Bug: install.ts --update overwrites custom CORE skill despite claiming to preserve config

[eccentricnode]

Summary

The install.ts --update mode claims to preserve existing configuration and "only update infrastructure files," but it overwrites the custom skills/CORE/SKILL.md file with a basic template, losing all user customizations.

Version

• PAI Bundle: v2.1.0
• File: Bundles/Official/install.ts
• Tested: 2026-01-15

Expected Behavior

According to the installer output when run with --update:

📦 Update mode: Preserving existing configuration.

   ✓ Skipping backup (your files stay in place)
   ✓ Will use existing .env values as defaults
   ✓ Only updating infrastructure files

The user's custom CORE skill (containing identity, goals, projects, personality calibration, etc.) should be preserved.

Actual Behavior

The installer overwrites ~/.claude/skills/CORE/SKILL.md with a minimal template:

• Before: 287 lines, 8920 bytes of custom configuration
• After: 70 lines, 1604 bytes generic template

All custom content lost:

• Detailed identity and goals
• Current projects and priorities
• Personality calibration settings
• Custom contacts and infrastructure navigation
• 5-year vision and learning philosophy

Impact

Critical data loss for users running --update:

1. CORE skill is the primary identity/configuration file
2. Contains irreplaceable user-specific context
3. No backup created in update mode (by design)
4. File history may not capture SKILL.md (depends on if it was edited via Claude Code)

Reproduction

# 1. Create custom CORE skill with personal content
echo "Custom content..." > ~/.claude/skills/CORE/SKILL.md

# 2. Run update (claims to preserve config)
cd /path/to/PAI/Bundles/Official
bun run install.ts --update

# 3. CORE skill is now the default template
cat ~/.claude/skills/CORE/SKILL.md  # Shows generic template

Root Cause

The installer's "update infrastructure" logic doesn't distinguish between:

• Infrastructure files (that should be updated)
• User configuration files (that should be preserved)

The CORE SKILL.md is treated as infrastructure and gets overwritten.

Suggested Fixes

Option A: Exclude CORE from updates

// In install.ts, skip CORE skill if it exists and differs from template
const coreSkillPath = `${paiDir}/skills/CORE/SKILL.md`;
if (isUpdateMode && existsSync(coreSkillPath)) {
  const existing = await Bun.file(coreSkillPath).text();
  const template = await Bun.file(coreSk illTemplate).text();
  
  if (existing !== template) {
    console.log("   ✓ Preserving custom CORE skill");
    // Skip overwriting CORE
  }
}

Option B: Merge instead of replace

Preserve user sections (## Identity, ## Goals, etc.) while updating structure.

Option C: Always backup in update mode

Even though docs say "no backup", create timestamped backup of critical files:

~/.claude/skills/CORE/SKILL.md.backup-20260115

Workaround

Users must manually back up CORE skill before running --update:

cp ~/.claude/skills/CORE/SKILL.md ~/SKILL.md.backup
bun run install.ts --update
# Restore custom content manually

Additional Context

The .env file has similar issues:

• Lost PAI_DIR="$HOME/.claude" line
• Lost quotes around TIME_ZONE value
• But at least .env is smaller and easier to recreate

---

Discovered during attempted upgrade to PAI 2.1.0 on existing installation.

[eccentricnode]

I trying to work on my own fix, I will push a branch, with the changes, if it's helpful.

Otherwise I can just get it working till 2.1.0 stabilizes.

[renoirb]

I had been thinking about this problem too. Maybe these files should be always generated automatically instead of being pasted as-is.

Or maybe some way to set conventions in title and preserving them. Some data structure where the title text, optional note that one would be warned not to change, and the example text we can check for existence, and not replace that chunk when absent. Basically a way to grab all Markdown text between title (with predictable pattern) and next title with some logic

[kaimagnus]

Thanks for reporting! The Bundles/install.ts system was completely replaced in v3.0 (now released) with a new installer that doesn't overwrite custom configurations. Please upgrade to v3.0.