Manifest Update

Update your Manifest project from the upstream Manifest repository using diff-based atomic sync.

When to use: The user says "manifest update", "update from upstream", "pull upstream changes", or similar.

Philosophy

You control what enters your app. The agent computes what changed upstream since your last sync, shows the changes grouped by area, and applies them as a single atomic diff. No per-commit cherry-picking, no replay of already-applied changes, no cascade of false conflicts.

The manifest branch is your local read-only copy of the upstream framework. main is your application. Updates flow from manifest-upstream remote → manifest branch → aggregate diff onto main.

How It Works

A .manifest-sync file in the project root stores the upstream commit hash that main was last synced to. On update:

•Fetch upstream and fast-forward the manifest branch
•Diff between .manifest-sync hash and current manifest HEAD
•Show what changed (commits for context, files for review)
•Apply the aggregate diff as a single commit
•Update .manifest-sync to the new upstream hash

Conflicts are resolved once per file — not once per upstream commit.

Steps

1. Ensure Setup Is Correct

bash

# Check manifest-upstream remote
git remote get-url manifest-upstream 2>/dev/null || echo "MISSING"

# Check manifest branch exists
git branch --list manifest | grep -q manifest || echo "MISSING"

# Check .manifest-sync exists
test -f .manifest-sync && echo "Sync file: $(cat .manifest-sync)" || echo "MISSING"

If manifest-upstream remote is missing:

bash

git remote add manifest-upstream https://github.com/HazAT/manifest.git

If manifest branch is missing:

bash

git fetch manifest-upstream
git branch manifest manifest-upstream/main

If .manifest-sync is missing:

This means the project hasn't synced before with the new mechanism. Set it to the current manifest HEAD so that future updates diff from here:

bash

echo "$(git rev-parse manifest)" > .manifest-sync
git add .manifest-sync
git commit -m "chore: initialize manifest sync marker"

Then tell the user: "Sync marker initialized. Run manifest update again next time upstream has new changes."

2. Sync the Manifest Branch

Fast-forward manifest to match upstream:

bash

git fetch manifest-upstream
git checkout manifest
git merge --ff-only manifest-upstream/main
git checkout -    # back to previous branch

If fast-forward fails: Someone committed directly to the manifest branch. This should never happen — manifest is a read-only mirror. Warn the user and offer git reset --hard manifest-upstream/main on the manifest branch.

3. Check for New Changes

bash

LAST_SYNC=$(cat .manifest-sync)
UPSTREAM=$(git rev-parse manifest)

If $LAST_SYNC equals $UPSTREAM, tell the user they're up to date and stop.

Show upstream commits for context (the "why"):

bash

git log --oneline "$LAST_SYNC".."$UPSTREAM"

Show aggregate file changes (the "what"):

bash

git diff --stat "$LAST_SYNC".."$UPSTREAM"

Read the full commit messages to understand intent:

bash

git log --format="medium" "$LAST_SYNC".."$UPSTREAM"

4. Categorize and Present

Group changed files by area:

Area	Path pattern	Description
Framework	`manifest/`	Core framework improvements
Skills	`.claude/skills/`	Prompt and workflow refinements
Docs	`AGENTS.md`, `SPARK.md`, `README.md`	Documentation updates
Extensions	`extensions/`	New or updated extensions
Config	`config/`	Config structure changes
Root	`index.ts`, `package.json`, `tsconfig.json`	Project root files

For each area, check if the user has locally modified any of the same files since the last sync:

bash

UPSTREAM_FILES=$(git diff --name-only "$LAST_SYNC".."$UPSTREAM")

for file in $UPSTREAM_FILES; do
  LOCAL_CHANGE=$(git diff --name-only "$LAST_SYNC"..HEAD -- "$file")
  if [ -n "$LOCAL_CHANGE" ]; then
    echo "⚠️  $file — changed both upstream and locally (will need merge)"
  fi
done

Present a summary like:

code

### Framework (manifest/)
Files: manifest/server.ts, manifest/frontend.ts
Status: Clean — no local changes ✅

### Docs
Files: AGENTS.md
Status: ⚠️ Locally modified — will need merge

Ask the user to confirm before applying.

5. Apply the Diff

Generate and apply the aggregate patch:

bash

git diff "$LAST_SYNC".."$UPSTREAM" > /tmp/manifest-update.patch
git apply --3way /tmp/manifest-update.patch

If everything applies cleanly — proceed to step 6.

If git apply --3way reports conflicts:

The working tree will have conflict markers in affected files. Resolve them:

•Read both versions of each conflicted file
•
Resolution rules:
- •Framework file not locally customized → take upstream's version: git checkout manifest -- <file>
- •Framework file locally customized → merge both changes, preserving local customizations while incorporating the upstream improvement
- •App-specific file (VISION.md, user features, user services) → keep your version
•Stage resolved files: git add <resolved-file>

If git apply --3way fails entirely (e.g., binary files, renames), fall back to per-file application:

bash

# For each changed file, decide:
# - No local changes → take upstream version directly
git checkout manifest -- <file>

# - Local changes exist → 3-way merge manually
# Read the base (last sync), upstream, and local versions, then merge

6. Commit the Sync

bash

# Update the sync marker
echo "$UPSTREAM" > .manifest-sync

# Stage all changes
git add -A

# Commit
git commit -m "sync: update manifest framework to $(echo $UPSTREAM | head -c 7)

Synced from $(echo $LAST_SYNC | head -c 7) to $(echo $UPSTREAM | head -c 7).

Upstream commits:
$(git log --oneline "$LAST_SYNC".."$UPSTREAM")

Changed files:
$(git diff --stat "$LAST_SYNC".."$UPSTREAM" | tail -1)"

7. Verify

bash

bun test
bunx tsc --noEmit

Both must pass. If something fails, investigate and fix before considering the update complete.

Rules

•Always show what changed before applying. The agent presents areas and conflict risk. The user confirms.
•Never modify the manifest branch. It's a read-only mirror of upstream.
•Always update .manifest-sync after syncing so the next update starts from the right place.
•Always use GIT_EDITOR=true when git commands might open an editor.
•Always read upstream commits first. The commit messages explain why things changed — show them to the user.
•Always test after syncing. bun test, bunx tsc --noEmit.
•Warn about local modifications. Flag files changed on both sides before applying.
•Preserve app identity. VISION.md, user features, user services, and deployment configs are the user's — never overwrite them with upstream versions.
•One commit per sync. The entire update is a single descriptive commit, not a replay of upstream history.