Smart Upgrade

Pulls the latest claudesidian from GitHub and merges it into the user's vault, preserving customizations.

Layout assumptions (READ FIRST)

claudesidian stores skills under .agents/skills/<name>/SKILL.md as the canonical location. Symlinks live at .claude/skills/<name> and .pi/skills/<name> pointing back to canonical. Edit canonical, all consumers follow.

If the user is on a pre-conversion claudesidian (anything before the commands→skills migration) they will have .claude/commands/*.md instead and no .agents/skills/. Do not run a normal upgrade in that case — see "Migration from legacy layout" at the bottom of this file.

If the user's local repo has .agents/skills/ populated, proceed normally.

Process

1. Version check

• Read current version from package.json
• Fetch upstream version:

  CURRENT=$(grep '"version"' package.json | head -1 | cut -d'"' -f4)
  LATEST=$(curl -s https://raw.githubusercontent.com/heyitsnoah/claudesidian/main/package.json | grep '"version"' | head -1 | cut -d'"' -f4)
  if [ "$CURRENT" = "$LATEST" ]; then
    echo "✅ Already on $CURRENT"
    exit 0
  fi

• Detect layout: test -d .agents/skills && echo NEW || echo LEGACY. If LEGACY, jump to "Migration from legacy layout".

2. Backup

BACKUP_DIR=".backup/upgrade-$(date +%Y-%m-%d-%H%M%S)"
mkdir -p "$BACKUP_DIR"
cp -r .agents .claude .pi .scripts package.json "$BACKUP_DIR/" 2>/dev/null
cp CHANGELOG.md README.md "$BACKUP_DIR/" 2>/dev/null || true
echo "✅ Backup created at $BACKUP_DIR"

3. Fetch upstream

git clone --depth=1 --branch=main \
  https://github.com/heyitsnoah/claudesidian.git \
  .tmp/claudesidian-upgrade

The user's working repo stays disconnected from origin throughout — we only ever read from .tmp/.

4. Build upgrade checklist

System files we care about:

• Skills: .agents/skills/<name>/SKILL.md (canonical) — also resources inside skill dirs (helper scripts, references).
• Hooks: .claude/hooks/*.sh
• Settings: .claude/settings.json
• MCP servers: .claude/mcp-servers/*
• Scripts: .scripts/*
• Core: package.json, CHANGELOG.md, README.md

Files we never touch:

• User content folders: 00_Inbox/, 01_Projects/, 02_Areas/, 03_Resources/, 04_Archive/, 05_Attachments/, 06_Metadata/ (except 06_Metadata/Templates/ if upstream changes them)
• The user's CLAUDE.md
• .obsidian/ (user's Obsidian settings)
• vault-config.json
• .mcp.json (contains API keys)
• Anything in .git/

Build the checklist:

# Skills that exist in both, or only upstream, or only local
diff -qr .agents/skills .tmp/claudesidian-upgrade/.agents/skills 2>/dev/null

# Hooks, settings, mcp-servers, scripts
diff -qr .claude/hooks .tmp/claudesidian-upgrade/.claude/hooks 2>/dev/null
diff -q .claude/settings.json .tmp/claudesidian-upgrade/.claude/settings.json 2>/dev/null
diff -qr .claude/mcp-servers .tmp/claudesidian-upgrade/.claude/mcp-servers 2>/dev/null
diff -qr .scripts .tmp/claudesidian-upgrade/.scripts 2>/dev/null

# Core files
diff -q package.json .tmp/claudesidian-upgrade/package.json
diff -q README.md .tmp/claudesidian-upgrade/README.md
diff -q CHANGELOG.md .tmp/claudesidian-upgrade/CHANGELOG.md

Write findings to .upgrade-checklist.md, grouped by category, with status markers [ ] pending, [x] updated, [-] skipped.

5. File-by-file review

Hard rules — do not skip:

• Always show the diff before modifying anything.
• Always wait for the user's choice. Never auto-pick.
• Never use cp -f. Use cat src > dest for non-interactive overwrite.
• Update .upgrade-checklist.md after every file.

For each file in the checklist:

1. Show diff -u local upstream.
2. Determine state:
   • No local edits, no upstream edits → mark [-] skipped, move on.
   • Upstream changed, no local edits → ask: apply / keep / view full diff.
   • Both changed (local customization) → ask: keep yours / take upstream / view full diff / AI-merge.
3. Ask the user:

   File: <path> has updates.
   1. Apply update (take upstream)
   2. Keep your version
   3. View full diff
   4. AI-merge
   
   Choice (1/2/3/4):

   Wait for input. Do not auto-select.
4. Apply the chosen action:

   # Option 1
   if [ -f ".tmp/claudesidian-upgrade/$path" ]; then
     mkdir -p "$(dirname "$path")"
     cat ".tmp/claudesidian-upgrade/$path" > "$path"
     echo "✅ Updated $path"
   fi

5. Mark in checklist and continue.

6. Symlink hygiene (skills only)

After updating any skill in .agents/skills/<name>/, verify the symlinks in .claude/skills/<name> and .pi/skills/<name> still resolve:

for name in $(ls .agents/skills); do
  for agent in claude pi; do
    link=".${agent}/skills/${name}"
    target="../../.agents/skills/${name}"
    mkdir -p ".${agent}/skills"
    if [ -L "$link" ]; then
      # Symlink exists — verify it points to the right place
      current="$(readlink "$link")"
      if [ "$current" != "$target" ]; then
        rm "$link"
        ln -s "$target" "$link"
        echo "✅ Repaired symlink $link (was → $current)"
      fi
    elif [ -e "$link" ]; then
      # Real file or directory at this path — do not trample user data
      echo "⚠️  $link exists as a real file/dir, not a symlink. Skipping."
      echo "    Manual fix: inspect, back up if needed, then rm and rerun."
    else
      # Nothing there — create
      ln -s "$target" "$link"
      echo "✅ Created symlink $link"
    fi
  done
done

The -L test is critical: a broken symlink (target missing) returns false from -e but true from -L, so checking -e alone would try to ln -s over the existing broken link and fail with "File exists". Conversely, a symlink pointing the wrong way would pass -e (because the wrong target still exists) and silently stay wrong. Always check -L first, then verify the target with readlink, then fall through to -e for real files, then create if nothing exists.

If upstream introduced a brand-new skill, this loop also creates its symlinks.

7. Verification

Re-run the diff commands from step 4. The only differences should be files the user explicitly chose to keep (marked [-] or [x] customized in the checklist). Anything still pending [ ] is a bug — report it and let the user decide whether to retry.

8. Final steps

• Update package.json version to match upstream
• rm -rf .tmp/claudesidian-upgrade
• Save the final .upgrade-checklist.md to the backup dir for reference
• Print a summary: updated count, skipped count, customized count

Conflict resolution philosophy

When a skill has both upstream and local edits, prefer AI-merge over "take upstream." The user's local edit usually represents an intentional preference (their voice, their workflow conventions). The upstream edit usually represents a new feature or bug fix. Almost always you can keep both.

Show your merge proposal as a concrete diff before applying. Don't paraphrase.

Update categories

Auto-safe (low risk, default to "apply")

• Brand-new skills upstream introduced (additive — just symlink in)
• Hook script updates (.claude/hooks/*.sh) when local hasn't changed
• package.json dependency bumps in dependencies / devDependencies (preserve user-added scripts in the scripts section)
• CHANGELOG.md (always replace with upstream version)
• New files in .scripts/

Needs review (always ask)

• Skills the user has touched
• .claude/settings.json (often has user-added hooks)
• package.json scripts section
• README.md
• MCP server files

Never touch

See the "files we never touch" list in step 4.

Error handling

• No internet → fail gracefully, suggest retry
• GitHub rate limit → wait + retry once, then fail with the rate-limit reset time
• Merge conflict during AI-merge → show both versions, ask user to pick
• rm -rf .tmp/claudesidian-upgrade fails → leave it, warn the user

Rollback

The backup directory from step 2 is the rollback target. Manual rollback:

cp -r .backup/upgrade-<timestamp>/.agents .
cp -r .backup/upgrade-<timestamp>/.claude .
cp .backup/upgrade-<timestamp>/package.json .
# etc.

Don't try to be clever with selective rollbacks — restore the whole snapshot.

Migration from legacy layout

If test -d .agents/skills returns false, the user is on a pre-conversion claudesidian. Their skills live in .claude/commands/*.md. A normal upgrade will not work — the diff will show every command as "removed locally" and every skill as "added upstream."

The migration path:

1. Stop and explain. Tell the user their layout predates the commands→skills conversion and offer to migrate.

2. Backup first (step 2 above, but include .claude/commands/).

3. Move command files to skill dirs:

   mkdir -p .agents/skills
   for f in .claude/commands/*.md; do
     [ -f "$f" ] || continue
     name=$(basename "$f" .md)
     [ "$name" = "README" ] && continue
     mkdir -p ".agents/skills/$name"
     mv "$f" ".agents/skills/$name/SKILL.md"
   done

4. Add name/description frontmatter to any file that lacks it. Use the add-frontmatter skill.

5. Create symlinks for .claude/skills/ and .pi/skills/ (see step 6).

6. Validate frontmatter. Use the quick_validate.py script bundled with the skill-creator skill in this repo:

   for d in .agents/skills/*/; do
     uv run --with pyyaml python \
       .agents/skills/skill-creator/scripts/quick_validate.py "$d"
   done

   This enforces the full skill schema (name, description, allowed-tools, compatibility, license, metadata) and will reject any file with extra or missing required keys.

   If uv is not installed or skill-creator is somehow missing, fall back to this minimal inline check that only verifies name and description are present:

   for f in .agents/skills/*/SKILL.md; do
     dir=$(basename "$(dirname "$f")")
     awk '
       BEGIN { in_fm=0; has_name=0; has_desc=0 }
       /^---$/ { in_fm++; next }
       in_fm==1 && /^name:/ { has_name=1 }
       in_fm==1 && /^description:/ { has_desc=1 }
       END {
         if (!has_name) print "  ✗ missing name"
         if (!has_desc) print "  ✗ missing description"
         if (has_name && has_desc) print "  ✓ ok"
       }
     ' "$f" | sed "s|^|  $dir: |"
   done

7. Then run the normal upgrade flow to pull in any additional upstream changes.

This migration is one-time. After it runs successfully, future upgrades use the normal flow.

Selective upgrades

Common subset commands the user may ask for:

• "Just update skills" → only diff .agents/skills/
• "Just dependencies" → only update package.json deps
• "Just hooks" → only diff .claude/hooks/

Treat these as filters on the checklist. Same review/confirm rules apply.