~/.claude/skills being wiped on agent run

[BelgianNoise]

Context:

I use multiple LLM providers/tools. Mainly Claude Code with a Team subscription through work. I manage by skill inside a centralised folder on my computer and sync them using symlinks to specific folders like ~/.claude/skills, ~/.copilot/skills, ...

My paperclip LLM setup:

I have my Claude Team subscription set up. I also have OpenCode running with models through OpenRouter.

My goal:

Set up a weekly routine on deepseek v4 pro that uses a skill to do some relatively basic stuff.

What's happening?

Whenever my agent starts running, Paperclip will clear my ~/.claude/skills folder and populate it with only the skills i assigned to the agent in Paperclip itself. I understand that this is like a feature now, but it literally clears my claude's skills folder everytime. I don't want my workflow outside of Paperclip to be effected by an agent configured in Paperclip.
The thing that confuses me most is that the agent isn't event using Claude Code, but is configured to use OpenCode.

---

Do you know of any way to fix my issue ?
Or just let all agents use any skill that they can find ?

[Etogerman]

This looks like a collision with Paperclip's OpenCode cleanup rather than Claude Code itself.

On current master, the OpenCode adapter deliberately uses the shared ~/.claude/skills directory. Before a local run, it removes unselected symlinks when their target path contains /.agents/skills/.

So if your central store is something like ~/.agents/skills, Paperclip classifies those links as maintainer-only and unlinks them.

You can confirm it with:

for link in ~/.claude/skills/*; do
  [ -L "$link" ] && printf '%s -> %s\n' "$link" "$(readlink "$link")"
done

If the targets contain /.agents/skills/, a practical workaround is to relocate the canonical store, after backing it up, to a path such as ~/.local/share/llm-skills and recreate the tool-specific links. External directories and valid links whose targets do not match that marker are otherwise preserved.

Relevant code:

• OpenCode uses the shared Claude skills home
• The /.agents/skills/ cleanup heuristic

If this is a remote execution target, use a managed home or a dedicated remote user: the remote path currently replaces the entire remote .claude/skills directory.

One more caveat: setting HOME only in the agent adapter config is not a reliable local workaround today. Skill sync reads the configured HOME, but local execution uses os.homedir(). I would consider that mismatch, and the broad path heuristic, worth reporting as a Paperclip bug.