -47,7 +48,7 @@ const processRoutes=(routes:Route[]) :ProcessedRoutes => {
                 pattern: route.path,
                 path: expressRequest.originalUrl,
                 method,
-                parameters: { one: 1, two: 2 },
+                parameters: params,
                 request: expressRequest,
                 user: auth.user,
                 session: new Session(auth.session, auth.user),

backend/diachron/types.ts

@@ -29,13 +29,13 @@ export type Call = {
     pattern: string;
     path: string;
     method: Method;
-    parameters: object;
+    parameters: Record<string, string>;
     request: ExpressRequest;
     user: User;
     session: Session;
 };
 
-export type InternalHandler = (req: ExpressRequest) => Promise<Result>;
+export type InternalHandler = (req: ExpressRequest, params: Record<string, string>) => Promise<Result>;
 
 export type Handler = (call: Call) => Promise<Result>;
 export type ProcessedRoute = {

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

@@ -137,6 +137,14 @@ Do not edit:           master/*, logger/*, diachron/*, backend/diachron/*
 ```
 
 If a task requires framework changes, confirm with the user first.
+When framework files are modified, the changes can be extracted as a
+diff against upstream with `./diff-upstream.sh` (or `--stat` to list
+changed files only).
+
+When committing framework changes, keep them in separate commits from
+application code.  Each framework commit should have a clear message
+explaining what was changed and why.  This makes it much easier to
+upstream the changes later.
 
 ### Command safety tiers
 
@@ -179,6 +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

@@ -0,0 +1,116 @@
+#!/bin/bash
+
+# Generate a diff of framework files against the upstream version this
+# project is based on.  Useful for contributing changes back to diachron.
+#
+# Usage:
+#   ./diff-upstream.sh              # diff against .diachron-version
+#   ./diff-upstream.sh <ref>        # diff against a specific ref
+#   ./diff-upstream.sh --stat       # show changed files only
+
+set -eu
+set -o pipefail
+IFS=$'\n\t'
+
+DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+stat_only=false
+ref=""
+
+for arg in "$@"; do
+    case "$arg" in
+        --stat) stat_only=true ;;
+        *)      ref="$arg" ;;
+    esac
+done
+
+if [ -z "$ref" ]; then
+    if [ ! -f "$DIR/.diachron-version" ]; then
+        echo "Error: .diachron-version not found and no ref specified." >&2
+        echo "Usage: $0 [--stat] [<ref>]" >&2
+        exit 1
+    fi
+    ref=$(cat "$DIR/.diachron-version")
+fi
+
+cached_repo="$HOME/.cache/diachron/v1/repositories/diachron.git"
+
+if [ ! -d "$cached_repo" ]; then
+    echo "Error: cached repository not found at $cached_repo" >&2
+    echo "Run ./update-cached-repository.sh first." >&2
+    exit 1
+fi
+
+# Update cached repo
+"$DIR/update-cached-repository.sh"
+
+# Verify ref exists
+if ! git -C "$cached_repo" rev-parse --verify "$ref^{commit}" >/dev/null 2>&1; then
+    echo "Error: ref '$ref' not found in cached repository." >&2
+    exit 1
+fi
+
+# Read file-list (strip ? prefix from sample entries)
+files=()
+while IFS= read -r line; do
+    [[ "$line" =~ ^[[:space:]]*# ]] && continue
+    [[ -z "$line" ]] && continue
+    files+=("${line#\?}")
+done < "$DIR/file-list"
+
+# Check out upstream into a temp directory
+tmpdir=$(mktemp -d)
+cleanup() { rm -rf "$tmpdir"; }
+trap cleanup EXIT
+
+git clone --quiet "$cached_repo" "$tmpdir/upstream"
+git -C "$tmpdir/upstream" checkout --quiet "$ref"
+
+# Generate diff
+if $stat_only; then
+    diff -rq "$tmpdir/upstream" "$DIR" \
+        --no-dereference \
+        2>/dev/null \
+        | grep -v '^\.' \
+        || true
+
+    # Simpler: just list files that differ
+    for f in "${files[@]}"; do
+        # Skip directories
+        [ -d "$DIR/$f" ] && continue
+
+        upstream="$tmpdir/upstream/$f"
+        local="$DIR/$f"
+
+        if [ ! -f "$upstream" ] && [ -f "$local" ]; then
+            echo "added:    $f"
+        elif [ -f "$upstream" ] && [ ! -f "$local" ]; then
+            echo "removed:  $f"
+        elif [ -f "$upstream" ] && [ -f "$local" ]; then
+            if ! diff -q "$upstream" "$local" >/dev/null 2>&1; then
+                echo "modified: $f"
+            fi
+        fi
+    done
+else
+    for f in "${files[@]}"; do
+        [ -d "$DIR/$f" ] && continue
+
+        upstream="$tmpdir/upstream/$f"
+        local="$DIR/$f"
+
+        if [ ! -f "$upstream" ] && [ -f "$local" ]; then
+            diff -u /dev/null "$local" \
+                --label "a/$f" --label "b/$f" \
+                || true
+        elif [ -f "$upstream" ] && [ ! -f "$local" ]; then
+            diff -u "$upstream" /dev/null \
+                --label "a/$f" --label "b/$f" \
+                || true
+        elif [ -f "$upstream" ] && [ -f "$local" ]; then
+            diff -u "$upstream" "$local" \
+                --label "a/$f" --label "b/$f" \
+                || true
+        fi
+    done
+fi

file-list

@@ -1,31 +1,37 @@
 # 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
 develop
+diff-upstream.sh
 diachron
 diachron/AGENTS.md
 file-list

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"