Claude Code Plugin Bug Causes Skills to Load Twice, Increasing Context Compaction

A bug in Claude Code causes plugins to load every skill twice, significantly increasing system prompt size and triggering frequent context compaction. The issue stems from stale plugin cache directories not being cleaned up during auto-updates and duplicate symlinks in the skills directory.

The Problem

When plugins update (e.g., from version 4.3.0 to 4.3.1), the old version directory remains in ~/.claude/plugins/cache/. Claude Code loads skills from ALL cached versions, not just the active one listed in installed_plugins.json. This causes every skill to appear twice in the system prompt.

One user reported having 11 stale version directories across 6 plugins, which doubled their ~30 skills to ~60 entries. Additional duplication vectors include a bug in prompt construction itself (confirmed in issue #29520) and symlinks created in ~/.claude/skills/ pointing back to the plugin cache (issue #23819), where one reporter had 83 symlinks batch-created.

Check if You're Affected

Run these scripts to check for the issue:

Check 1: Stale plugin versions

for d in ~/.claude/plugins/cache/claude-plugins-official/*/; do
    name=$(basename "$d")
    count=$(ls -d "$d"*/ 2>/dev/null | wc -l)
    if [ "$count" -gt 1 ]; then
        echo "AFFECTED: $name has $count versions (should be 1)"
        ls -d "$d"*/
    fi
done

Check 2: Duplicate symlinks

ls -la ~/.claude/skills/ 2>/dev/null | grep -c "plugins/"

If this returns a number > 0, you have symlink duplicates.

Check 3: From inside a session — run /context and look at the Skills table. If every skill appears twice, you're affected.

Fix the Issue

Fix stale versions:

python3 << 'EOF'
import json, os, shutil

with open(os.path.expanduser("~/.claude/plugins/installed_plugins.json")) as f:
    data = json.load(f)
cache = os.path.expanduser("~/.claude/plugins/cache/claude-plugins-official")
for full_name, installs in data["plugins"].items():
    plugin = full_name.split("@")[0]
    active = installs[0]["version"]
    plugin_dir = os.path.join(cache, plugin)
    if os.path.isdir(plugin_dir):
        for ver in os.listdir(plugin_dir):
            path = os.path.join(plugin_dir, ver)
            if os.path.isdir(path) and ver != active:
                print(f"Removing stale: {plugin}/{ver}")
                shutil.rmtree(path)
EOF

Fix duplicate symlinks:

find ~/.claude/skills/ -type l -lname "*plugins/*" -delete 2>/dev/null

Restart Claude Code after running these fixes.

Additional Context Savings

The source also recommends:

• Audit your enabled plugins in ~/.claude/settings.json → enabledPlugins. Disable what you don't need for your current project.
• Disconnect unused MCP connectors (Gmail, GCal, etc.).
• Run /context in your next session to see the difference.
• Thumbs-up issue #27721 so it gets prioritized — it's the root issue with no response yet.